Query 009300
Match_columns 538
No_of_seqs 165 out of 208
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 22:52:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1793 Uncharacterized conser 100.0 2E-74 4.2E-79 593.5 24.1 339 172-536 65-417 (417)
2 COG5139 Uncharacterized conser 100.0 1.3E-49 2.9E-54 398.1 13.4 275 224-534 118-397 (397)
3 PF08711 Med26: TFIIS helical 99.1 1.1E-10 2.4E-15 90.5 3.6 53 337-396 1-53 (53)
4 cd00183 TFIIS_I N-terminal dom 98.2 2.7E-06 5.8E-11 71.1 6.6 58 330-395 18-75 (76)
5 smart00509 TFS2N Domain in the 97.7 4.5E-05 9.8E-10 63.8 4.1 54 335-396 21-74 (75)
6 TIGR01385 TFSII transcription 96.6 0.0018 3.8E-08 67.3 3.9 53 337-397 25-77 (299)
7 KOG1105 Transcription elongati 94.7 0.047 1E-06 57.0 5.4 73 314-397 7-80 (296)
8 PLN02976 amine oxidase 93.8 0.17 3.6E-06 62.6 8.0 86 302-398 1272-1359(1713)
9 PF06371 Drf_GBD: Diaphanous G 47.6 67 0.0015 29.8 6.9 56 290-345 83-143 (187)
10 PF10498 IFT57: Intra-flagella 42.8 61 0.0013 35.1 6.5 102 286-400 5-130 (359)
11 PF11176 DUF2962: Protein of u 38.3 67 0.0014 30.8 5.4 78 250-332 64-145 (155)
12 PF14278 TetR_C_8: Transcripti 38.1 68 0.0015 25.0 4.6 19 304-322 59-77 (77)
13 KOG3050 COP9 signalosome, subu 33.4 1E+02 0.0022 32.3 6.1 81 315-396 208-298 (299)
14 COG1390 NtpE Archaeal/vacuolar 30.2 5E+02 0.011 25.8 10.1 54 305-377 79-133 (194)
15 cd03567 VHS_GGA VHS domain fam 29.4 2.2E+02 0.0049 26.7 7.2 60 285-345 55-114 (139)
16 KOG2973 Uncharacterized conser 25.2 2.2E+02 0.0048 31.0 7.0 72 329-404 255-328 (353)
17 PRK13916 plasmid segregation p 21.5 88 0.0019 28.0 2.7 30 315-345 18-47 (97)
18 PF00514 Arm: Armadillo/beta-c 20.1 2.3E+02 0.005 20.3 4.4 37 303-345 3-39 (41)
No 1
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2e-74 Score=593.46 Aligned_cols=339 Identities=42% Similarity=0.616 Sum_probs=276.0
Q ss_pred HHHHHHHhhCCCCCCCc---cccccCCCCC-----CcccCCCCCCCCCCCCCCCCCCCCCCCccccCCCchHHHHHHhhc
Q 009300 172 MLNEMWNAVAPTGDSED---DQEGVRTLDD-----DNFIDDSGVDPSDRYGSDSEPRFAHDAPQAEEGDEDEEIKELFKM 243 (538)
Q Consensus 172 ~~~e~~~~i~~~~d~~~---~~e~~~t~~D-----d~fiDd~g~d~~d~~g~d~e~~~~~d~~~aee~e~Dd~i~~~lk~ 243 (538)
+..++|+.+. .+-+. +..+.++..+ -+|+.++|+++-+-++.+.........+.++..|...++.++|+|
T Consensus 65 ~~~~~~~~~~--~~~~r~~Kd~k~~~s~~~~e~~~~d~~~e~~~~~~e~~~~d~~d~~~~r~~~~~~~ed~~e~~~~~k~ 142 (417)
T KOG1793|consen 65 PADEDENSNL--EDRKRERKDEKGLDSDGDNEKEHEDESQETGQEFPESQDDDFGDTGGRRPKLKAKLEDILEKKAVRKM 142 (417)
T ss_pred ccchhhcccc--cchhhhhccccccccccccchhhhHhhhccccccccccccccccccccchhhHhhhhhHHHHHHHHhh
Confidence 6778888776 44443 3344444443 458889998877666555444556666778888999999999998
Q ss_pred cccccccCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHcCChHHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhc
Q 009300 244 GKKRKKNEKSPAEIA-LLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLE 322 (538)
Q Consensus 244 ~Kkkkk~~~~~~ei~-~~v~~Li~~M~~AAe~D~ean~~gkPAl~KLkmLpeV~~~L~K~~Lq~~fLd~giL~vl~~WLe 322 (538)
+++++++...+++|. .+|..|+.+|+.||+.|+++|.+++|||+||+|||.|+++|.|++||.+|||||||++|+.||+
