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Superfamily :     Homeodomain-like Class :     All alpha proteins Fold :     DNA/RNA-binding 3-helical bundle Number of Members :     48 Average Size :     65

Representative Superpose

Alignment

Matrices

Tree

PCA

CUSP

HMM (?)

Structural Motifs

SCOP PDBid	Start Residue	Start Chain	End Residue	End Chain	Domain Size	Name	Source	Resolution	R-factor
d1bl0a2	63	A	124	A	62	DNA (5'-	ESCHERICHIA COLI	2.30	0.225
d1d5ya2	57	A	121	A	65	ROB TRANSCRIPTION FACTOR	ESCHERICHIA COLI	2.70	0.254
d2gfna1	4	A	80	A	77	HTH-TYPE TRANSCRIPTIONAL REGULATOR PKSA RELATED	RHODOCOCCUS SP.	1.90	0.173
d2g3ba1	2	A	73	A	71	PUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR	RHODOCOCCUS SP.	2.00	0.185
d2id3a1	13	A	80	A	67	PUTATIVE TRANSCRIPTIONAL REGULATOR	STREPTOMYCES COELICOLOR	1.70	0.164
d2fq4a1	9	A	77	A	68	TRANSCRIPTIONAL REGULATOR, TETR FAMILY	BACILLUS CEREUS ATCC 14579	1.79	0.235
d2gena1	6	A	75	A	69	PROBABLE TRANSCRIPTIONAL REGULATOR	PSEUDOMONAS AERUGINOSA	1.70	0.210
d1jt6a1	2	A	72	A	71	HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA	STAPHYLOCOCCUS AUREUS	2.54	0.209
d2fx0a1	4	A	76	A	71	HEMOLYSIN II REGULATORY PROTEIN	BACILLUS CEREUS	2.40	0.221
d1z77a1	2	A	75	A	72	TRANSCRIPTIONAL REGULATOR (TETR FAMILY)	THERMOTOGA MARITIMA	2.00	0.229
d2fbqa1	2	A	80	A	79	PROBABLE TRANSCRIPTIONAL REGULATOR	PSEUDOMONAS AERUGINOSA	1.80	0.183
d1pb6a1	14	A	85	A	72	HYPOTHETICAL TRANSCRIPTIONAL REGULATOR YCDC	ESCHERICHIA COLI	2.50	0.238
d1fjla-	0	A	64	A	65	PROTEIN (SEGMENTATION PROTEIN PAIRED)	DROSOPHILA MELANOGASTER	2.00	0.198
d1p7ia-	3	A	55	A	53	SEGMENTATION POLARITY HOMEOBOX PROTEIN ENGRAILED	DROSOPHILA MELANOGASTER	2.10	0.200
d2e1oa1	8	A	64	A	57	HOMEOBOX PROTEIN PRH	HOMO SAPIENS	NA	NA
d1uhsa-	1	A	72	A	72	HOMEODOMAIN ONLY PROTEIN	MUS MUSCULUS	NA	NA
d2d6ya1	7	A	74	A	67	PUTATIVE TETR FAMILY REGULATORY PROTEIN	STREPTOMYCES COELICOLOR	2.30	0.207
d1rkta1	2	A	82	A	79	PROTEIN YFIR	BACILLUS SUBTILIS	1.95	0.208
d2fd5a1	1	A	76	A	76	TRANSCRIPTIONAL REGULATOR	PSEUDOMONAS AERUGINOSA PAO1	1.70	0.211
d1t56a1	22	A	94	A	73	ETHR REPRESSOR	MYCOBACTERIUM TUBERCULOSIS H37RV	1.70	0.208
d1v7ba1	1	A	74	A	74	TRANSCRIPTIONAL REGULATOR	CORYNEBACTERIUM GLUTAMICUM ATCC 13032	1.90	0.208
