Query 005513
Match_columns 693
No_of_seqs 132 out of 181
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 00:39:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005513hhsearch_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 2.3E-63 5E-68 499.2 23.9 237 121-384 1-240 (240)
2 KOG2181 LIM domain binding pro 100.0 1.2E-31 2.5E-36 276.8 15.9 217 109-389 40-261 (415)
3 KOG3598 Thyroid hormone recept 68.4 2.2 4.7E-05 54.1 1.0 10 124-133 2195-2204(2220)
4 PF09849 DUF2076: Uncharacteri 59.8 20 0.00044 38.1 6.1 32 34-65 5-36 (247)
5 KOG3598 Thyroid hormone recept 52.1 14 0.00031 47.4 3.9 9 113-121 2174-2182(2220)
6 PF06249 EutQ: Ethanolamine ut 29.4 49 0.0011 33.0 3.0 36 229-264 76-111 (152)
7 KOG4369 RTK signaling protein 27.7 73 0.0016 40.9 4.5 14 546-559 2073-2086(2131)
8 COG3185 4-hydroxyphenylpyruvat 22.4 64 0.0014 36.2 2.6 144 125-285 165-330 (363)
9 PRK15457 ethanolamine utilizat 22.3 1.1E+02 0.0023 32.7 4.1 40 226-265 153-192 (233)
10 KOG3648 Golgi apparatus protei 13.8 1.6E+02 0.0034 35.9 3.2 19 658-676 536-554 (1179)
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=2.3e-63 Score=499.21 Aligned_cols=237 Identities=38% Similarity=0.581 Sum_probs=211.0
Q ss_pred HHHHHHHHHHHhCC-CCCCchhHHHHHHHHhcCCCCcEEEEeeccCCCCCCccccccccccccccccccCCCCCceeEEc
Q 005513 121 ARRLMQYLYHQRQR-PPDNTIAYWRKFVAEYYSPRAKKRWCLSLYDNVGHHALGVFPQAAMDAWQCDICGSKSGRGFEAT 199 (693)
Q Consensus 121 ~lRLlQfiehLs~r-p~~ndI~YWrkFV~EFFSP~AvlR~tls~~d~~g~hs~GvfPq~a~d~W~cdic~sk~~K~FEIt 199 (693)
++||++|+++|+++ ++++|++||++||+|||+|+|++|||++..++. ..+|+|||+
T Consensus 1 ilRl~~~~~~l~~~~~~~~~~~yW~~fv~~fF~~~a~lr~~~~~~~~~-----------------------~~~k~FEi~ 57 (240)
T PF01803_consen 1 ILRLLEFIERLSNFSPNLNDIEYWQKFVHEFFSPDAVLRISLWNEDGN-----------------------GSPKQFEIT 57 (240)
T ss_pred CchHHHHHHHHHhhcCCCCcHHHHHHHHHHHcCCCeeEEEEEEcCCCC-----------------------CCCeeEEEc
Confidence 58999999999998 889999999999999999999999998643221 125999999
Q ss_pred ccchhHHHHHHhhcCcceEEEeeCCCcceecCCCcEEEEeCceEEEEEec-CeEEEEEEEEEEEeCcccceEEEEEeecc
Q 005513 200 FEVLPRLNEIKFGSGVIDELMFLDLPRECRFPSGIMMLEYGKAVQESVYE-QLRIVREGQLRIIFTNDLKILSWEFCARR 278 (693)
Q Consensus 200 ~~vLPRfF~t~FeSGV~~~qL~Ld~prE~vLpNGsi~LEc~KAs~~y~Ye-gS~Vv~~GqLRiiFd~dLKIEswEF~~~s 278 (693)
+++|||||+++|++||++|+|++++++|++|+||+|+|||+||+++|||+ |++|+++|+||++||++|||||||||+++
T Consensus 58 ~~~lPR~f~~~~~sGv~~~~~~l~~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v~~~G~lr~~f~~~lKIe~~df~~~~ 137 (240)