T Consensus 143 r~kk~~~d~~~~~I~d~~v~~l~~~m~~aa~~D~~~N~e~kPA~~Klk~Lp~v~~vL~k~~L~et~LDngvL~~lk~WLe 222 (417)
T KOG1793|consen 143 RTKKRKNDDGPEEILDDEVSRLMERMEDAAEKDRELNREGKPATQKLKLLPLVVAVLSKKALQETFLDNGVLDSLKEWLE 222 (417)
T ss_pred hhhhccccCchHHHHHHHHHHHHHHHHHHHHHHHhhccccCchHHHHhccHHHHHHHhhhhHHHHHHhhhHHHHHHHHhc
Confidence 888888999999999 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhhhhhcCCccc
Q 009300 323 PLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIFNKSTRF 402 (538)
Q Consensus 323 PLPDgSLPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsRPI~~~ss~Y 402 (538)
||||||||||+||.+||+||.+|||.+ +|||++||||||||||++||+||++|++||..||++|+||||+++++|
T Consensus 223 PLPD~SLPal~Ir~~ll~iL~dlpi~~-----~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~st~y 297 (417)
T KOG1793|consen 223 PLPDGSLPALNIRKSLLDILNDLPIDK-----REHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKLSTNY 297 (417)
T ss_pred cCCCCCCcchHHHHHHHHHHhcCCcch-----HHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCCCCCc
Confidence 999999999999999999999999976 489999999999999999999999999999999999999999999999
Q ss_pred hhhhhh--h--hcc-CCCCCCCCCCchhhHhhhhcCCCCchhhhhhhhccCCCCCCccccCCCCcccccccCCCCCCCCC
Q 009300 403 EDMKTV--E--DDR-VPFRRPSAKKPASKAAAMESRDGDFDDLVISRERKSGQSSSGQHASRSDSSSRQHASRPEATPLD 477 (538)
Q Consensus 403 ~d~~~~--e--~er-~~~rr~~~kk~~~k~a~~esr~~dld~~~~~~~~k~G~~~~~~~a~r~~~~~r~rArvP~~s~~D 477 (538)
++|++. + ..+ .++|++..+.+.. .+. +..++. ..+ .++++++ -.+|+||+||+++++|
T Consensus 298 ~dm~~~~e~~de~r~~~~Rr~~~~~~~~--~~~--~~~d~~-~~i--------~~~e~g~----~~gr~Ra~vP~~s~~D 360 (417)
T KOG1793|consen 298 RDMRRMREERDEKRMPQSRRDSAKARKK--SGT--DPRDRG-SEI--------DTDEEGL----TTGRARARVPAPSTKD 360 (417)
T ss_pred hhhHHHHhhhhhhhhhhhhccccccccc--cCC--Cccccc-ccc--------chhhhcc----ccccccccCCCCCCCc
Confidence 999864 1 122 3344444332221 111 112221 001 0111111 1228999999999999
Q ss_pred eeeCCCCCCChHHHHHHhhhhchHHHHHHHHHHHHhhhccccccccccccccccCCccc
Q 009300 478 FVVRPQSKIDPEEVRARAKQVMQDQRRMKMNKKLQQLKAPRKKQLQATKLSVEGRGMLK 536 (538)
Q Consensus 478 YviRPkskvd~~~~rar~Kk~~~derr~Kl~kkL~qlk~~kKK~~RA~~ISIEGR~M~~ 536 (538)
|+|||+|+|+++ .+++.+.+....+.+++++++|++..|+|+.+|++||||||+|.+
T Consensus 361 y~irP~s~v~~~--~~~~~~~~~~~~r~~~~krk~q~k~kKsk~~~a~kvSiEGr~M~~ 417 (417)
T KOG1793|consen 361 YVIRPVSNVDPV--AARAEGVSSGLNREDMYKRKFQRKNKKSKSNQAVKVSIEGRGMGK 417 (417)
T ss_pred ceecCccccCHH--HHhhhcccccccHHHHHHHHHHHHhhhhccccceeeeeecCCCCC
Confidence 999999999997 455666666777888999999999999999999999999999974
No 2
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.3e-49 Score=398.06 Aligned_cols=275 Identities=28% Similarity=0.436 Sum_probs=216.8
Q ss_pred CCccccCCCchHHHHHHhhcccccc---ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHhhhHHHHHHHh
Q 009300 224 DAPQAEEGDEDEEIKELFKMGKKRK---KNEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLS 300 (538)
Q Consensus 224 d~~~aee~e~Dd~i~~~lk~~Kkkk---k~~~~~~ei~~~v~~Li~~M~~AAe~D~ean~~gkPAl~KLkmLpeV~~~L~ 300 (538)
+.+.|..+|.++.+.++++.++..+ +....+.-+++++..|..+|..||..|++.|..+.|||.||+|||+|.++|.
