Query psy17141
Match_columns 141
No_of_seqs 139 out of 1254
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 23:00:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12777 MT: Microtubule-bindi 99.9 4E-27 8.7E-32 190.5 3.3 126 10-140 139-281 (344)
2 KOG3595|consensus 99.5 3.4E-13 7.4E-18 125.1 10.7 113 9-126 850-970 (1395)
3 PF12780 AAA_8: P-loop contain 98.5 1.3E-08 2.8E-13 80.2 -1.4 88 39-126 100-215 (268)
4 COG5245 DYN1 Dynein, heavy cha 98.5 5.6E-07 1.2E-11 83.7 8.2 89 6-99 2223-2316(3164)
5 KOG3595|consensus 95.6 0.028 6.1E-07 53.5 6.0 60 67-126 592-651 (1395)
6 KOG0994|consensus 73.1 77 0.0017 30.7 11.4 28 42-69 1474-1501(1758)
7 PF10664 NdhM: Cyanobacterial 60.7 15 0.00032 25.0 3.4 38 103-140 34-84 (108)
8 PRK00578 prfB peptide chain re 52.8 1.3E+02 0.0029 24.9 8.7 51 43-93 30-82 (367)
9 COG0216 PrfA Protein chain rel 51.9 1.4E+02 0.003 24.8 8.8 51 44-94 15-67 (363)
10 TIGR00019 prfA peptide chain r 49.6 1.5E+02 0.0033 24.6 9.2 48 44-91 15-64 (360)
11 TIGR00020 prfB peptide chain r 48.5 1.6E+02 0.0034 24.5 8.8 51 43-93 30-82 (364)
12 PRK00591 prfA peptide chain re 47.9 1.6E+02 0.0035 24.4 9.1 50 44-93 14-65 (359)
13 PF13495 Phage_int_SAM_4: Phag 47.1 42 0.00091 20.7 3.9 42 36-77 37-79 (85)
14 PHA01346 hypothetical protein 43.4 27 0.00058 20.1 2.2 20 44-63 18-38 (53)
15 COG3489 Predicted periplasmic 43.0 9.5 0.00021 31.0 0.4 63 12-77 82-151 (359)
16 PRK06746 peptide chain release 36.5 1.9E+02 0.0041 23.7 6.9 42 53-94 2-45 (326)
17 PF10979 DUF2786: Protein of u 33.7 91 0.002 17.5 3.4 30 43-72 2-34 (43)
18 KOG3647|consensus 32.2 2.1E+02 0.0045 23.1 6.3 55 84-138 116-177 (338)
19 PRK05589 peptide chain release 29.8 3E+02 0.0064 22.6 7.0 40 53-92 2-43 (325)
20 PF10929 DUF2811: Protein of u 28.8 1.4E+02 0.003 18.1 3.9 27 39-65 5-32 (57)
21 PRK04964 hypothetical protein; 27.0 97 0.0021 19.2 2.9 31 43-73 29-59 (66)
22 PF06786 UPF0253: Uncharacteri 25.6 96 0.0021 19.2 2.7 31 43-73 29-59 (66)
23 PF02899 Phage_int_SAM_1: Phag 22.9 1.8E+02 0.004 17.4 4.5 42 36-77 40-81 (84)
24 PF02284 COX5A: Cytochrome c o 22.5 2.4E+02 0.0053 19.3 4.5 30 57-86 43-72 (108)
25 PHA03256 BDLF3; Provisional 22.4 1.4E+02 0.003 19.0 3.1 38 38-77 15-52 (77)
26 COG5245 DYN1 Dynein, heavy cha 22.3 7.6E+02 0.016 25.9 9.0 79 50-128 2614-2698(3164)
27 PF05184 SapB_1: Saposin-like 22.3 98 0.0021 16.2 2.2 27 43-69 9-35 (39)
28 PF12983 DUF3867: Protein of u 22.2 74 0.0016 23.8 2.1 43 21-68 40-84 (186)
29 KOG4403|consensus 22.1 3.5E+02 0.0075 23.4 6.2 45 95-139 243-290 (575)
30 COG2231 Uncharacterized protei 20.6 83 0.0018 24.2 2.1 18 3-20 35-52 (215)
31 PHA02335 hypothetical protein 20.4 58 0.0013 22.4 1.1 40 4-49 75-116 (118)
32 PF11593 Med3: Mediator comple 20.1 5.3E+02 0.011 21.6 8.8 29 45-73 10-39 (379)
No 1
>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.