T PF01803_consen 58 RPLLPRYFRTLFESGVKRMQLVLDGPREQVLPNGSIFIECPRATFIYWYEDGSQVVHEGQLRAQFDPDLKIEWWDFCTRS 137 (240)
T ss_pred hHHHHHHHHHHhcCCceEEEEEecCCceEEcCCCeEEEEECCEEEEEEECCceEEEEEeEEEEEECccccEEEEEEEeec
Confidence 99999999999999999999999999999999999999999999999997 79999999999999999999999999999
Q ss_pred eeccccccchhhhHHHHHHhhhhccccccccCCCCCchhhhhhchhhhHhhhhhhccccccCCCCCCCcchhhhhHhhHH
Q 005513 279 HEELLPRRLVAPQVNQLLQVAQKCQSTISESGSEGISQQDLQTNSNMVLTAGRQLAKSLELQSLNDLGFSKRYVRCLQIS 358 (693)
Q Consensus 279 HEEyIpR~~Le~qvn~lie~aqK~Qs~i~EsgsdgvS~eD~k~np~m~k~karQLaksLp~s~Vn~~GIpe~vMRcLQIa 358 (693)
|+|||+|++|++++.....++++++... . +....+|+.+++.....+.+++.+.||.++|+++|||+++||||||+
T Consensus 138 ~~e~I~r~~l~~~~~~~~~~~~~~~~~~--~--~~k~~~~~~~~~~~~~~~~~~~~~~Lp~~~v~~~Gi~~~~mr~Lqi~ 213 (240)
T PF01803_consen 138 HEEYIPRSALEQQASNLHPSVQIFQKLS--P--DQKQSPDMSKNSKARQQKSPQLPPSLPSSNVNEFGIPERVMRCLQIA 213 (240)
T ss_pred ccccCcHHHHHHhhccchhhhHHhhhcc--c--ccccccchhhhhhhhhhcccccCCCcccCCCCcCCCCHHHHHHHHHH
Confidence 9999999999998766555555554443 1 12245577777666666677888889999999999999999999999
Q ss_pred HHHhchHHHHHHHHHhC-CCHHHHHhh
Q 005513 359 EVVSSMKDLINFCWEQK-VGPIEGLKS 384 (693)
Q Consensus 359 EVMSqMKdLM~FSk~Nn-LSPiEALk~ 384 (693)
|||++|+|||.|++.|+ +||+|||++
T Consensus 214 evms~M~~Lm~fs~~~~~~sP~eaL~~ 240 (240)
T PF01803_consen 214 EVMSQMKDLMSFSKQNNILSPLEALEQ 240 (240)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHhcC
Confidence 99999999999999998 899999985
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=99.97 E-value=1.2e-31 Score=276.81 Aligned_cols=217 Identities=18% Similarity=0.329 Sum_probs=190.3
Q ss_pred ccCCCcCCchhHHHHHHHHHHHHhCCCCCCchhHHHHHHHHhcCCCCcEEEEeeccCCCCCCcccccccccccccccccc
Q 005513 109 NATKRPYDSGVCARRLMQYLYHQRQRPPDNTIAYWRKFVAEYYSPRAKKRWCLSLYDNVGHHALGVFPQAAMDAWQCDIC 188 (693)
Q Consensus 109 ~~~~~py~~G~c~lRLlQfiehLs~rp~~ndI~YWrkFV~EFFSP~AvlR~tls~~d~~g~hs~GvfPq~a~d~W~cdic 188 (693)
-..+.+| ....-.||+++..+|..+.+..|-.||+.|..|||.++|+|.+++ |
T Consensus 40 ~~rh~~y-~s~~e~Ri~emNkRLq~~se~sdN~WWDaFstEFFeDDa~Lt~~f--------------------------c 92 (415)
T KOG2181|consen 40 FQRHGNY-VSPLEFRIHEMNKRLQIFSEVSDNQWWDAFSTEFFEDDAKLTFVF--------------------------C 92 (415)
T ss_pred ccccCCC-cCcchhhHHHHHHHHHHhcccchhhhHHhhhhhhhcCCceEEEEE--------------------------E
Confidence 3566788 456689999999999999999999999999999999999999875 5
