Query 012329
Match_columns 466
No_of_seqs 126 out of 179
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 01:29:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012329hhsearch_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 1.4E-57 3E-62 460.9 17.2 283 171-464 64-361 (417)
2 COG5139 Uncharacterized conser 100.0 2.9E-42 6.4E-47 340.6 13.3 181 223-409 117-300 (397)
3 PF08711 Med26: TFIIS helical 99.2 3.4E-11 7.3E-16 91.3 4.3 53 337-396 1-53 (53)
4 cd00183 TFIIS_I N-terminal dom 98.4 6.1E-07 1.3E-11 73.2 7.2 58 330-395 18-75 (76)
5 smart00509 TFS2N Domain in the 98.0 1.1E-05 2.4E-10 66.1 4.7 58 331-396 17-74 (75)
6 TIGR01385 TFSII transcription 97.1 0.00053 1.1E-08 69.5 4.4 53 337-397 25-77 (299)
7 KOG1105 Transcription elongati 95.8 0.018 3.8E-07 58.9 6.1 74 313-397 6-80 (296)
8 PLN02976 amine oxidase 95.3 0.058 1.2E-06 65.1 8.8 86 302-398 1272-1359(1713)
9 PF11176 DUF2962: Protein of u 56.9 28 0.00061 32.6 5.9 79 249-332 63-145 (155)
10 PF06371 Drf_GBD: Diaphanous G 44.4 1.4E+02 0.003 26.9 8.2 56 290-345 83-143 (187)
11 PF14278 TetR_C_8: Transcripti 43.1 50 0.0011 25.0 4.5 19 304-322 59-77 (77)
12 cd03567 VHS_GGA VHS domain fam 36.8 1.5E+02 0.0033 27.3 7.2 60 285-345 55-114 (139)
13 PF10498 IFT57: Intra-flagella 34.3 1.5E+02 0.0033 31.4 7.7 102 286-400 5-130 (359)
14 KOG2973 Uncharacterized conser 27.4 1.1E+02 0.0024 32.7 5.2 72 329-404 255-328 (353)
15 cd00197 VHS_ENTH_ANTH VHS, ENT 27.1 3.4E+02 0.0074 23.1 7.4 78 257-344 35-112 (115)
16 PF00514 Arm: Armadillo/beta-c 21.1 2.2E+02 0.0049 19.9 4.4 37 303-345 3-39 (41)
17 PLN02777 photosystem I P subun 21.0 3.4E+02 0.0074 26.4 6.8 90 288-397 75-165 (167)
18 PRK13916 plasmid segregation p 20.7 95 0.0021 27.4 2.8 29 316-345 19-47 (97)
19 cd03569 VHS_Hrs_Vps27p VHS dom 20.5 3.3E+02 0.0071 25.0 6.4 56 285-346 58-113 (142)
No 1
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.4e-57 Score=460.91 Aligned_cols=283 Identities=40% Similarity=0.581 Sum_probs=230.1
Q ss_pred hHHHHHHHhhCCCCCCCc---chhcccCccCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCcHHHHHHHhh
Q 012329 171 KMLNEMWNAVAPTGDSED---DQEGVRTLDDD-----NFIDDSGVDPSDRYGSDSEPRFAHDAPQAEEGDEDEEIKELFK 242 (466)
Q Consensus 171 ~~~~e~~~~i~~~~ds~d---~~e~~rt~~Dd-----~fiD~~G~d~~d~~g~d~e~r~~~d~~~aee~E~Ddei~~l~k 242 (466)
.+..++|+.+. .+-++ ++.+.++..+. +|+.++|.++-+-++.+.......++++++..|...++.++|+
T Consensus 64 e~~~~~~~~~~--~~~~r~~Kd~k~~~s~~~~e~~~~d~~~e~~~~~~e~~~~d~~d~~~~r~~~~~~~ed~~e~~~~~k 141 (417)
T KOG1793|consen 64 EPADEDENSNL--EDRKRERKDEKGLDSDGDNEKEHEDESQETGQEFPESQDDDFGDTGGRRPKLKAKLEDILEKKAVRK 141 (417)
T ss_pred cccchhhcccc--cchhhhhccccccccccccchhhhHhhhccccccccccccccccccccchhhHhhhhhHHHHHHHHh
Confidence 36778888776 44333 44455555544 4999999887777666655556677788888899999999999
Q ss_pred ccccccccCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhh
Q 012329 243 MGKKRKKNEKSPAEIA-LLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWL 321 (466)
Q Consensus 243 ~~KKKKk~~~s~~Ei~-~iv~~Ll~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WL 321 (466)
|++|++++...+.+|. .+|..|+.+|..||+.|+++|.+++||++||+|||.|.++|.|.+||.+|||||||+.|+.||
T Consensus 142 ~r~kk~~~d~~~~~I~d~~v~~l~~~m~~aa~~D~~~N~e~kPA~~Klk~Lp~v~~vL~k~~L~et~LDngvL~~lk~WL 221 (417)
T KOG1793|consen 142 MRTKKRKNDDGPEEILDDEVSRLMERMEDAAEKDRELNREGKPATQKLKLLPLVVAVLSKKALQETFLDNGVLDSLKEWL 221 (417)
T ss_pred hhhhhccccCchHHHHHHHHHHHHHHHHHHHHHHHhhccccCchHHHHhccHHHHHHHhhhhHHHHHHhhhHHHHHHHHh
Confidence 8888889999999999 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhhhhhcCCcc
Q 012329 322 EPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIFNKSTR 401 (466)
Q Consensus 322 ePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSRPI~~~ss~ 401 (466)
+||||||||||+||.+||+||..|||.+ +|||++||||||||||++||+||++||+||..||++|+||||+++++
T Consensus 222 ePLPD~SLPal~Ir~~ll~iL~dlpi~~-----~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~st~ 296 (417)
T KOG1793|consen 222 EPLPDGSLPALNIRKSLLDILNDLPIDK-----REHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKLSTN 296 (417)
T ss_pred ccCCCCCCcchHHHHHHHHHHhcCCcch-----HHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCCCCC
Confidence 9999999999999999999999999976 58999999999999999999999999999999999999999999999
Q ss_pred cccchhcccc----c-CCCCCCCCCCchhhhhhhhcccCCCCceeeecccccc-cceeeeeeccccCcc
Q 012329 402 FEDMKTVEDD----R-VPFRRPSAKKPASKAAAMESRDGDFDDLVISRYDLTI-DLIFLRILYCSSMSF 464 (466)
Q Consensus 402 Y~d~~~~e~~----~-~~~rr~~~kk~~~kaa~~~sR~~~ld~~~~~~~~~~~-~~~~~~~~~~~~~~~ 464 (466)
|++|++..++ + +++||.....+. .+..+.+++...|=..+..++ =.++-|||-.+.+-|
T Consensus 297 y~dm~~~~e~~de~r~~~~Rr~~~~~~~----~~~~~~~d~~~~i~~~e~g~~~gr~Ra~vP~~s~~Dy 361 (417)
T KOG1793|consen 297 YRDMRRMREERDEKRMPQSRRDSAKARK----KSGTDPRDRGSEIDTDEEGLTTGRARARVPAPSTKDY 361 (417)
T ss_pred chhhHHHHhhhhhhhhhhhhcccccccc----ccCCCccccccccchhhhccccccccccCCCCCCCcc
Confidence 9999974111 1 223343332222 244455555544333322221 147778887777665
No 2
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.9e-42 Score=340.56 Aligned_cols=181 Identities=33% Similarity=0.598 Sum_probs=164.6
Q ss_pred CCCCcccCCCcHHHHHHHhhccccc---cccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHH
Q 012329 223 HDAPQAEEGDEDEEIKELFKMGKKR---KKNEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVL 299 (466)
Q Consensus 223 ~d~~~aee~E~Ddei~~l~k~~KKK---Kk~~~s~~Ei~~iv~~Ll~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L 299 (466)
.+.++|...|.++.++++++..+.. ++....++-+..++..|..+|..||..|+..|.++.||+.||+|||+|..+|
T Consensus 117 ~d~t~a~~~El~~~~dr~lK~p~~sr~rr~eD~leq~~de~~lrLk~~M~~aa~~D~~~n~e~~pAt~Kik~lp~V~~VL 196 (397)
T COG5139 117 QDFTEAQSGELGDTGDRQLKAPAASRARRKEDLLEQTVDEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSDVL 196 (397)