Probab=99.93 E-value=4e-27 Score=190.47 Aligned_cols=126 Identities=31% Similarity=0.490 Sum_probs=107.8
Q ss_pred cCChHHHHhcc---HhhhcccccccccccccCCCCHHHHHHHHhhhCCCCCCHHHHHHHHHHHHhhchHHhhhhhhHHHH
Q psy17141 10 ATGFSTAKVRF---PNYRKNCTRISLYEYDKDHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQLF 86 (141)
Q Consensus 10 ~~~W~~ak~~l---~~f~~~~~~~~L~~fd~d~i~~~~l~~i~~~l~~p~F~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~ 86 (141)
+++|.+||++| ++|++ +|.+||+|+|++.++.+|++|+.+|+|+|+.+.++|.||++||.||+||+.|++|+
T Consensus 139 ~~~W~~ak~~l~~~~~Fl~-----~L~~fd~~~i~~~~~~~l~~~~~~p~F~~e~v~~~S~Aa~~Lc~WV~A~~~Y~~v~ 213 (344)
T PF12777_consen 139 DTSWESAKKLLSDSDNFLQ-----RLKNFDKDNIPEATIKKLKKYLKNPDFNPEKVRKASKAAGSLCKWVRAMVKYYEVN 213 (344)
T ss_dssp --HHHHHHCHHCSSTTHHH-----HHHHS-GGG--HHHHHHHHCTTTSTTSSHHHHHHH-TTHHHHHHHHHHHHHHHHHC
T ss_pred cccHHHHHHHHHhHHHHHH-----HHHhhccccccHHHHHHHHHHhcCCCCCHHHHHHHhhcchHHHHHHHHHHHHHHHH
Confidence 57899999988 37999 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcchhhHHHHH----HHhHHhhchHHHHHHHHHHHHHHhhh----------hHHHHHHHHHhhhc
Q psy17141 87 KDIQRQYPSIIDCT----TIDWILDCPEQSLMEVAERFLETVDI----------LETNVLEVQIRLYF 140 (141)
Q Consensus 87 ~~v~Pk~~~L~~~~----~~~~~l~~~~~~L~~V~~~l~~l~~~----------~~~~~~~~~~rl~~ 140 (141)
+.|.|++.++.++. .+...|...+..|.++.+++..++.. ++.++..|++||..
T Consensus 214 ~~V~P~~~~l~~a~~~l~~~~~~L~~~~~~l~~l~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~kl~r 281 (344)
T PF12777_consen 214 KEVEPKRQKLEEAEAELEEAEEQLAEKQAELAELEEKLAALQKEYEEAQKEKQELEEEIEETERKLER 281 (344)
T ss_dssp CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 99999999999884 46677888888899998888888743 56667788888764
No 2
>KOG3595|consensus
Probab=99.46 E-value=3.4e-13 Score=125.10 Aligned_cols=113 Identities=28% Similarity=0.451 Sum_probs=98.9
Q ss_pred ccCChHHHHhcc--H-hhhcccccccccccccCCCCHHHHHHHH-hhhCCCCCCHHHHHHHHHHHHhhchHHhhhhhhHH
Q psy17141 9 YATGFSTAKVRF--P-NYRKNCTRISLYEYDKDHIPEKILKKIT-NYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQ 84 (141)
Q Consensus 9 ~~~~W~~ak~~l--~-~f~~~~~~~~L~~fd~d~i~~~~l~~i~-~~l~~p~F~~e~i~~~S~Aa~~l~~WV~a~~~y~~ 84 (141)
..++|..+.++| . .|+. .+.+|+++++++.+.+.+. .|+.+|+|.|+.+.++|.||+++|.||.|+.+|+.
T Consensus 850 ~~~~w~~~~~~~~~~~~fl~-----~l~~~~~~~i~~~~~k~i~~~~~~~p~f~~~~v~~~s~a~~~l~~wv~a~~~~~k 924 (1395)
T KOG3595|consen 850 SSTDWKNISKLLLSDDFFLI-----ILREFDKDEIPEEIMKLIKKFYFQNPDFVPEKVNRASLACEGLCLWVIAIDKYSK 924 (1395)
T ss_pred cCCChHHHHHHhhcccHHHH-----HhhcCccccChHHHHHHHHHhhcCCccCCHHHHHhhhhhhhhHHHHHHHHHHHHH
Confidence 467777777766 4 5888 9999999999999999996 69999999999999999999999999999999999
Q ss_pred HHHHHhcchhhHHHHH----HHhHHhhchHHHHHHHHHHHHHHhhh
Q psy17141 85 LFKDIQRQYPSIIDCT----TIDWILDCPEQSLMEVAERFLETVDI 126 (141)
Q Consensus 85 v~~~v~Pk~~~L~~~~----~~~~~l~~~~~~L~~V~~~l~~l~~~ 126 (141)
++..|.|++..+..++ .....+....+.+.++.++++.+.+.
T Consensus 925 v~~~v~p~~~~~~~~e~~~~~~~~~l~~~~~~l~~~e~~~~~~~~~ 970 (1395)
T KOG3595|consen 925 VLKVVEPKRQELARLEAELKAAMKELEEKSAELQDLEEKLQRLKDE 970 (1395)
T ss_pred HHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999885 34667778888888888888877643
No 3
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=98.49 E-value=1.3e-08 Score=80.19 Aligned_cols=88 Identities=26% Similarity=0.571 Sum_probs=70.3
Q ss_pred CCCHHHHHHHHhhhCCCC----CCHHHHHHHH------------------------HHHHhhchHHhhhhhhHHHHHHHh
Q psy17141 39 HIPEKILKKITNYVNLPD----FDPEEIGMVS------------------------VAAKSLSKWVMAIEKYAQLFKDIQ 90 (141)
Q Consensus 39 ~i~~~~l~~i~~~l~~p~----F~~e~i~~~S------------------------~Aa~~l~~WV~a~~~y~~v~~~v~ 90 (141)
-..+..++.|+.++++++ |++|+...+. ..+..++|.|++|++.+..++...
