Query 007092
Match_columns 618
No_of_seqs 128 out of 179
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 18:49:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007092hhsearch_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 7.4E-64 1.6E-68 498.2 23.8 237 46-309 1-240 (240)
2 KOG2181 LIM domain binding pro 100.0 1.7E-32 3.7E-37 280.1 15.5 212 38-313 44-260 (415)
3 KOG3648 Golgi apparatus protei 45.2 9.2 0.0002 45.0 0.9 19 583-601 536-554 (1179)
4 PF06249 EutQ: Ethanolamine ut 26.3 60 0.0013 31.9 2.9 36 154-189 76-111 (152)
5 KOG3598 Thyroid hormone recept 25.6 59 0.0013 41.9 3.3 14 33-46 2169-2182(2220)
6 PRK15457 ethanolamine utilizat 20.1 1.3E+02 0.0028 31.6 4.1 40 151-190 153-192 (233)
7 KOG3648 Golgi apparatus protei 19.8 1.2E+02 0.0025 36.5 4.0 14 4-17 67-80 (1179)
8 KOG1819 FYVE finger-containing 17.5 1.1E+02 0.0024 35.5 3.2 22 7-28 814-835 (990)
9 PF09943 DUF2175: Uncharacteri 17.4 65 0.0014 29.8 1.1 10 107-116 2-11 (101)
10 KOG3598 Thyroid hormone recept 15.4 1.3E+02 0.0028 39.1 3.2 14 45-58 2191-2204(2220)
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=7.4e-64 Score=498.16 Aligned_cols=237 Identities=38% Similarity=0.581 Sum_probs=211.0
Q ss_pred HHHHHHHHHHHhCC-CCCCchhHHHHHHHHhcCCCccEEEEeeccCCCCCCccccccccccccccccccCCCCCceeEEc
Q 007092 46 ARRLMQYLYHQRQR-PPDNTIAYWRKFVAEYYSPRAKKRWCLSLYDNVGHHALGVFPQAAMDAWQCDICGSKSGRGFEAT 124 (618)
Q Consensus 46 ~lRLlqfiehLs~r-p~~ndI~YW~kFV~EFFSP~AvlR~tls~~d~~g~~s~Gvfp~~a~d~w~cdic~sk~~K~FEIt 124 (618)
++||++|+++|+++ ++++|++||++||+|||+|+|++|||++.+++. ..+|+|||+
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 889999999999999999999999999643221 125999999
Q ss_pred ccchhHHHHHHhhcCcceEEEEeCCCcceecCCCcEEEEeCceEEEEEec-CeEEEEEEEEEEEeCcccceEEEEEeecc
Q 007092 125 FEVLPRLNEIKFGSGVIDELMFLDLPRECRFPSGIMMLEYGKAVQESVYE-QLRIVREGQLRIIFTNDLKILSWEFCARR 203 (618)
Q Consensus 125 ~~vLPRfF~t~FeSGV~~~qL~Ld~prE~~LpNGsi~lE~~KAs~~y~Ye-gs~Vv~~G~LRiiFd~~LKIEs~EF~~~s 203 (618)
+++|||||+++|++||++|+|++++++|++++||+|+|||+||+++|||+ |++|+++|+||++||++|||||||||+++
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 99999999999999999999999999999999999999999999999998 79999999999999999999999999999
Q ss_pred eeccccccchhhhhHHHHHhhhhccccccccCCCCCChhhhhhhhhhhhhhhhhhccccccCCCCCCCcchhhhhHhhHH
Q 007092 204 HEELLPRRLVAPQVNQLLQVAQKCQSTISESGSEGISQQDLQTNSNMVLTAGRQLAKSLELQSLNDLGFSKRYVRCLQIS 283 (618)
Q Consensus 204 HEEyIpR~~L~~qvn~Lie~aqK~Qs~i~es~s~g~s~~D~k~n~~m~~~k~rQLak~Lp~s~Vn~~Gip~~vmR~LQIa 283 (618)
|+|||+|++|++++.....+.++++... ++....+|+.+++.....+.+++.+.||.++|+++|+|+++||||||+
T Consensus 138 ~~e~I~r~~l~~~~~~~~~~~~~~~~~~----~~~k~~~~~~~~~~~~~~~~~~~~~~Lp~~~v~~~Gi~~~~mr~Lqi~ 213 (240)
T PF01803_consen 138 HEEYIPRSALEQQASNLHPSVQIFQKLS----PDQKQSPDMSKNSKARQQKSPQLPPSLPSSNVNEFGIPERVMRCLQIA 213 (240)
T ss_pred ccccCcHHHHHHhhccchhhhHHhhhcc----cccccccchhhhhhhhhhcccccCCCcccCCCCcCCCCHHHHHHHHHH
Confidence 9999999999998766555555554432 222345677777666656677888889999999999999999999999
Q ss_pred HHHhchHHHHHHHHHhC-CCHHHHHhh
Q 007092 284 EVVSSMKDLINFCWEQK-VGPIEGLKS 309 (618)
Q Consensus 284 EVMS~MkdLm~FSk~nn-LsP~EALk~ 309 (618)
|||++|+|||.|++.|+ +||+|||++
T Consensus 214 evms~M~~Lm~fs~~~~~~sP~eaL~~ 240 (240)
