Query 005633
Match_columns 686
No_of_seqs 136 out of 180
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 11:23:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005633hhsearch_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 7.3E-64 1.6E-68 501.4 22.5 236 71-356 2-240 (240)
2 KOG2181 LIM domain binding pro 100.0 7.5E-35 1.6E-39 300.0 12.8 225 62-363 34-263 (415)
3 COG4907 Predicted membrane pro 42.0 17 0.00036 42.0 2.2 19 605-623 571-589 (595)
4 KOG1883 Cofactor required for 33.0 24 0.00051 44.5 1.8 28 66-93 1476-1503(1517)
5 KOG3598 Thyroid hormone recept 28.5 31 0.00066 44.6 1.7 35 17-51 2133-2184(2220)
6 PF06249 EutQ: Ethanolamine ut 28.5 52 0.0011 32.7 3.0 36 202-237 76-111 (152)
7 PF06752 E_Pc_C: Enhancer of P 23.4 57 0.0012 34.5 2.3 15 212-226 137-151 (230)
8 KOG4369 RTK signaling protein 23.3 1E+02 0.0022 39.7 4.6 7 16-22 1866-1872(2131)
9 PRK15457 ethanolamine utilizat 20.3 1.3E+02 0.0029 31.9 4.3 39 200-238 154-192 (233)
10 KOG3875 Peroxisomal biogenesis 20.0 1.3E+02 0.0028 33.6 4.1 21 553-573 33-53 (362)
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=7.3e-64 Score=501.41 Aligned_cols=236 Identities=36% Similarity=0.611 Sum_probs=219.7
Q ss_pred HHHHHHHHHhhcC-ccccccCCccchhhhhhhheeeccccccccCCCHHHHHHHHHHhcCCCCceeEEeeecCCCCCccc
Q 005633 71 RRLTHYMYQQQHR-PEVRFSHHDESVVSLWCITIVICNSRVFVQDNNIEFWRKFVAEYFAPNAKKKWCVSMYGSGRQATG 149 (686)
Q Consensus 71 ~rl~~y~~~q~~r-p~~~~~~~~~~~~~~~~~~~~~c~~~v~kq~ndIeYWqkFV~EFFSP~AvlR~~~s~~~~~~~~tG 149 (686)
.||++|+++...| ++ ++|++||++||+|||+|+|++|||++.+++.
T Consensus 2 lRl~~~~~~l~~~~~~----------------------------~~~~~yW~~fv~~fF~~~a~lr~~~~~~~~~----- 48 (240)
T PF01803_consen 2 LRLLEFIERLSNFSPN----------------------------LNDIEYWQKFVHEFFSPDAVLRISLWNEDGN----- 48 (240)
T ss_pred chHHHHHHHHHhhcCC----------------------------CCcHHHHHHHHHHHcCCCeeEEEEEEcCCCC-----
Confidence 5999999999998 77 9999999999999999999999998875521
Q ss_pred cCccccccccccCCCCCceeeEcccchhHHHHHHhhcCcceEEEeecCCcceecCCCeEEEEeCceEEEEEec-CeEEEE
Q 005633 150 VFPQDVWHCEICNRKPGRGFEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVFE-QLRVVR 228 (686)
Q Consensus 150 vfpqdlW~cd~c~tk~~KqFEItt~vLPRfF~t~FeSGV~~iqLvLd~pRE~vLsNGsI~LEc~KAs~iy~Ye-gS~Vv~ 228 (686)
..+|+|||++++|||||+++|++||++++|+++++||++++||+|+|||+||+++|||+ |++|++
T Consensus 49 --------------~~~k~FEi~~~~lPR~f~~~~~sGv~~~~~~l~~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v~~ 114 (240)
T PF01803_consen 49 --------------GSPKQFEITRPLLPRYFRTLFESGVKRMQLVLDGPREQVLPNGSIFIECPRATFIYWYEDGSQVVH 114 (240)
T ss_pred --------------CCCeeEEEchHHHHHHHHHHhcCCceEEEEEecCCceEEcCCCeEEEEECCEEEEEEECCceEEEE
Confidence 12599999999999999999999999999999999999999999999999999999997 699999
Q ss_pred eeEEEEEeCCCcceeEEEEeecceeeccccchhhhHHhhhhhHHHHHHHHhhcCCCCCCchHhhhhhhhhHHHHHHHHHh
Q 005633 229 DGQLRIVFSPDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCNMFVASARQLAKA 308 (686)
Q Consensus 229 ~GqLRiiFdpdLKIE~wEF~~~sHEEyIpRs~L~~qv~~L~~~akk~qs~~qN~sd~ksspElsKN~n~fl~a~rQLas~ 308 (686)
+|+||++||++|||||||||+++|+|||+|++|++++.+.+.++++|++.. ++.|.++|+.|+++.+..+.+++.+.
