Query psy6282
Match_columns 251
No_of_seqs 193 out of 1665
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 22:27:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6282.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6282hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315|consensus 100.0 3.9E-54 8.4E-59 370.5 13.0 213 1-225 68-283 (307)
2 KOG1311|consensus 100.0 6.8E-45 1.5E-49 318.7 11.1 179 42-222 103-292 (299)
3 KOG1314|consensus 100.0 1.1E-44 2.3E-49 308.4 6.7 207 1-245 70-308 (414)
4 PF01529 zf-DHHC: DHHC palmito 100.0 6.7E-41 1.5E-45 271.4 8.5 128 46-173 42-173 (174)
5 KOG1313|consensus 100.0 7.2E-41 1.6E-45 276.9 6.8 175 48-222 98-304 (309)
6 COG5273 Uncharacterized protei 100.0 6.2E-38 1.3E-42 273.5 9.3 180 45-224 102-304 (309)
7 KOG0509|consensus 100.0 2E-29 4.2E-34 230.2 5.2 140 53-200 421-585 (600)
8 KOG1312|consensus 100.0 1.8E-29 3.9E-34 210.3 2.3 62 53-114 149-210 (341)
9 PF01529 zf-DHHC: DHHC palmito 95.1 0.14 3E-06 40.9 7.9 52 49-111 59-110 (174)
10 KOG1311|consensus 94.1 0.1 2.2E-06 45.7 5.4 50 65-114 112-172 (299)
11 PF13240 zinc_ribbon_2: zinc-r 90.6 0.15 3.3E-06 26.8 1.2 21 54-74 1-21 (23)
12 COG5273 Uncharacterized protei 89.1 1.5 3.3E-05 38.7 6.9 46 51-107 122-167 (309)
13 PRK04136 rpl40e 50S ribosomal 86.3 0.46 9.9E-06 29.6 1.4 27 52-78 14-40 (48)
14 PF13248 zf-ribbon_3: zinc-rib 85.4 0.5 1.1E-05 25.5 1.2 22 53-74 3-24 (26)
15 KOG1315|consensus 83.2 4 8.6E-05 36.0 6.4 45 51-106 122-166 (307)
16 PF06906 DUF1272: Protein of u 77.3 1.1 2.3E-05 28.9 0.7 36 54-92 7-50 (57)
17 PTZ00303 phosphatidylinositol 76.4 1.8 3.9E-05 42.5 2.2 22 53-74 461-489 (1374)
18 PF12773 DZR: Double zinc ribb 74.5 3.7 8.1E-05 25.5 2.7 34 52-85 12-48 (50)
19 KOG0509|consensus 71.6 1.1 2.4E-05 42.6 -0.4 55 52-107 325-379 (600)
20 PF10571 UPF0547: Uncharacteri 69.8 3.1 6.7E-05 22.5 1.3 22 53-74 1-22 (26)
21 PF12773 DZR: Double zinc ribb 68.8 4.1 8.8E-05 25.3 1.9 24 50-73 27-50 (50)
22 PF01363 FYVE: FYVE zinc finge 66.8 2 4.4E-05 28.7 0.2 26 52-77 9-36 (69)
23 PF01020 Ribosomal_L40e: Ribos 64.2 4 8.6E-05 25.9 1.1 25 51-75 16-42 (52)
24 smart00064 FYVE Protein presen 58.1 8.3 0.00018 25.5 2.0 26 52-77 10-37 (68)
25 PF00641 zf-RanBP: Zn-finger i 57.1 4.2 9.1E-05 22.4 0.3 21 54-74 6-26 (30)
26 PF07649 C1_3: C1-like domain; 54.3 3.8 8.3E-05 22.6 -0.2 21 54-74 2-23 (30)
27 COG1552 RPL40A Ribosomal prote 53.9 3.5 7.5E-05 25.8 -0.4 27 52-78 14-40 (50)
28 KOG1842|consensus 53.5 5.1 0.00011 36.8 0.4 27 51-77 179-207 (505)
29 KOG1314|consensus 49.4 6.5 0.00014 35.1 0.4 46 51-107 104-149 (414)
30 PF07282 OrfB_Zn_ribbon: Putat 49.0 9.5 0.00021 25.3 1.1 35 41-75 17-55 (69)
31 PF03107 C1_2: C1 domain; Int 49.0 11 0.00024 20.8 1.2 20 54-73 2-22 (30)
32 PHA02680 ORF090 IMV phosphoryl 41.9 1.2E+02 0.0027 21.4 6.2 25 149-173 59-83 (91)
33 PRK03681 hypA hydrogenase nick 41.5 14 0.00031 27.5 1.2 24 51-74 69-95 (114)
34 COG4640 Predicted membrane pro 40.6 15 0.00032 33.4 1.3 26 52-77 1-26 (465)
35 smart00661 RPOL9 RNA polymeras 40.4 14 0.00031 22.8 0.9 21 53-73 1-27 (52)
36 COG2093 DNA-directed RNA polym 40.3 16 0.00035 24.1 1.1 24 52-75 4-27 (64)
37 cd00065 FYVE FYVE domain; Zinc 40.2 20 0.00043 22.6 1.5 23 54-76 4-28 (57)
38 PF09788 Tmemb_55A: Transmembr 39.2 1.4E+02 0.0031 25.6 6.8 23 90-112 189-212 (256)
39 KOG3183|consensus 38.7 15 0.00033 31.0 1.0 12 76-87 38-49 (250)
40 PF02150 RNA_POL_M_15KD: RNA p 36.6 11 0.00024 21.8 -0.1 7 53-59 2-8 (35)
41 PF03842 Silic_transp: Silicon 36.5 1.4E+02 0.0031 27.6 6.7 26 96-121 171-196 (512)
42 PF00751 DM: DM DNA binding do 36.3 13 0.00028 23.2 0.1 22 66-87 2-28 (47)
43 PRK13130 H/ACA RNA-protein com 35.7 24 0.00052 22.9 1.3 22 51-74 4-25 (56)
44 PRK14559 putative protein seri 34.9 27 0.00059 34.2 2.2 39 52-92 15-53 (645)
45 PF07754 DUF1610: Domain of un 34.1 28 0.0006 18.4 1.2 19 55-73 1-23 (24)
46 PF09889 DUF2116: Uncharacteri 33.9 27 0.00059 22.9 1.4 23 52-74 3-26 (59)
47 KOG4017|consensus 33.8 19 0.0004 30.6 0.8 35 50-84 101-139 (274)
48 KOG2927|consensus 33.1 62 0.0013 29.1 3.9 32 61-92 156-188 (372)
49 PF08600 Rsm1: Rsm1-like; Int 31.3 27 0.00058 24.9 1.2 10 81-90 56-65 (91)
50 PRK15103 paraquat-inducible me 30.7 4E+02 0.0088 24.6 9.0 33 51-83 220-252 (419)
51 PRK14559 putative protein seri 30.0 30 0.00066 33.8 1.6 24 53-76 2-25 (645)
52 cd00350 rubredoxin_like Rubred 29.9 38 0.00082 19.1 1.4 21 54-74 3-25 (33)