d1s7ea1	103	A	152	A	50	HEPATOCYTE NUCLEAR FACTOR 6	MUS MUSCULUS	NA	NA
d1e3oc1	104	C	160	C	57	5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3'	HOMO SAPIENS	1.90	0.220
d1sgma1	5	A	77	A	73	PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YXAF	BACILLUS SUBTILIS	2.00	0.233
d2np5a1	9	A	77	A	68	TRANSCRIPTIONAL REGULATOR	RHODOCOCCUS SP.	1.80	0.177
d2o7oa1	2	A	67	A	66	TETRACYCLINE REPRESSOR PROTEIN CLASS D	ESCHERICHIA COLI	1.89	0.202
d1z0xa1	4	A	71	A	66	TRANSCRIPTIONAL REGULATOR, TETR FAMILY	ENTEROCOCCUS FAECALIS V583	2.40	0.219
d2g7ga1	9	A	73	A	64	RHA04620, PUTATIVE TRANSCRIPTIONAL REGULATOR	RHODOCOCCUS SP. RHA1	2.01	0.191
d1zk8a1	6	A	77	A	72	TRANSCRIPTIONAL REGULATOR, TETR FAMILY	BACILLUS CEREUS	2.15	0.182
d1akha-	77	A	125	A	49	PROTEIN (MATING-TYPE PROTEIN A-1)	SACCHAROMYCES CEREVISIAE	2.50	0.201
d1lfba-	13	A	89	A	77	LIVER TRANSCRIPTION FACTOR (LFB1)	RATTUS NORVEGICUS	2.80	0.212
d2i10a1	10	A	78	A	66	PUTATIVE TETR TRANSCRIPTIONAL REGULATOR	RHODOCOCCUS SP.	2.05	0.202
d2g7sa1	3	A	76	A	74	TRANSCRIPTIONAL REGULATOR, TETR FAMILY	AGROBACTERIUM TUMEFACIENS	1.40	0.136
d1hcra-	139	A	190	A	52	PROTEIN (HIN RECOMBINASE)	2.30	0.228	All alpha proteins
d2g7la1	16	A	83	A	66	TETR-FAMILY TRANSCRIPTIONAL REGULATOR	STREPTOMYCES COELICOLOR	2.10	0.225
d1gdta1	141	A	183	A	43	PROTEIN (GAMMA DELTA RESOLVASE)	ESCHERICHIA COLI	3.00	0.235
d1fexa-	1	A	59	A	59	TRF2-INTERACTING TELOMERIC RAP1 PROTEIN	NA	NA	All alpha proteins
d1gv2a2	144	A	190	A	47	MYB PROTO-ONCOGENE PROTEIN	MUS MUSCULUS	1.68	0.193
d1igna1	360	A	445	A	86	PROTEIN (RAP1)	SACCHAROMYCES CEREVISIAE	2.25	0.219
d1x41a1	8	A	54	A	47	TRANSCRIPTIONAL ADAPTOR 2-LIKE, ISOFORM B	HOMO SAPIENS	NA	NA
d2cu7a1	8	A	72	A	65	KIAA1915 PROTEIN	HOMO SAPIENS	NA	NA
d1x58a1	8	A	56	A	49	HYPOTHETICAL PROTEIN 4930532D21RIK	MUS MUSCULUS	NA	NA
d2cqqa1	8	A	66	A	59	DNAJ HOMOLOG SUBFAMILY C MEMBER 1	HOMO SAPIENS	NA	NA
d1u78a2	55	A	104	A	50	TRANSPOSABLE ELEMENT TC3 TRANSPOSASE	CAENORHABDITIS ELEGANS	2.69	0.233
d2cjja1	8	A	70	A	63	RADIALIS	ANTIRRHINUM MAJUS	1.90	0.215
d2crga1	8	A	64	A	57	METASTASIS ASSOCIATED PROTEIN MTA3	MUS MUSCULUS	NA	NA
d1hlva1	1	A	66	A	66	MAJOR CENTROMERE AUTOANTIGEN B	HOMO SAPIENS	2.50	0.222
d1tc3c-	202	C	252	C	51	DNA (5'-	CAENORHABDITIS ELEGANS	2.45	NULL

