Query 016190
Match_columns 393
No_of_seqs 116 out of 184
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:37:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016190.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016190hhsearch_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 1.1E-50 2.3E-55 403.7 16.3 215 172-393 65-288 (417)
2 COG5139 Uncharacterized conser 100.0 7.8E-39 1.7E-43 311.1 13.2 167 221-393 115-284 (397)
3 PF08711 Med26: TFIIS helical 99.0 2.1E-10 4.5E-15 85.2 3.7 50 337-393 1-50 (53)
4 cd00183 TFIIS_I N-terminal dom 98.4 1.3E-06 2.8E-11 69.9 7.2 55 330-392 18-72 (76)
5 smart00509 TFS2N Domain in the 97.9 1.4E-05 3E-10 64.2 4.8 54 331-392 17-70 (75)
6 TIGR01385 TFSII transcription 96.9 0.001 2.2E-08 66.2 4.7 48 337-392 25-72 (299)
7 PLN02976 amine oxidase 95.4 0.051 1.1E-06 64.3 8.8 81 301-392 1271-1353(1713)
8 KOG1105 Transcription elongati 95.4 0.029 6.3E-07 56.2 6.0 69 313-392 6-75 (296)
9 PF11176 DUF2962: Protein of u 61.6 22 0.00048 32.5 5.9 79 249-332 63-145 (155)
10 PF06371 Drf_GBD: Diaphanous G 54.9 88 0.0019 27.5 8.5 95 290-389 83-183 (187)
11 PF14278 TetR_C_8: Transcripti 51.6 33 0.00072 25.4 4.5 19 304-322 59-77 (77)
12 cd03567 VHS_GGA VHS domain fam 49.0 80 0.0017 28.4 7.3 60 285-345 55-114 (139)
13 cd00197 VHS_ENTH_ANTH VHS, ENT 31.5 2.8E+02 0.006 23.1 7.5 61 283-344 52-112 (115)
14 cd03569 VHS_Hrs_Vps27p VHS dom 28.4 2E+02 0.0043 25.7 6.4 56 285-346 58-113 (142)
15 KOG2973 Uncharacterized conser 28.4 1.1E+02 0.0024 32.0 5.3 58 329-390 255-312 (353)
16 PF10498 IFT57: Intra-flagella 26.6 1.9E+02 0.0041 30.0 6.7 82 286-371 5-106 (359)
17 PF00514 Arm: Armadillo/beta-c 24.5 1.8E+02 0.004 19.9 4.4 37 303-345 3-39 (41)
18 PRK13916 plasmid segregation p 22.6 84 0.0018 27.2 2.8 29 316-345 19-47 (97)
19 PF11985 DUF3486: Protein of u 20.7 1.1E+02 0.0023 28.1 3.3 38 285-326 3-42 (180)
20 PF09701 Cas_Cmr5: CRISPR-asso 20.2 51 0.0011 28.5 1.1 50 334-392 24-74 (122)
No 1
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.1e-50 Score=403.72 Aligned_cols=215 Identities=44% Similarity=0.666 Sum_probs=191.8
Q ss_pred HHHHHHHhcCCCCCCCc---hhhcccCccCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCchHHHHHHhhc
Q 016190 172 MLNEMWNAVAPTGDSED---DQEGVRTLDDD-----NFIDDSGVDPSDRYGSDSEPRFAHDAPQAEEGDEDEEIKELFKM 243 (393)
Q Consensus 172 ~~~e~~~~~~~~~ds~~---~~e~~rt~~Dd-----~fiD~~g~d~~d~~g~d~e~~~~~d~p~aee~E~Ddei~~llk~ 243 (393)
...++|+.+. .+-+. ++.+.++..+. +|+.++|.++-+-++.+.......+.+++...|...++.++|+|
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 6677887776 33333 33445554444 49999998877666665556567777888888999999999999
Q ss_pred cccccccCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHHhhHHHHHHHHhhhhHHHHHHhhc
Q 016190 244 GKKRKKNEKSPAEIA-LLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLE 322 (393)
Q Consensus 244 ~KkKKk~~~s~~Ei~-~iv~~Li~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLe 322 (393)
+++++++...+.+|. .+|..|+.+|..||+.|+++|.+++|||+||+|||.|.++|.|++||.+|||||||+.|+.||+
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 888899999999999 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHhhcC
Q 016190 323 PLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWVM 393 (393)
Q Consensus 323 PLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSR 393 (393)
||||||||||+||.+||+||..|||.+ +|||++||||||||||++||+||++||+||..||++|+|
T Consensus 223 PLPD~SLPal~Ir~~ll~iL~dlpi~~-----~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsR 288 (417)
T KOG1793|consen 223 PLPDGSLPALNIRKSLLDILNDLPIDK-----REHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSR 288 (417)
T ss_pred cCCCCCCcchHHHHHHHHHHhcCCcch-----HHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhc
Confidence 999999999999999999999999976 589999999999999999999999999999999999998
No 2
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7.8e-39 Score=311.11 Aligned_cols=167 Identities=32% Similarity=0.571 Sum_probs=151.7
Q ss_pred CCCCCccccCCCchHHHHHHhhccccc---cccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHH
Q 016190 221 FAHDAPQAEEGDEDEEIKELFKMGKKR---KKNEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTE 297 (393)
Q Consensus 221 ~~~d~p~aee~E~Ddei~~llk~~KkK---Kk~~~s~~Ei~~iv~~Li~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~ 297 (393)
+..+++.|...|.++.+.++|+..+.. ++....++=+..++..|..+|..||..|+..|.++.|||.||+|||+|..