53 PF00130 C1_1: Phorbol esters/ 29.3 22 0.00048 22.0 0.4 28 50-77 9-39 (53)
54 smart00423 PSI domain found in 29.0 22 0.00049 21.5 0.4 14 72-85 7-20 (46)
55 PLN00186 ribosomal protein S26 29.0 23 0.0005 26.1 0.5 14 66-79 20-33 (109)
56 PRK00432 30S ribosomal protein 28.9 32 0.00069 21.6 1.1 23 52-74 20-45 (50)
57 KOG3611|consensus 28.8 20 0.00044 35.6 0.3 27 66-92 491-523 (737)
58 PHA02942 putative transposase; 28.2 33 0.00071 31.3 1.5 34 41-74 314-350 (383)
59 PF14015 DUF4231: Protein of u 27.9 73 0.0016 23.0 3.1 25 162-186 79-103 (112)
60 smart00547 ZnF_RBZ Zinc finger 27.7 33 0.00071 17.9 0.9 21 54-74 4-24 (26)
61 COG0603 Predicted PP-loop supe 26.7 22 0.00048 29.8 0.1 19 61-79 187-205 (222)
62 PRK09335 30S ribosomal protein 26.6 27 0.00058 25.2 0.5 19 66-84 20-38 (95)
63 TIGR00155 pqiA_fam integral me 25.7 5.3E+02 0.011 23.7 9.5 32 52-83 215-247 (403)
64 PTZ00172 40S ribosomal protein 25.4 28 0.00061 25.6 0.4 14 66-79 20-33 (108)
65 PRK12380 hydrogenase nickel in 25.1 39 0.00086 25.1 1.2 24 51-74 69-94 (113)
66 smart00301 DM Doublesex DNA-bi 24.8 44 0.00095 21.5 1.2 6 82-87 23-28 (54)
67 PF01437 PSI: Plexin repeat; 24.5 13 0.00028 23.2 -1.4 17 70-86 6-22 (51)
68 PF00539 Tat: Transactivating 24.1 45 0.00098 22.5 1.2 13 53-72 30-42 (68)
69 KOG1819|consensus 23.8 39 0.00084 31.8 1.1 22 53-74 902-925 (990)
70 PF03461 TRCF: TRCF domain; I 23.4 98 0.0021 22.3 3.0 34 4-37 5-42 (101)
71 PRK12286 rpmF 50S ribosomal pr 22.7 49 0.0011 21.4 1.1 20 52-73 27-47 (57)
72 KOG1729|consensus 22.5 27 0.00058 30.6 -0.2 25 52-76 168-195 (288)
73 cd01995 ExsB ExsB is a transcr 22.5 27 0.00058 27.4 -0.2 23 54-79 142-164 (169)
74 PRK00564 hypA hydrogenase nick 22.3 50 0.0011 24.7 1.3 25 50-74 69-96 (117)
75 TIGR02487 NrdD anaerobic ribon 22.3 1.4E+02 0.003 28.9 4.6 59 26-92 499-558 (579)
76 TIGR00100 hypA hydrogenase nic 22.2 49 0.0011 24.6 1.2 24 51-74 69-94 (115)
77 COG5270 PUA domain (predicted 21.7 46 0.001 27.1 1.0 22 51-74 13-34 (202)
78 TIGR00364 exsB protein. This p 21.6 46 0.001 27.0 1.1 13 66-78 189-201 (201)
79 PF09297 zf-NADH-PPase: NADH p 21.5 39 0.00085 18.8 0.4 22 52-73 3-28 (32)
80 TIGR00811 sit silicon transpor 20.3 4.7E+02 0.01 24.7 7.2 13 156-168 239-251 (545)
81 COG2248 Predicted hydrolase (m 20.2 91 0.002 27.0 2.5 17 2-18 29-47 (304)
82 smart00109 C1 Protein kinase C 20.1 66 0.0014 19.0 1.3 26 51-76 10-37 (49)
No 1
>KOG1315|consensus
Probab=100.00 E-value=3.9e-54 Score=370.46 Aligned_cols=213 Identities=47% Similarity=0.920 Sum_probs=183.0
Q ss_pred CCCCCCCCCCCCCChhhhhhhccCCChHHHHHHHHHhhccCCcccccCCCCcccCcccccccCCCCCCCCccCccccCCc
Q psy6282 1 MTPLGTAPKHFKLSPSLQHALFTTDNDVERKQILEQFSASLPVLNKSIDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMD 80 (251)
Q Consensus 1 ~~dPG~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 80 (251)
|||||.+|..|.|+.++.+...+....+ +.+++...++++..|||.+|+.+||+||||||+|++||+|||
T Consensus 68 f~~pg~vp~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmD 137 (307)
T KOG1315|consen 68 FTDPGRVPDSYRPSVEDEDSLENGSDNE----------RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMD 137 (307)
T ss_pred EecCCCCccccCCCcCccccccccCccc----------ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccc
Confidence 6899999999999999876554443333 466777888999999999999999999999999999999999
Q ss_pred ccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhhhhhccccc--cCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q psy6282 81 HHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFIQFWEGSFV--HSGKFHILFLCFVAAMFSLSLVALFGYHL 158 (251)
Q Consensus 81 HHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~h~ 158 (251)
|||||+|||||.+|||+|++||+|+.+++++.+++.+..+...+..... ....+.++++.++++.+++.++.|+++|+
T Consensus 138 HHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~ 217 (307)
T KOG1315|consen 138 HHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHT 217 (307)
T ss_pred cCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999888888777766632111 11345566777788888888888999999
Q ss_pred HHhccCceeeccccCCCcccC-CCCCCCChHHHHHHHHhcCCCCCceeeccccCCCCCceecCcCCCc
Q psy6282 159 YLVAQNKTTLEAIRPPVFSYG-PDKQGYNLGCKRNFIEIFGENKLLWFFPVHTHLGDGIRFPVRGSNV 225 (251)
Q Consensus 159 ~li~~n~TtiE~~~~~~~~~~-~~~npyd~G~~~Nl~~vfG~~~~~Wl~P~~~~~~dG~~~~~~~~~~ 225 (251)
+||.+|+||+|..+.+.++.+ ..++.+++ ..|++++||.++..|++|..++.+||.+++.+.+..
