Query 009855
Match_columns 523
No_of_seqs 125 out of 173
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 18:08:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009855.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009855hhsearch_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 1.7E-53 3.7E-58 412.9 16.8 188 3-193 51-240 (240)
2 KOG2181 LIM domain binding pro 100.0 5.4E-30 1.2E-34 257.8 10.2 163 3-201 97-264 (415)
3 PF11197 DUF2835: Protein of u 45.3 56 0.0012 27.6 5.3 55 16-83 11-67 (68)
4 PF06249 EutQ: Ethanolamine ut 40.5 25 0.00055 33.7 2.9 36 39-74 76-111 (152)
5 PF03249 TSA: Type specific an 30.5 49 0.0011 36.4 3.4 11 82-92 200-210 (503)
6 COG4907 Predicted membrane pro 30.3 32 0.0007 38.6 2.1 19 442-460 571-589 (595)
7 PRK15457 ethanolamine utilizat 30.2 70 0.0015 32.9 4.3 37 39-75 156-192 (233)
8 PF07202 Tcp10_C: T-complex pr 27.7 1.5E+02 0.0032 29.2 5.9 43 31-73 80-125 (179)
9 KOG3361 Iron binding protein i 24.3 1.4E+02 0.0031 28.7 4.9 62 68-152 68-129 (157)
10 PF07202 Tcp10_C: T-complex pr 22.1 2.9E+02 0.0063 27.2 6.7 42 32-73 99-142 (179)
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=1.7e-53 Score=412.89 Aligned_cols=188 Identities=37% Similarity=0.593 Sum_probs=175.1
Q ss_pred CceeeeCcchhhHHHHHHhhcCceEEEEEecCCceeecCCCeEEEEeCceEEEEEec-CeEEEEeeeEEEEeCCCCceeE
Q 009855 3 TVVAEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVFE-QLRVVRDGQLRIVFSPDLKICS 81 (523)
Q Consensus 3 ~KqFEIt~~vLPRyF~t~FeSGV~~mqLvLd~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 009855 82 WEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYTKRYV 161 (523)
Q Consensus 82 wEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~Ns~d~KsspdmsKn~n~Fls~~rQLas~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 009855 162 RCLQISEVVNSMKDLIDYSR-VTGTGPMESLAK 193 (523)
Q Consensus 162 RcLQIsEVMSqMKdLM~FSk-nn~LSPlEALe~ 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=5.4e-30 Score=257.81 Aligned_cols=163 Identities=18% Similarity=0.340 Sum_probs=144.6
Q ss_pred CceeeeCcchhhHHHHHHhhcCceEEEEEecCCceeecCCCeEEEEeCceEEEEEecC---eEEEEeeeEEEEe--CCCC
Q 009855 3 TVVAEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVFEQ---LRVVRDGQLRIVF--SPDL 77 (523)
Q Consensus 3 ~KqFEIt~~vLPRyF~t~FeSGV~~mqLvLd~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 009855 78 KICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYT 157 (523)
Q Consensus 78 KIEswEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~Ns~d~KsspdmsKn~n~Fls~~rQLas~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 9999999999999999999876421 011211223334 37999999
Q ss_pred ccchhhhhHHHHHhchHHHHHHhhhcCCChHHHHhhhhcccCCC
Q 009855 158 KRYVRCLQISEVVNSMKDLIDYSRVTGTGPMESLAKFPRRTSGA 201 (523)
Q Consensus 158 e~vMRcLQIsEVMSqMKdLM~FSknn~LSPlEALe~fv~~~~~~ 201 (523)
+.+++||++|.|+++|++||+.+|.+.|+|+||||.++.+.+..
T Consensus 221 nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLFQkwQr 264 (415)
T KOG2181|consen 221 NSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLFQKWQR 264 (415)
T ss_pred hhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999754
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=45.31 E-value=56 Score=27.56 Aligned_cols=55 Identities=20% Similarity=0.256 Sum_probs=37.0
Q ss_pred HHHHHhhcCceEEEEEecCCceeecCCCeE--EEEeCceEEEEEecCeEEEEeeeEEEEeCCCCceeEEE
Q 009855 16 LFKIKYESGTLEELLYVDMPREYQNASGQI--VLDYAKAIQESVFEQLRVVRDGQLRIVFSPDLKICSWE 83 (523)
Q Consensus 16 yF~t~FeSGV~~mqLvLd~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 355667777888877776666544443332 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=40.48 E-value=25 Score=33.72 Aligned_cols=36 Identities=17% Similarity=0.317 Sum_probs=26.4
Q ss_pred ecCCCeEEEEeCceEEEEEecCeEEEEeeeEEEEeC
Q 009855 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 456777788765555555556799999999998765
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=30.52 E-value=49 Score=36.40 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=7.5
Q ss_pred EEEeecceeec
Q 009855 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 46677777765
No 6
>COG4907 Predicted membrane protein [Function unknown]
Probab=30.33 E-value=32 Score=38.65 Aligned_cols=19 Identities=37% Similarity=0.589 Sum_probs=11.4
Q ss_pred CCCCcCCCCCCCCCCCCCc
Q 009855 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=30.19 E-value=70 Score=32.85 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=28.7
Q ss_pred ecCCCeEEEEeCceEEEEEecCeEEEEeeeEEEEeCC
Q 009855 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 3567777887777667777777999999999998863
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=27.72 E-value=1.5e+02 Score=29.21 Aligned_cols=43 Identities=26% Similarity=0.359 Sum_probs=19.7
Q ss_pred EecCCceeecCCCeEEEEeCceEEEEEec-C--eEEEEeeeEEEEe
Q 009855 31 YVDMPREYQNASGQIVLDYAKAIQESVFE-Q--LRVVRDGQLRIVF 73 (523)
Q Consensus 31 vLd~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 33444444445555444444444444453 3 3344455555555
No 9
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=24.30 E-value=1.4e+02 Score=28.67 Aligned_cols=62 Identities=19% Similarity=0.138 Sum_probs=41.0
Q ss_pred eEEEEeCCCCceeEEEEeecceeecccccchhhHHhhhhhHHHHHHHhhhcCCCCCCchhhhhhhhhhHHHHHHHHHhhc
Q 009855 68 QLRIVFSPDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKALE 147 (523)
Q Consensus 68 ~LRa~Fd~~LKIEswEF~t~sHEEyIpRs~L~~qv~ql~~~aKk~qsl~~Ns~d~KsspdmsKn~n~Fls~~rQLas~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 467888999999999999999877666655543 2322 3444454432 2266777777
Q ss_pred CCccc
Q 009855 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 77665
No 10
>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=22.06 E-value=2.9e+02 Score=27.19 Aligned_cols=42 Identities=17% Similarity=0.060 Sum_probs=21.6
Q ss_pred ecCCceeecCCCeEEEEeCceEEEEEecC--eEEEEeeeEEEEe
Q 009855 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 34444455666665555555555555543 3444444444454
Done!