YRC Public Data Repository - Protein Structure Prediction

Protein:	HMI1
Organism:	Saccharomyces cerevisiae
Length:	706 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for HMI1.

Description	E-value	Query Range	Subject Range
gi\|2625021 - gi\|2625021\|gb\|AAC46278.1\| DNA helicase II [Serratia marcescens]	0.0	[1..675]	[7..658]
gi\|253326607, gi... - gi\|254290505\|ref\|YP_003056253.1\| DNA-dependent ATPase I and helicase II [Escherichia coli BL21(DE3)]... gi\|13364219, gi\|... - gi\|15833997\|ref\|NP_312770.1\| DNA-dependent helicase II [Escherichia coli O157:H7 str. Sakai], gi\|133... gi\|253975656, gi... - gi\|254163755\|ref\|YP_003046863.1\| DNA-dependent ATPase I and helicase II [Escherichia coli B str. REL... gi\|110345730, gi... - gi\|110644138\|ref\|YP_671868.1\| DNA-dependent helicase II [Escherichia coli 536], gi\|110345730\|gb\|ABG7... gi\|227888602, gi... - gi\|227888602\|ref\|ZP_04006407.1\| excision endonuclease subunit UvrD [Escherichia coli 83972], gi\|2278... gi\|251787070, gi... - gi\|251787070\|ref\|YP_003001374.1\| hypothetical protein B21_03638 [Escherichia coli BL21], gi\|24237934... gi\|74314325, gi\|... - gi\|74314325\|ref\|YP_312744.1\| DNA-dependent helicase II [Shigella sonnei Ss046], gi\|73857802\|gb\|AAZ90... gi\|254795809, gi... - gi\|254795809\|ref\|YP_003080646.1\| DNA-dependent ATPase I and helicase II [Escherichia coli O157:H7 st... gi\|115515196, gi... - gi\|117626072\|ref\|YP_859395.1\| DNA-dependent helicase II [Escherichia coli APEC O1], gi\|115515196\|gb\|... gi\|25290766, gi\|... - pir\|\|B86068 DNA-dependent ATPase I and helicase II [imported] - Escherichia coli (strain O157:H7, su... gi\|15804402, gi\|... - gi\|15804402\|ref\|NP_290442.1\| DNA-dependent helicase II [Escherichia coli O157:H7 EDL933], gi\|1251868... gi\|13364219, gi\|... - gi\|15833997\|ref\|NP_312770.1\| DNA-dependent ATPase I and helicase II [Escherichia coli O157:H7], gi\|1... gi\|195938102 - gi\|195938102\|ref\|ZP_03083484.1\| DNA-dependent helicase II [Escherichia coli O157:H7 str. EC4024] gi\|208727159, gi... - gi\|208807358\|ref\|ZP_03249695.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4206], gi\|208727159... gi\|208735256, gi... - gi\|208813979\|ref\|ZP_03255308.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4045], gi\|208735256... gi\|208739927, gi... - gi\|208819804\|ref\|ZP_03260124.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4042], gi\|208739927... gi\|168801123, gi... - gi\|189376660\|gb\|EDU95076.1\| DNA helicase II [Escherichia coli O157:H7 str. EC508], gi\|168801123\|ref\|... gi\|170679582, gi... - gi\|170679582\|ref\|YP_001746130.1\| DNA helicase II [Escherichia coli SMS-3-5], gi\|170517300\|gb\|ACB1547... gi\|191174264, gi... - gi\|191174264\|ref\|ZP_03035773.1\| DNA helicase II [Escherichia coli F11], gi\|190905447\|gb\|EDV65077.1\| ... gi\|194438675, gi... - gi\|194438675\|ref\|ZP_03070763.1\| DNA helicase II [Escherichia coli 101-1], gi\|194422479\|gb\|EDX38478.1... gi\|168768094, gi... - gi\|189362636\|gb\|EDU81055.