T ss_pred CCCChhhhhhhhhhhhhhhccchhhhhhccccchHHHHHHHHHHHHHHHHHHHHhhhhhhhccCcchhhhhccHHHHHHH
Confidence 3466788899999999999933322 2333445667788999999999999999999999999999999999999999
Q ss_pred hhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHH
Q 012329 300 SKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTS 379 (466)
Q Consensus 300 ~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~e 379 (466)
.|.+||.+|||+|||+.|+.||+||||+||||++||+.||.+|..|||.+ |||++||||+||+||+.+|++.++
T Consensus 197 ~k~~L~dtiLDnniLdsVr~WLEPLPD~SlP~~~IqksL~dvL~~lpI~t------EHL~eSgvGrIV~FYtiskk~e~~ 270 (397)
T COG5139 197 MKKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKSLLDVLKTLPIHT------EHLVESGVGRIVYFYTISKKEEKE 270 (397)
T ss_pred HHHHHHHHHhhcchHHHHHhhhccCCCCCCcchHHHHHHHHHHhhCCchH------HHhhhcCCceEEEEEecCCcccHH
Confidence 99999999999999999999999999999999999999999999999987 699999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhhhcCCcccccchhcc
Q 012329 380 NRKLAKDLVDKWSRPIFNKSTRFEDMKTVE 409 (466)
Q Consensus 380 NKrlA~~LI~kWSRPI~~~ss~Y~d~~~~e 409 (466)
++++|+.||++|+||||+.+.+|+|.+.-.
T Consensus 271 v~r~A~~LV~eWtrpIik~s~nyRDk~i~~ 300 (397)
T COG5139 271 VRRSAKALVQEWTRPIIKPSGNYRDKRIMQ 300 (397)
T ss_pred HHHHHHHHHHHhhccccCcCCCcchhhhhe
Confidence 999999999999999999999999966443
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=99.15 E-value=3.4e-11 Score=91.31 Aligned_cols=53 Identities=45% Similarity=0.737 Sum_probs=47.3
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhhhhh
Q 012329 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIF 396 (466)
Q Consensus 337 ~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSRPI~ 396 (466)
.+|+.|..|||+. ++|++|+||++|.+|+|| .++++|+++|+.||.+|.++|+
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 4899999999964 799999999999999999 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=98.45 E-value=6.1e-07 Score=73.24 Aligned_cols=58 Identities=29% Similarity=0.563 Sum_probs=53.7
Q ss_pred CCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhhhh
Q 012329 330 PNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPI 395 (466)
Q Consensus 330 Pnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSRPI 395 (466)
|+...--.+|..|..+||+. +.|+.++||++|.+|++|+. +.++.+|..||.+|...|
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 79999999999999999987 999999999999999876
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=97.95 E-value=1.1e-05 Score=66.07 Aligned_cols=58 Identities=31% Similarity=0.558 Sum_probs=48.4
Q ss_pred CHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhhhhh
Q 012329 331 NINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIF 396 (466)
Q Consensus 331 nl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSRPI~ 396 (466)
+..-=-.+|+.|..||++. +.|+.+.||++|..|++|+ .++++.+|..||..|...|.