T Consensus 115 ~~~d~t~a~~~El~~~~dr~lK~p~~sr~rr~eD~leq~~de~~lrLk~~M~~aa~~D~~~n~e~~pAt~Kik~lp~V~~ 194 (397)
T COG5139 115 SGQDFTEAQSGELGDTGDRQLKAPAASRARRKEDLLEQTVDEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSD 194 (397)
T ss_pred ccCCCChhhhhhhhhhhhhhhccchhhhhhccccchHHHHHHHHHHHHHHHHHHHHhhhhhhhccCcchhhhhccHHHHH
Confidence 344567888999999999999833332 23334455567789999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhc
Q 016190 298 VLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEET 377 (393)
Q Consensus 298 ~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET 377 (393)
+|.|.+||.+|||+|||+.|+.||+||||+|||||+||+.||.+|..|||.+ |||++||||+||+||+.+|++.
T Consensus 195 VL~k~~L~dtiLDnniLdsVr~WLEPLPD~SlP~~~IqksL~dvL~~lpI~t------EHL~eSgvGrIV~FYtiskk~e 268 (397)
T COG5139 195 VLMKKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKSLLDVLKTLPIHT------EHLVESGVGRIVYFYTISKKEE 268 (397)
T ss_pred HHHHHHHHHHHhhcchHHHHHhhhccCCCCCCcchHHHHHHHHHHhhCCchH------HHhhhcCCceEEEEEecCCccc
Confidence 9999999999999999999999999999999999999999999999999987 6999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcC
Q 016190 378 TSNRKLAKDLVDKWVM 393 (393)
Q Consensus 378 ~eNKrlA~~LI~kWSR 393 (393)
++++++|..||++|+|
T Consensus 269 ~~v~r~A~~LV~eWtr 284 (397)
T COG5139 269 KEVRRSAKALVQEWTR 284 (397)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999999997
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=99.02 E-value=2.1e-10 Score=85.20 Aligned_cols=50 Identities=46% Similarity=0.727 Sum_probs=44.8
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHhhcC
Q 016190 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWVM 393 (393)
Q Consensus 337 ~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWSR 393 (393)
.+|+.|..|||+ .++|++|+||++|.+|+|| .++++|+++|+.||.+|.+
T Consensus 1 ~iL~~L~~l~it------~~~L~~T~IGk~V~~l~k~-~~~~~i~~~A~~Li~~Wk~ 50 (53)
T PF08711_consen 1 EILKVLEKLPIT------VELLKSTGIGKAVNKLRKH-SENPEIRKLAKELIKKWKR 50 (53)
T ss_dssp HHHHHHHCSS-S------HHHHHHHSHHHHHHHHHHC-TS-HHHHHHHHHHHHHHHH
T ss_pred CHHHHhhcCCCC------HHHHHhCChhHHHHHHHcC-CCCHHHHHHHHHHHHHHhH
Confidence 489999999985 4799999999999999999 9999999999999999974
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=98.37 E-value=1.3e-06 Score=69.89 Aligned_cols=55 Identities=31% Similarity=0.561 Sum_probs=51.2
Q ss_pred CCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHhhc
Q 016190 330 PNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWV 392 (393)
Q Consensus 330 Pnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWS 392 (393)
|+...--.+|..|..|||+. +.|+.++||++|.+|++|+. +.++.+|+.||.+|.