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4486], gi\|168768094\|ref... gi\|168775636, gi... - gi\|187768818\|gb\|EDU32662.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4196], gi\|168775636\|ref... gi\|189001426, gi... - gi\|189001426\|gb\|EDU70412.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4076], gi\|168780712\|ref... gi\|189373276, gi... - gi\|189373276\|gb\|EDU91692.1\| DNA helicase II [Escherichia coli O157:H7 str. EC869], gi\|168786651\|ref\|... gi\|161486051 - gi\|161486051\|ref\|NP_756593.2\| DNA-dependent helicase II [Escherichia coli CFT073] gi\|162138327 - gi\|162138327\|ref\|YP_543324.2\| DNA-dependent helicase II [Escherichia coli UTI89] gi\|168750375, gi... - gi\|188015427\|gb\|EDU53549.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4113], gi\|168750375\|ref... gi\|189359023, gi... - gi\|189359023\|gb\|EDU77442.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4401], gi\|168753710\|ref... gi\|209157402, gi... - gi\|209396002\|ref\|YP_002273330.1\| DNA helicase II [Escherichia coli O157:H7 str. EC4115], gi\|20915740... gi\|215489141, gi... - gi\|215489141\|ref\|YP_002331572.1\| DNA-dependent helicase II [Escherichia coli O127:H6 str. E2348/69],... gi\|218550963, gi... - gi\|218550963\|ref\|YP_002384754.1\| DNA-dependent helicase II [Escherichia fergusonii ATCC 35469], gi\|2...	0.0	[1..675]	[7..658]
gi\|16762183 - gi\|16762183\|ref\|NP_457800.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serovar ... gi\|213425413 - gi\|213425413\|ref\|ZP_03358163.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|213649574 - gi\|213649574\|ref\|ZP_03379627.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|25290775, gi\|... - gi\|25290775\|pir\|\|AG0918 DNA helicase II [imported] - Salmonella enterica subsp. enterica serovar Typ... gi\|213865062 - gi\|213865062\|ref\|ZP_03387181.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov... gi\|29139307, gi\|... - gi\|29143672\|ref\|NP_807014.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serovar ... gi\|213161539 - gi\|213161539\|ref\|ZP_03347249.1\| DNA-dependent helicase II [Salmonella enterica subsp. enterica serov...	0.0	[1..675]	[7..658]
gi\|85676237, gi\|... - gi\|89110206\|ref\|AP_003986.1\| DNA-dependent ATPase I and helicase II [Escherichia coli str. K-12 subs... gi\|194429230, gi... - gi\|194429230\|ref\|ZP_03061758.1\| DNA helicase II [Escherichia coli B171], gi\|194412742\|gb\|EDX29036.1\|... gi\|194434041, gi... - gi\|194434041\|ref\|ZP_03066311.1\| DNA helicase II [Shigella dysenteriae 1012], gi\|194417699\|gb\|EDX3379... gi\|238902889, gi... - gi\|238902889\|ref\|YP_002928685.1\| DNA-dependent ATPase I and helicase II [Escherichia coli BW2952], g... gi\|218354263, gi... - gi\|218697531\|ref\|YP_002405198.1\| DNA-dependent helicase II [Escherichia coli 55989], gi\|218354263\|em... UVRD_ECOLI - DNA helicase II (EC 3.6.1.-) - Escherichia coli gi\|170083295, gi... - gi\|170083295\|ref\|YP_001732615.1\| DNA-dependent ATPase I and helicase II [Escherichia coli str. K-12 ... gi\|192926639, gi... - gi\|193065672\|ref\|ZP_03046737.1\| DNA helicase II [Escherichia coli E22], gi\|192926639\|gb\|EDV81268.1\| ... EG11064 - DNA-dependent ATPase I and helicase II / ATP-dependent 3'-5' DNA helicase II; unwinds forked DNA str... EG11064 - DNA-dependent ATPase I and helicase II / ATP-dependent 3'-5' DNA helicase II; unwinds forked DNA str...	0.0	[1..675]	[7..658]
UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium GN=uvrD PE=3 SV=2 lcl\|NC_016856.1_... - [gene=uvrD] [protein=DNA-dependent helicase II] [protein_id=YP_005240211.1] [location=4169232..41713... UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium GN=uvrD PE=3 SV=2 gi\|197242160, gi... - gi\|197263905\|ref\|ZP_03163979.1\| DNA helicase II [Salmonella enterica subsp. enterica serovar Saintpa... UVRD_SALTY - DNA helicase II OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=uvrD PE=3 SV=2 gi\|167993889, gi... - gi\|205328129\|gb\|EDZ14893.1\| DNA helicase II [Salmonella enterica subsp. enterica serovar 4,[5],12:i:...	0.0	[1..675]	[7..658]
gi\|148212\|gb\|AAA... - DNA helicase II [Escherichia coli] gi\|148212 - gi\|148212\|gb\|AAA67609.1\| DNA helicase II [Escherichia coli]	0.0	[1..675]	[7..658]
gi\|10173262, gi\|... - gi\|15613211\|ref\|NP_241514.1\| ATP-dependent DNA helicase [Bacillus halodurans C-125], gi\|10173262\|dbj... gi\|25290764 - pir\|\|H83730 ATP-dependent DNA helicase pcrA [imported] - Bacillus halodurans (strain C-125)	0.0	[1..701]	[17..693]
gi\|25290780 - pir\|\|H97606 probable DNA helicase II homolog [imported] - Agrobacterium tumefaciens (strain C58, Cer... gi\|15157185, gi\|... - gi\|15889343\|ref\|NP_355024.1\| hypothetical protein AGR_C_3725 [Agrobacterium tumefaciens str. C58], g...	0.0	[1..704]	[56..754]

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Predicted Domain #1

Region A:
Residues: [1-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDKLTPSQWK VINKSYEPAS TIKVIAGPGS GKTLTLLYKV LHLITVENIK PEEILIFSLT  60
   61 NKAVDSIIEN LLSIFENSHT NKEIVHQIGC YTVHGLANRI VVENEGMINI IEEIGWRGLM 120
  121 KLLPPSKRTP HHFRSYKELE KVVKDYKLNN AKNNNPVIEK LVELMDNCKV MTNDDLIIRA 180
  181 KKYLELDSSD SDASSFTQDL RNKYKVVLID EFQDLYPSLA PLITMICKGK QLIMFGDTNQ 240
  241 SIYGFLGSNN EIMSQLDNLH PKNSTTVLKL FDNF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	362.0
Match:	1pjr__
Description:	DEXX box DNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [275-706]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RSTPEIISLA SKIINRPLAE KQIIDDTDET PSELVRKLPS GVSPQIMTFD DLAAESEFII  60
   61 DKITQLICSS AKFSDIAILS RTNSHLTAIA SILKKYGIPY QKLKSQPDWM DDLRIQFLLD 120
  121 ILKVCSLASD EKHNREFNTG DKWQSNFSIL VTMSALKGIG DASIQALYKA CSLKNLSIWK 180
  181 YLTMVPNFEW PLGLSIKKKM ENYTSNLYEM IENDQVHQLD DPMELLEKVA SITNNLNLNP 240
  241 TYFQSLSDAQ SSLEFKTHLQ EMAQVMKVSK SNKPPGISFV KWFLETYFDQ TMVFHQSQQA 300
  301 LQTTGPGTVK LSTIHSAKGL EFPIVFLTNG SMSNFPMDTN ALYVGITRAR NLLYMCNMKH 360
  361 ERLVSKSSPY SRNIMSNNLF WTYYNKDLKR SVCDVKVTHG YNVQRYNQLR KNFGFYRAYS 420
  421 SLRGCKSVFR RI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	362.0
Match:	1pjr__
Description:	DEXX box DNA helicase
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits