Query 042790
Match_columns 617
No_of_seqs 128 out of 180
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:31:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042790.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042790hhsearch_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 6.1E-65 1.3E-69 506.6 23.8 237 262-524 1-240 (240)
2 KOG2181 LIM domain binding pro 100.0 2.1E-35 4.5E-40 301.2 15.2 231 254-551 44-279 (415)
3 KOG4369 RTK signaling protein 69.2 2.2 4.9E-05 52.5 1.3 37 212-248 1856-1892(2131)
4 KOG3598 Thyroid hormone recept 51.5 8.6 0.00019 48.6 2.0 9 266-274 2196-2204(2220)
5 KOG3598 Thyroid hormone recept 44.9 16 0.00035 46.4 2.9 26 136-161 2000-2026(2220)
6 PF06249 EutQ: Ethanolamine ut 31.3 46 0.00099 32.7 3.1 36 370-405 76-111 (152)
7 PRK15457 ethanolamine utilizat 20.6 1.3E+02 0.0027 31.7 4.1 40 367-406 153-192 (233)
8 KOG3648 Golgi apparatus protei 20.2 61 0.0013 38.6 1.9 15 227-241 69-83 (1179)
9 PF07202 Tcp10_C: T-complex pr 15.7 3E+02 0.0065 27.7 5.4 50 354-404 73-125 (179)
10 COG5380 LimK Lipase chaperone 14.8 92 0.002 33.0 1.6 74 216-298 168-247 (283)
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=6.1e-65 Score=506.60 Aligned_cols=237 Identities=35% Similarity=0.584 Sum_probs=215.1
Q ss_pred HHHHHHHHHHhcCC-CCCCchhHHHHHHHHhcCCCCeeeeEeecccCCCCCcccccccccccccccccCCCCCCceeEEc
Q 042790 262 SRRIMQYMYHLRHR-PSENGIAYWRKFVAEYYAPCAKKRWCFSMYDNAGHHAFGFFPKAAVDAWQCDLCGTKPGRGFEAN 340 (617)
Q Consensus 262 ~lRLmqf~e~Ls~r-~~~ndIeYWqkFV~EFFSP~AvlR~tls~~d~~g~~a~Gvf~q~~~~~w~cd~~gsk~~KqFEIt 340 (617)
++||++|+++|+++ ++.+|++||++||+|||+|+|++|||++.+++.| .+|+|||+
T Consensus 1 ilRl~~~~~~l~~~~~~~~~~~yW~~fv~~fF~~~a~lr~~~~~~~~~~-----------------------~~k~FEi~ 57 (240)
T PF01803_consen 1 ILRLLEFIERLSNFSPNLNDIEYWQKFVHEFFSPDAVLRISLWNEDGNG-----------------------SPKQFEIT 57 (240)
T ss_pred CchHHHHHHHHHhhcCCCCcHHHHHHHHHHHcCCCeeEEEEEEcCCCCC-----------------------CCeeEEEc
Confidence 58999999999998 8899999999999999999999999998765421 25999999
Q ss_pred ccchhHHHHHHhhcCceeEEEeeCCCceeeccCCcEEEEeCceEEEEEe-cCeEEEEeEEEEEEeCcccceeEEEEEeec
Q 042790 341 LEAFPRLNKVMFESGVIDELLYLDMPHERVQFSGLMILEYGKAVQETVF-EQCRVVREGKLRIVFTPDLKILSWEFCAWQ 419 (617)
Q Consensus 341 ~~vLPRyF~t~FeSGV~~iqL~Ld~prE~vLpNG~ivlE~~KAs~iy~Y-dGs~Vv~~G~LR~~F~~dLKIEs~EF~~~~ 419 (617)
+++|||||+++|++||++++|++++++|++|+||+|+|||+||+++||| ||++|+++|+||++|++++||||||||+++
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 9999999999999999999999999999999999999999999999999 599999999999999999999999999999
Q ss_pred eeecccccchhhhhhHHHHhhhccccccccCCCCCCchhhhhhhhhhhhhhcccccccCCCCCCCCCcchhhhhHHHHHH
Q 042790 420 HEEFLPRNLVAPQVNQLVQTAQKYESTIYSGSDGATPHNLQANCNMFLVAGCQLARNTELDLVDDLGFPKRYVRSLQIAE 499 (617)
Q Consensus 420 HeEyIpR~~L~~qvn~l~q~aqK~qs~i~s~s~gks~eel~kN~n~fl~a~rqLa~~Lp~s~Vn~~Gip~~vmR~LQIsE 499 (617)
|+|||||++|++++.+....+++.+... ++.|..+++.+|++....+.+++++.||.++|+++|+|+++||||||+|
T Consensus 138 ~~e~I~r~~l~~~~~~~~~~~~~~~~~~---~~~k~~~~~~~~~~~~~~~~~~~~~~Lp~~~v~~~Gi~~~~mr~Lqi~e 214 (240)