T Consensus 18 ~~~~~~~~~L~~L~~~~it~------~~L~~T~iG~~V~~Lrkh~~--~~i~~~A~~Lv~~Wk 72 (76)
T cd00183 18 EEVSRLLDLLRLLKKLPLTV------EILKETRIGKKVNSLRKHSN--EKIRKLAKALIKSWK 72 (76)
T ss_pred CCHHHHHHHHHHHhcCCCCH------HHHHHCCHHHHHHHHHcCCc--HHHHHHHHHHHHHHH
Confidence 78888889999999999854 79999999999999999987 999999999999996
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=97.93 E-value=1.4e-05 Score=64.18 Aligned_cols=54 Identities=33% Similarity=0.511 Sum_probs=45.6
Q ss_pred CHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHhhc
Q 016190 331 NINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWV 392 (393)
Q Consensus 331 nl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWS 392 (393)
+..-=-.+|+.|..|||+ .++|+.+.||++|..|++|+ .++++.+|..||..|.
T Consensus 17 ~~~~~l~~L~~L~~~~~t------~~~L~~T~iG~~v~~Lrkh~--~~~I~~~A~~Li~~WK 70 (75)
T smart00509 17 EVSRCLDILKKLKKLPIT------VDLLEETRIGKKVNGLRKHK--NEEIRKLAKKLIKSWK 70 (75)
T ss_pred CHHHHHHHHHHHhcCCCC------HHHHHHCcHHHHHHHHHcCC--cHHHHHHHHHHHHHHH
Confidence 333334678888888985 47999999999999999996 5999999999999995
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=96.93 E-value=0.001 Score=66.16 Aligned_cols=48 Identities=33% Similarity=0.521 Sum_probs=42.1
Q ss_pred HHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHhhc
Q 016190 337 AILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDKWV 392 (393)
Q Consensus 337 ~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~kWS 392 (393)
.+|+.|..|||. .+.|+.+.||++|..|+||+. ++|+.+|+.||..|.
T Consensus 25 ~~L~~L~~~~~t------~~lL~~T~IG~~Vn~lrkh~~--~~I~~lAk~li~~WK 72 (299)
T TIGR01385 25 DILHQLKEFPPT------EELLQETKVGVKVNKLRKHPN--EDISKLAKKIIKSWK 72 (299)
T ss_pred HHHHHHhcCCCc------HHHHhhCchhHHHHHHHcCCc--HHHHHHHHHHHHHHH
Confidence 467888888885 479999999999999999975 679999999999995
No 7
>PLN02976 amine oxidase
Probab=95.44 E-value=0.051 Score=64.29 Aligned_cols=81 Identities=22% Similarity=0.323 Sum_probs=62.3
Q ss_pred hHHHHHHHHhhhhHHHHHHhhc--cCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcH
Q 016190 301 KKQLQQEFLDHGVLTLLKNWLE--PLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETT 378 (393)
Q Consensus 301 K~~Lq~~fLD~GiL~vLk~WLe--PLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~ 378 (393)
-.+|..+-+....|.+|..||. --++| -++-+.++.+|.-+|.+. -.|+.|||||+|--=. |--..+
T Consensus 1271 ~~~~~~~a~~~~gl~~l~~w~~~~~~~~~----~~l~~~~~~ll~~~~~d~------~a~r~sg~~~~~k~~~-~~h~~~ 1339 (1713)
T PLN02976 1271 VETLKSFAGTKEGLATLNSWILDSMGKDG----TQLLRHCVRLLVLVSTDL------LAVRLSGIGKTVKEKV-CVHTSR 1339 (1713)
T ss_pred HHHHHHHhcccchHHHHHHHHHHHhcccH----HHHHHHHHHHHhhcchhH------HHHHhccchHHHHhhh-hhcccH
Confidence 3455566666788999999998 33555 346678889998888765 4899999999984322 445678
Q ss_pred HHHHHHHHHHHhhc
Q 016190 379 SNRKLAKDLVDKWV 392 (393)
Q Consensus 379 eNKrlA~~LI~kWS 392 (393)
+||.||.+|++.|+
T Consensus 1340 ~~r~~a~~~~~~w~ 1353 (1713)
T PLN02976 1340 DIRAIASQLVSVWL 1353 (1713)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999996
No 8
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=95.42 E-value=0.029 Score=56.19 Aligned_cols=69 Identities=30% Similarity=0.440 Sum_probs=55.7
Q ss_pred hHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhH-hhhcCchhcHHHHHHHHHHHHhh
Q 016190 313 VLTLLKNWLEPLPDGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIM-FLSKSDEETTSNRKLAKDLVDKW 391 (393)
Q Consensus 313 iL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVm-fL~K~p~ET~eNKrlA~~LI~kW 391 (393)
++.+.+. |+-++.. +|+.---.+|+-|.++||. .++|..+.||..|. ++.+|+.+ +++.+|+.||..|
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--KNVEAALDLLKRLKKIPVT------LELLQETRTGMGVNEVLKKHKNE--EVRSLAKKLIKSW 74 (296)
T ss_pred HHHHHHH-HHhhccc--ccHHHHHHHHHHHHhcccH------HHHHHHhhHHHHHHHHHHhCCCH--HHHHHHHHHHHHH
Confidence 3444444 6666665 8887777889999999984 47999999999999 88888875 7889999999999
Q ss_pred c
Q 016190 392 V 392 (393)
Q Consensus 392 S 392 (393)
.