Q ss_pred CCCCCceeEEcccchhHHHHHHhhcCcceEEEeeCCCcceecCCCcEEEEeCceEEEEEec---CeEEEEEEEEEEEe--
Q 005513 189 GSKSGRGFEATFEVLPRLNEIKFGSGVIDELMFLDLPRECRFPSGIMMLEYGKAVQESVYE---QLRIVREGQLRIIF-- 263 (693)
Q Consensus 189 ~sk~~K~FEIt~~vLPRfF~t~FeSGV~~~qL~Ld~prE~vLpNGsi~LEc~KAs~~y~Ye---gS~Vv~~GqLRiiF-- 263 (693)
.++++|.|.|++.+|||||++.|++||++++++|..++|. +.||++.+||+.+++++.|. ...|+.+|.|.+.|
T Consensus 93 lEdgpkRYtIgRtlIPrfFrsIfegG~~eLyyvLkh~ket-~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~f 171 (415)
T KOG2181|consen 93 LEDGPKRYTIGRTLIPRFFRSIFEGGMRELYYVLKHPKET-LHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAF 171 (415)
T ss_pred ecCCcceeeeccchhHHHHHHHHhcchhhhhhhhcCchhh-hcCCceeeeccceeEEeecCCccceeeeccceEEEEeeh
Confidence 6788999999999999999999999999999999999776 89999999999999999997 49999999999875
Q ss_pred CcccceEEEEEeecceeccccccchhhhHHHHHHhhhhccccccccCCCCCchhhhhhchhhhHhhhhhhccccccCCCC
Q 005513 264 TNDLKILSWEFCARRHEELLPRRLVAPQVNQLLQVAQKCQSTISESGSEGISQQDLQTNSNMVLTAGRQLAKSLELQSLN 343 (693)
Q Consensus 264 d~dLKIEswEF~~~sHEEyIpR~~Le~qvn~lie~aqK~Qs~i~EsgsdgvS~eD~k~np~m~k~karQLaksLp~s~Vn 343 (693)
|..+||+.|+|.++.|.|+|+|+.|.... + . |. + ...|+.| +++
T Consensus 172 Dd~MRIK~Wh~~ik~~rElvprsil~~~a-------~--------~--------dp----~----~ldq~~k-----Nit 215 (415)
T KOG2181|consen 172 DDVMRIKAWHLEIKRSRELVPRSILQNTA-------D--------Y--------DP----E----ALDQEQK-----NIT 215 (415)
T ss_pred hhhhhhhheeeeeeccccccchhhhhccC-------C--------C--------Ch----h----hhChhhc-----ccc
Confidence 78899999999999999999999985311 1 0 10 1 1123333 789
Q ss_pred CCCcchhhhhHhhHHHHHhchHHHHHHHHHhCCCHHHHHhhhHhhh
Q 005513 344 DLGFSKRYVRCLQISEVVSSMKDLINFCWEQKVGPIEGLKSFPRHA 389 (693)
Q Consensus 344 ~~GIpe~vMRcLQIaEVMSqMKdLM~FSk~NnLSPiEALk~yv~~~ 389 (693)
++||++.++.+|.+|.|+..|++||+-.|...|+|+||||..+.+-
T Consensus 216 R~G~~nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLFQk 261 (415)
T KOG2181|consen 216 RMGFFNSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLFQK 261 (415)
T ss_pred ccccchhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999998653
No 3
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=68.45 E-value=2.2 Score=54.10 Aligned_cols=10 Identities=10% Similarity=0.009 Sum_probs=4.6
Q ss_pred HHHHHHHHhC
Q 005513 124 LMQYLYHQRQ 133 (693)
Q Consensus 124 LlQfiehLs~ 133 (693)
+-|+-.+|++
T Consensus 2195 VRQlQ~qLs~ 2204 (2220)
T KOG3598|consen 2195 VRQLQMQLSA 2204 (2220)