T Consensus 118 d~t~a~~~El~~~~dr~lK~p~~sr~rr~eD~leq~~de~~lrLk~~M~~aa~~D~~~n~e~~pAt~Kik~lp~V~~VL~ 197 (397)
T COG5139 118 DFTEAQSGELGDTGDRQLKAPAASRARRKEDLLEQTVDEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSDVLM 197 (397)
T ss_pred CCChhhhhhhhhhhhhhhccchhhhhhccccchHHHHHHHHHHHHHHHHHHHHhhhhhhhccCcchhhhhccHHHHHHHH
Confidence 4677888999999999999555433 2233455667889999999999999999999999999999999999999999
Q ss_pred hHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHH
Q 009300 301 KKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSN 380 (538)
Q Consensus 301 K~~Lq~~fLd~giL~vl~~WLePLPDgSLPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eN 380 (538)
|.+||.+|||||||+.|+.||+||||+|||||+||+.||.+|..|||.+ |||++||||+||+||+.+|++++++
T Consensus 198 k~~L~dtiLDnniLdsVr~WLEPLPD~SlP~~~IqksL~dvL~~lpI~t------EHL~eSgvGrIV~FYtiskk~e~~v 271 (397)
T COG5139 198 KKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKSLLDVLKTLPIHT------EHLVESGVGRIVYFYTISKKEEKEV 271 (397)
T ss_pred HHHHHHHHhhcchHHHHHhhhccCCCCCCcchHHHHHHHHHHhhCCchH------HHhhhcCCceEEEEEecCCcccHHH
Confidence 9999999999999999999999999999999999999999999999987 5899999999999999999999999
Q ss_pred HHHHHHHHHHhhhhhhcCCccchhhhhhhhc--cCCCCCCCCCCchhhHhhhhcCCCCchhhhhhhhccCCCCCCccccC
Q 009300 381 RKLAKDLVDKWSRPIFNKSTRFEDMKTVEDD--RVPFRRPSAKKPASKAAAMESRDGDFDDLVISRERKSGQSSSGQHAS 458 (538)
Q Consensus 381 KrlA~~LI~kWsRPI~~~ss~Y~d~~~~e~e--r~~~rr~~~kk~~~k~a~~esr~~dld~~~~~~~~k~G~~~~~~~a~ 458 (538)
+++|..||++|+||||+.|.+|+|.+....+ -..++.. .....+..++.++.- .+...+...-++.|+++++
T Consensus 272 ~r~A~~LV~eWtrpIik~s~nyRDk~i~~~~F~~E~~~~k----~~~D~A~~~~~~~s~--~~~T~R~~~~~tl~~~~~~ 345 (397)
T COG5139 272 RRSAKALVQEWTRPIIKPSGNYRDKRIMQLEFDSEKLRKK----SVMDSAKNRKKKSSG--EDPTSRGSSVQTLYEQAAA 345 (397)
T ss_pred HHHHHHHHHHhhccccCcCCCcchhhhheeecCHHHHHHH----HHHHHHhhhcccccc--cCCCCCCcchhhHHHHHhh
Confidence 9999999999999999999999997654322 1112211 111112222111100 0111112234678888877
Q ss_pred CCCcccccccCCCCCCCCCeeeCCCCCCChHHHHHHhhhhchHHHHHHHHHHHHhhhccccccccccccccccCCc
Q 009300 459 RSDSSSRQHASRPEATPLDFVVRPQSKIDPEEVRARAKQVMQDQRRMKMNKKLQQLKAPRKKQLQATKLSVEGRGM 534 (538)
Q Consensus 459 r~~~~~r~rArvP~~s~~DYviRPkskvd~~~~rar~Kk~~~derr~Kl~kkL~qlk~~kKK~~RA~~ISIEGR~M 534 (538)
+ +++|+.|.+.|++|.+.|.++.-..-..+++++ .+.+...+..+||+|++|
T Consensus 346 ~-----~~~~~~Pa~~T~~~k~~P~~~~~~~~~~Ar~~~-------------------v~S~~~~~~~~~~~~~~L 397 (397)
T COG5139 346 R-----RNRAAAPAQTTTDYKYAPVSNLSAVPTNARAVG-------------------VGSTLNNSEMYKRLTSRL 397 (397)
T ss_pred c-----cccccCccccccccccccccccccccccchhhh-------------------hhcccccchhhhhhccCC
Confidence 7 999999999999999999988754333333332 334455677899999875
No 3
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.06 E-value=1.1e-10 Score=90.50 Aligned_cols=53 Identities=45% Similarity=0.737 Sum_probs=47.3