T Consensus 100 i~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~~~~~~~~~~~~F~~rvr~nLHivl~~sp~~~~~r~~~ 179 (268)
T PF12780_consen 100 IVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEGISDSRESLYEFFIERVRKNLHIVLCMSPVGPNFRDRC 179 (268)
T ss_dssp SSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT--SSHHHHHHHHHHHHCCCEEEEEEESTTTTCCCHHH
T ss_pred cchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcCCCCchHHHHHHHHHHHHhheeEEEEECCCCchHHHHH
Confidence 345678888888888765 7776655432 346677889999999999999999
Q ss_pred cchhhHHHHHHHhHHhhchHHHHHHHHHHHHHHhhh
Q psy17141 91 RQYPSIIDCTTIDWILDCPEQSLMEVAERFLETVDI 126 (141)
Q Consensus 91 Pk~~~L~~~~~~~~~l~~~~~~L~~V~~~l~~l~~~ 126 (141)
..+|+|.++|+++|+.+||+++|..|+.++.+..+.
T Consensus 180 ~~fPaL~~~ctIdW~~~W~~eaL~~Va~~~l~~~~~ 215 (268)
T PF12780_consen 180 RSFPALVNCCTIDWFDPWPEEALLSVANKFLSDIEL 215 (268)
T ss_dssp HHHCCHHHHSEEEEEES--HHHHHHHHHHHCCHHHT
T ss_pred HhCcchhcccEEEeCCcCCHHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999988766543
No 4
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=98.47 E-value=5.6e-07 Score=83.69 Aligned_cols=89 Identities=10% Similarity=0.091 Sum_probs=78.4
Q ss_pred ecc-ccCChHHHHhcc--HhhhcccccccccccccC-CCCHHHHHHHH-hhhCCCCCCHHHHHHHHHHHHhhchHHhhhh
Q psy17141 6 VLY-YATGFSTAKVRF--PNYRKNCTRISLYEYDKD-HIPEKILKKIT-NYVNLPDFDPEEIGMVSVAAKSLSKWVMAIE 80 (141)
Q Consensus 6 ~~~-~~~~W~~ak~~l--~~f~~~~~~~~L~~fd~d-~i~~~~l~~i~-~~l~~p~F~~e~i~~~S~Aa~~l~~WV~a~~ 80 (141)
+|+ ....|...++.+ ++|+. .+.+|+.+ +++++....++ .+.+||.|+.+.+.++|+||+++..|+.+..
T Consensus 2223 LLgf~a~~w~~~qQ~LrrDDfi~-----~i~~y~~e~e~~~~~Rr~~E~~~~Sdp~ft~~~lnRaskacGPl~~Wl~~~c 2297 (3164)
T COG5245 2223 LLGFEAKIWFGEQQSLRRDDFIR-----IIGKYPDEIEFDLEARRFREARECSDPSFTGSILNRASKACGPLKRWLVREC 2297 (3164)
T ss_pred HhcchhHHhhhHHHHhhhhhHHH-----HhccCCceeecCHHHHHHHHHHhcCCCcchhHHhhhhhhccCcHHHHHHHHh
Confidence 443 468899999999 79999 99999754 47888888887 7999999999999999999999999999999
Q ss_pred hhHHHHHHHhcchhhHHHH
Q psy17141 81 KYAQLFKDIQRQYPSIIDC 99 (141)
Q Consensus 81 ~y~~v~~~v~Pk~~~L~~~ 99 (141)
.|..|...+.|.+.....-
T Consensus 2298 n~skvLE~~~plr~E~kRI 2316 (3164)
T COG5245 2298 NRSKVLEVKIPLREEEKRI 2316 (3164)
T ss_pred hHHHhhhhcccchhHHHhh
Confidence 9999999999999876643
No 5
>KOG3595|consensus
Probab=95.57 E-value=0.028 Score=53.49 Aligned_cols=60 Identities=28% Similarity=0.563 Sum_probs=55.1
Q ss_pred HHHHhhchHHhhhhhhHHHHHHHhcchhhHHHHHHHhHHhhchHHHHHHHHHHHHHHhhh
Q psy17141 67 VAAKSLSKWVMAIEKYAQLFKDIQRQYPSIIDCTTIDWILDCPEQSLMEVAERFLETVDI 126 (141)
Q Consensus 67 ~Aa~~l~~WV~a~~~y~~v~~~v~Pk~~~L~~~~~~~~~l~~~~~~L~~V~~~l~~l~~~ 126 (141)
..+....|.|+++++.++.++.+..++|++.+.|+++|+.+|+.++|..|.+.+...+..