T Consensus 218 ~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~--~~n~~~vfg~~~~~wl~P~~~s~~~~~~~~~~~~~~ 283 (307)
T KOG1315|consen 218 YLILKNKTTIEAYKSPVFRSGLHNKNGFNL--YVNFREVFGSNLLYWLLPIDSSWGDGVSFPLRGDGL 283 (307)
T ss_pred HHHHcCchhHhhhccccccccccccCCcce--eecHHHHhCCCceEEeccccCccccCccccccccCC
Confidence 999999999999998766643 67788887 899999999999999999999999999999988843
No 2
>KOG1311|consensus
Probab=100.00 E-value=6.8e-45 Score=318.66 Aligned_cols=179 Identities=34% Similarity=0.638 Sum_probs=137.9
Q ss_pred CcccccCCCCcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhh
Q psy6282 42 PVLNKSIDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFI 121 (251)
Q Consensus 42 ~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~ 121 (251)
...+.+...+++||.+|+.+||+|||||++||+||+||||||+|+|||||++|||+|+.|++++.+++++.++..+..+.
T Consensus 103 ~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~ 182 (299)
T KOG1311|consen 103 NVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELL 182 (299)
T ss_pred CcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456777889999999999999999999999999999999999999999999999999999999999888776665544
Q ss_pred hhhcccc---c----cCCchhhHHHHHHHHHHHHHHHHHHHHHHHHhccCceeeccccCCCcccCCCCCCCChHHHHHHH
Q psy6282 122 QFWEGSF---V----HSGKFHILFLCFVAAMFSLSLVALFGYHLYLVAQNKTTLEAIRPPVFSYGPDKQGYNLGCKRNFI 194 (251)
Q Consensus 122 ~~~~~~~---~----~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TtiE~~~~~~~~~~~~~npyd~G~~~Nl~ 194 (251)
....... . .......+++.++++++.+.++.|+.+|++++.+|+||+|.++. .+.....++||.|.++|++
T Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~--~~~~~~~~~~~~g~~~n~~ 260 (299)
T KOG1311|consen 183 QRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKS--LDFVSRSNPYDLGLLKNLQ 260 (299)
T ss_pred HhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhc--cccccccCCCchhHHHHHH
Confidence 3222111 1 11122233445566666777778999999999999999999886 2222335899999999999
Q ss_pred HhcCCCCCc-eeeccccC---CCCCceecCcC
Q psy6282 195 EIFGENKLL-WFFPVHTH---LGDGIRFPVRG 222 (251)
Q Consensus 195 ~vfG~~~~~-Wl~P~~~~---~~dG~~~~~~~ 222 (251)
++||.+... |+.|...+ +.||..++...
T Consensus 261 ~~~~~~~~~~~~~p~~~~~~~p~~~~~~~~~~ 292 (299)
T KOG1311|consen 261 EVFGGPLPLSWLSPFARSGPLPHDGEGGPPTP 292 (299)
T ss_pred HHhCCCCCcccccccccCCCCCCCCCCCCccc
Confidence 999987655 99887743 46666555443
No 3
>KOG1314|consensus
Probab=100.00 E-value=1.1e-44 Score=308.38 Aligned_cols=207 Identities=33% Similarity=0.545 Sum_probs=150.5
Q ss_pred CCCCCCCCCCCCCChhhhhhhccCCChHHHHHHHHHhhccCCcccccCCCCcccCcccccccCCCCCCCCccCccccCCc
Q psy6282 1 MTPLGTAPKHFKLSPSLQHALFTTDNDVERKQILEQFSASLPVLNKSIDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMD 80 (251)
Q Consensus 1 ~~dPG~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 80 (251)
|+.||++|++|+|+.+.-++ -..||.+|+.||+||||||+.|||||.+||
T Consensus 70 ~~gPG~vp~~wkPe~~~D~~------------------------------~lqfCk~CqgYKapRSHHCrkCnrCvmkMD 119 (414)
T KOG1314|consen 70 FTGPGFVPLGWKPENPKDEM------------------------------FLQFCKKCQGYKAPRSHHCRKCNRCVMKMD 119 (414)
T ss_pred hcCCCCCCCCCCCCCChhHH------------------------------HHHHHhhccCcCCCccccchHHHHHHHhhc
Confidence 68899999999996543111 147999999999999999999999999999
Q ss_pred ccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhh----hhhhc--cccccC--------CchhhHHHHHHHHHH
Q psy6282 81 HHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYF----IQFWE--GSFVHS--------GKFHILFLCFVAAMF 146 (251)
Q Consensus 81 HHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~----~~~~~--~~~~~~--------~~~~~~~~~~~~~~~ 146 (251)
|||||+|||||..||.+|+.||++..++|+-..+..+..+ +..|. ...... .....+|.+.+++..
T Consensus 120 HHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv 199 (414)
T KOG1314|consen 120 HHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGV 199 (414)
T ss_pred cCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHH
Confidence 9999999999999999999999999998766544333322 22331 111110 111122333445555
Q ss_pred HHHHHHHHHHHHHHhccCceeeccccCC--C------ccc--CCCCCCCChHHHHHHHHhcCCCCCceeeccccCCCCCc
Q psy6282 147 SLSLVALFGYHLYLVAQNKTTLEAIRPP--V------FSY--GPDKQGYNLGCKRNFIEIFGENKLLWFFPVHTHLGDGI 216 (251)
Q Consensus 147 ~~~~~~l~~~h~~li~~n~TtiE~~~~~--~------~~~--~~~~npyd~G~~~Nl~~vfG~~~~~Wl~P~~~~~~dG~ 216 (251)
.+++++|++.|+..|.+|+|.||.+--. . ... +....|||+|++.|+++||-... .+.|||+
T Consensus 200 ~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~--------~~~gdg~ 271 (414)
T KOG1314|consen 200 VLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNK--------KEEGDGI 271 (414)
T ss_pred HHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhcc--------ccCCCCc
Confidence 6677788999999999999999976411 1 112 45678999999899999997652 3679999
Q ss_pred eecCcCCCcc--------cccccCCCccceeeecccc
Q psy6282 217 RFPVRGSNVN--------QYNSMGNTQGTDLTVNCHI 245 (251)
Q Consensus 217 ~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~ 245 (251)
+||+.+...+ ..+...+.|++.+.....+
T Consensus 272 ~wPv~~gc~qytlt~eql~qk~~kr~rsr~~~~~~~~ 308 (414)
T KOG1314|consen 272 EWPVVEGCVQYTLTIEQLTQKLDKRGRSRLFKCIEDV 308 (414)
T ss_pred cccccCcccccceeHHHHHHHHHhhcCeEEEEeccCC
Confidence 9999998654 3445556666666655544
No 4
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=6.7e-41 Score=271.40 Aligned_cols=128 Identities=39% Similarity=0.834 Sum_probs=103.8
Q ss_pred ccCCCCcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhhhhhc
Q psy6282 46 KSIDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFIQFWE 125 (251)
Q Consensus 46 ~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~~~~~ 125 (251)
.+.....++|.+|+..||+|||||+.||+||+|+||||+|+|||||++|||+|++|++++.+++++.++..+.++.....