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhhhhh
Q 009300 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIF 396 (538)
Q Consensus 337 ~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsRPI~ 396 (538)
++|+.|..|||+. ++|++|+||++|.+|++| .++++++.+|..||.+|.++|+
T Consensus 1 ~iL~~L~~l~it~------~~L~~T~IGk~V~~l~k~-~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITV------ELLKSTGIGKAVNKLRKH-SENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SH------HHHHHHSHHHHHHHHHHC-TS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCH------HHHHhCChhHHHHHHHcC-CCCHHHHHHHHHHHHHHhHhcC
Confidence 5899999999964 689999999999999999 9999999999999999999985
No 4
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=98.24 E-value=2.7e-06 Score=71.06 Aligned_cols=58 Identities=29% Similarity=0.563 Sum_probs=53.5
Q ss_pred CCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhhhh
Q 009300 330 PNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPI 395 (538)
Q Consensus 330 Pnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsRPI 395 (538)
|+...--.+|..|..|||+. +.|+.++||++|.+|++|+. +.++.+|..||..|...|
T Consensus 18 ~~~~~~~~~L~~L~~~~it~------~~L~~T~iG~~V~~Lrkh~~--~~i~~~A~~Lv~~Wk~~v 75 (76)
T cd00183 18 EEVSRLLDLLRLLKKLPLTV------EILKETRIGKKVNSLRKHSN--EKIRKLAKALIKSWKKLV 75 (76)
T ss_pred CCHHHHHHHHHHHhcCCCCH------HHHHHCCHHHHHHHHHcCCc--HHHHHHHHHHHHHHHHhc
Confidence 78888889999999999864 68999999999999999987 999999999999999876
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=97.67 E-value=4.5e-05 Score=63.85 Aligned_cols=54 Identities=33% Similarity=0.583 Sum_probs=46.8
Q ss_pred HHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhhhhh
Q 009300 335 RAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIF 396 (538)
Q Consensus 335 R~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsRPI~ 396 (538)
=-.+|..|..||+.. +.|+.+.||++|..|++|+ .++++.+|..||..|..-|.
T Consensus 21 ~l~~L~~L~~~~~t~------~~L~~T~iG~~v~~Lrkh~--~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 21 CLDILKKLKKLPITV------DLLEETRIGKKVNGLRKHK--NEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHHHHHhcCCCCH------HHHHHCcHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHHhc
Confidence 346788888899854 6899999999999999996 59999999999999987663
No 6
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=96.60 E-value=0.0018 Score=67.27 Aligned_cols=53 Identities=30% Similarity=0.465 Sum_probs=46.6
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhhhhhc
Q 009300 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIFN 397 (538)
Q Consensus 337 ~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsRPI~~ 397 (538)
.||+.|..|||.. +.|+.+.||++|..|.+|+. +++..+|..||..|..-|..
T Consensus 25 ~~L~~L~~~~~t~------~lL~~T~IG~~Vn~lrkh~~--~~I~~lAk~li~~WK~~v~~ 77 (299)
T TIGR01385 25 DILHQLKEFPPTE------ELLQETKVGVKVNKLRKHPN--EDISKLAKKIIKSWKKVVDK 77 (299)
T ss_pred HHHHHHhcCCCcH------HHHhhCchhHHHHHHHcCCc--HHHHHHHHHHHHHHHHHHhh
Confidence 4678888888853 68999999999999999975 56999999999999999976
No 7
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=94.75 E-value=0.047 Score=56.98 Aligned_cols=73 Identities=29% Similarity=0.423 Sum_probs=59.5
Q ss_pred HHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceeh-hhccCchhcHHHHHHHHHHHHHhh
Q 009300 314 LTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIM-FLSKSDEETTSNRKLAKDLVDKWS 392 (538)
Q Consensus 314 L~vl~~WLePLPDgSLPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVm-fl~K~p~ET~eNKrlA~~LI~kWs 392 (538)
+.+.+. |+-++.. +|+.-=-.+|+-|.++||. .++|..+.||..|. ++.+|+.+ +++.+|+.||..|.
T Consensus 7 ~r~ak~-l~~~~~~--~n~~~~ld~l~~L~~~pvt------~ell~~Tr~g~~vn~~~Kk~~n~--ev~~~ak~Lik~Wk 75 (296)
T KOG1105|consen 7 LRAAKA-LEKDKQS--KNVEAALDLLKRLKKIPVT------LELLQETRTGMGVNEVLKKHKNE--EVRSLAKKLIKSWK 75 (296)
T ss_pred HHHHHH-HHhhccc--ccHHHHHHHHHHHHhcccH------HHHHHHhhHHHHHHHHHHhCCCH--HHHHHHHHHHHHHH
Confidence 333344 6666665 7877777889999999994 36899999999999 88888876 68889999999999
Q ss_pred hhhhc
Q 009300 393 RPIFN 397 (538)
Q Consensus 393 RPI~~ 397 (538)
+-|..
T Consensus 76 k~~~~ 80 (296)
T KOG1105|consen 76 KLVDK 80 (296)
T ss_pred HHhhc
Confidence 99986
No 8
>PLN02976 amine oxidase
Probab=93.77 E-value=0.17 Score=62.56 Aligned_cols=86 Identities=21% Similarity=0.288 Sum_probs=65.2
Q ss_pred HhHHHHHHhhhhHHHHHHhhc--cCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHH
Q 009300 302 KQLQQEFLDHGVLTLLKNWLE--PLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTS 379 (538)
Q Consensus 302 ~~Lq~~fLd~giL~vl~~WLe--PLPDgSLPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~e 379 (538)
.+|..+-+....|..|..||. --++| -++-+.++.+|.-+|.+. -.|+.|||||+|---. +--..++
T Consensus 1272 ~~~~~~a~~~~gl~~l~~w~~~~~~~~~----~~l~~~~~~ll~~~~~d~------~a~r~sg~~~~~k~~~-~~h~~~~ 1340 (1713)
T PLN02976 1272 ETLKSFAGTKEGLATLNSWILDSMGKDG----TQLLRHCVRLLVLVSTDL------LAVRLSGIGKTVKEKV-CVHTSRD 1340 (1713)
T ss_pred HHHHHHhcccchHHHHHHHHHHHhcccH----HHHHHHHHHHHhhcchhH------HHHHhccchHHHHhhh-hhcccHH
Confidence 455556666788999999998 44555 356678888888888654 3799999999994322 4457789
Q ss_pred HHHHHHHHHHHhhhhhhcC
Q 009300 380 NRKLAKDLVDKWSRPIFNK 398 (538)
Q Consensus 380 NKrlA~~LI~kWsRPI~~~ 398 (538)
+|.||.+|++.|+-..-..