| CLUSTAL | PIR | postscript | superposed-coordinates | Alistat | MeanRms | AVGSSTEQUI | Outliers | README |

Alignment Based On Similarities In Structural Features (COMPARER Alignment) 10 20 30 40 50 d1bl0a2 ( 63 ) rkmTeIAqkLkes----------nepilyLAerygfe d1d5ya2 ( 57 ) rrlSkSAvaLrlt----------arpildIAlqyrfd d2gfna1 ( 4 ) ivdhderrraLAdaVlaLiareg------isaVttraVaeesgw- d2g3ba1 ( 2 ) serrdaIlkASAtAiaqrgir------gLrvndVAevAgv- d2id3a1 ( 13 ) ggrtarireaVLlaAgdalaadg------fdaLdLgeIArrAgV- d2fq4a1 ( 9 ) rnietqkaIlsASyelllesgfk------aVtvdkIaerAkv- d2gena1 ( 6 ) rkdeIlqaAlacFsehgvd------aTti-eIrdrSga- d1jt6a1 ( 2 ) nlkdkILgvAkelFikngyn------aTttgeIvklSeS- d2fx0a1 ( 4 ) sreqtenIlkaAkkkFgergye------gTsiqeIAkeAkv- d1z77a1 ( 2 ) lskrdaIlkAAvevFgkkgyd------rAttdeIAekagv- d2fbqa1 ( 2 ) aqsetverILdAAeqlFaekgfa------eTslrlItskAgv- d1pb6a1 ( 14 ) avsakkkaIlsAAldTFsqfgfh------gTrleqIAelAgv- d1fjla- ( 0 ) k---qrrsrttfsasqldeLeraFertq-----yPdiytreeLaqrT--- d1p7ia- ( 3 ) rprtafsseqlarLkrefnenr-----ylterrrqqLssel--- d2e1oa1 ( 8 ) kggqvrfsndqtielekkfetqk-----ylspperkrlakml--- d1uhsa- ( 1 ) gsegaa--tmtedqveileynfnkvnk----hpdpttlcliaaeagl- d2d6ya1 ( 7 ) eatkarIfeaAvaEFarhgia------gAridrIaaeArA- d1rkta1 ( 2 ) spkvtkehkdkrqaeIleaAktVfkrkgfe------lTt-kdVveeSgf- d2fd5a1 ( 1 ) msdkktqtrarIlgaAtqallergav------ePsvgeVMgaagl- d1t56a1 ( 22 ) gddrelaILatAenlledrpla------dIsvddLAkgAgi- d1v7ba1 ( 1 ) mrtskkemILrtAidyigeysle------tLsydsLaeaTgl- d1s7ea1 ( 103 ) prlvftdvqrrtlhaifkenk-----rpskelqitisqql--- d1e3oc1 ( 104 ) krtsietnirvaLeksFmenq-----kPtseditliAeql--- d1sgma1 ( 5 ) gdsrekILhTAsrLsqlqgyh------aTglnqIvkeSgA- d2np5a1 ( 9 ) tsperLAaaLfdVaaesg------legAsvreVAkragv- d2o7oa1 ( 2 ) srlnresVIdaAleLlnetgid------gLttrkLAqkLgi- d1z0xa1 ( 4 ) klskdtIiaaAfslleks-----ptleqLs-rkVAkqlgv- d2g7ga1 ( 9 ) ldrerIAeaAleLvdrdg---------dFrpdLArhLnv- d1zk8a1 ( 6 ) igltlqkIVetAaeiadang------vqeVtlasLaqtlgv- d1akha- ( 77 ) ispqArafLeevfrrkq-----sLnskekeevAkkC--- d1lfba- ( 13 ) rfkwgpaSqqiLfqayerqk-nPskeeretlveeCnraeCiq d2i10a1 ( 10 ) ddqvalqtA-eLFwrqgye------gTsitdLtkaLgi- d2g7sa1 ( 3 ) npqskaddIlqcArtliirgg------ynsFsyadIsqvvgi- d1hcra- ( 139 ) grpraInkheqeqIsrllek-------ghp---rqqLAiif--- d2g7la1 ( 16 ) kpalsrrwIvdtAvaL-raegle------kVt-rrLAqeLdt- d1gdta1 ( 141 ) grkrki---drdaVlnmwqq-------gl---gAshIsktm--- d1fexa- ( 1 ) griaftdaddvailtyvkenarspssvtgnalwkameksslt- d1gv2a2 ( 144 ) ktswteeedriIyqAhkrlg-----n----rwaeIaklLp-- d1igna1 ( 360 ) kasftdeeDefILdvVrknPtrrtth---tLYdeIshyvp-- d1x41a1 ( 8 ) dpswtaqeemalleavmdcg-----f---gnwqdvanqmc-- d2cu7a1 ( 8 ) ysvkwtieekelfeqglakfg-----r----rwtkisklig-- d1x58a1 ( 8 ) rkdftkeevnylfhgvktmg-----n----hwnsilwsfpf- d2cqqa1 ( 8 ) apewteedlsqltrsmvkfp-----ggtpgrwekiahel--- d1u78a2 ( 55 ) aprrkaLsvrdernViraasns------ck---tArdIrnelqL- d2cjja1 ( 8 ) grpwsakenkaFeralavyd-----kdtpdrwanVAraVe-- d2crga1 ( 8 ) meewsaseaclfeealekyg-----k----dfndirqdflp- d1hlva1 ( 1 ) mgpkrrqLtfreksrIIqeveenp--------dlrkgeIArrfnI- d1tc3c- ( 202 ) prgsaLsdteraqLdvmkll-------nvs---lheMsrki--- aaaaaaaaaaaaa aaaaaaa 60 70 80 90 100 d1bl0a2 ( 90 ) ---sqqtLtrtF-----knyFdvpPhkYrm---tn------mqgesrflh d1d5ya2 ( 84 ) ---sqqtFtraF-----kkqFaqtPalyrr---sp---ewsafgirpplr d2gfna1 ( 42 ) ---stgvLnhyFg---srheLllAAlrrag---diqgdryrtildeeg