T Consensus 115 ~G~lr~~f~~~lKIe~~df~~~~~~e~I~r~~l~~~~~~~~~~~~~~~~~~---~~~k~~~~~~~~~~~~~~~~~~~~~~ 191 (240)
T PF01803_consen 115 EGQLRAQFDPDLKIEWWDFCTRSHEEYIPRSALEQQASNLHPSVQIFQKLS---PDQKQSPDMSKNSKARQQKSPQLPPS 191 (240)
T ss_pred EeEEEEEECccccEEEEEEEeecccccCcHHHHHHhhccchhhhHHhhhcc---cccccccchhhhhhhhhhcccccCCC
Confidence 999999999999999999999999999999999999999999999999884 55789999999988877777788877
Q ss_pred ccCCcccCCCccccchhhhhHHHHHhchHHHHHHhhhcC-CChHHHHhh
Q 005633 309 LEVPLVNDLGYTKRYVRCLQISEVVNSMKDLIDYSRVTG-TGPMESLAK 356 (686)
Q Consensus 309 le~p~Vn~~GIpk~vMR~LQIsEVMSqMKdLM~FSk~n~-lSPiEALk~ 356 (686)
|+.++|+++|+++++||||||+|||++|+|||.|++.++ +||+|||++
T Consensus 192 Lp~~~v~~~Gi~~~~mr~Lqi~evms~M~~Lm~fs~~~~~~sP~eaL~~ 240 (240)
T PF01803_consen 192 LPSSNVNEFGIPERVMRCLQIAEVMSQMKDLMSFSKQNNILSPLEALEQ 240 (240)
T ss_pred cccCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHhcC
Confidence 888899999999999999999999999999999999655 999999985
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=100.00 E-value=7.5e-35 Score=300.03 Aligned_cols=225 Identities=20% Similarity=0.380 Sum_probs=185.0
Q ss_pred CCCCcchHHHHHHHHHHHhhcCccccccCCccchhhhhhhheeeccccccccCCCHHHHHHHHHHhcCCCCceeEEeeec
Q 005633 62 PVYEPGMCARRLTHYMYQQQHRPEVRFSHHDESVVSLWCITIVICNSRVFVQDNNIEFWRKFVAEYFAPNAKKKWCVSMY 141 (686)
Q Consensus 62 ~~~~~g~c~~rl~~y~~~q~~rp~~~~~~~~~~~~~~~~~~~~~c~~~v~kq~ndIeYWqkFV~EFFSP~AvlR~~~s~~ 141 (686)
.++|+| -+|...|+-|.-+|.- |+ --|+ +...+.+|..||+.|..|||.++|+|+|.|++.
T Consensus 34 ~~~~pg--~~rh~~y~s~~e~Ri~--------------em--NkRL-q~~se~sdN~WWDaFstEFFeDDa~Lt~~fclE 94 (415)
T KOG2181|consen 34 QATEPG--FQRHGNYVSPLEFRIH--------------EM--NKRL-QIFSEVSDNQWWDAFSTEFFEDDAKLTFVFCLE 94 (415)
T ss_pred ccCCCc--ccccCCCcCcchhhHH--------------HH--HHHH-HHhcccchhhhHHhhhhhhhcCCceEEEEEEec
Confidence 456776 4566666665555443 11 1111 223468888999999999999999999999885
Q ss_pred CCCCCccccCccccccccccCCCCCceeeEcccchhHHHHHHhhcCcceEEEeecCCcceecCCCeEEEEeCceEEEEEe
Q 005633 142 GSGRQATGVFPQDVWHCEICNRKPGRGFEATVEVLPRLFKIKYESGTLEELLYVDMPREYQNASGQIVLDYAKAIQESVF 221 (686)
Q Consensus 142 ~~~~~~tGvfpqdlW~cd~c~tk~~KqFEItt~vLPRfF~t~FeSGV~~iqLvLd~pRE~vLsNGsI~LEc~KAs~iy~Y 221 (686)
+ ++|.|.|++.+|||||+++||+||++++++|.+++| .+.||++.+||+.|++++.|
T Consensus 95 d----------------------gpkRYtIgRtlIPrfFrsIfegG~~eLyyvLkh~ke-t~hn~s~~~dcdq~~~iTqh 151 (415)
T KOG2181|consen 95 D----------------------GPKRYTIGRTLIPRFFRSIFEGGMRELYYVLKHPKE-TLHNGSQAYDCDQVLQITQH 151 (415)
T ss_pred C----------------------CcceeeeccchhHHHHHHHHhcchhhhhhhhcCchh-hhcCCceeeeccceeEEeec
Confidence 4 479999999999999999999999999999999988 69999999999999999999
Q ss_pred cC---eEEEEeeEEEEEeC--CCcceeEEEEeecceeeccccchhhhHHhhhhhHHHHHHHHhhcCCCCCCchHhhhhhh