T Consensus 1341 ~r~~a~~~~~~w~~~~~~~ 1359 (1713)
T PLN02976 1341 IRAIASQLVSVWLEVFRRE 1359 (1713)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999765433
No 9
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=47.62 E-value=67 Score=29.81 Aligned_cols=56 Identities=34% Similarity=0.367 Sum_probs=44.0
Q ss_pred hhhHHHHHHHhhH--hHHHHHHhhhhHHHHHHhhccCCC---CCCCCHHHHHHHHHHHhcC
Q 009300 290 KKLSLLTEVLSKK--QLQQEFLDHGVLTLLKNWLEPLPD---GSLPNINIRAAILKILTEF 345 (538)
Q Consensus 290 kmLpeV~~~L~K~--~Lq~~fLd~giL~vl~~WLePLPD---gSLPnl~IR~~LLkiL~~L 345 (538)
+.|..+.-.|+.. .|...|+++|.+.+|..+|.-+.. .+-..+.+...+|.||..+
T Consensus 83 ~~L~~L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~~~~~~~~~~~~l~Clkal 143 (187)
T PF06371_consen 83 KILKSLRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEKSEEDIDIEHECLRCLKAL 143 (187)
T ss_dssp HHHHHHHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCTCTTCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhhcchhHHHHHHHHHHHHHH
Confidence 5666676777765 678899999999999999987753 3456788999999998775
No 10
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=42.82 E-value=61 Score=35.09 Aligned_cols=102 Identities=27% Similarity=0.520 Sum_probs=67.6
Q ss_pred HHHHhhhHHHHHHHhhHhH----HHHHH--------hhhhHHHHHHhhccCCCCCC--------CCHHHHHHHHHHHhcC
Q 009300 286 INKLKKLSLLTEVLSKKQL----QQEFL--------DHGVLTLLKNWLEPLPDGSL--------PNINIRAAILKILTEF 345 (538)
Q Consensus 286 l~KLkmLpeV~~~L~K~~L----q~~fL--------d~giL~vl~~WLePLPDgSL--------Pnl~IR~~LLkiL~~L 345 (538)
+.||+||.-=...|.+..+ ..+|. ....+..|+.||--+-...+ || .+-..||..|..|
T Consensus 5 ~dKLklL~Ye~~f~~~~~~kpl~r~yFa~~~~Np~eQF~~F~~L~~WL~~~~g~~f~~p~e~DDPn-~~~~~Il~~lr~~ 83 (359)
T PF10498_consen 5 LDKLKLLNYEKDFCKKRKMKPLSRHYFAVPSTNPGEQFYYFTSLCAWLISKAGRKFEQPQEYDDPN-ATISNILDELRKL 83 (359)
T ss_pred HHHHHhhhhHHHHhhhcCCCCCCHHHhcCCCCCchHHHHHHHHHHHHHHHhcCCCCCCCcccCCHH-HHHHHHHHHHHcc
Confidence 6799999876666665544 33465 24789999999965433333 45 5667788888877
Q ss_pred CCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHH----HhhhhhhcCCc
Q 009300 346 PIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVD----KWSRPIFNKST 400 (538)
Q Consensus 346 PI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~----kWsRPI~~~ss 400 (538)
-+..+ | .-..| .+|-|..|+|+- -.||..-+. .|.||+|....
T Consensus 84 g~~~d-f-~p~kL-k~G~Ge~vc~VL---------d~Lad~AL~~~~F~~~~p~~~~e~ 130 (359)
T PF10498_consen 84 GVPVD-F-PPSKL-KQGSGEHVCYVL---------DQLADEALKRKNFKWKRPIYPKEE 130 (359)
T ss_pred CCCCC-C-ChHHh-hCCCCHHHHHHH---------HHHHHHHHHhcCcCccCCCCCccc
Confidence 54332 1 12344 589999999875 225544444 59999998755
No 11
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=38.32 E-value=67 Score=30.76 Aligned_cols=78 Identities=21% Similarity=0.319 Sum_probs=46.7
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHhhhHHHHHHHhhHhH----HHHHHhhhhHHHHHHhhccCC
Q 009300 250 NEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQL----QQEFLDHGVLTLLKNWLEPLP 325 (538)
Q Consensus 250 ~~~~~~ei~~~v~~Li~~M~~AAe~D~ean~~gkPAl~KLkmLpeV~~~L~K~~L----q~~fLd~giL~vl~~WLePLP 325 (538)