T Consensus 592 ~~~~~~l~~vl~~~~~g~~~~~r~~~~pal~~~~~i~w~~~w~~~al~~v~~~~l~~~~~ 651 (1395)
T KOG3595|consen 592 FRVRRNLHVVLSVSPVGDAFRLRARKFPALVNRCTIDWFDSWPTEALLSVAEEFLASQDI 651 (1395)
T ss_pred HHHHHhcceeEEeCchhhHHHHHHHhChhhhccchhhhcccCCHHHHHHHHHHHHhhhcC
Confidence 457777889999999999999999999999999999999999999999999999887643
No 6
>KOG0994|consensus
Probab=73.07 E-value=77 Score=30.70 Aligned_cols=28 Identities=21% Similarity=0.593 Sum_probs=18.0
Q ss_pred HHHHHHHHhhhCCCCCCHHHHHHHHHHH
Q psy17141 42 EKILKKITNYVNLPDFDPEEIGMVSVAA 69 (141)
Q Consensus 42 ~~~l~~i~~~l~~p~F~~e~i~~~S~Aa 69 (141)
..+++.|+.++.++.-+|+.|+.++..+
T Consensus 1474 ~~Li~~v~~Flt~~~adp~si~~vA~~v 1501 (1758)
T KOG0994|consen 1474 RNLIQQVRDFLTQPDADPDSIEEVAEEV 1501 (1758)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence 3456666777777777777776665443
No 7
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=60.70 E-value=15 Score=24.97 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=29.7
Q ss_pred hHHhhchHHHHHHHHHHHHHHhhh-------------hHHHHHHHHHhhhc
Q psy17141 103 DWILDCPEQSLMEVAERFLETVDI-------------LETNVLEVQIRLYF 140 (141)
Q Consensus 103 ~~~l~~~~~~L~~V~~~l~~l~~~-------------~~~~~~~~~~rl~~ 140 (141)
+-++.|.+++|++|..++.+|.+. +-.+++..+|.|-.
T Consensus 34 dNEF~W~~~~l~kVy~~F~eLVe~~~G~~LtdYnLRrIGSdLE~~iR~LLq 84 (108)
T PF10664_consen 34 DNEFNWNEEALQKVYRKFDELVESYAGEDLTDYNLRRIGSDLEHFIRSLLQ 84 (108)
T ss_pred CcccccCHHHHHHHHHHHHHHHHhhcCCCchhhhHHHhccHHHHHHHHHHH
Confidence 456789999999999999999842 45667777777654
No 8
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=52.83 E-value=1.3e+02 Score=24.94 Aligned_cols=51 Identities=24% Similarity=0.318 Sum_probs=39.5
Q ss_pred HHHHHHHhhhCCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcch
Q psy17141 43 KILKKITNYVNLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQY 93 (141)
Q Consensus 43 ~~l~~i~~~l~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~ 93 (141)
.-+..+..-+.+|+| +++.+...++.-..+-.+|.....|-....+..-..
T Consensus 30 ~~~~~l~~~l~~p~~~~d~~~~~~l~ke~~~L~~iv~~~~~l~~~~~e~~~~~ 82 (367)
T PRK00578 30 ERLEELEAEAEDPDFWNDQERAQKVTKELSSLKAKLDTLEELRQRLDDLEELL 82 (367)
T ss_pred HHHHHHHHHhcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667778899997 788888999888888888888888877766655444
No 9
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=51.90 E-value=1.4e+02 Score=24.80 Aligned_cols=51 Identities=18% Similarity=0.264 Sum_probs=38.0
Q ss_pred HHHHHHhhhCCCC--CCHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcchh
Q psy17141 44 ILKKITNYVNLPD--FDPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQYP 94 (141)
Q Consensus 44 ~l~~i~~~l~~p~--F~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~~ 94 (141)
....|...|.+|+ -+++.+.+.|+.-+.|-..|.+...|-.+..++.-.+.
T Consensus 15 r~~el~~~L~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~~~~~~~l~~a~~ 67 (363)
T COG0216 15 RYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKE 67 (363)
T ss_pred HHHHHHHHhcCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566778999998 67899999999888888777777777766555444333
No 10
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=49.59 E-value=1.5e+02 Score=24.59 Aligned_cols=48 Identities=19% Similarity=0.310 Sum_probs=37.7
Q ss_pred HHHHHHhhhCCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhc
Q psy17141 44 ILKKITNYVNLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQR 91 (141)
Q Consensus 44 ~l~~i~~~l~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~P 91 (141)
-+..+..-+.+|+| +++....+++..+.|-.||.....|.....++.-
T Consensus 15 ~~~~le~~~~~p~~w~d~~~~~~~~k~~~~l~~~v~~~~~~~~~~~~~~~ 64 (360)
T TIGR00019 15 RYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQEDIKE 64 (360)
T ss_pred HHHHHHHHhcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566777889998 6888889999899999999888888776665543
No 11
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=48.52 E-value=1.6e+02 Score=24.51 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=39.3
Q ss_pred HHHHHHHhhhCCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcch
Q psy17141 43 KILKKITNYVNLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQY 93 (141)
Q Consensus 43 ~~l~~i~~~l~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~ 93 (141)
..+..+..-+.+|+| +++.+..+++.-+.+-.++.....|-....++.-..