T Consensus 42 ~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~ 121 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIP 121 (174)
T ss_pred cccCCCCEECcccCCcCCCcceeccccccccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34566789999999999999999999999999999999999999999999999999999999998887766665554433
Q ss_pred cccccC-Cchh---hHHHHHHHHHHHHHHHHHHHHHHHHhccCceeeccccC
Q psy6282 126 GSFVHS-GKFH---ILFLCFVAAMFSLSLVALFGYHLYLVAQNKTTLEAIRP 173 (251)
Q Consensus 126 ~~~~~~-~~~~---~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TtiE~~~~ 173 (251)
...... .... .+++++++++++++++.++++|++++++|+||+|.+++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~~ 173 (174)
T PF01529_consen 122 SISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYERIKR 173 (174)
T ss_pred cccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHc
Confidence 221111 1111 14555666777778888999999999999999999874
No 5
>KOG1313|consensus
Probab=100.00 E-value=7.2e-41 Score=276.86 Aligned_cols=175 Identities=31% Similarity=0.557 Sum_probs=131.7
Q ss_pred CCCCcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhhhhhcc-
Q psy6282 48 IDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFIQFWEG- 126 (251)
Q Consensus 48 ~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~~~~~~- 126 (251)
....-.+|.+|+.+||||+||||+||+||++|||||||+|||||.+|||||++|++|+.+++.|+.+...+.++.....
T Consensus 98 ~~~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~ 177 (309)
T KOG1313|consen 98 GLENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPI 177 (309)
T ss_pred CCccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchH
Confidence 3445689999999999999999999999999999999999999999999999999999999999776644433321110
Q ss_pred -cc-----c-----c----------CCchhhHHHHHHHHHHHHHHHHHHHHHHHHhccCceeeccccCCC----cccCCC
Q psy6282 127 -SF-----V-----H----------SGKFHILFLCFVAAMFSLSLVALFGYHLYLVAQNKTTLEAIRPPV----FSYGPD 181 (251)
Q Consensus 127 -~~-----~-----~----------~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TtiE~~~~~~----~~~~~~ 181 (251)
+. + . .....+..+.++++.+.++++.+..+|.++|.+|.|++|...+.. +.....
T Consensus 178 ~~~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R 257 (309)
T KOG1313|consen 178 EEITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLR 257 (309)
T ss_pred hhcccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhcc
Confidence 00 0 0 011123346666777777888899999999999999999875332 222344
Q ss_pred CCCCChHHHHHHHHhcCCC--CCce---eeccccCC-CCCceecCcC
Q psy6282 182 KQGYNLGCKRNFIEIFGEN--KLLW---FFPVHTHL-GDGIRFPVRG 222 (251)
Q Consensus 182 ~npyd~G~~~Nl~~vfG~~--~~~W---l~P~~~~~-~dG~~~~~~~ 222 (251)
+||++.|.++||+.++|-. +..| ++|....+ +.|.++++++
T Consensus 258 ~~~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p~~~~~~~~~~d 304 (309)
T KOG1313|consen 258 SNPTNFGGKANWRNFLGLFRGRHFWKTVLLPTIRKPVKYGDSKEKSD 304 (309)
T ss_pred CCCcccchHHHHHHhhccccCCceeEEEeccccccccccCCcccccc
Confidence 8999999999999999942 2245 67876544 8888887443
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=6.2e-38 Score=273.49 Aligned_cols=180 Identities=34% Similarity=0.655 Sum_probs=128.0
Q ss_pred cccCCCCcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhhhhh
Q psy6282 45 NKSIDGGTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFIQFW 124 (251)
Q Consensus 45 ~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~~~~ 124 (251)
..+..+..++|.+|+.+||+|||||+.||+||+||||||+|+|||||.+|||+|++||+++...++++++....++...+
T Consensus 102 ~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~ 181 (309)
T COG5273 102 DDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIF 181 (309)
T ss_pred hcCccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34667788999999999999999999999999999999999999999999999999999998888887776665554444
Q ss_pred ccccc-cCCchhhHHH-HHHHHHHHHHHHHHHHHHHHHhccCceeeccccCCCccc---------------------CCC
Q psy6282 125 EGSFV-HSGKFHILFL-CFVAAMFSLSLVALFGYHLYLVAQNKTTLEAIRPPVFSY---------------------GPD 181 (251)
Q Consensus 125 ~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~l~~~h~~li~~n~TtiE~~~~~~~~~---------------------~~~ 181 (251)
...-. ......+++. ...+..+++.+..++.++.+++..|+|++|.....+... ...
T Consensus 182 ~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~ 261 (309)
T COG5273 182 SIRHDTSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEG 261 (309)
T ss_pred cccCChHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCcc
Confidence 32111 1111112221 223333455566778899999999999999775433221 012
Q ss_pred CCCCChHHHHHHHHhcCCCCCceeeccccCCCCCceecCcCCC
Q psy6282 182 KQGYNLGCKRNFIEIFGENKLLWFFPVHTHLGDGIRFPVRGSN 224 (251)
Q Consensus 182 ~npyd~G~~~Nl~~vfG~~~~~Wl~P~~~~~~dG~~~~~~~~~ 224 (251)
..|++.|.-+|+..++|.+...|+.|......++..++.+++.
T Consensus 262 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (309)
T COG5273 262 ALPLDLGIGQNLSTIKGSNALYWLTPLHTNYCNSYDFSLRSDT 304 (309)
T ss_pred ccccccCccccceeecCCCceeeccccccCCCCccCcccchhh
Confidence 3466777777888888877777877754433556666655543
No 7
>KOG0509|consensus
Probab=99.95 E-value=2e-29 Score=230.16 Aligned_cols=140 Identities=31% Similarity=0.597 Sum_probs=100.1
Q ss_pred ccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcccchhhhhhhhccccccCC
Q psy6282 53 RFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSLSTLPYFIQFWEGSFVHSG 132 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 132 (251)
+||.+|...||.||+||++||+||.||||||||++||||.+|||+|+.|++.+...+.+.++....++...-. ..