d2g3ba1 ( 36 ) ---spglLyyhFk---drigLleaAlnyin---drarayrsegegg d2id3a1 ( 51 ) ---gkttVyrrWg---tpggLaadllad-a---eqslp------------ d2fq4a1 ( 45 ) ---skatIykwWp---nkaaVV-dGflsaa---aar----------lpvp d2gena1 ( 38 ) ---sigsLyhhFg---nkerIhgelylagi---gqyaalleagfar-a d1jt6a1 ( 35 ) ---skgnLyyhFk---tkenLfleilniee---skwqeqwkkeqik-a d2fx0a1 ( 40 ) ---nv-aAsyyFn---gkenLyyevfkkyg----lanelpnflekn-q d1z77a1 ( 36 ) ---akglIfhyFk---nkeeLyyqaysvte---klqkefenflknr-n d2fbqa1 ( 38 ) ---nlaaVnyhfg---skkaLiqavfsrfl---gpfcaslekeldrrqak d1pb6a1 ( 50 ) ---sktnLlyyfp---skeaLyiaVlrqil---diwlaplkafre d1fjla- ( 39 ) ---n--ltearI-----qvwFq-nrrarlr---kqhtsv--s d1p7ia- ( 39 ) ---g--lneaqI-----kiwFq-narak d2e1oa1 ( 45 ) ---q--lserqv-----ktwfq-nrrakwr---r d1uhsa- ( 42 ) ---t----eeqt-----qkwfkqrlaewrr---seglp------secrsv d2d6ya1 ( 41 ) ---nkqlIyayyg---nkgeLfasvlekkl---dlaisvpv--------- d1rkta1 ( 45 ) ---srggVylyFs---steef-rriietgl---deglrkldksaehq d2fd5a1 ( 40 ) ---tvggFyahFq---skdaLMleAfeqll---gkrrellgeld--pg d1t56a1 ( 57 ) ---srptFyfyFp---skeaVlltlldrvv---nqadmalqtlaen-p d1v7ba1 ( 37 ) ---sksgLiyhFp---srhaLllgMhella---ddwdkelrditrd-p d1s7ea1 ( 138 ) ---g--lelstv-----snffm-nar d1e3oc1 ( 139 ) ---n--mekevI-----rvwFs-nrrqkek---rin d1sgma1 ( 39 ) ---p-kgslyhFf-pngkeeLaieAvtytg---kivehliqqsmde-s d2np5a1 ( 42 ) ---sigaVqhhFs---tkdefa-falrtlv---dkllarlsever d2o7oa1 ( 37 ) ---eqptLywhvk---nkraLldaLaveil---arhhd------------ d1z0xa1 ( 39 ) ---qapaIywyFk---nkqaLlqs-aeaie---ehfq----------epa d2g7ga1 ( 40 ) ---qvssIyhhAk---graaVveLvrhrvv---reidgsafer d1zk8a1 ( 41 ) ---rspsLynhVk---glqdVrknlgiygi---kklhnrleeaaed d1akha- ( 108 ) ---g--itplqV-----rvwFi-nkrmrs d1lfba- ( 54 ) rgvspsqaqgLgsnlVtevrVynWFanrrk---eeafrh d2i10a1 ( 42 ) ---nppsLyaafg---skrdLfekTldryc---ertlqleeavr d2g7sa1 ( 39 ) ---rnasIhhhFp---sksdLvckLvsqyr---qeaeagiaelekni d1hcra- ( 170 ) ---g--igvstL-----yryfp---a---s---sikkrm--n d2g7la1 ( 52 ) ---gpasLyvyVa---ntaeLhaAVldall---g-----------evdlt d1gdta1 ( 169 ) ---n--IarstV-----ykVin-esn d1fexa- ( 43 ) ---q--hswqsl-----kdrylkhlr---------------------g d1gv2a2 ( 175 ) -----grtdnaI-----knhwnstmr d1igna1 ( 397 ) -----nHtgnsI-----rhrfrvyLskrleyVyevdkfgklvrdddgnli d1x41a1 ( 40 ) -----tktkeec-----ekhymkyf d2cu7a1 ( 40 ) -----srtvlqv-----ksyar-qyfknkv---kcgldketpnqkt-g d1x58a1 ( 40 ) ---qkgrravdl-----ahkyh-rli d2cqqa1 ( 42 ) ---g--rsvtdv-----ttkak-qlkdsv------tcspgmv d1u78a2 ( 90 ) ---s--askrtI-----lnVik-rsg d2cjja1 ( 43 ) -----gRtpeeV-----kkhye-ilvedik---yiesgkvpf d2crga1 ( 40 ) -----wksltsi-----ieyyy-mwkttd-----------ryvqqk-r d1hlva1 ( 38 ) ---ppstLstIlk---nkrailaserkygv---aStcr d1tc3c- ( 233 ) ---s--rsrhcI-----rvYlk-dpvsygt---s aaa aaaaa aaaaa d1bl0a2 ( 123 ) p-------l d1d5ya2 ( 120 ) l-------g d2gfna1 d2g3ba1 d2id3a1 ( 80 ) --------r d2fq4a1 ( 76 ) d-------t d2gena1 d1jt6a1 d2fx0a1 d1z77a1 d2fbqa1 ( 79 ) p-------e d1pb6a1 d1fjla- d1p7ia- d2e1oa1 d1uhsa- ( 71 ) t-------d d2d6ya1 ( 74 ) --------d d1rkta1 d2fd5a1 d1t56a1 d1v7ba1 d1s7ea1 d1e3oc1 d1sgma1 d2np5a1 d2o7oa1 ( 66 ) y-------s d1z0xa1 ( 70 ) l-------c d2g7ga1 d1zk8a1 d1akha- d1lfba- d2i10a1 d2g7sa1 d1hcra- d2g7la1 ( 82 ) g-------a d1gdta1 d1fexa- d1gv2a2 d1igna1 ( 437 ) ktkvlppsi d1x41a1 d2cu7a1 d1x58a1 d2cqqa1 d1u78a2 d2cjja1 d2crga1 d1hlva1 d1tc3c-