T ss_pred HHHHHHHhhh
Confidence 3444444554
No 4
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=59.76 E-value=20 Score=38.06 Aligned_cols=32 Identities=28% Similarity=0.524 Sum_probs=21.7
Q ss_pred HHHHHHHHHhccCccccccCChHHHHHHHHHH
Q 005513 34 QQQVLQQLLQRQDPVQLQGRNPQLQALLQQQQ 65 (693)
Q Consensus 34 ~q~~~qq~~~~q~~~~~~~~~~~~~~l~~q~~ 65 (693)
.++||+.|+.|-......-+.|++.+||+++-
T Consensus 5 E~qLI~~lf~RL~~ae~~prD~eAe~lI~~~~ 36 (247)
T PF09849_consen 5 ERQLIDDLFSRLKQAEAQPRDPEAEALIAQAL 36 (247)
T ss_pred HHHHHHHHHHHHHhccCCCCCHHHHHHHHHHH
Confidence 35677777776655555667777777777765
No 5
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=52.14 E-value=14 Score=47.37 Aligned_cols=9 Identities=11% Similarity=-0.045 Sum_probs=3.4
Q ss_pred CcCCchhHH
Q 005513 113 RPYDSGVCA 121 (693)
Q Consensus 113 ~py~~G~c~ 121 (693)
.|....+++
T Consensus 2174 qplf~RQgl 2182 (2220)
T KOG3598|consen 2174 QPLFRRQGL 2182 (2220)
T ss_pred chhhHHHHH
Confidence 343333333
No 6
>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=29.36 E-value=49 Score=32.98 Aligned_cols=36 Identities=31% Similarity=0.460 Sum_probs=28.4
Q ss_pred ecCCCcEEEEeCceEEEEEecCeEEEEEEEEEEEeC
Q 005513 229 RFPSGIMMLEYGKAVQESVYEQLRIVREGQLRIIFT 264 (693)
Q Consensus 229 vLpNGsi~LEc~KAs~~y~YegS~Vv~~GqLRiiFd 264 (693)
.|.-|.+-+|-....|++.|+-..+|++|+|.+..+
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 577888888876666667777899999999998765
No 7
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=27.75 E-value=73 Score=40.91 Aligned_cols=14 Identities=43% Similarity=0.389 Sum_probs=6.3
Q ss_pred CCChhHHHHHHHHH
Q 005513 546 QGNQAMQQQMIQQL 559 (693)
Q Consensus 546 ~~~~~~~~~~~~ql 559 (693)
.-|+..+|+|-++|
T Consensus 2073 ~~n~s~~qq~~~~~ 2086 (2131)
T KOG4369|consen 2073 TTNPSRTQQMYQQY 2086 (2131)
T ss_pred CCCccHHHHHHHHh
Confidence 34444444444444
No 8
>COG3185 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]
Probab=22.38 E-value=64 Score=36.20 Aligned_cols=144 Identities=16% Similarity=0.193 Sum_probs=86.5
Q ss_pred HHHHHHHhCCCCCCchhHHHHHHHHhcCCCCcEEEEeeccCCCCCCcccccccccccc----ccccccCCCCCceeEEcc
Q 005513 125 MQYLYHQRQRPPDNTIAYWRKFVAEYYSPRAKKRWCLSLYDNVGHHALGVFPQAAMDA----WQCDICGSKSGRGFEATF 200 (693)
Q Consensus 125 lQfiehLs~rp~~ndI~YWrkFV~EFFSP~AvlR~tls~~d~~g~hs~GvfPq~a~d~----W~cdic~sk~~K~FEIt~ 200 (693)
+.++||+...-.-..+.=|-.|-.+.|.=.-+--+-+ +++ -+||..+. |.+ -...+..+.+. .