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~---~~-- 495 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLEN---AS-- 495 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcch---hH--
Confidence 7999999999999999999999999999999999999999999999999999988887766655544321100 00
Q ss_pred chhhHHHHHHHHHHHHH-------------------H-HHHHHHHHHHhccCceeeccccCCCcc-----cCCCCCCCCh
Q psy6282 133 KFHILFLCFVAAMFSLS-------------------L-VALFGYHLYLVAQNKTTLEAIRPPVFS-----YGPDKQGYNL 187 (251)
Q Consensus 133 ~~~~~~~~~~~~~~~~~-------------------~-~~l~~~h~~li~~n~TtiE~~~~~~~~-----~~~~~npyd~ 187 (251)
.+...++..+..+. . ...-..|...++.++||+|.++.++++ .++.++|++.
T Consensus 496 ---~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~ 572 (600)
T KOG0509|consen 496 ---TIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSP 572 (600)
T ss_pred ---HHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCc
Confidence 11111111111110 0 011112333578899999999876554 3456789999
Q ss_pred HHHHHHHHhcCCC
Q psy6282 188 GCKRNFIEIFGEN 200 (251)
Q Consensus 188 G~~~Nl~~vfG~~ 200 (251)
|+.+|+.+++=.+
T Consensus 573 g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 573 GPIRNLVDFFLCS 585 (600)
T ss_pred hhhhcchheeecc
Confidence 9999999998543
No 8
>KOG1312|consensus
Probab=99.95 E-value=1.8e-29 Score=210.30 Aligned_cols=62 Identities=44% Similarity=0.958 Sum_probs=58.4
Q ss_pred ccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHHhcc
Q psy6282 53 RFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIYGSL 114 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~~~~ 114 (251)
..|+||+..||.||+|||+||+||.|+||||.|+|||||.+|.|||++||++.+.++.++.+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaiv 210 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIV 210 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHH
Confidence 67999999999999999999999999999999999999999999999999999887777654
No 9
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=95.07 E-value=0.14 Score=40.91 Aligned_cols=52 Identities=27% Similarity=0.588 Sum_probs=39.7
Q ss_pred CCCcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHHHHHH
Q psy6282 49 DGGTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALLYCIY 111 (251)
Q Consensus 49 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i~~~~ 111 (251)
..+.++|..|+.--..+-|||..-|.||-+.-| +.+=.|++++.-..+..++
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~ 110 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFI 110 (174)
T ss_pred CCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHH
Confidence 345799999999999999999999999998776 5555676666554444443
No 10
>KOG1311|consensus
Probab=94.08 E-value=0.1 Score=45.75 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=40.2
Q ss_pred CCCCCCccCccccCCcccCcccccccchhhH-----------HHHHHHHhHHHHHHHHhcc
Q psy6282 65 RSHHCSVCGKCVLKMDHHCPWVNNCVSFTNY-----------KYFLLFLGYALLYCIYGSL 114 (251)
Q Consensus 65 Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~-----------r~Filfl~~~~i~~~~~~~ 114 (251)
+.++|..|+.-+..+-|||..-|+||-..-| |.+-.|+.+++...+..++
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~ 172 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLL 172 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999998876 6688888666644443333
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.59 E-value=0.15 Score=26.76 Aligned_cols=21 Identities=29% Similarity=0.855 Sum_probs=18.6
Q ss_pred cCcccccccCCCCCCCCccCc
Q psy6282 54 FCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 54 ~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
||..|+..-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999985
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=89.07 E-value=1.5 Score=38.75 Aligned_cols=46 Identities=24% Similarity=0.432 Sum_probs=28.6
Q ss_pred CcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHH
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALL 107 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i 107 (251)
+.+.|..|+.=-...-|||..=|+||-+..| +=.=.|++++...++
T Consensus 122 RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~ 167 (309)
T COG5273 122 RSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVAL 167 (309)
T ss_pred CCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHH
Confidence 4566777776666667777777777766544 555566666544333
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=86.30 E-value=0.46 Score=29.55 Aligned_cols=27 Identities=26% Similarity=0.645 Sum_probs=23.1
Q ss_pred cccCcccccccCCCCCCCCccCccccC
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKCVLK 78 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~ 78 (251)
...|..|...-|+|+..|+.||.=-+|
T Consensus 14 k~ICrkC~ARnp~~A~~CRKCg~~~LR 40 (48)
T PRK04136 14 KKICMRCNARNPWRATKCRKCGYKNLR 40 (48)
T ss_pred ccchhcccCCCCccccccccCCCCCcC
Confidence 589999999999999999999864333
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.42 E-value=0.5 Score=25.47 Aligned_cols=22 Identities=27% Similarity=0.726 Sum_probs=19.1
Q ss_pred ccCcccccccCCCCCCCCccCc
Q psy6282 53 RFCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
++|..|+..-++-+..|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6799999988899999999875
No 15
>KOG1315|consensus
Probab=83.20 E-value=4 Score=36.02 Aligned_cols=45 Identities=20% Similarity=0.432 Sum_probs=33.2
Q ss_pred CcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHH
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYAL 106 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~ 106 (251)
+...|+.|+.=--..-|||..-|+||--.++ +=.-.|+.+....+
T Consensus 122 RaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny-----------KfF~lfl~y~~l~~ 166 (307)
T KOG1315|consen 122 RAHHCSVCNRCVLKMDHHCPWINNCVGFRNY-----------KFFLLFLFYTNLYS 166 (307)
T ss_pred ccccchhhhhhhhccccCCcceeceecccch-----------HHHHHHHHHHHHHH
Confidence 4578888887667778999999999997665 55566666655444
No 16
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=77.31 E-value=1.1 Score=28.89 Aligned_cols=36 Identities=31% Similarity=0.745 Sum_probs=29.2
Q ss_pred cCcccccccCCCC-------CCCCccCccccCC-cccCcccccccch
Q psy6282 54 FCDKCYQVKADRS-------HHCSVCGKCVLKM-DHHCPWVNNCVSF 92 (251)
Q Consensus 54 ~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHHC~wl~nCIG~ 92 (251)
-|..|..--|+-+ +-|..|..|+..+ +++|| ||=|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 4778887777766 6799999999999 99999 66664
No 17
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=76.36 E-value=1.8 Score=42.45 Aligned_cols=22 Identities=36% Similarity=0.862 Sum_probs=18.4
Q ss_pred ccCcccccccC-------CCCCCCCccCc
Q psy6282 53 RFCDKCYQVKA-------DRSHHCSVCGK 74 (251)
Q Consensus 53 ~~C~~C~~~kP-------~Rs~HC~~C~~ 74 (251)
..|..|+..-. .|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 67999997764 39999999876