Key solvent inaccessible UPPER CASE X solvent accesible lower case x alpha helix red x beta strand blue x 3 - 10 helix maroon x hydrogen bond to main chain amide bold x hydrogen bond to mainchain carbonyl underline x disulphide bond cedilla ç positive phi italic x

List of outliers  

SCOP PDBid
d1bl0a1
d1bw5a-
d1etxa-
d1g2ha-
d1gvda-
d1hlva2
d1igna2
d1irza-
d1iufa1
d1iufa2
d1k61a-
d1k78a1
d1k78a2
d1mija-
d1ntca-
d1ofcx1
d1ofcx2
d1pufa-
d1pufb-
d1qrya-
d1rr7a-
d1t33a1
d1ug2a-
d1ui5a1
d1umqa-
d1vi0a1
d1w0ua-
d1wgxa-
d1wh7a-
d1x2ma1
d1x2na1
d1xc5a1
d2ao9a1
d2aqea1
d2coba1
d2coma1
d2cqra1
d2cufa1
d2ecca1
d2ezia-
d2ezla-
d2fq3a1
d2ga1a1
d2iw5b1
d2np3a1

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Computational Approaches to Protein Science
NCBS
Bangalore, India

 Your suggestions and further clarifications are most welcome.

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 PASS2 group: 

     Prof. R. Sowdhamini
     K. Kanagarajadurai
     P. Nagarajan
     S. Kalaimathy