T Consensus 17 ~~~~~l~~L~~L~~~~~t~------~~L~~T~iG~~v~~Lrkh~--~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 17 EVSRCLDILKKLKKLPITV------DLLEETRIGKKVNGLRKHK--NEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred CHHHHHHHHHHHhcCCCCH------HHHHHCcHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHHhc
Confidence 3333346788888888854 7999999999999999996 59999999999999998763
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=97.08 E-value=0.00053 Score=69.51 Aligned_cols=53 Identities=30% Similarity=0.485 Sum_probs=46.9
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhhhhhc
Q 012329 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSRPIFN 397 (466)
Q Consensus 337 ~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSRPI~~ 397 (466)
.+|+.|..|||+ .+.|+++.||++|..|+||+. ++|+.+|+.||..|...|..
T Consensus 25 ~~L~~L~~~~~t------~~lL~~T~IG~~Vn~lrkh~~--~~I~~lAk~li~~WK~~v~~ 77 (299)
T TIGR01385 25 DILHQLKEFPPT------EELLQETKVGVKVNKLRKHPN--EDISKLAKKIIKSWKKVVDK 77 (299)
T ss_pred HHHHHHhcCCCc------HHHHhhCchhHHHHHHHcCCc--HHHHHHHHHHHHHHHHHHhh
Confidence 467888888885 479999999999999999975 57999999999999999986
No 7
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=95.79 E-value=0.018 Score=58.90 Aligned_cols=74 Identities=30% Similarity=0.445 Sum_probs=60.4
Q ss_pred hHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchh-hhccCchhcHHHHHHHHHHHHHh
Q 012329 313 VLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIM-FLSKSDEETTSNRKLAKDLVDKW 391 (466)
Q Consensus 313 iL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVm-fL~K~p~ET~eNKrlA~~LI~kW 391 (466)
++.+.+. |+-++.. +|+.---.+|+-|.++||.. ++|..+.||+.|. ++.+|+.+ +++.+|+.||..|
T Consensus 6 ~~r~ak~-l~~~~~~--~n~~~~ld~l~~L~~~pvt~------ell~~Tr~g~~vn~~~Kk~~n~--ev~~~ak~Lik~W 74 (296)
T KOG1105|consen 6 ALRAAKA-LEKDKQS--KNVEAALDLLKRLKKIPVTL------ELLQETRTGMGVNEVLKKHKNE--EVRSLAKKLIKSW 74 (296)
T ss_pred HHHHHHH-HHhhccc--ccHHHHHHHHHHHHhcccHH------HHHHHhhHHHHHHHHHHhCCCH--HHHHHHHHHHHHH
Confidence 3444444 6666655 88777778899999999843 7999999999999 88888875 7889999999999
Q ss_pred hhhhhc
Q 012329 392 SRPIFN 397 (466)
Q Consensus 392 SRPI~~ 397 (466)
.+.|..
T Consensus 75 kk~~~~ 80 (296)
T KOG1105|consen 75 KKLVDK 80 (296)
T ss_pred HHHhhc
Confidence 999987
No 8
>PLN02976 amine oxidase
Probab=95.29 E-value=0.058 Score=65.12 Aligned_cols=86 Identities=21% Similarity=0.288 Sum_probs=65.4
Q ss_pred HhHHHHHHhhhhHHHHHHhhc--cCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHH
Q 012329 302 KQLQQEFLDHGVLTLLKNWLE--PLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTS 379 (466)
Q Consensus 302 ~~Lq~~fLD~GiL~vLk~WLe--PLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~e 379 (466)
.+|..+-+....|..|..||. --++| -++-+.++.+|.-+|.+. -.|+.|||||+|--=. |-...++
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 455555566778999999998 33555 346688889998888765 4899999999994222 4457889
Q ss_pred HHHHHHHHHHHhhhhhhcC
Q 012329 380 NRKLAKDLVDKWSRPIFNK 398 (466)
Q Consensus 380 NKrlA~~LI~kWSRPI~~~ 398 (466)
||.||.+|++.|+...-..