No 18
>PF12773 DZR: Double zinc ribbon
Probab=74.49 E-value=3.7 Score=25.47 Aligned_cols=34 Identities=24% Similarity=0.565 Sum_probs=25.0
Q ss_pred cccCcccccccC---CCCCCCCccCccccCCcccCcc
Q psy6282 52 TRFCDKCYQVKA---DRSHHCSVCGKCVLKMDHHCPW 85 (251)
Q Consensus 52 ~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHHC~w 85 (251)
.+||..|...-+ .....|..|+.=+...+.+|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 578888886666 4466788888877777777764
No 19
>KOG0509|consensus
Probab=71.58 E-value=1.1 Score=42.58 Aligned_cols=55 Identities=11% Similarity=-0.111 Sum_probs=47.2
Q ss_pred cccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHH
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALL 107 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i 107 (251)
...|.+|....+-+..++..+-.++..+++||+|+. +|+..|...|.+..+...+
T Consensus 325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l 379 (600)
T KOG0509|consen 325 TCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVL 379 (600)
T ss_pred heeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHH
Confidence 567999999999999999999999999999999999 9999998776554443333
No 20
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=69.80 E-value=3.1 Score=22.45 Aligned_cols=22 Identities=23% Similarity=0.705 Sum_probs=18.3
Q ss_pred ccCcccccccCCCCCCCCccCc
Q psy6282 53 RFCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
|.|..|...-|.-+.-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688899888998888888874
No 21
>PF12773 DZR: Double zinc ribbon
Probab=68.82 E-value=4.1 Score=25.29 Aligned_cols=24 Identities=21% Similarity=0.699 Sum_probs=21.3
Q ss_pred CCcccCcccccccCCCCCCCCccC
Q psy6282 50 GGTRFCDKCYQVKADRSHHCSVCG 73 (251)
Q Consensus 50 ~~~~~C~~C~~~kP~Rs~HC~~C~ 73 (251)
....+|..|+...++.+..|..||
T Consensus 27 ~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 27 QSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCCcCCcCCCcCCcCccCccc
Confidence 346899999999999999999986
No 22
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=66.77 E-value=2 Score=28.67 Aligned_cols=26 Identities=35% Similarity=0.709 Sum_probs=13.2
Q ss_pred cccCccccc--ccCCCCCCCCccCcccc
Q psy6282 52 TRFCDKCYQ--VKADRSHHCSVCGKCVL 77 (251)
Q Consensus 52 ~~~C~~C~~--~kP~Rs~HC~~C~~CV~ 77 (251)
...|..|+. ---.|-|||+.||+-|=
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 467888873 33478999999988553
No 23
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=64.18 E-value=4 Score=25.87 Aligned_cols=25 Identities=32% Similarity=0.848 Sum_probs=17.1
Q ss_pred CcccCcccccccCCCCCCCCc--cCcc
Q psy6282 51 GTRFCDKCYQVKADRSHHCSV--CGKC 75 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 75 (251)
....|.+|...-|+|+-.|+. ||.+
T Consensus 16 ~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 16 DKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp S-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cceecccccCcCCCCccceecccCCCC
Confidence 358999999999999999998 8754
No 24
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=57.15 E-value=4.2 Score=22.43 Aligned_cols=21 Identities=24% Similarity=0.719 Sum_probs=14.8
Q ss_pred cCcccccccCCCCCCCCccCc
Q psy6282 54 FCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 54 ~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
.|..|...-+++..+|..|+.
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--
T ss_pred cCCCCcCCchHHhhhhhCcCC
Confidence 478888888888888888863
No 26
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=54.34 E-value=3.8 Score=22.64 Aligned_cols=21 Identities=29% Similarity=0.502 Sum_probs=9.1
Q ss_pred cCcccccccCC-CCCCCCccCc
Q psy6282 54 FCDKCYQVKAD-RSHHCSVCGK 74 (251)
Q Consensus 54 ~C~~C~~~kP~-Rs~HC~~C~~ 74 (251)
.|..|+..... ..++|..|+-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 57788776666 7888988874
No 27
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=53.88 E-value=3.5 Score=25.77 Aligned_cols=27 Identities=30% Similarity=0.846 Sum_probs=23.1
Q ss_pred cccCcccccccCCCCCCCCccCccccC
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKCVLK 78 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~ 78 (251)
.+.|..|...-|+|+--|+.|+.=-+|
T Consensus 14 kkIC~rC~Arnp~~A~kCRkC~~k~LR 40 (50)
T COG1552 14 KKICRRCYARNPPRATKCRKCGYKNLR 40 (50)
T ss_pred HHHHHHhcCCCCcchhHHhhccCCCcc
Confidence 488999999999999999999765444
No 28
>KOG1842|consensus
Probab=53.45 E-value=5.1 Score=36.79 Aligned_cols=27 Identities=33% Similarity=0.941 Sum_probs=20.5
Q ss_pred CcccCccccc--ccCCCCCCCCccCcccc
Q psy6282 51 GTRFCDKCYQ--VKADRSHHCSVCGKCVL 77 (251)
Q Consensus 51 ~~~~C~~C~~--~kP~Rs~HC~~C~~CV~ 77 (251)
...+|..|.. ----|-|||+.||+-+=
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHH
Confidence 3589999974 44568999999997443
No 29
>KOG1314|consensus
Probab=49.36 E-value=6.5 Score=35.13 Aligned_cols=46 Identities=28% Similarity=0.554 Sum_probs=36.0
Q ss_pred CcccCcccccccCCCCCCCCccCccccCCcccCcccccccchhhHHHHHHHHhHHHH
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSFTNYKYFLLFLGYALL 107 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~~N~r~Filfl~~~~i 107 (251)
+...|.+|+.=-..--|||..-|.||--..| .-.-+|++|...+.+
T Consensus 104 RSHHCrkCnrCvmkMDHHCPWinnCVG~aNh-----------~~F~~FLlf~ivG~i 149 (414)
T KOG1314|consen 104 RSHHCRKCNRCVMKMDHHCPWINNCVGWANH-----------AYFLRFLLFSIVGCI 149 (414)
T ss_pred ccccchHHHHHHHhhccCCcchhhccccccc-----------HHHHHHHHHHHHhcc
Confidence 3578999987666678999999999987666 456788888887544
No 30
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=49.04 E-value=9.5 Score=25.33 Aligned_cols=35 Identities=20% Similarity=0.450 Sum_probs=24.6
Q ss_pred CCcccccCCCCcccCccccccc----CCCCCCCCccCcc
Q psy6282 41 LPVLNKSIDGGTRFCDKCYQVK----ADRSHHCSVCGKC 75 (251)
Q Consensus 41 ~~~~~~~~~~~~~~C~~C~~~k----P~Rs~HC~~C~~C 75 (251)
.++..-++....+.|..|+... ..|.++|..||.-
T Consensus 17 ~~v~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 17 IQVVEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CEEEEECCCCCccCccCcccccccccccceEEcCCCCCE
Confidence 4444445556789999998654 4578889998865
No 31
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=48.99 E-value=11 Score=20.82 Aligned_cols=20 Identities=35% Similarity=0.740 Sum_probs=14.6
Q ss_pred cCcccccccCCC-CCCCCccC
Q psy6282 54 FCDKCYQVKADR-SHHCSVCG 73 (251)
Q Consensus 54 ~C~~C~~~kP~R-s~HC~~C~ 73 (251)
.|..|+..--.. .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477777666666 88888777
No 32
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=41.94 E-value=1.2e+02 Score=21.41 Aligned_cols=25 Identities=20% Similarity=0.393 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHhccCceeeccccC
Q psy6282 149 SLVALFGYHLYLVAQNKTTLEAIRP 173 (251)
Q Consensus 149 ~~~~l~~~h~~li~~n~TtiE~~~~ 173 (251)
.+++++++..|--+++.++.|+++.