Q 005633 222 EQ---LRVVRDGQLRIVFS--PDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKYQAATQNASSNLSAPELQNNCN 296 (686)
Q Consensus 222 eg---S~Vv~~GqLRiiFd--pdLKIE~wEF~~~sHEEyIpRs~L~~qv~~L~~~akk~qs~~qN~sd~ksspElsKN~n 296 (686)
+. .+|+.+|+|.++|. .-+||+.|+|.+++|.|+|+|+.|...+. .|....
T Consensus 152 gkp~ft~VctegrL~lEF~fDd~MRIK~Wh~~ik~~rElvprsil~~~a~----------------~dp~~l-------- 207 (415)
T KOG2181|consen 152 GKPSFTEVCTEGRLYLEFAFDDVMRIKAWHLEIKRSRELVPRSILQNTAD----------------YDPEAL-------- 207 (415)
T ss_pred CCccceeeeccceEEEEeehhhhhhhhheeeeeeccccccchhhhhccCC----------------CChhhh--------
Confidence 85 99999999999974 45999999999999999999998764210 011111
Q ss_pred hhHHHHHHHHHhccCCcccCCCccccchhhhhHHHHHhchHHHHHHhhhcCCChHHHHhhhhhccCC
Q 005633 297 MFVASARQLAKALEVPLVNDLGYTKRYVRCLQISEVVNSMKDLIDYSRVTGTGPMESLAKFPRRTSG 363 (686)
Q Consensus 297 ~fl~a~rQLas~le~p~Vn~~GIpk~vMR~LQIsEVMSqMKdLM~FSk~n~lSPiEALk~fv~~~~~ 363 (686)
+|+.| ++++.|+++.++.+|++|.|+++|++||+.+|.+.|+|+||||..+.+.-.
T Consensus 208 ------dq~~k-----NitR~G~~nsTlNylrlcvILePMQelMSrhKayalsPRdclKttLFQkwQ 263 (415)
T KOG2181|consen 208 ------DQEQK-----NITRMGFFNSTLNYLRLCVILEPMQELMSRHKAYALSPRDCLKTTLFQKWQ 263 (415)
T ss_pred ------Chhhc-----cccccccchhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHHHHHHHHHhh
Confidence 22222 389999999999999999999999999999999999999999999987643
No 3
>COG4907 Predicted membrane protein [Function unknown]
Probab=42.02 E-value=17 Score=41.97 Aligned_cols=19 Identities=37% Similarity=0.589 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCCCCCCCCc
Q 005633 605 NNPGIGTGGYGNMGGGLGQ 623 (686)
Q Consensus 605 ~~~~~~~~~~g~~g~g~~~ 623 (686)
..+|.||||+|.-|||+|-
T Consensus 571 ~~~~~~GGG~G~~gGg~GG 589 (595)
T COG4907 571 RRSSSSGGGGGFSGGGSGG 589 (595)
T ss_pred ccCCCCCCCCCcCCCCCCC
Confidence 3455666666656666654
No 4
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=32.99 E-value=24 Score=44.54 Aligned_cols=28 Identities=14% Similarity=0.202 Sum_probs=21.7
Q ss_pred cchHHHHHHHHHHHhhcCccccccCCcc
Q 005633 66 PGMCARRLTHYMYQQQHRPEVRFSHHDE 93 (686)
Q Consensus 66 ~g~c~~rl~~y~~~q~~rp~~~~~~~~~ 93 (686)
.|-.+..+|+|++|.+.+|-.-+++..-
T Consensus 1476 ~g~~~~~~~~y~qHmqqH~h~~~~~~~~ 1503 (1517)
T KOG1883|consen 1476 SGPVGHVPMQYGQHMQQHPHLPHHQQMP 1503 (1517)
T ss_pred cccccccchhhHHHHHhccCCCccccCC
Confidence 4677889999999999999865555443
No 5
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=28.53 E-value=31 Score=44.63 Aligned_cols=35 Identities=40% Similarity=0.409 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHH-----------------HHhhcccCCCCCchhhhhh
Q 005633 17 QQQRYLQLQQQHQQQQ-----------------LLKAMPQQRPQLPQHFVQQ 51 (686)