T Consensus 75 k 75 (296)
T KOG1105|consen 75 K 75 (296)
T ss_pred H
Confidence 5
No 9
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=61.57 E-value=22 Score=32.49 Aligned_cols=79 Identities=22% Similarity=0.329 Sum_probs=48.1
Q ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHhhhHHHHHHHhhHHH----HHHHHhhhhHHHHHHhhccC
Q 016190 249 KNEKSPAEIALLVENVMAELEVTAEEDAELNRQGKPAINKLKKLSLLTEVLSKKQL----QQEFLDHGVLTLLKNWLEPL 324 (393)
Q Consensus 249 k~~~s~~Ei~~iv~~Li~~M~~AAeeD~eank~gkPAl~KLkmLpeV~~~L~K~~L----q~~fLD~GiL~vLk~WLePL 324 (393)
...-+.+|+..+|..+|.+-..=.++=....+.|+|+.++..+|...++...+..- .+-|.+..-+..|+.|
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 44677899999999999887666655455578899999999999987776544332 1124555667889999
Q ss_pred CCCCCCCH
Q 016190 325 PDGSLPNI 332 (393)
Q Consensus 325 PDgSLPnl 332 (393)
||++-.+
T Consensus 139 -~G~~~~l 145 (155)
T PF11176_consen 139 -NGDWGYL 145 (155)
T ss_dssp -SS-STHH
T ss_pred -CCChhhC
Confidence 7776554
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=54.92 E-value=88 Score=27.54 Aligned_cols=95 Identities=26% Similarity=0.295 Sum_probs=58.3
Q ss_pred hhhHHHHHHHhhH--HHHHHHHhhhhHHHHHHhhccCC---CCCCCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcc
Q 016190 290 KKLSLLTEVLSKK--QLQQEFLDHGVLTLLKNWLEPLP---DGSLPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLG 364 (393)
Q Consensus 290 kmLpeV~~~L~K~--~Lq~~fLD~GiL~vLk~WLePLP---DgSLPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLG 364 (393)
+.|..+.-.|+.. .|...|+++|++.+|..+|.-+. ..+-..+.+...+|.||..+ +++..+ ....|...++=
T Consensus 83 ~~L~~L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~~~~~~~~~~~~l~Clkal-~n~~~G-~~~v~~~~~~v 160 (187)
T PF06371_consen 83 KILKSLRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEKSEEDIDIEHECLRCLKAL-MNTKYG-LEAVLSHPDSV 160 (187)
T ss_dssp HHHHHHHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCTCTTCHHHHHHHHHHHHHH-TSSHHH-HHHHHCSSSHH
T ss_pred HHHHHHHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhhcchhHHHHHHHHHHHHHH-HccHHH-HHHHHcCcHHH
Confidence 5555666666654 78899999999999999998874 34456788999999999876 232211 12333433332
Q ss_pred hh-hHhhhcCchhcHHHHHHHHHHHH
Q 016190 365 KV-IMFLSKSDEETTSNRKLAKDLVD 389 (393)
Q Consensus 365 KV-VmfL~K~p~ET~eNKrlA~~LI~ 389 (393)
.. +..|. ...+..|.+|-+|+.