T Consensus 59 l~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 59 LLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHhcccCCCceeecccC
Confidence 3445677777777788888887764
No 33
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.51 E-value=14 Score=27.50 Aligned_cols=24 Identities=21% Similarity=0.596 Sum_probs=18.6
Q ss_pred CcccCcccccccCCCCCC---CCccCc
Q psy6282 51 GTRFCDKCYQVKADRSHH---CSVCGK 74 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~H---C~~C~~ 74 (251)
..-+|..|+..-|...++ |+.|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 468999999888776555 999884
No 34
>COG4640 Predicted membrane protein [Function unknown]
Probab=40.63 E-value=15 Score=33.44 Aligned_cols=26 Identities=35% Similarity=0.810 Sum_probs=22.2
Q ss_pred cccCcccccccCCCCCCCCccCcccc
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKCVL 77 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~CV~ 77 (251)
+++|..|+..+-.-+..|..||.=+-
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFT 26 (465)
T ss_pred CCcccccccccccccccccccCCcCC
Confidence 47999999999999999999986544
No 35
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.36 E-value=14 Score=22.84 Aligned_cols=21 Identities=33% Similarity=0.920 Sum_probs=11.3
Q ss_pred ccCcccccccCCC------CCCCCccC
Q psy6282 53 RFCDKCYQVKADR------SHHCSVCG 73 (251)
Q Consensus 53 ~~C~~C~~~kP~R------s~HC~~C~ 73 (251)
+||..|+....++ -+-|+.|+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg 27 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCC
Confidence 3677776444332 23466666
No 36
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=40.28 E-value=16 Score=24.15 Aligned_cols=24 Identities=25% Similarity=0.851 Sum_probs=21.1
Q ss_pred cccCcccccccCCCCCCCCccCcc
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKC 75 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~C 75 (251)
.+-|..|+..-|+-+.-|.+|+.=
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCCc
Confidence 367999999999999999999863
No 37
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=40.21 E-value=20 Score=22.63 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=14.9
Q ss_pred cCccccc--ccCCCCCCCCccCccc
Q psy6282 54 FCDKCYQ--VKADRSHHCSVCGKCV 76 (251)
Q Consensus 54 ~C~~C~~--~kP~Rs~HC~~C~~CV 76 (251)
-|..|+. -.-.|.|||+.|++-+
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred cCcccCccccCCccccccCcCcCCc
Confidence 4566642 3356789999887643
No 38
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=39.20 E-value=1.4e+02 Score=25.56 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=12.1
Q ss_pred cch-hhHHHHHHHHhHHHHHHHHh
Q psy6282 90 VSF-TNYKYFLLFLGYALLYCIYG 112 (251)
Q Consensus 90 IG~-~N~r~Filfl~~~~i~~~~~ 112 (251)
||. ...|-.++|++.+.+..+..
T Consensus 189 VG~~faRkR~i~f~llgllfliia 212 (256)
T PF09788_consen 189 VGPRFARKRAIIFFLLGLLFLIIA 212 (256)
T ss_pred ccchHhhhHHHHHHHHHHHHHHHH
Confidence 674 45555555555555544433
No 39
>KOG3183|consensus
Probab=38.73 E-value=15 Score=31.01 Aligned_cols=12 Identities=33% Similarity=0.379 Sum_probs=9.4
Q ss_pred ccCCcccCcccc
Q psy6282 76 VLKMDHHCPWVN 87 (251)
Q Consensus 76 V~~~DHHC~wl~ 87 (251)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 456799999974
No 40
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=36.61 E-value=11 Score=21.76 Aligned_cols=7 Identities=57% Similarity=1.483 Sum_probs=4.2
Q ss_pred ccCcccc
Q psy6282 53 RFCDKCY 59 (251)
Q Consensus 53 ~~C~~C~ 59 (251)
++|.+|+
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 5677776
No 41
>PF03842 Silic_transp: Silicon transporter; InterPro: IPR004693 Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms, which make their "glass houses" out of silicon.
Probab=36.50 E-value=1.4e+02 Score=27.57 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=16.9
Q ss_pred HHHHHHHhHHHHHHHHhcccchhhhh
Q psy6282 96 KYFLLFLGYALLYCIYGSLSTLPYFI 121 (251)
Q Consensus 96 r~Filfl~~~~i~~~~~~~~~~~~~~ 121 (251)
-||.+|.+|..+..=+.-+.-..|++
T Consensus 171 nyFalFTlyvam~IEfsGvmHssYLI 196 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFSGVMHSSYLI 196 (512)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence 58999999988765444444334444
No 42
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=36.28 E-value=13 Score=23.18 Aligned_cols=22 Identities=36% Similarity=0.774 Sum_probs=8.9
Q ss_pred CCCCCcc---CccccCCcc--cCcccc
Q psy6282 66 SHHCSVC---GKCVLKMDH--HCPWVN 87 (251)
Q Consensus 66 s~HC~~C---~~CV~~~DH--HC~wl~ 87 (251)
..+|..| |.-+...+| .|+|-+
T Consensus 2 ~p~C~RCrnHG~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 2 SPTCARCRNHGVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp -SS-HHHHTTT---TTTT-GGG-TTTT
T ss_pred CCcCcchhcCCcccchhhhccccCcCC
Confidence 4445555 445566666 688864
No 43
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.73 E-value=24 Score=22.85 Aligned_cols=22 Identities=36% Similarity=0.729 Sum_probs=18.1
Q ss_pred CcccCcccccccCCCCCCCCccCc
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
.++.|..|+.+-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4688999998888 778888875
No 44
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.88 E-value=27 Score=34.16 Aligned_cols=39 Identities=31% Similarity=0.623 Sum_probs=21.3
Q ss_pred cccCcccccccCCCCCCCCccCccccCCcccCcccccccch
Q psy6282 52 TRFCDKCYQVKADRSHHCSVCGKCVLKMDHHCPWVNNCVSF 92 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wl~nCIG~ 92 (251)
.|||..|+..-+ ...|..||.=+..-..+|+=-|.=.|.