Q Consensus 17 ~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~ 51 (686)
|||++.|.|||+|+|+ -+++++|++|+++-|-+||
T Consensus 2133 qQq~~~q~qQqqq~q~qq~~q~~q~~q~Qq~~~~~qa~qq~qplf~RQglqq 2184 (2220)
T KOG3598|consen 2133 QQQEAYQKQQQQQEQKQQIEQNNQIMQEQQREEAYQAEQQRQPLFRRQGLQQ 2184 (2220)
T ss_pred HHHHHHHHHhhhhhhhhcccchhHHHHHHhhhcccccccccchhhHHHHHHH
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=28.47 E-value=52 Score=32.72 Aligned_cols=36 Identities=17% Similarity=0.317 Sum_probs=28.4
Q ss_pred ecCCCeEEEEeCceEEEEEecCeEEEEeeEEEEEeC
Q 005633 202 QNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFS 237 (686)
Q Consensus 202 vLsNGsI~LEc~KAs~iy~YegS~Vv~~GqLRiiFd 237 (686)
.++-|.+.+|-....|+|.||-..+|++|+|.+..+
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 578888888876666666667799999999999865
No 7
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=23.42 E-value=57 Score=34.54 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=6.2
Q ss_pred eCceEEEEEecCeEE
Q 005633 212 YAKAIQESVFEQLRV 226 (686)
Q Consensus 212 c~KAs~iy~YegS~V 226 (686)
|.-..++..-.++++
T Consensus 137 ~~~t~Q~L~gnn~~l 151 (230)
T PF06752_consen 137 CTSTTQVLIGNNIRL 151 (230)
T ss_pred CCCCceecccCcccc
Confidence 444444443333333
No 8
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=23.31 E-value=1e+02 Score=39.70 Aligned_cols=7 Identities=71% Similarity=0.733 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 005633 16 LQQQRYL 22 (686)
Q Consensus 16 ~~~~~~~ 22 (686)
|||+.-+
T Consensus 1866 lq~~q~l 1872 (2131)
T KOG4369|consen 1866 LQQQQAL 1872 (2131)
T ss_pred HHHHHHH
Confidence 3333333
No 9
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=20.28 E-value=1.3e+02 Score=31.93 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=32.8
Q ss_pred ceecCCCeEEEEeCceEEEEEecCeEEEEeeEEEEEeCC
Q 005633 200 EYQNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFSP 238 (686)
Q Consensus 200 E~vLsNGsI~LEc~KAs~iy~YegS~Vv~~GqLRiiFdp 238 (686)
+..++-|.+.+|.....|+|.|+....+++|.+++..+.
T Consensus 154 ~s~m~aGf~~~~~~sf~wtl~~dEi~YVLEGe~~l~IdG 192 (233)
T PRK15457 154 GSSMAAGFMQWENAFFPWTLNYDEIDMVLEGELHVRHEG 192 (233)
T ss_pred CCceeeEEEEEecCccceeccceEEEEEEEeEEEEEECC
Confidence 346888999999888888888888999999999998864
No 10
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.02 E-value=1.3e+02 Score=33.61 Aligned_cols=21 Identities=33% Similarity=0.551 Sum_probs=10.2
Q ss_pred ccccCCCCCCCCccccccccC
Q 005633 553 CSHLNGGSGGGGGMVGVGSLG 573 (686)
Q Consensus 553 s~~~~~~~~~~~~~~~~g~~g 573 (686)
+++.+|....+.|.-|-+..|
T Consensus 33 ~s~s~~~~~T~~G~~~~~~~g 53 (362)
T KOG3875|consen 33 SSVSNGNANTGPGIYGNSNYG 53 (362)
T ss_pred ccccCCcccCCCCccccccCC
Confidence 344455444445544455554
Done!