T PF01803_consen 138 HEEYIPRSALEQQASNLHPSVQIFQKLS---PDQKQSPDMSKNSKARQQKSPQLPPSLPSSNVNEFGIPERVMRCLQIAE 214 (240)
T ss_pred ccccCcHHHHHHhhccchhhhHHhhhcc---cccccccchhhhhhhhhhcccccCCCcccCCCCcCCCCHHHHHHHHHHH
Confidence 9999999999988765444443332221 4466888999999888888888888899999999999999999999999
Q ss_pred HHhchHHHHHHhHhcC-CCHHHHHHH
Q 042790 500 IVNSMKDLISFSLNSN-TGPIESLKN 524 (617)
Q Consensus 500 VmsqMkdLM~FSk~n~-lSP~EALk~ 524 (617)
||++|++||.|+++|+ +||+|||++
T Consensus 215 vms~M~~Lm~fs~~~~~~sP~eaL~~ 240 (240)
T PF01803_consen 215 VMSQMKDLMSFSKQNNILSPLEALEQ 240 (240)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHhcC
Confidence 9999999999999995 999999984
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=100.00 E-value=2.1e-35 Score=301.22 Aligned_cols=231 Identities=21% Similarity=0.298 Sum_probs=197.2
Q ss_pred ccccchhHHHHHHHHHHHhcCCCCCCchhHHHHHHHHhcCCCCeeeeEeecccCCCCCcccccccccccccccccCCCCC
Q 042790 254 YALHSGVCSRRIMQYMYHLRHRPSENGIAYWRKFVAEYYAPCAKKRWCFSMYDNAGHHAFGFFPKAAVDAWQCDLCGTKP 333 (617)
Q Consensus 254 ~py~~G~c~lRLmqf~e~Ls~r~~~ndIeYWqkFV~EFFSP~AvlR~tls~~d~~g~~a~Gvf~q~~~~~w~cd~~gsk~ 333 (617)
.+|... --.|+++++.+|..+.+..|..||+.|..|||.++|+|. +..|.++|
T Consensus 44 ~~y~s~-~e~Ri~emNkRLq~~se~sdN~WWDaFstEFFeDDa~Lt--~~fclEdg------------------------ 96 (415)
T KOG2181|consen 44 GNYVSP-LEFRIHEMNKRLQIFSEVSDNQWWDAFSTEFFEDDAKLT--FVFCLEDG------------------------ 96 (415)
T ss_pred CCCcCc-chhhHHHHHHHHHHhcccchhhhHHhhhhhhhcCCceEE--EEEEecCC------------------------
Confidence 456643 568999999999999999999999999999999999994 44555554
Q ss_pred CceeEEcccchhHHHHHHhhcCceeEEEeeCCCceeeccCCcEEEEeCceEEEEEec---CeEEEEeEEEEEEeCcc--c
Q 042790 334 GRGFEANLEAFPRLNKVMFESGVIDELLYLDMPHERVQFSGLMILEYGKAVQETVFE---QCRVVREGKLRIVFTPD--L 408 (617)
Q Consensus 334 ~KqFEIt~~vLPRyF~t~FeSGV~~iqL~Ld~prE~vLpNG~ivlE~~KAs~iy~Yd---Gs~Vv~~G~LR~~F~~d--L 408 (617)
+|+|.|++.+|||||++.||+||++++++|.+++|. +.||++.+||+.+++++.|+ ...|+.+|+|.+.|..| +
T Consensus 97 pkRYtIgRtlIPrfFrsIfegG~~eLyyvLkh~ket-~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~fDd~M 175 (415)
T KOG2181|consen 97 PKRYTIGRTLIPRFFRSIFEGGMRELYYVLKHPKET-LHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAFDDVM 175 (415)
T ss_pred cceeeeccchhHHHHHHHHhcchhhhhhhhcCchhh-hcCCceeeeccceeEEeecCCccceeeeccceEEEEeehhhhh
Confidence 489999999999999999999999999999999775 99999999999999999996 69999999999999876 9
Q ss_pred ceeEEEEEeeceeecccccchhhhhhHHHHhhhccccccccCCCCCCchhhhhhhhhhhhhhcccccccCCCCCCCCCcc
Q 042790 409 KILSWEFCAWQHEEFLPRNLVAPQVNQLVQTAQKYESTIYSGSDGATPHNLQANCNMFLVAGCQLARNTELDLVDDLGFP 488 (617)
Q Consensus 409 KIEs~EF~~~~HeEyIpR~~L~~qvn~l~q~aqK~qs~i~s~s~gks~eel~kN~n~fl~a~rqLa~~Lp~s~Vn~~Gip 488 (617)
||+.|+|.+++|.|+|||+.|... |+. |. .+..++.++ ++++|++
T Consensus 176 RIK~Wh~~ik~~rElvprsil~~~-------a~~---------dp--------------~~ldq~~kN-----itR~G~~ 220 (415)
T KOG2181|consen 176 RIKAWHLEIKRSRELVPRSILQNT-------ADY---------DP--------------EALDQEQKN-----ITRMGFF 220 (415)
T ss_pred hhhheeeeeeccccccchhhhhcc-------CCC---------Ch--------------hhhChhhcc-----ccccccc
Confidence 999999999999999999998732 111 11 012233333 4899999