T Consensus 30 ~~~~~le~~~~~p~~w~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~d~~~l~ 82 (364)
T TIGR00020 30 ARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSELL 82 (364)
T ss_pred HHHHHHHHHhcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346667778899998 789999999888888888888888877666655433
No 12
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=47.92 E-value=1.6e+02 Score=24.42 Aligned_cols=50 Identities=18% Similarity=0.251 Sum_probs=39.0
Q ss_pred HHHHHHhhhCCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcch
Q psy17141 44 ILKKITNYVNLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQY 93 (141)
Q Consensus 44 ~l~~i~~~l~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~ 93 (141)
.+..++.-+.+|+| +++....+++-...|-.+|..+..+.....+..-..
T Consensus 14 ~~~~le~~~~~~~~w~d~~~~~~~~~e~~~L~~~v~~~~~~~~~~~~~~~~~ 65 (359)
T PRK00591 14 RYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQEDLEEAK 65 (359)
T ss_pred HHHHHHHHhcCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667778899998 688888888888888899988888877766655433
No 13
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=47.14 E-value=42 Score=20.67 Aligned_cols=42 Identities=21% Similarity=0.438 Sum_probs=27.0
Q ss_pred ccCCCCHHHHHHHHhhhC-CCCCCHHHHHHHHHHHHhhchHHh
Q psy17141 36 DKDHIPEKILKKITNYVN-LPDFDPEEIGMVSVAAKSLSKWVM 77 (141)
Q Consensus 36 d~d~i~~~~l~~i~~~l~-~p~F~~e~i~~~S~Aa~~l~~WV~ 77 (141)
+.+.+++..+..--.++. ..+..|..+...-.|....+.|+.
T Consensus 37 ~~~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~~l~~ff~~~~ 79 (85)
T PF13495_consen 37 PPDEITPEDIEQYLNYLQNERGLSPSTINQYLSALRSFFRWLL 79 (85)
T ss_dssp -GGG--HHHHHHHHHHHHTTT---HHHHHHHHHHHHHHHHCTS
T ss_pred ccchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 456777777766555555 667889999988888888888865
No 14
>PHA01346 hypothetical protein
Probab=43.35 E-value=27 Score=20.06 Aligned_cols=20 Identities=40% Similarity=0.597 Sum_probs=15.4
Q ss_pred HHHHHH-hhhCCCCCCHHHHH
Q psy17141 44 ILKKIT-NYVNLPDFDPEEIG 63 (141)
Q Consensus 44 ~l~~i~-~~l~~p~F~~e~i~ 63 (141)
-+++++ ..+++|+|+.|++.
T Consensus 18 elkrlrlsavsdpdfsqekih 38 (53)
T PHA01346 18 ELKRLRLSAVSDPDFSQEKIH 38 (53)
T ss_pred HHHHHHhhhcCCCCccHHHHH
Confidence 455666 57799999998876
No 15
>COG3489 Predicted periplasmic lipoprotein [General function prediction only]
Probab=42.96 E-value=9.5 Score=31.05 Aligned_cols=63 Identities=19% Similarity=0.227 Sum_probs=40.4
Q ss_pred ChHHHHhcc-Hhhhcccccccccccc-cCCCCHHHHHHHHhhhCCCC---CCHHHHHHHHHHHHhh--chHHh
Q psy17141 12 GFSTAKVRF-PNYRKNCTRISLYEYD-KDHIPEKILKKITNYVNLPD---FDPEEIGMVSVAAKSL--SKWVM 77 (141)
Q Consensus 12 ~W~~ak~~l-~~f~~~~~~~~L~~fd-~d~i~~~~l~~i~~~l~~p~---F~~e~i~~~S~Aa~~l--~~WV~ 77 (141)
.|.++.-+. .-...+....+++.|. +.. -.+++++.++++++ .+++.+.+.|.|+-|| +.||+
T Consensus 82 ~Wstleii~~GP~~e~Nr~ervlfwPDkK~---~glkQVq~lLa~kd~s~~~a~~LagkSVavQGLgAlEfvL 151 (359)
T COG3489 82 AWSTLEIIRRGPSAELNRFERVLFWPDKKD---TGLKQVQQLLANKDESAWDADDLAGKSVAVQGLGALEFVL 151 (359)
T ss_pred HHHHhhhhhcCchhhhhhhhhheeCCCccc---chHHHHHHHHcCCCccccCHHHhccCeeeeecccceeeee
Confidence 488777655 1111122222666663 333 35777888888864 7899999999998887 56654
No 16
>PRK06746 peptide chain release factor 2; Provisional
Probab=36.49 E-value=1.9e+02 Score=23.73 Aligned_cols=42 Identities=17% Similarity=0.187 Sum_probs=31.1
Q ss_pred CCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcchh
Q psy17141 53 NLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQYP 94 (141)
Q Consensus 53 ~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~~ 94 (141)
..|+| +++.+..+++-...|-.+|.....|.....++.-...