T Consensus 165 ~~~IDHl~~nv~~~~md~w~~FY~~if~~~~~~~fdi-----~~p-~tgl~Sra-m~Sp~G~vrlplN~s~~~------~ 231 (363)
T COG3185 165 LTAIDHLTHNVKAGQMDTWVLFYESLFGFREIQYFDI-----PGP-ITGLRSRA-MVSPCGKVRLPLNESADD------K 231 (363)
T ss_pred ceeechhhhhcchhhHHHHHHHHHHHhCccceeeEec-----cCC-cccEEEee-EecCCCcEEeecccCCCc------h
Confidence 3578999887777888889999999985432222111 111 12333221 110 00011111222 2
Q ss_pred cchhHHHHHHhhcCcceEEEeeCCC---cceecCCCcEEEEeCceEEEEEecC--eEEEEEE-------EEEEEeCcccc
Q 005513 201 EVLPRLNEIKFGSGVIDELMFLDLP---RECRFPSGIMMLEYGKAVQESVYEQ--LRIVREG-------QLRIIFTNDLK 268 (693)
Q Consensus 201 ~vLPRfF~t~FeSGV~~~qL~Ld~p---rE~vLpNGsi~LEc~KAs~~y~Yeg--S~Vv~~G-------qLRiiFd~dLK 268 (693)
+.+-+|....+.+||-.|-+..+.. .+....+|.-+++.++ .+|+. -+|..++ ...|+.|.+--
T Consensus 232 sqi~efl~~y~G~GIQHIA~~T~dI~~tv~~lr~rG~~fl~ip~----tYYd~~~~R~~~~~e~ld~Lr~~~IL~D~~~~ 307 (363)
T COG3185 232 SQIGEFLREYRGEGIQHIAFGTDDIYATVAALRERGVKFLPIPE----TYYDDLDARFPLHGEFLDALRELEILYDGDGG 307 (363)
T ss_pred hHHHHHHHHhCCCcceEEEecccHHHHHHHHHHHcCCccCCCch----hHHHHHhhcCCCChHHHHHHHhcCeEeecCCC
Confidence 3688999999999999999988875 3344568999998666 56774 4444444 35577775333
Q ss_pred e-EEEEEeeccee-----ccccc
Q 005513 269 I-LSWEFCARRHE-----ELLPR 285 (693)
Q Consensus 269 I-EswEF~~~sHE-----EyIpR 285 (693)
= +.+.+-++.+. |.|.|
T Consensus 308 ~~~lLQift~~~~g~~FFEiIeR 330 (363)
T COG3185 308 GGELLQIFTRTFIGPFFFEIIER 330 (363)
T ss_pred CcEEEEEecccccCceeEEEEEe
Confidence 3 88888888854 45555
No 9
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=22.30 E-value=1.1e+02 Score=32.65 Aligned_cols=40 Identities=20% Similarity=0.302 Sum_probs=33.1
Q ss_pred cceecCCCcEEEEeCceEEEEEecCeEEEEEEEEEEEeCc
Q 005513 226 RECRFPSGIMMLEYGKAVQESVYEQLRIVREGQLRIIFTN 265 (693)
Q Consensus 226 rE~vLpNGsi~LEc~KAs~~y~YegS~Vv~~GqLRiiFd~ 265 (693)
.+..+.-|.+.+|.....|++.|+....+++|.+++..+.
T Consensus 153 d~s~m~aGf~~~~~~sf~wtl~~dEi~YVLEGe~~l~IdG 192 (233)
T PRK15457 153 DGSSMAAGFMQWENAFFPWTLNYDEIDMVLEGELHVRHEG 192 (233)
T ss_pred CCCceeeEEEEEecCccceeccceEEEEEEEeEEEEEECC
Confidence 4456788899999888888888888999999999998763
No 10
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=13.82 E-value=1.6e+02 Score=35.85 Aligned_cols=19 Identities=16% Similarity=0.356 Sum_probs=11.2
Q ss_pred hhhhHHhhhhhccCCCCcc
Q 005513 658 DDIDQDIANEFTENGFFNN 676 (693)
Q Consensus 658 ~~~~~~~~~~~~~~~~~~~ 676 (693)
+|||.+-.|.|.|--+|.+
T Consensus 536 ~~MV~~CE~RLLE~QYF~s 554 (1179)
T KOG3648|consen 536 EKMVEDCEHRLLELQYFIS 554 (1179)
T ss_pred chhhHHHHHHHHHHHHHHh
Confidence 3566666666666655543
Done!