T Consensus 1341 ~r~~a~~~~~~w~~~~~~~ 1359 (1713)
T PLN02976 1341 IRAIASQLVSVWLEVFRRE 1359 (1713)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999765443
No 9
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=56.94 E-value=28 Score=32.57 Aligned_cols=79 Identities=22% Similarity=0.329 Sum_probs=47.9
Q ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHHhhHhH----HHHHHhhhhHHHHHHhhccC
Q 012329 249 KNEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQL----QQEFLDHGVLTLLKNWLEPL 324 (466)
Q Consensus 249 k~~~s~~Ei~~iv~~Ll~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L~K~~L----q~~fLD~GiL~vLk~WLePL 324 (466)
...-+.+|+..+|...|.+-..=.++=....+.|+|+.++..+|....+...+..- .+-|.+..-+..|+.|
T Consensus 63 ~~~~t~~e~~~lI~~yl~R~DeEleql~~~rR~gRp~s~re~~L~~~~~~E~~ey~~G~~vPDLtd~~nv~~Lr~W---- 138 (155)
T PF11176_consen 63 KKPFTLEEIHELIERYLHRFDEELEQLKKERRKGRPPSNREDLLEQKIEREEEEYKTGFEVPDLTDEKNVKLLREW---- 138 (155)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHHHHHGGGT---TTHHHHHHHHHHHHHHHHHTTEEEE-S--HHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHhcCHHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHhhCeeCCCCCCHHHHHHHHhc----
Confidence 34577899999999999887666655555578899999999999987776543322 1124455667889999
Q ss_pred CCCCCCCH
Q 012329 325 PDGSLPNI 332 (466)
Q Consensus 325 PDgSLPnl 332 (466)
||++-.+
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 10
>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=44.42 E-value=1.4e+02 Score=26.93 Aligned_cols=56 Identities=34% Similarity=0.380 Sum_probs=43.2
Q ss_pred hhhHHHHHHHhhH--hHHHHHHhhhhHHHHHHhhccCC---CCCCCCHHHHHHHHHHHhcC
Q 012329 290 KKLSLLTEVLSKK--QLQQEFLDHGVLTLLKNWLEPLP---DGSLPNINIRAAILKILTEF 345 (466)
Q Consensus 290 kmLpeV~~~L~K~--~Lq~~fLD~GiL~vLk~WLePLP---DgSLPnl~IRt~LLkiL~~L 345 (466)
+.|..+.-.|+.. .|...|+++|++.+|..+|.-+. ..+-....+...+|.||..+
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 5566666666654 78899999999999999998874 33456788999999998775
No 11
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=43.13 E-value=50 Score=25.02 Aligned_cols=19 Identities=26% Similarity=0.686 Sum_probs=17.0
Q ss_pred HHHHHHhhhhHHHHHHhhc
Q 012329 304 LQQEFLDHGVLTLLKNWLE 322 (466)
Q Consensus 304 Lq~~fLD~GiL~vLk~WLe 322 (466)
+.-.|+-+|++.+|..||+
T Consensus 59 y~~~f~~sg~igvi~~Wl~ 77 (77)
T PF14278_consen 59 YLISFIVSGIIGVIQWWLE 77 (77)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 6678999999999999995
No 12
>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=36.80 E-value=1.5e+02 Score=27.27 Aligned_cols=60 Identities=18% Similarity=0.247 Sum_probs=46.8
Q ss_pred HHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 012329 285 AINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (466)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (466)
++.-|.+|..++.-|- ..+|..+-...+|+.|..=+.|-..|+-++..||..+|.+|...