...+.+|+..+|...|.+-..=.++=....+.|+|+.++..+|........+..- .+-|.+..-+..|+.|
T Consensus 64 ~~~t~~e~~~lI~~yl~R~DeEleql~~~rR~gRp~s~re~~L~~~~~~E~~ey~~G~~vPDLtd~~nv~~Lr~W----- 138 (155)
T PF11176_consen 64 KPFTLEEIHELIERYLHRFDEELEQLKKERRKGRPPSNREDLLEQKIEREEEEYKTGFEVPDLTDEKNVKLLREW----- 138 (155)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHHGGGT---TTHHHHHHHHHHHHHHHHHTTEEEE-S--HHHHHHHHT------
T ss_pred CCCCHHHHHHHHHHHHhcCHHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHhhCeeCCCCCCHHHHHHHHhc-----
Confidence 4578899999999999877655554444567899999999999987776544332 1124445567889999
Q ss_pred CCCCCCH
Q 009300 326 DGSLPNI 332 (538)
Q Consensus 326 DgSLPnl 332 (538)
||++-.+
T Consensus 139 ~G~~~~l 145 (155)
T PF11176_consen 139 NGDWGYL 145 (155)
T ss_dssp SS-STHH
T ss_pred CCChhhC
Confidence 7776544
No 12
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=38.07 E-value=68 Score=24.99 Aligned_cols=19 Identities=26% Similarity=0.686 Sum_probs=17.0
Q ss_pred HHHHHHhhhhHHHHHHhhc
Q 009300 304 LQQEFLDHGVLTLLKNWLE 322 (538)
Q Consensus 304 Lq~~fLd~giL~vl~~WLe 322 (538)
+.-.|+-+|++.+|..||+
T Consensus 59 y~~~f~~sg~igvi~~Wl~ 77 (77)
T PF14278_consen 59 YLISFIVSGIIGVIQWWLE 77 (77)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 5668999999999999995
No 13
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=33.43 E-value=1e+02 Score=32.34 Aligned_cols=81 Identities=20% Similarity=0.338 Sum_probs=48.1
Q ss_pred HHHHHhhccCCCCCC-CCHHHHHHHHHHHhcCCC-CccccchHHHHhhcCccceehhh---ccCch-----hcHHHHHHH
Q 009300 315 TLLKNWLEPLPDGSL-PNINIRAAILKILTEFPI-DLEQFDRREQLKKSGLGKVIMFL---SKSDE-----ETTSNRKLA 384 (538)
Q Consensus 315 ~vl~~WLePLPDgSL-Pnl~IR~~LLkiL~~LPI-~~e~~d~re~Lk~SGLGKvVmfl---~K~p~-----ET~eNKrlA 384 (538)
..|-.+|++.-+|.| ||+.|=++...++..||+ +++.|- -+-+.+..=--++-|| +++-. ..+-|-..+
T Consensus 208 klil~Y~k~~e~G~l~~N~eILrea~~L~~~Lp~~~~~~F~-d~F~~e~nd~~l~syl~~iT~~~~nMn~~vnKfn~~yd 286 (299)
T KOG3050|consen 208 KLILAYLKKVEAGTLQPNFEILREAYALCHRLPVMESEKFQ-DNFYMECNDVGLISYLGTITKCCNNMNEVVNKFNTLYD 286 (299)
T ss_pred HHHHHHHhhhhcCCcCccHHHHHHHHHHHhhccccchHHHh-HHHHHhcchhhHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 445568888999986 689999999999999995 332210 1223333222222222 22222 223355566
Q ss_pred HHHHHHhhhhhh
Q 009300 385 KDLVDKWSRPIF 396 (538)
Q Consensus 385 ~~LI~kWsRPI~ 396 (538)
+.+..+|.|++|
T Consensus 287 r~gt~R~~r~~~ 298 (299)
T KOG3050|consen 287 RQGTRRRMRGLF 298 (299)
T ss_pred hhhhhccccccC
Confidence 667888888876
No 14
>COG1390 NtpE Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]
Probab=30.17 E-value=5e+02 Score=25.82 Aligned_cols=54 Identities=15% Similarity=0.410 Sum_probs=39.1
Q ss_pred HHHHHhhhhHHHHHHhhccCCCC-CCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhc
Q 009300 305 QQEFLDHGVLTLLKNWLEPLPDG-SLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEET 377 (538)
Q Consensus 305 q~~fLd~giL~vl~~WLePLPDg-SLPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET 377 (538)
+..+|+. +++.+..||.-++-. .+.. +++-|-.++..+.- |.+|+|..++....