T Consensus 2 ~~~~fw~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~d~~~~~e 45 (326)
T PRK06746 2 MGAGFWDDQQGAQAVINEANALKDMVGKFRQLDETFENLEITHE 45 (326)
T ss_pred CCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35665 5677888888888888899888888887776655443
No 17
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=33.67 E-value=91 Score=17.55 Aligned_cols=30 Identities=27% Similarity=0.302 Sum_probs=19.2
Q ss_pred HHHHHHHhhh---CCCCCCHHHHHHHHHHHHhh
Q psy17141 43 KILKKITNYV---NLPDFDPEEIGMVSVAAKSL 72 (141)
Q Consensus 43 ~~l~~i~~~l---~~p~F~~e~i~~~S~Aa~~l 72 (141)
.++.+|++.+ .++.+++.+...+...+..|
T Consensus 2 kil~kI~kLLalA~~~~~~~~EA~~A~~kAq~L 34 (43)
T PF10979_consen 2 KILEKIRKLLALAESTGSNEHEAEAALAKAQRL 34 (43)
T ss_pred hHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4667777655 45668887766665555554
No 18
>KOG3647|consensus
Probab=32.19 E-value=2.1e+02 Score=23.10 Aligned_cols=55 Identities=7% Similarity=0.054 Sum_probs=34.2
Q ss_pred HHHHHHhcchhhHHHHH----HHhHHhhchHHHHHHHHHHHHHHh---hhhHHHHHHHHHhh
Q psy17141 84 QLFKDIQRQYPSIIDCT----TIDWILDCPEQSLMEVAERFLETV---DILETNVLEVQIRL 138 (141)
Q Consensus 84 ~v~~~v~Pk~~~L~~~~----~~~~~l~~~~~~L~~V~~~l~~l~---~~~~~~~~~~~~rl 138 (141)
.+...+...+..|.++. .....+...+.+|......|..|+ +.+-++.++|+.+|
T Consensus 116 ~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~EeeL 177 (338)
T KOG3647|consen 116 AIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCEEEL 177 (338)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH
Confidence 34556666666666663 233444555666777777777776 45667777777766
No 19
>PRK05589 peptide chain release factor 2; Provisional
Probab=29.83 E-value=3e+02 Score=22.56 Aligned_cols=40 Identities=20% Similarity=0.251 Sum_probs=30.2
Q ss_pred CCCCC--CHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcc
Q psy17141 53 NLPDF--DPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQ 92 (141)
Q Consensus 53 ~~p~F--~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk 92 (141)
.+|+| +++....+++..+.+-.++.+...|.....+..-.
T Consensus 2 ~~p~~w~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~~~~~~ 43 (325)
T PRK05589 2 QEPNFWNDIKEAQEITSEEKYLKDKLDKYNHLRNRIEDIEVL 43 (325)
T ss_pred CCchhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46765 57788888888888888988888887766655433
No 20
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=28.78 E-value=1.4e+02 Score=18.08 Aligned_cols=27 Identities=19% Similarity=0.519 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHhhh-CCCCCCHHHHHHH
Q psy17141 39 HIPEKILKKITNYV-NLPDFDPEEIGMV 65 (141)
Q Consensus 39 ~i~~~~l~~i~~~l-~~p~F~~e~i~~~ 65 (141)
.||+...+.++.|+ .+|+++...+-.+
T Consensus 5 eiPe~L~~~m~~fie~hP~WDQ~Rl~~a 32 (57)
T PF10929_consen 5 EIPEDLHQAMKDFIETHPNWDQYRLFQA 32 (57)
T ss_pred cccHHHHHHHHHHHHcCCCchHHHHHHH
Confidence 58888889999988 4688887665433
No 21
>PRK04964 hypothetical protein; Provisional
Probab=26.97 E-value=97 Score=19.17 Aligned_cols=31 Identities=16% Similarity=0.082 Sum_probs=24.4
Q ss_pred HHHHHHHhhhCCCCCCHHHHHHHHHHHHhhc
Q psy17141 43 KILKKITNYVNLPDFDPEEIGMVSVAAKSLS 73 (141)
Q Consensus 43 ~~l~~i~~~l~~p~F~~e~i~~~S~Aa~~l~ 73 (141)
..++.+..+..++....+.-+++..|+++|+
T Consensus 29 ca~k~L~~IAad~~Lp~~vRe~AAfAAANLl 59 (66)
T PRK04964 29 CVLKALNEIAADEALPESVREKAAYAAANLL 59 (66)
T ss_pred HHHHHHHHHhccccCCHHHHHHHHHHHHHHH
Confidence 4566677788888887777788999998875
No 22
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=25.63 E-value=96 Score=19.19 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=24.4
Q ss_pred HHHHHHHhhhCCCCCCHHHHHHHHHHHHhhc
Q psy17141 43 KILKKITNYVNLPDFDPEEIGMVSVAAKSLS 73 (141)
Q Consensus 43 ~~l~~i~~~l~~p~F~~e~i~~~S~Aa~~l~ 73 (141)
..++.+..+..++....+.-+++..||++|+
T Consensus 29 calk~Ln~iAad~~Lp~~vRE~AAfAAANLl 59 (66)
T PF06786_consen 29 CALKTLNDIAADEALPEDVREQAAFAAANLL 59 (66)
T ss_pred HHHHHHHHHHcccccCHHHHHHHHHHHHHHH
Confidence 4466667788888888888888999998875
No 23
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=22.92 E-value=1.8e+02 Score=17.43 Aligned_cols=42 Identities=17% Similarity=0.332 Sum_probs=26.7
Q ss_pred ccCCCCHHHHHHHHhhhCCCCCCHHHHHHHHHHHHhhchHHh
Q psy17141 36 DKDHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVM 77 (141)
Q Consensus 36 d~d~i~~~~l~~i~~~l~~p~F~~e~i~~~S~Aa~~l~~WV~ 77 (141)
+-+.++...+..--..+...+..+..+.....|....+.|..