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 5666666666666543 45777788889998888888877778889999999999999865
No 13
>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=34.33 E-value=1.5e+02 Score=31.37 Aligned_cols=102 Identities=26% Similarity=0.492 Sum_probs=66.8
Q ss_pred HHHHhhhHHHHHHHhhHhH----HHHHH--------hhhhHHHHHHhhccCCCCCC--------CCHHHHHHHHHHHhcC
Q 012329 286 INKLKKLSLLTEVLSKKQL----QQEFL--------DHGVLTLLKNWLEPLPDGSL--------PNINIRAAILKILTEF 345 (466)
Q Consensus 286 l~KLkmLpeV~~~L~K~~L----q~~fL--------D~GiL~vLk~WLePLPDgSL--------Pnl~IRt~LLkiL~~L 345 (466)
+.||++|.-=...|++..+ ..+|. ....+..|+.||--+-...+ || .+-..||..|..|
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 5799999865655554433 33455 23788999999964433333 45 5667788888887
Q ss_pred CCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHH----HhhhhhhcCCc
Q 012329 346 PIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVD----KWSRPIFNKST 400 (466)
Q Consensus 346 PId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~----kWSRPI~~~ss 400 (466)
-+..+. .-..| .+|-|..|+|+-. .||..-+. .|.||+|....
T Consensus 84 g~~~df--~p~kL-k~G~Ge~vc~VLd---------~Lad~AL~~~~F~~~~p~~~~e~ 130 (359)
T PF10498_consen 84 GVPVDF--PPSKL-KQGSGEHVCYVLD---------QLADEALKRKNFKWKRPIYPKEE 130 (359)
T ss_pred CCCCCC--ChHHh-hCCCCHHHHHHHH---------HHHHHHHHhcCcCccCCCCCccc
Confidence 543332 12344 5799999998762 25554444 59999998865
No 14
>KOG2973 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.36 E-value=1.1e+02 Score=32.68 Aligned_cols=72 Identities=24% Similarity=0.317 Sum_probs=60.9
Q ss_pred CCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccchhhhccCchhcHHHHHHHHHHHHHhhh--hhhcCCccccc
Q 012329 329 LPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWSR--PIFNKSTRFED 404 (466)
Q Consensus 329 LPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSR--PI~~~ss~Y~d 404 (466)
-|.-.||..++.+|..|-.+. . -|++|+.-|+=.++--|++.- +.+.+++.|.++|+--.| |-.|.-..|..
T Consensus 255 epdpdIrk~llEai~lLcaT~-~--GRe~lR~kgvYpilRElhk~e-~ded~~~ace~vvq~Lv~~e~~~G~~~~~~s 328 (353)
T KOG2973|consen 255 EPDPDIRKMLLEALLLLCATR-A--GREVLRSKGVYPILRELHKWE-EDEDIREACEQVVQMLVRLEPEIGILDEYES 328 (353)
T ss_pred CCChHHHHHHHHHHHHHHhhh-H--hHHHHHhcCchHHHHHHhcCC-CcHHHHHHHHHHHHHHHhcccccchhhhcCc
Confidence 456779999999999986532 2 499999999999999888876 889999999999998888 77787778874
No 15
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=27.07 E-value=3.4e+02 Score=23.11 Aligned_cols=78 Identities=12% Similarity=0.139 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHH
Q 012329 257 IALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRA 336 (466)
Q Consensus 257 i~~iv~~Ll~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt 336 (466)
+..++..|..+|.. .+-.-++.=|.+|..++.-+... ++..|-.+.++..+-....+-..|.-++.+||+
T Consensus 35 ~~~~~~~l~kRl~~---------~~~~~~lkaL~lLe~lvkN~g~~-f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~ 104 (115)
T cd00197 35 PKEAVDAIKKRINN---------KNPHVVLKALTLLEYCVKNCGER-FHQEVASNDFAVELLKFDKSKLLGDDVSTNVRE 104 (115)
T ss_pred HHHHHHHHHHHhcC---------CcHHHHHHHHHHHHHHHHHccHH-HHHHHHHhHHHHHHHHhhccccccCCCChHHHH
Confidence 44455555555531 12334556666677666665544 445577776666665545555688889999999
Q ss_pred HHHHHHhc
Q 012329 337 AILKILTE 344 (466)
Q Consensus 337 ~LLkiL~~ 344 (466)
.++.++..