T Consensus 79 ~ee~l~~-~~~~~~e~L~~i~~~~~~~~--l~~ll~~~~~~~~~----------------~~~iV~~~e~d~~~ 133 (194)
T COG1390 79 KEEILES-VFEAVEEKLRNIASDPEYES--LQELLIEALEKLLG----------------GELVVYLNEKDKAL 133 (194)
T ss_pred HHHHHHH-HHHHHHHHHHcCcCCcchHH--HHHHHHHHHHhcCC----------------CCeEEEeCcccHHH
Confidence 5567777 999999999999843 3444 78888888877764 46677777666554
No 15
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=29.43 E-value=2.2e+02 Score=26.71 Aligned_cols=60 Identities=18% Similarity=0.247 Sum_probs=46.9
Q ss_pred HHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 009300 285 AINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (538)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLd~giL~vl~~WLePLPDgSLPnl~IR~~LLkiL~~L 345 (538)
++.=|.+|..++.-+- ..+|..+-...+|+.|..=+.|-.+|+-++..|+..+|.+|...
T Consensus 55 ~l~AL~LLe~~vkNCG-~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W 114 (139)
T cd03567 55 ALQALTVLEACMKNCG-ERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSW 114 (139)
T ss_pred HHHHHHHHHHHHHHcC-HHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHH
Confidence 5666666776666543 45677788889998888888777778889999999999999865
No 16
>KOG2973 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.17 E-value=2.2e+02 Score=30.98 Aligned_cols=72 Identities=24% Similarity=0.323 Sum_probs=60.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCccceehhhccCchhcHHHHHHHHHHHHHhhh--hhhcCCccchh
Q 009300 329 LPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSR--PIFNKSTRFED 404 (538)
Q Consensus 329 LPnl~IR~~LLkiL~~LPI~~e~~d~re~Lk~SGLGKvVmfl~K~p~ET~eNKrlA~~LI~kWsR--PI~~~ss~Y~d 404 (538)
-|.-.||..+|.+|..|-. |.+ -|++|+.-|.=.++--|++.- +.+.+++.|.++|+--.| |-+|.-..|..
T Consensus 255 epdpdIrk~llEai~lLca-T~~--GRe~lR~kgvYpilRElhk~e-~ded~~~ace~vvq~Lv~~e~~~G~~~~~~s 328 (353)
T KOG2973|consen 255 EPDPDIRKMLLEALLLLCA-TRA--GREVLRSKGVYPILRELHKWE-EDEDIREACEQVVQMLVRLEPEIGILDEYES 328 (353)
T ss_pred CCChHHHHHHHHHHHHHHh-hhH--hHHHHHhcCchHHHHHHhcCC-CcHHHHHHHHHHHHHHHhcccccchhhhcCc
Confidence 5677899999999999965 333 389999999999998888777 888999999999998888 77787777874
No 17
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=21.46 E-value=88 Score=27.95 Aligned_cols=30 Identities=27% Similarity=0.492 Sum_probs=25.2
Q ss_pred HHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 009300 315 TLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (538)
Q Consensus 315 ~vl~~WLePLPDgSLPnl~IR~~LLkiL~~L 345 (538)
..|-.+|+-||||+.|++ ||..|-+-|...
T Consensus 18 ~~iF~FL~~~P~GT~~~~-iR~~L~rYI~~~ 47 (97)
T PRK13916 18 PQIFDFLENVPRGTKTAH-IREALRRYIEEI 47 (97)
T ss_pred HHHHHHHHHCCCCCccHH-HHHHHHHHHHhc
Confidence 345678999999999998 999988888765
No 18
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=20.12 E-value=2.3e+02 Score=20.28 Aligned_cols=37 Identities=16% Similarity=0.264 Sum_probs=30.9
Q ss_pred hHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 009300 303 QLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (538)
Q Consensus 303 ~Lq~~fLd~giL~vl~~WLePLPDgSLPnl~IR~~LLkiL~~L 345 (538)
.....+++.|++..|-.-|. -++..|++..+-+|.+|
T Consensus 3 ~~~~~i~~~g~i~~Lv~ll~------~~~~~v~~~a~~al~nl 39 (41)
T PF00514_consen 3 ENKQAIVEAGGIPPLVQLLK------SPDPEVQEEAAWALGNL 39 (41)
T ss_dssp HHHHHHHHTTHHHHHHHHTT------SSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcccHHHHHHHHc------CCCHHHHHHHHHHHHHH
Confidence 45678999999999999988 67888999988888764
Done!