Query 009901
Match_columns 523
No_of_seqs 123 out of 172
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 18:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01803 LIM_bind: LIM-domain 100.0 2E-53 4.3E-58 412.4 16.8 188 3-193 51-240 (240)
2 KOG2181 LIM domain binding pro 100.0 4.5E-30 9.8E-35 258.4 10.3 163 3-201 97-264 (415)
3 PF11197 DUF2835: Protein of u 44.1 58 0.0013 27.4 5.2 55 16-83 11-67 (68)
4 PF06249 EutQ: Ethanolamine ut 41.5 23 0.00051 33.9 2.9 36 39-74 76-111 (152)
5 PF03249 TSA: Type specific an 32.2 44 0.00096 36.7 3.4 11 82-92 200-210 (503)
6 COG4907 Predicted membrane pro 30.4 32 0.00069 38.7 2.1 19 442-460 571-589 (595)
7 PRK15457 ethanolamine utilizat 30.1 70 0.0015 32.9 4.3 37 39-75 156-192 (233)
8 PF07202 Tcp10_C: T-complex pr 25.9 1.7E+02 0.0037 28.8 5.9 43 31-73 80-125 (179)
9 PF07202 Tcp10_C: T-complex pr 21.1 3.2E+02 0.0068 26.9 6.8 42 32-73 99-142 (179)
10 KOG3361 Iron binding protein i 20.8 1.9E+02 0.004 28.0 4.9 62 68-152 68-129 (157)
No 1
>PF01803 LIM_bind: LIM-domain binding protein; InterPro: IPR002691 The LIM-domain binding protein, binds to the LIM domain IPR001781 from INTERPRO of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) P70662 from SWISSPROT is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons []. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development []. The Drosophila melanogaster protein Chip O18353 from SWISSPROT is required for segmentation and activity of a remote wing margin enhancer []. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development []. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [].; GO: 0003712 transcription cofactor activity, 0005634 nucleus
Probab=100.00 E-value=2e-53 Score=412.41 Aligned_cols=188 Identities=37% Similarity=0.593 Sum_probs=175.2
Q ss_pred CceeeeCccchhHHHHHHhhcCceEEEEEecCCceeecCCCeEEEEeCceEEEEEec-CeEEEEeeeEEEEeCCCCceeE
Q 009901 3 TVVAEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVFE-QLRVVRDGQLRIVFSPDLKICS 81 (523)
Q Consensus 3 ~KqFEIt~~vLPRyF~t~FeSGV~~mqLiLd~pRE~~lsNG~I~LEc~KAs~iy~Ye-gs~Vv~~G~LRa~Fd~~LKIEs 81 (523)
+|+|||++++|||||+++|++||++|+|+|+++||++++||.|+|||+||+++|||+ |++|+++|+||++||++|||||
T Consensus 51 ~k~FEi~~~~lPR~f~~~~~sGv~~~~~~l~~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v~~~G~lr~~f~~~lKIe~ 130 (240)
T PF01803_consen 51 PKQFEITRPLLPRYFRTLFESGVKRMQLVLDGPREQVLPNGSIFIECPRATFIYWYEDGSQVVHEGQLRAQFDPDLKIEW 130 (240)
T ss_pred CeeEEEchHHHHHHHHHHhcCCceEEEEEecCCceEEcCCCeEEEEECCEEEEEEECCceEEEEEeEEEEEECccccEEE
Confidence 399999999999999999999999999999999999999999999999999999997 5999999999999999999999
Q ss_pred EEEeecceeecccccchhhHHhhhhhHHHHHHHhhhcCCCCCCchHhhhhhhhhHHHHHHHHHhhcCCcccCCCccccch
Q 009901 82 WEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYTKRYV 161 (523)
Q Consensus 82 wEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~N~~d~KsspdmsKn~n~Fl~a~rQLak~l~lP~Vn~~Gipe~vM 161 (523)