T Consensus 40 ~~~~i~~~~v~~f~~~~~~~~~s~~T~~~~~~alr~f~~~l~ 81 (84)
T PF02899_consen 40 DWEDITEEDVRDFLEYLAKEGLSPSTINRRLSALRAFFRFLY 81 (84)
T ss_dssp CGGG--HHHHHHHHHHHHCTT--HHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHH
Confidence 345677666666555666666888888888888888888764
No 24
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=22.51 E-value=2.4e+02 Score=19.31 Aligned_cols=30 Identities=13% Similarity=0.234 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHHhhchHHhhhhhhHHHH
Q psy17141 57 FDPEEIGMVSVAAKSLSKWVMAIEKYAQLF 86 (141)
Q Consensus 57 F~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~ 86 (141)
-.|+.+..+-.||..+-....||.-+-.+-
T Consensus 43 P~P~ii~aALrAcRRvND~a~AVR~lE~iK 72 (108)
T PF02284_consen 43 PEPKIIEAALRACRRVNDFALAVRILEGIK 72 (108)
T ss_dssp --HHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred CChHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 467888888899999888877775544433
No 25
>PHA03256 BDLF3; Provisional
Probab=22.41 E-value=1.4e+02 Score=19.02 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHhhhCCCCCCHHHHHHHHHHHHhhchHHh
Q psy17141 38 DHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVM 77 (141)
Q Consensus 38 d~i~~~~l~~i~~~l~~p~F~~e~i~~~S~Aa~~l~~WV~ 77 (141)
+.|+++-+..+..+...| -|..|..+|++.++++..|.
T Consensus 15 ~~IsE~df~~~~~ff~rp--Lp~lVaevska~~~~~elv~ 52 (77)
T PHA03256 15 GTIGEREFGELLSWDPTD--LPRTVARVYVAVGGLFEQEV 52 (77)
T ss_pred CccCHHHHHHHHHHcCCc--HHHHHHHHHHHhccceeeee
Confidence 678888888888777766 46788888888888765543
No 26
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=22.34 E-value=7.6e+02 Score=25.88 Aligned_cols=79 Identities=23% Similarity=0.146 Sum_probs=51.9
Q ss_pred hhhCCCCCCHHHHHHHHHHHHhhchHHhhhhhhHHHHHHHhcchh--hHHHH----HHHhHHhhchHHHHHHHHHHHHHH
Q psy17141 50 NYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQRQYP--SIIDC----TTIDWILDCPEQSLMEVAERFLET 123 (141)
Q Consensus 50 ~~l~~p~F~~e~i~~~S~Aa~~l~~WV~a~~~y~~v~~~v~Pk~~--~L~~~----~~~~~~l~~~~~~L~~V~~~l~~l 123 (141)
+...-|-|..++.-.++++|..+.-|+++=+.|.+..-...|... .+... .+-.........++.++..++..+
T Consensus 2614 ~~~~~~lf~~~~~l~~lk~~~~l~L~~L~~~ll~~L~~s~~nm~~tDEI~vll~NlKk~~~~Ie~~~sEs~ei~~riD~L 2693 (3164)
T COG5245 2614 KLVSGPLFVHEKALNALKACGSLFLWVLARYLLAKLMLSISNMEQTDEIAVLLHNLKKSRKEIEEEESESMEIEDRIDAL 2693 (3164)
T ss_pred hhhccchhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHhcccccccchHHHHHHHhHHHHHHHHHHHHhhHhhHHHHHHHH
Confidence 444556688888888999999999999999999998877777665 22211 111222334455556666666666
Q ss_pred hhhhH
Q psy17141 124 VDILE 128 (141)
Q Consensus 124 ~~~~~ 128 (141)
...+.