T Consensus 161 ~~i~~~L~---s~~~~~r~~~leiL~ 183 (187)
T PF06371_consen 161 NLIALSLD---SPNIKTRKLALEILA 183 (187)
T ss_dssp HHHHHT-----TTSHHHHHHHHHHHH
T ss_pred HHHHHHHC---CCCHHHHHHHHHHHH
Confidence 22 23332 233567777766653
No 11
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=51.58 E-value=33 Score=25.40 Aligned_cols=19 Identities=26% Similarity=0.686 Sum_probs=17.0
Q ss_pred HHHHHHhhhhHHHHHHhhc
Q 016190 304 LQQEFLDHGVLTLLKNWLE 322 (393)
Q Consensus 304 Lq~~fLD~GiL~vLk~WLe 322 (393)
+.-.|+-+|++.+|..||+
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=48.97 E-value=80 Score=28.36 Aligned_cols=60 Identities=18% Similarity=0.247 Sum_probs=47.5
Q ss_pred HHHHHhhhHHHHHHHhhHHHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 016190 285 AINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (393)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (393)
++.-|.+|..++.-+- ..+|..+-...+|+.|..=+.|-..|+-++..||..+|.+|...
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 5667777777766543 45677788888898888888776678889999999999999865
No 13
>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=31.54 E-value=2.8e+02 Score=23.08 Aligned_cols=61 Identities=13% Similarity=0.156 Sum_probs=42.0
Q ss_pred ChHHHHHhhhHHHHHHHhhHHHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhc
Q 016190 283 KPAINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTE 344 (393)
Q Consensus 283 kPAl~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~ 344 (393)
+-++.=|.+|..++.-+... ++..|-.+.++..+-.-..+-..|.-++.+||+.++.++..
T Consensus 52 ~~~lkaL~lLe~lvkN~g~~-f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~ 112 (115)
T cd00197 52 HVVLKALTLLEYCVKNCGER-FHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQL 112 (115)
T ss_pred HHHHHHHHHHHHHHHHccHH-HHHHHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHHHH
Confidence 34566666777777665544 34456677666665554555567888999999999999864
No 14
>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=28.37 E-value=2e+02 Score=25.71 Aligned_cols=56 Identities=16% Similarity=0.268 Sum_probs=42.1
Q ss_pred HHHHHhhhHHHHHHHhhHHHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcCC
Q 016190 285 AINKLKKLSLLTEVLSKKQLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEFP 346 (393)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~LP 346 (393)
++.-|.+|..++.-+ -..+|..+-+..+|+.|..=+.+ -++..|+..+|.+|...-
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 445555666666544 35677888899999999988776 578889999999998763
No 15
>KOG2973 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.36 E-value=1.1e+02 Score=31.95 Aligned_cols=58 Identities=24% Similarity=0.323 Sum_probs=48.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhhcCchhcHHHHHHHHHHHHh
Q 016190 329 LPNINIRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLSKSDEETTSNRKLAKDLVDK 390 (393)
Q Consensus 329 LPnl~IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~K~p~ET~eNKrlA~~LI~k 390 (393)
-|.--||..+|.+|..|-.. .. -|++|+.-|+=.++--|++.- +.+.+++.|.++|+-
T Consensus 255 epdpdIrk~llEai~lLcaT-~~--GRe~lR~kgvYpilRElhk~e-~ded~~~ace~vvq~ 312 (353)
T KOG2973|consen 255 EPDPDIRKMLLEALLLLCAT-RA--GREVLRSKGVYPILRELHKWE-EDEDIREACEQVVQM 312 (353)
T ss_pred CCChHHHHHHHHHHHHHHhh-hH--hHHHHHhcCchHHHHHHhcCC-CcHHHHHHHHHHHHH
Confidence 45667999999999998653 22 499999999999999998876 789999999999874
No 16
>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=26.62 E-value=1.9e+02 Score=30.05 Aligned_cols=82 Identities=23% Similarity=0.368 Sum_probs=54.1