T Consensus 105 k~~~l~~~ 112 (115)
T cd00197 105 KAIELVQL 112 (115)
T ss_pred HHHHHHHH
Confidence 99998864
No 16
>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=21.08 E-value=2.2e+02 Score=19.93 Aligned_cols=37 Identities=16% Similarity=0.264 Sum_probs=30.9
Q ss_pred hHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 012329 303 QLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (466)
Q Consensus 303 ~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (466)
.....+++.|++..|-.-|. -++..|++..+-+|.+|
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 57888999988888765
No 17
>PLN02777 photosystem I P subunit (PSI-P)
Probab=21.01 E-value=3.4e+02 Score=26.41 Aligned_cols=90 Identities=14% Similarity=0.187 Sum_probs=62.7
Q ss_pred HH-hhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcccc
Q 012329 288 KL-KKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKV 366 (466)
Q Consensus 288 KL-kmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKV 366 (466)
.+ .++..|.+..-+.+=.-+++--++...|+.| |-..+|..|..+|+-. ..|.=-|||-.
T Consensus 75 ~~~ei~k~~~e~Wd~~EdK~av~~l~~aaiVal~-------------v~~~VL~AId~lPLlP------~lLELVGigYs 135 (167)
T PLN02777 75 ELPEIVKTVQEAWDKVEDKYAVSSLAFAGVVALW-------------GSAGMISAIDRLPLVP------GVLELVGIGYT 135 (167)
T ss_pred cHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHH-------------HHHHHHHHHhcccccc------chHHHhhhhhh
Confidence 44 5666666666666667778888999999999 6789999999999844 36888899999
Q ss_pred hhhhccCchhcHHHHHHHHHHHHHhhhhhhc
Q 012329 367 IMFLSKSDEETTSNRKLAKDLVDKWSRPIFN 397 (466)
Q Consensus 367 VmfL~K~p~ET~eNKrlA~~LI~kWSRPI~~ 397 (466)
..|.+++=--.+.=+.+..++ +....-|+|
T Consensus 136 ~WF~yRyLLfke~ReeL~~ki-~~lk~~IlG 165 (167)
T PLN02777 136 GWFAYKNLVFKPDREALIEKI-KDTYKEIIG 165 (167)
T ss_pred hhhhhhHhcCcccHHHHHHHH-HHHHHHhhC
Confidence 999886543333333344444 333344445
No 18
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=20.74 E-value=95 Score=27.42 Aligned_cols=29 Identities=28% Similarity=0.508 Sum_probs=25.0
Q ss_pred HHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 012329 316 LLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (466)
Q Consensus 316 vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (466)
.|=.+|+-||+|+.|++ ||..|-+-|...
T Consensus 19 ~iF~FL~~~P~GT~~~~-iR~~L~rYI~~~ 47 (97)
T PRK13916 19 QIFDFLENVPRGTKTAH-IREALRRYIEEI 47 (97)
T ss_pred HHHHHHHHCCCCCccHH-HHHHHHHHHHhc
Confidence 45578999999999998 999998888775
No 19
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=20.54 E-value=3.3e+02 Score=24.96 Aligned_cols=56 Identities=16% Similarity=0.268 Sum_probs=41.1
Q ss_pred HHHHHhhhHHHHHHHhhHhHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCC
Q 012329 285 AINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFP 346 (466)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LP 346 (466)
++.-|.+|..++.-| -..+|..+-+..+|+.|..=+.+ -++..|+..+|.+|...-
T Consensus 58 ql~AL~LLe~~vkNC-G~~fh~evas~~fl~~l~~l~~~-----~~~~~Vk~kil~li~~W~ 113 (142)
T cd03569 58 QLYALLLLESCVKNC-GTHFHDEVASREFMDELKDLIKT-----TKNEEVRQKILELIQAWA 113 (142)
T ss_pred HHHHHHHHHHHHHHC-CHHHHHHHhhHHHHHHHHHHHcc-----cCCHHHHHHHHHHHHHHH
Confidence 344455555555543 34578888899999999998876 578889999999998763
Done!