Q ss_pred hhhhhHHHHHHHHhchHHHHHHhHhcCCCHHHHHHHHHhhhcCCCCccchhhhhhccccCCCC
Q 042790 489 KRYVRSLQIAEIVNSMKDLISFSLNSNTGPIESLKNYCCEASGSKPLKDESLEKRSAQDLLND 551 (617)
Q Consensus 489 ~~vmR~LQIsEVmsqMkdLM~FSk~n~lSP~EALk~yv~~~~~~~~~~~~~~~q~~~~~lp~~ 551 (617)
+.++++|.+|.|+++|++||+.+|+..|+|+||||..+. +|||.|..+..++...-|+.
T Consensus 221 nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLF----QkwQrMvaPp~ep~~qkp~~ 279 (415)
T KOG2181|consen 221 NSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLF----QKWQRMVAPPPEPEKQKPAR 279 (415)
T ss_pred hhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHH----HHhhhhhcCCCCCCCCCCch
Confidence 999999999999999999999999889999999999997 67888877776655554554
No 3
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=69.22 E-value=2.2 Score=52.53 Aligned_cols=37 Identities=16% Similarity=0.212 Sum_probs=28.9
Q ss_pred hhHHhhhhccCCcccchhhhhhHHHhhhHhhhcCCCC
Q 042790 212 KSEQQNILHSTPEFGAVDIDKMQQQQMRHHQLQQPMH 248 (617)
Q Consensus 212 ~~~~~~~~~~~~~~q~~~~~~~~q~Q~r~~~qq~~~~ 248 (617)
++||||-||.+-+.|..|-+||+|||+|++.||-..+
T Consensus 1856 q~~qqq~iq~lq~~q~lqqqqq~~qq~~~~~~q~~sq 1892 (2131)
T KOG4369|consen 1856 QQQQQQQIQHLQQQQALQQQQQRIQQFQQQYQQHQSQ 1892 (2131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccCC
Confidence 5677777788878888888888888999998875544
No 4
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=51.45 E-value=8.6 Score=48.64 Aligned_cols=9 Identities=22% Similarity=0.150 Sum_probs=3.7
Q ss_pred HHHHHHhcC
Q 042790 266 MQYMYHLRH 274 (617)
Q Consensus 266 mqf~e~Ls~ 274 (617)
-|.-.+|++
T Consensus 2196 RQlQ~qLs~ 2204 (2220)
T KOG3598|consen 2196 RQLQMQLSA 2204 (2220)
T ss_pred HHHHHHhhh
Confidence 333334444
No 5
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=44.89 E-value=16 Score=46.41 Aligned_cols=26 Identities=15% Similarity=0.141 Sum_probs=11.0
Q ss_pred CCCCcCCCc-cccccCCCCCCCchhhH
Q 042790 136 GSSNTDGSS-TLQQTSHLGINSSQPRK 161 (617)
Q Consensus 136 gs~~~~~~~-~~~~~~~~~~~~~~~~~ 161 (617)
||-++.|.+ -|+|+.++.-+.++++-
T Consensus 2000 ~~m~p~g~~mp~~qs~q~~~~~~~l~p 2026 (2220)
T KOG3598|consen 2000 SSMPPSGPPMPMGQSMQSAGATQQLQP 2026 (2220)
T ss_pred CCcCCCCCCCCcccccccCCCceecCc
Confidence 344444433 34444444444444433
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=31.27 E-value=46 Score=32.67 Aligned_cols=36 Identities=25% Similarity=0.290 Sum_probs=28.4
Q ss_pred eccCCcEEEEeCceEEEEEecCeEEEEeEEEEEEeC
Q 042790 370 VQFSGLMILEYGKAVQETVFEQCRVVREGKLRIVFT 405 (617)
Q Consensus 370 vLpNG~ivlE~~KAs~iy~YdGs~Vv~~G~LR~~F~ 405 (617)
.|..|-+-+|-....|+|.||...+|++|+|.+..+
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 577888888876666666668999999999999866
No 7
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=20.56 E-value=1.3e+02 Score=31.69 Aligned_cols=40 Identities=18% Similarity=0.183 Sum_probs=33.1
Q ss_pred ceeeccCCcEEEEeCceEEEEEecCeEEEEeEEEEEEeCc
Q 042790 367 HERVQFSGLMILEYGKAVQETVFEQCRVVREGKLRIVFTP 406 (617)
Q Consensus 367 rE~vLpNG~ivlE~~KAs~iy~YdGs~Vv~~G~LR~~F~~ 406 (617)
.+..|.-|.+.+|.....|++.|+....+++|.+++..+.