T Consensus 2694 ~~eY~ 2698 (3164)
T COG5245 2694 KSEYN 2698 (3164)
T ss_pred HHHHH
Confidence 55443
No 27
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=22.31 E-value=98 Score=16.19 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=14.5
Q ss_pred HHHHHHHhhhCCCCCCHHHHHHHHHHH
Q psy17141 43 KILKKITNYVNLPDFDPEEIGMVSVAA 69 (141)
Q Consensus 43 ~~l~~i~~~l~~p~F~~e~i~~~S~Aa 69 (141)
.++..++.++.++....+.+..+..+|
T Consensus 9 ~~v~~i~~~l~~~~t~~~I~~~l~~~C 35 (39)
T PF05184_consen 9 FVVKEIEKLLKNNKTEEEIKKALEKAC 35 (39)
T ss_dssp HHHHHHHHHHHSTCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCccHHHHHHHHHHHH
Confidence 356667777776654444444444433
No 28
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=22.20 E-value=74 Score=23.77 Aligned_cols=43 Identities=23% Similarity=0.472 Sum_probs=35.4
Q ss_pred Hhhhcccccccccccc-cCCCCHHHHHHHH-hhhCCCCCCHHHHHHHHHH
Q psy17141 21 PNYRKNCTRISLYEYD-KDHIPEKILKKIT-NYVNLPDFDPEEIGMVSVA 68 (141)
Q Consensus 21 ~~f~~~~~~~~L~~fd-~d~i~~~~l~~i~-~~l~~p~F~~e~i~~~S~A 68 (141)
.+|.+ .+..|- ..+|+.+-+-.|+ +++..-+|+|+.+++.-+.
T Consensus 40 ~dFsk-----~I~~YmeeNNISqeKf~niQkk~mERYGfd~~~iE~q~K~ 84 (186)
T PF12983_consen 40 ADFSK-----KIMEYMEENNISQEKFLNIQKKFMERYGFDPSEIEKQMKS 84 (186)
T ss_pred HHHHH-----HHHHHHHHcCCcHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 68888 888885 4679999988898 6888899999999876543
No 29
>KOG4403|consensus
Probab=22.10 E-value=3.5e+02 Score=23.43 Aligned_cols=45 Identities=18% Similarity=0.113 Sum_probs=21.7
Q ss_pred hHHHHHHHhHHhhchHHHHHHHHHHHHHHh---hhhHHHHHHHHHhhh
Q psy17141 95 SIIDCTTIDWILDCPEQSLMEVAERFLETV---DILETNVLEVQIRLY 139 (141)
Q Consensus 95 ~L~~~~~~~~~l~~~~~~L~~V~~~l~~l~---~~~~~~~~~~~~rl~ 139 (141)
.+.++..-...|...+.+|..+++.|...+ .+...+..+.++||.
T Consensus 243 hv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ 290 (575)
T KOG4403|consen 243 HVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLD 290 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHh
Confidence 344333333345556666666666665543 223333444444443
No 30
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=20.60 E-value=83 Score=24.19 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=14.7
Q ss_pred eeeeccccCChHHHHhcc
Q psy17141 3 ITMVLYYATGFSTAKVRF 20 (141)
Q Consensus 3 ~~~~~~~~~~W~~ak~~l 20 (141)
|.+||...++|..+.+-|
T Consensus 35 igAILtQNT~WknvekAl 52 (215)
T COG2231 35 IGAILTQNTSWKNVEKAL 52 (215)
T ss_pred HHHHHhccccHHHHHHHH
Confidence 457888999999998766
No 31
>PHA02335 hypothetical protein
Probab=20.35 E-value=58 Score=22.40 Aligned_cols=40 Identities=15% Similarity=0.324 Sum_probs=24.1
Q ss_pred eeeccc--cCChHHHHhccHhhhcccccccccccccCCCCHHHHHHHH
Q psy17141 4 TMVLYY--ATGFSTAKVRFPNYRKNCTRISLYEYDKDHIPEKILKKIT 49 (141)
Q Consensus 4 ~~~~~~--~~~W~~ak~~l~~f~~~~~~~~L~~fd~d~i~~~~l~~i~ 49 (141)
.|++++ +..|+..|..| -|++ ++..+.....++++++.++
T Consensus 75 plLfyKte~~~wp~iKafl-lfLn-----~~p~~~n~e~D~e~L~~L~ 116 (118)
T PHA02335 75 PLLFYKLEAEYWPAIKSFL-LFLN-----RLPIFPNEEVDQECLKQLN 116 (118)
T ss_pred hhhHHhhhHHHHHHHHHHH-HHHH-----hcCCCCCCCccHHHHHHHh
Confidence 344443 56799999866 4454 5554544455667776654
No 32
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=20.12 E-value=5.3e+02 Score=21.65 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=15.7
Q ss_pred HHHHHhhhCCCCCCHHHHH-HHHHHHHhhc
Q psy17141 45 LKKITNYVNLPDFDPEEIG-MVSVAAKSLS 73 (141)
Q Consensus 45 l~~i~~~l~~p~F~~e~i~-~~S~Aa~~l~ 73 (141)
++.++..+...|+..+.|. .++.+=.+++
T Consensus 10 LeeLe~kLa~~d~~Kd~V~~~I~ea~~sIL 39 (379)
T PF11593_consen 10 LEELEEKLASNDNSKDSVMDKISEAQDSIL 39 (379)
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHHhccc
Confidence 5666655555566666655 4444444433
Done!