T PF01803_consen 214 EVMSQMKDLMSFSKQNNILSPLEALEQ 240 (240)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHhcC
Confidence 99999999999999998 799999985
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=100.00 E-value=1.7e-32 Score=280.06 Aligned_cols=212 Identities=19% Similarity=0.343 Sum_probs=187.6
Q ss_pred CCcCcchHHHHHHHHHHHHhCCCCCCchhHHHHHHHHhcCCCccEEEEeeccCCCCCCccccccccccccccccccCCCC
Q 007092 38 RPYDSGVCARRLMQYLYHQRQRPPDNTIAYWRKFVAEYYSPRAKKRWCLSLYDNVGHHALGVFPQAAMDAWQCDICGSKS 117 (618)
Q Consensus 38 ~py~~G~c~lRLlqfiehLs~rp~~ndI~YW~kFV~EFFSP~AvlR~tls~~d~~g~~s~Gvfp~~a~d~w~cdic~sk~ 117 (618)
.+| ....-.||++++++|..+.+..|..||+.|..|||.++|+|.+++ |.+++
T Consensus 44 ~~y-~s~~e~Ri~emNkRLq~~se~sdN~WWDaFstEFFeDDa~Lt~~f--------------------------clEdg 96 (415)
T KOG2181|consen 44 GNY-VSPLEFRIHEMNKRLQIFSEVSDNQWWDAFSTEFFEDDAKLTFVF--------------------------CLEDG 96 (415)
T ss_pred CCC-cCcchhhHHHHHHHHHHhcccchhhhHHhhhhhhhcCCceEEEEE--------------------------EecCC
Confidence 355 455679999999999999999999999999999999999999876 66788
Q ss_pred CceeEEcccchhHHHHHHhhcCcceEEEEeCCCcceecCCCcEEEEeCceEEEEEec---CeEEEEEEEEEEE--eCccc
Q 007092 118 GRGFEATFEVLPRLNEIKFGSGVIDELMFLDLPRECRFPSGIMMLEYGKAVQESVYE---QLRIVREGQLRII--FTNDL 192 (618)
Q Consensus 118 ~K~FEIt~~vLPRfF~t~FeSGV~~~qL~Ld~prE~~LpNGsi~lE~~KAs~~y~Ye---gs~Vv~~G~LRii--Fd~~L 192 (618)
+|.|.|++.+|||||++.|++||++++++|..++|. +.||++.+||+.+++++.|. -..|+.+|+|.+. ||..+
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 999999999999999999999999999999999776 89999999999999999997 3999999999986 57889
Q ss_pred ceEEEEEeecceeccccccchhhhhHHHHHhhhhccccccccCCCCCChhhhhhhhhhhhhhhhhhccccccCCCCCCCc
Q 007092 193 KILSWEFCARRHEELLPRRLVAPQVNQLLQVAQKCQSTISESGSEGISQQDLQTNSNMVLTAGRQLAKSLELQSLNDLGF 272 (618)
Q Consensus 193 KIEs~EF~~~sHEEyIpR~~L~~qvn~Lie~aqK~Qs~i~es~s~g~s~~D~k~n~~m~~~k~rQLak~Lp~s~Vn~~Gi 272 (618)
||+.|+|.++.|.|+|+|+.|.... +. |.. ...|+.| ++++.|+
T Consensus 176 RIK~Wh~~ik~~rElvprsil~~~a-------~~----------------dp~--------~ldq~~k-----NitR~G~ 219 (415)
T KOG2181|consen 176 RIKAWHLEIKRSRELVPRSILQNTA-------DY----------------DPE--------ALDQEQK-----NITRMGF 219 (415)
T ss_pred hhhheeeeeeccccccchhhhhccC-------CC----------------Chh--------hhChhhc-----ccccccc
Confidence 9999999999999999999985311 10 111 1233333 6899999
Q ss_pred chhhhhHhhHHHHHhchHHHHHHHHHhCCCHHHHHhhhHHh
Q 007092 273 SKRYVRCLQISEVVSSMKDLINFCWEQKVGPIEGLKSFPRH 313 (618)
Q Consensus 273 p~~vmR~LQIaEVMS~MkdLm~FSk~nnLsP~EALk~yv~~ 313 (618)
++.++.+|.+|.|+..|++||.-+|...|+|+||||..+-+
T Consensus 220 ~nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLFQ 260 (415)
T KOG2181|consen 220 FNSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLFQ 260 (415)
T ss_pred chhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999865
No 3
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.17 E-value=9.2 Score=44.95 Aligned_cols=19 Identities=16% Similarity=0.356 Sum_probs=10.4
Q ss_pred hhhhHHhhhhhccCCCCcc
Q 007092 583 DDIDQDIANEFTENGFFNN 601 (618)
Q Consensus 583 ~~~~~~~~~~~~~~~~~~~ 601 (618)
+|||.+-.|.|.|--+|.+
T Consensus 536 ~~MV~~CE~RLLE~QYF~s 554 (1179)
T KOG3648|consen 536 EKMVEDCEHRLLELQYFIS 554 (1179)