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 4446888888899877777777789999999999999874
No 8
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.16 E-value=61 Score=38.57 Aligned_cols=15 Identities=27% Similarity=0.421 Sum_probs=7.6
Q ss_pred chhhhhhHHHhhhHh
Q 042790 227 AVDIDKMQQQQMRHH 241 (617)
Q Consensus 227 ~~~~~~~~q~Q~r~~ 241 (617)
-.||+||||||..++
T Consensus 69 ~~~~~~~~~~~~~~~ 83 (1179)
T KOG3648|consen 69 SSQLQQQQQQQQQQQ 83 (1179)
T ss_pred HHHHHHHHHHHHHHH
Confidence 346666655544333
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=15.71 E-value=3e+02 Score=27.70 Aligned_cols=50 Identities=28% Similarity=0.347 Sum_probs=26.8
Q ss_pred cCceeEEEeeCCCceeeccCCcEEEEeCceEEEEEe-cCe--EEEEeEEEEEEe
Q 042790 354 SGVIDELLYLDMPHERVQFSGLMILEYGKAVQETVF-EQC--RVVREGKLRIVF 404 (617)
Q Consensus 354 SGV~~iqL~Ld~prE~vLpNG~ivlE~~KAs~iy~Y-dGs--~Vv~~G~LR~~F 404 (617)
.|.++. .+.|+.+|-.+|+|.+-+-++.-.-+.+| ||. .+..+|.-++.|
T Consensus 73 ngQ~E~-h~pDG~keI~fPDGt~k~~~~dG~e~~~fpDGT~~~~~~nG~k~i~~ 125 (179)
T PF07202_consen 73 NGQIEK-HYPDGSKEIVFPDGTIKYIHPDGREETVFPDGTIVTIDPNGDKTITF 125 (179)
T ss_pred CCceEE-EcCCCCEEEEeCCCcEEEEeCCCcEEEECCCceEEEEeCCCcEEEEe
Confidence 444444 24455555566666665555555556666 453 333456655555
No 10
>COG5380 LimK Lipase chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=14.85 E-value=92 Score=32.96 Aligned_cols=74 Identities=20% Similarity=0.192 Sum_probs=51.8
Q ss_pred hhhhccCCcccchhhhhhHHH---hhhHhhhcCCCCCC-ccc-cc-ccchhHHHHHHHHHHHhcCCCCCCchhHHHHHHH
Q 042790 216 QNILHSTPEFGAVDIDKMQQQ---QMRHHQLQQPMHQV-PAA-YA-LHSGVCSRRIMQYMYHLRHRPSENGIAYWRKFVA 289 (617)
Q Consensus 216 ~~~~~~~~~~q~~~~~~~~q~---Q~r~~~qq~~~~~~-~~~-~p-y~~G~c~lRLmqf~e~Ls~r~~~ndIeYWqkFV~ 289 (617)
+.+++++|..|.--+++|+|+ |+-++||+.|.-+- -+. +. -.+-.+.-||-++- ..-+-|+.-..
T Consensus 168 ~aL~~~lPkvQeeri~iQ~q~~~~q~~~qLq~ag~gp~~iRl~rv~LvG~e~a~Rlaeld---------rqr~~w~~~~~ 238 (283)
T COG5380 168 QALLLDLPKVQEERIFIQRQEATAQLLPQLQQAGQGPTQIRLARVALVGEEGAQRLAELD---------RQRATWEQQFQ 238 (283)
T ss_pred HHHHhhCchhhHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHhhHHHHHHHHHHH---------HHHHHHHHHHH
Confidence 778999999999989998887 56677877766522 112 32 23336777877653 34567998889
Q ss_pred HhcCCCCee
Q 042790 290 EYYAPCAKK 298 (617)
Q Consensus 290 EFFSP~Avl 298 (617)
+||..++.+
T Consensus 239 dY~a~r~~I 247 (283)
T COG5380 239 DYYAARAAI 247 (283)
T ss_pred HHHHHHHHH
Confidence 999887554
Done!