||||+++|+|||+|++|+.++.+.+.+.++|+++. ++.|+++|+.|+++.+..+.+++.+.++..+|+++|+++++|
T Consensus 131 ~df~~~~~~e~I~r~~l~~~~~~~~~~~~~~~~~~---~~~k~~~~~~~~~~~~~~~~~~~~~~Lp~~~v~~~Gi~~~~m 207 (240)
T PF01803_consen 131 WDFCTRSHEEYIPRSALEQQASNLHPSVQIFQKLS---PDQKQSPDMSKNSKARQQKSPQLPPSLPSSNVNEFGIPERVM 207 (240)
T ss_pred EEEEeecccccCcHHHHHHhhccchhhhHHhhhcc---cccccccchhhhhhhhhhcccccCCCcccCCCCcCCCCHHHH
Confidence 99999999999999999999999999999999983 668899999999876666666666665555999999999999
Q ss_pred hhhhHHHHHhchHHHHHHhh-hcCCChHHHHhh
Q 009901 162 RCLQISEVVNSMKDLIDYSR-VTGTGPMESLAK 193 (523)
Q Consensus 162 RcLQIsEVMSqMKdLM~FSk-nn~LSP~EALk~ 193 (523)
|||||+|||++|||||.|++ ++.++|+|||++
T Consensus 208 r~Lqi~evms~M~~Lm~fs~~~~~~sP~eaL~~ 240 (240)
T PF01803_consen 208 RCLQIAEVMSQMKDLMSFSKQNNILSPLEALEQ 240 (240)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCHHHHhcC
Confidence 99999999999999999999 555999999985
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=99.96 E-value=4.5e-30 Score=258.36 Aligned_cols=163 Identities=18% Similarity=0.340 Sum_probs=144.1
Q ss_pred CceeeeCccchhHHHHHHhhcCceEEEEEecCCceeecCCCeEEEEeCceEEEEEecC---eEEEEeeeEEEEe--CCCC
Q 009901 3 TVVAEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVFEQ---LRVVRDGQLRIVF--SPDL 77 (523)
Q Consensus 3 ~KqFEIt~~vLPRyF~t~FeSGV~~mqLiLd~pRE~~lsNG~I~LEc~KAs~iy~Yeg---s~Vv~~G~LRa~F--d~~L 77 (523)
.|+|.|++.+|||||+++||+||++++++|++++| .+.||.+.+||+.|++++.|.. .+|+++|+|.+.| |+.+
T Consensus 97 pkRYtIgRtlIPrfFrsIfegG~~eLyyvLkh~ke-t~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~fDd~M 175 (415)
T KOG2181|consen 97 PKRYTIGRTLIPRFFRSIFEGGMRELYYVLKHPKE-TLHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAFDDVM 175 (415)
T ss_pred cceeeeccchhHHHHHHHHhcchhhhhhhhcCchh-hhcCCceeeeccceeEEeecCCccceeeeccceEEEEeehhhhh
Confidence 58999999999999999999999999999999988 8999999999999999999985 8999999999865 8899
Q ss_pred ceeEEEEeecceeecccccchhhHHhhhhhHHHHHHHhhhcCCCCCCchHhhhhhhhhHHHHHHHHHhhcCCcccCCCcc
Q 009901 78 KICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYT 157 (523)
Q Consensus 78 KIEswEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~N~~d~KsspdmsKn~n~Fl~a~rQLak~l~lP~Vn~~Gip 157 (523)
||+.|+|++++|.|+|||+.|...+ ..|......++| ++++.||+
T Consensus 176 RIK~Wh~~ik~~rElvprsil~~~a----------------~~dp~~ldq~~k-------------------NitR~G~~ 220 (415)
T KOG2181|consen 176 RIKAWHLEIKRSRELVPRSILQNTA----------------DYDPEALDQEQK-------------------NITRMGFF 220 (415)
T ss_pred hhhheeeeeeccccccchhhhhccC----------------CCChhhhChhhc-------------------cccccccc
Confidence 9999999999999999998875421 011111122233 38999999
Q ss_pred ccchhhhhHHHHHhchHHHHHHhhhcCCChHHHHhhhhhccCCC
Q 009901 158 KRYVRCLQISEVVNSMKDLIDYSRVTGTGPMESLAKFPRRTSGA 201 (523)
Q Consensus 158 e~vMRcLQIsEVMSqMKdLM~FSknn~LSP~EALk~fv~~~~~~ 201 (523)
+.+++||++|.|+++|++||..+|.+.|+|+||||.++.+.+..