T ss_pred chhhHHHHHHHHHHHHHHh
Confidence 3455555666655555543
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=26.26 E-value=60 Score=31.89 Aligned_cols=36 Identities=31% Similarity=0.460 Sum_probs=27.9
Q ss_pred ecCCCcEEEEeCceEEEEEecCeEEEEEEEEEEEeC
Q 007092 154 RFPSGIMMLEYGKAVQESVYEQLRIVREGQLRIIFT 189 (618)
Q Consensus 154 ~LpNGsi~lE~~KAs~~y~Yegs~Vv~~G~LRiiFd 189 (618)
.|.-|.+-+|-....|++.|+-..+|++|+|.+..+
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 577788888876666666667899999999998755
No 5
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=25.59 E-value=59 Score=41.85 Aligned_cols=14 Identities=14% Similarity=0.109 Sum_probs=7.0
Q ss_pred cCcCCCCcCcchHH
Q 007092 33 ANATKRPYDSGVCA 46 (618)
Q Consensus 33 ~~~~~~py~~G~c~ 46 (618)
+.+-+.|....+++
T Consensus 2169 a~qq~qplf~RQgl 2182 (2220)
T KOG3598|consen 2169 AEQQRQPLFRRQGL 2182 (2220)
T ss_pred cccccchhhHHHHH
Confidence 33444555555554
No 6
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=20.09 E-value=1.3e+02 Score=31.64 Aligned_cols=40 Identities=20% Similarity=0.302 Sum_probs=32.7
Q ss_pred cceecCCCcEEEEeCceEEEEEecCeEEEEEEEEEEEeCc
Q 007092 151 RECRFPSGIMMLEYGKAVQESVYEQLRIVREGQLRIIFTN 190 (618)
Q Consensus 151 rE~~LpNGsi~lE~~KAs~~y~Yegs~Vv~~G~LRiiFd~ 190 (618)
-+..+.-|.+.+|.....|++.|+....+++|.+++..+.
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 4456778889999888777777778999999999998763
No 7
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=19.79 E-value=1.2e+02 Score=36.46 Aligned_cols=14 Identities=79% Similarity=0.767 Sum_probs=7.1
Q ss_pred hHHHHHHHHHHHHH
Q 007092 4 LQRAQLQQQQQQQM 17 (618)
Q Consensus 4 ~~~~~~~~~~~~~~ 17 (618)
||-.||||||||||
T Consensus 67 ~~~~~~~~~~~~~~ 80 (1179)
T KOG3648|consen 67 LQSSQLQQQQQQQQ 80 (1179)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555555554444
No 8
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=17.47 E-value=1.1e+02 Score=35.46 Aligned_cols=22 Identities=55% Similarity=0.536 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 007092 7 AQLQQQQQQQMQMRQQMQQQQQ 28 (618)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~q~ 28 (618)
+||.|..|||||+|-|.|||-|
T Consensus 814 aqlrqleqqqqqqqlqiqlqrq 835 (990)
T KOG1819|consen 814 AQLRQLEQQQQQQQLQIQLQRQ 835 (990)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 4555544444444444555533
No 9
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=17.37 E-value=65 Score=29.81 Aligned_cols=10 Identities=50% Similarity=1.517 Sum_probs=8.5
Q ss_pred cccccccCCC
Q 007092 107 AWQCDICGSK 116 (618)
Q Consensus 107 ~w~cdic~sk 116 (618)
.|+|.+|+.+
T Consensus 2 kWkC~iCg~~ 11 (101)
T PF09943_consen 2 KWKCYICGKP 11 (101)
T ss_pred ceEEEecCCe
Confidence 4999999876
No 10
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=15.36 E-value=1.3e+02 Score=39.13 Aligned_cols=14 Identities=14% Similarity=-0.014 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHhC
Q 007092 45 CARRLMQYLYHQRQ 58 (618)
Q Consensus 45 c~lRLlqfiehLs~ 58 (618)
.+-++-|+-.+|++
T Consensus 2191 taalVRQlQ~qLs~ 2204 (2220)
T KOG3598|consen 2191 TAALVRQLQMQLSA 2204 (2220)
T ss_pred HHHHHHHHHHHhhh
Confidence 34444455555554
Done!