Q ss_pred HHHHhhhHHHHHHHhhHHH----HHHHH--------hhhhHHHHHHhhccCCCCC--------CCCHHHHHHHHHHHhcC
Q 016190 286 INKLKKLSLLTEVLSKKQL----QQEFL--------DHGVLTLLKNWLEPLPDGS--------LPNINIRAAILKILTEF 345 (393)
Q Consensus 286 l~KLkmLpeV~~~L~K~~L----q~~fL--------D~GiL~vLk~WLePLPDgS--------LPnl~IRt~LLkiL~~L 345 (393)
+.||++|.-=...|++..+ .-+|. ..-.+..|+.||--+-... =|| .+-..||..|..|
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 5789999877766665544 33455 3478899999996443333 345 5667788888887
Q ss_pred CCCccccchHHHHhhcCcchhhHhhh
Q 016190 346 PIDLEQFDRREQLKKSGLGKVIMFLS 371 (393)
Q Consensus 346 PId~e~~d~rE~LK~SGLGKVVmfL~ 371 (393)
-+..+. .-..| .+|-|..|+|+-
T Consensus 84 g~~~df--~p~kL-k~G~Ge~vc~VL 106 (359)
T PF10498_consen 84 GVPVDF--PPSKL-KQGSGEHVCYVL 106 (359)
T ss_pred CCCCCC--ChHHh-hCCCCHHHHHHH
Confidence 543321 12344 579999998865
No 17
>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=24.54 E-value=1.8e+02 Score=19.86 Aligned_cols=37 Identities=16% Similarity=0.264 Sum_probs=30.8
Q ss_pred HHHHHHHhhhhHHHHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 016190 303 QLQQEFLDHGVLTLLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (393)
Q Consensus 303 ~Lq~~fLD~GiL~vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (393)
.....+++.|++..|-.-|. -++..||+..+-+|.+|
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 45678999999999999888 57888999988888764
No 18
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=22.56 E-value=84 Score=27.15 Aligned_cols=29 Identities=28% Similarity=0.508 Sum_probs=24.8
Q ss_pred HHHHhhccCCCCCCCCHHHHHHHHHHHhcC
Q 016190 316 LLKNWLEPLPDGSLPNINIRAAILKILTEF 345 (393)
Q Consensus 316 vLk~WLePLPDgSLPnl~IRt~LLkiL~~L 345 (393)
.|-.+|+-||+|+.|++ ||..|-+-|...
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 35578999999999998 999998888775
No 19
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.70 E-value=1.1e+02 Score=28.08 Aligned_cols=38 Identities=29% Similarity=0.453 Sum_probs=24.1
Q ss_pred HHHHHhhhHHHHHHHhhHHHHHHHHhhh--hHHHHHHhhccCCC
Q 016190 285 AINKLKKLSLLTEVLSKKQLQQEFLDHG--VLTLLKNWLEPLPD 326 (393)
Q Consensus 285 Al~KLkmLpeV~~~L~K~~Lq~~fLD~G--iL~vLk~WLePLPD 326 (393)
-..|+..||.-+ +..|+..|.+.| ..+.+..|++-++.
T Consensus 3 r~SkId~LP~ei----r~~l~~~L~~~~~t~~ei~~~~~~~~~~ 42 (180)
T PF11985_consen 3 RRSKIDLLPPEI----REWLDQMLRDGGFTQYEILAEWLEELAE 42 (180)
T ss_pred CCchHhhCCHHH----HHHHHHHHHhCCCChHHHHHHHHHhhhc
Confidence 345777777642 235666677765 56677777776665
No 20
>PF09701 Cas_Cmr5: CRISPR-associated protein (Cas_Cmr5); InterPro: IPR010160 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a family of Cas proteins as represented by TM1791.1 from Thermotoga maritima. This family of Cas proteins are found in both archaeal and bacterial species.; PDB: 2OEB_A 2ZOP_A.
Probab=20.21 E-value=51 Score=28.48 Aligned_cols=50 Identities=22% Similarity=0.501 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCCCccccchHHHHhhcCcchhhHhhh-cCchhcHHHHHHHHHHHHhhc
Q 016190 334 IRAAILKILTEFPIDLEQFDRREQLKKSGLGKVIMFLS-KSDEETTSNRKLAKDLVDKWV 392 (393)
Q Consensus 334 IRt~LLkiL~~LPId~e~~d~rE~LK~SGLGKVVmfL~-K~p~ET~eNKrlA~~LI~kWS 392 (393)
+++..-.....||. .+..+|||-+|-||. |...+....-.+....|..|.
T Consensus 24 ~~k~y~s~~~~lPa---------~I~~nGL~qtlAF~~sK~~~~~~~~~~~l~~~l~~wl 74 (122)
T PF09701_consen 24 VRKKYKSYAKKLPA---------MILQNGLGQTLAFLLSKGKDEHKAKHYLLLEHLAEWL 74 (122)
T ss_dssp CHHHHHHHHHHHHH---------HHHHH-HHHHHHHHHCTSSCHHCH-HHHHHHHHHHHC
T ss_pred HHHHHHHHHHHhHH---------HHHHcCHHHHHHHHHhcccccccchHHHHHHHHHHHH
Confidence 56677777888884 689999999999988 333322221235666666774
Done!