T Consensus 221 nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLFQkwQr 264 (415)
T KOG2181|consen 221 NSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLFQKWQR 264 (415)
T ss_pred hhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999854
No 3
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=44.13 E-value=58 Score=27.44 Aligned_cols=55 Identities=20% Similarity=0.256 Sum_probs=36.8
Q ss_pred HHHHHhhcCceEEEEEecCCceeecCCCeE--EEEeCceEEEEEecCeEEEEeeeEEEEeCCCCceeEEE
Q 009901 16 LFKIKYESGTLEELLYVDMPREYQNASGQI--VLDYAKAIQESVFEQLRVVRDGQLRIVFSPDLKICSWE 83 (523)
Q Consensus 16 yF~t~FeSGV~~mqLiLd~pRE~~lsNG~I--~LEc~KAs~iy~Yegs~Vv~~G~LRa~Fd~~LKIEswE 83 (523)
=|..+|..-++.++..-+..|--.+|-.++ ||. +-=+.|..|++||++-|+.++|
T Consensus 11 ~~l~~Y~G~a~~V~v~s~~Gr~v~~Pa~~lRpFvt-------------~~Gv~G~F~l~~d~~~kf~sle 67 (68)
T PF11197_consen 11 EFLAYYQGAASKVVVRSDDGRRVQFPARHLRPFVT-------------HDGVHGRFRLEFDDNNKFVSLE 67 (68)
T ss_pred HHHHhccccccEEEEEecCCcEEEEeHHHCcceec-------------CCCceEEEEEEECCCCCEEEeE
Confidence 355667777888877766666544443332 221 1226799999999999999886
No 4
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=41.53 E-value=23 Score=33.93 Aligned_cols=36 Identities=17% Similarity=0.317 Sum_probs=26.2
Q ss_pred ecCCCeEEEEeCceEEEEEecCeEEEEeeeEEEEeC
Q 009901 39 QNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFS 74 (523)
Q Consensus 39 ~lsNG~I~LEc~KAs~iy~Yegs~Vv~~G~LRa~Fd 74 (523)
.++-|.+.+|.....|+|.||-..+|++|+|.+..+
T Consensus 76 ~l~~Gf~~le~~~f~wtl~YDEi~~VlEG~L~i~~~ 111 (152)
T PF06249_consen 76 RLSAGFMELEKTSFPWTLTYDEIKYVLEGTLEISID 111 (152)
T ss_dssp SSEEEEEEEEEEEEEEE-SSEEEEEEEEEEEEEEET
T ss_pred ceeeEEEEEeCCCccEEeecceEEEEEEeEEEEEEC
Confidence 456777777765555555556799999999998765
No 5
>PF03249 TSA: Type specific antigen; InterPro: IPR004933 There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [, ]. TSA proteins are probably integral membrane proteins. ; GO: 0016021 integral to membrane
Probab=32.20 E-value=44 Score=36.72 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=7.6
Q ss_pred EEEeecceeec
Q 009901 82 WEFCARRHEEL 92 (523)
Q Consensus 82 wEF~t~sHEEy 92 (523)
.||.+..|++|
T Consensus 200 ~dfdIldH~qW 210 (503)
T PF03249_consen 200 CDFDILDHEQW 210 (503)
T ss_pred cCccccCHHHH
Confidence 46777777776
No 6
>COG4907 Predicted membrane protein [Function unknown]
Probab=30.36 E-value=32 Score=38.66 Aligned_cols=19 Identities=37% Similarity=0.589 Sum_probs=11.4
Q ss_pred CCCCcCCCCCCCCCCCCCc
Q 009901 442 NNPGIGTGGYGNMGGGLGQ 460 (523)
Q Consensus 442 ~~~~~~~~~~g~~g~g~~~ 460 (523)
..+|.||||+|.-|||+|-
T Consensus 571 ~~~~~~GGG~G~~gGg~GG 589 (595)
T COG4907 571 RRSSSSGGGGGFSGGGSGG 589 (595)
T ss_pred ccCCCCCCCCCcCCCCCCC
Confidence 3455666666666666654
No 7
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=30.06 E-value=70 Score=32.86 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=28.4
Q ss_pred ecCCCeEEEEeCceEEEEEecCeEEEEeeeEEEEeCC
Q 009901 39 QNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFSP 75 (523)
Q Consensus 39 ~lsNG~I~LEc~KAs~iy~Yegs~Vv~~G~LRa~Fd~ 75 (523)
.++-|.+.+|.....|+|.|+....+++|.+++..+.
T Consensus 156 ~m~aGf~~~~~~sf~wtl~~dEi~YVLEGe~~l~IdG 192 (233)
T PRK15457 156 SMAAGFMQWENAFFPWTLNYDEIDMVLEGELHVRHEG 192 (233)
T ss_pred ceeeEEEEEecCccceeccceEEEEEEEeEEEEEECC
Confidence 3566777777766666666677999999999998863
No 8
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=25.90 E-value=1.7e+02 Score=28.80 Aligned_cols=43 Identities=26% Similarity=0.359 Sum_probs=19.5
Q ss_pred EecCCceeecCCCeEEEEeCceEEEEEec-C--eEEEEeeeEEEEe
Q 009901 31 YVDMPREYQNASGQIVLDYAKAIQESVFE-Q--LRVVRDGQLRIVF 73 (523)
Q Consensus 31 iLd~pRE~~lsNG~I~LEc~KAs~iy~Ye-g--s~Vv~~G~LRa~F 73 (523)
+.|+.+|-.+++|.+.+-++.-.-+.+|+ | ..+..+|.-++.|
T Consensus 80 ~pDG~keI~fPDGt~k~~~~dG~e~~~fpDGT~~~~~~nG~k~i~~ 125 (179)
T PF07202_consen 80 YPDGSKEIVFPDGTIKYIHPDGREETVFPDGTIVTIDPNGDKTITF 125 (179)
T ss_pred cCCCCEEEEeCCCcEEEEeCCCcEEEECCCceEEEEeCCCcEEEEe
Confidence 33444444445554444334444444453 3 3344455555555
No 9
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=21.13 E-value=3.2e+02 Score=26.95 Aligned_cols=42 Identities=17% Similarity=0.060 Sum_probs=20.9
Q ss_pred ecCCceeecCCCeEEEEeCceEEEEEecC--eEEEEeeeEEEEe
Q 009901 32 VDMPREYQNASGQIVLDYAKAIQESVFEQ--LRVVRDGQLRIVF 73 (523)
Q Consensus 32 Ld~pRE~~lsNG~I~LEc~KAs~iy~Yeg--s~Vv~~G~LRa~F 73 (523)
.++..|.++++|.++...+.-.-+..|++ -.|...+.-|..|
T Consensus 99 ~dG~e~~~fpDGT~~~~~~nG~k~i~~pnGq~ei~t~~~krrey 142 (179)
T PF07202_consen 99 PDGREETVFPDGTIVTIDPNGDKTITFPNGQKEIHTADFKRREY 142 (179)
T ss_pred CCCcEEEECCCceEEEEeCCCcEEEEeCCCcEEEEccccEEEEc
Confidence 33334445566665555555555555542 3344444444444
No 10
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=20.83 E-value=1.9e+02 Score=27.95 Aligned_cols=62 Identities=19% Similarity=0.138 Sum_probs=40.5
Q ss_pred eEEEEeCCCCceeEEEEeecceeecccccchhhHHhhhhhHHHHHHHhhhcCCCCCCchHhhhhhhhhHHHHHHHHHhhc
Q 009901 68 QLRIVFSPDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALE 147 (523)
Q Consensus 68 ~LRa~Fd~~LKIEswEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~N~~d~KsspdmsKn~n~Fl~a~rQLak~l~ 147 (523)
+|.|.+|.+-+|+-..|-+.+.-.-|--+.+.. .|.| +|..+|..|- +-++++|.+.
T Consensus 68 kLqIkvd~~g~I~dakFKTFGCGSAIASSS~aT------ewvk-----------gkt~dea~kI------kNteIAKeL~ 124 (157)
T KOG3361|consen 68 KLQIKVDDSGVIEDAKFKTFGCGSAIASSSLAT------EWVK-----------GKTLDEALKI------KNTEIAKELS 124 (157)
T ss_pred eEEEEECCCCcEEEeeeeecccchHhhhhHHHH------HHHc-----------cccHHHHHhc------ccHHHHHhcc
Confidence 467888999999999999999876665555432 2222 3444444432 2266777777
Q ss_pred CCccc
Q 009901 148 VPLVN 152 (523)
Q Consensus 148 lP~Vn 152 (523)
||+|.
T Consensus 125 LPPVK 129 (157)
T KOG3361|consen 125 LPPVK 129 (157)
T ss_pred CCchh
Confidence 77765
Done!