T Consensus 15 akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCC--CCcCCCCCCCCCcccccccccCCcccc
Confidence 466666655432 235666666666666666644444443
No 45
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=34.11 E-value=28 Score=18.41 Aligned_cols=19 Identities=37% Similarity=0.875 Sum_probs=10.3
Q ss_pred CcccccccCCCC----CCCCccC
Q psy6282 55 CDKCYQVKADRS----HHCSVCG 73 (251)
Q Consensus 55 C~~C~~~kP~Rs----~HC~~C~ 73 (251)
|.+|+..-.+|- +.|..||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 555655544553 4566665
No 46
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=33.94 E-value=27 Score=22.85 Aligned_cols=23 Identities=22% Similarity=0.571 Sum_probs=16.0
Q ss_pred cccCcccccccCCCCCCCC-ccCc
Q psy6282 52 TRFCDKCYQVKADRSHHCS-VCGK 74 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~HC~-~C~~ 74 (251)
.+-|..|+..-|+--..|| .|+.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 3668888877777777775 6654
No 47
>KOG4017|consensus
Probab=33.76 E-value=19 Score=30.64 Aligned_cols=35 Identities=26% Similarity=0.540 Sum_probs=25.9
Q ss_pred CCcccCcccccccCC----CCCCCCccCccccCCcccCc
Q psy6282 50 GGTRFCDKCYQVKAD----RSHHCSVCGKCVLKMDHHCP 84 (251)
Q Consensus 50 ~~~~~C~~C~~~kP~----Rs~HC~~C~~CV~~~DHHC~ 84 (251)
....-|..|...-.+ -.++|++|+.|--.+|-|=.
T Consensus 101 ~~~~~C~eC~~i~mDs~L~~~F~~~VCd~CRd~~ekykL 139 (274)
T KOG4017|consen 101 ALAPKCEECDKIEMDSYLFDTFGCSVCDSCRDKDEKYKL 139 (274)
T ss_pred hhchhHHHhcCccchHHHHHhcCChhhhHhhhhhhhhhe
Confidence 345679999854433 46899999999999877543
No 48
>KOG2927|consensus
Probab=33.13 E-value=62 Score=29.09 Aligned_cols=32 Identities=13% Similarity=0.269 Sum_probs=22.3
Q ss_pred ccCCCCCCCCcc-CccccCCcccCcccccccch
Q psy6282 61 VKADRSHHCSVC-GKCVLKMDHHCPWVNNCVSF 92 (251)
Q Consensus 61 ~kP~Rs~HC~~C-~~CV~~~DHHC~wl~nCIG~ 92 (251)
.++-+..||-+= ++--..-|-|=.|+-+-+-.
T Consensus 156 ~kkkk~~~l~i~~dQ~F~d~de~YVW~yep~~~ 188 (372)
T KOG2927|consen 156 KKKKKKFELEIHDDQAFQDGDEHYVWIYEPRPL 188 (372)
T ss_pred hcccCccceeeccchhhcccCceEEEeccCCch
Confidence 567777777766 45555558888999776644
No 49
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=31.35 E-value=27 Score=24.88 Aligned_cols=10 Identities=50% Similarity=1.261 Sum_probs=7.9
Q ss_pred ccCccccccc
Q psy6282 81 HHCPWVNNCV 90 (251)
Q Consensus 81 HHC~wl~nCI 90 (251)
.||||++.-.
T Consensus 56 ~~CPwv~~~~ 65 (91)
T PF08600_consen 56 EYCPWVNPST 65 (91)
T ss_pred ccCCccCCcc
Confidence 6899998654
No 50
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=30.71 E-value=4e+02 Score=24.62 Aligned_cols=33 Identities=18% Similarity=0.363 Sum_probs=26.0
Q ss_pred CcccCcccccccCCCCCCCCccCccccCCcccC
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGKCVLKMDHHC 83 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC 83 (251)
...-|..|...-|....||..|+.-..+..++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 356799999888877779999998887766544
No 51
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.01 E-value=30 Score=33.84 Aligned_cols=24 Identities=21% Similarity=0.715 Sum_probs=16.6
Q ss_pred ccCcccccccCCCCCCCCccCccc
Q psy6282 53 RFCDKCYQVKADRSHHCSVCGKCV 76 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C~~CV 76 (251)
..|..|+..-|+.++.|..||.=.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l 25 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSL 25 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCC
Confidence 457777777777777777776543
No 52
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=29.85 E-value=38 Score=19.07 Aligned_cols=21 Identities=29% Similarity=0.822 Sum_probs=13.1
Q ss_pred cCcccccc-cCC-CCCCCCccCc
Q psy6282 54 FCDKCYQV-KAD-RSHHCSVCGK 74 (251)
Q Consensus 54 ~C~~C~~~-kP~-Rs~HC~~C~~ 74 (251)
.|..|+-. .+. ....|.+|+.
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCC
Confidence 47777744 444 4667777764
No 53
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=29.31 E-value=22 Score=22.04 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=19.7
Q ss_pred CCcccCccccccc---CCCCCCCCccCcccc
Q psy6282 50 GGTRFCDKCYQVK---ADRSHHCSVCGKCVL 77 (251)
Q Consensus 50 ~~~~~C~~C~~~k---P~Rs~HC~~C~~CV~ 77 (251)
..+.+|..|+..- -..+.+|+.|+.-+-
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H 39 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCH 39 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEE
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHh
Confidence 3468999998766 677889999975443
No 54
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=28.98 E-value=22 Score=21.49 Aligned_cols=14 Identities=43% Similarity=1.324 Sum_probs=6.4
Q ss_pred cCccccCCcccCcc
Q psy6282 72 CGKCVLKMDHHCPW 85 (251)
Q Consensus 72 C~~CV~~~DHHC~w 85 (251)
|..|+...|-||.|
T Consensus 7 C~~C~~~~~~~C~W 20 (46)
T smart00423 7 CSECLLARDPYCAW 20 (46)
T ss_pred HHHHHcCCCCCCCc
Confidence 44444444444444
No 55
>PLN00186 ribosomal protein S26; Provisional
Probab=28.96 E-value=23 Score=26.09 Aligned_cols=14 Identities=57% Similarity=1.042 Sum_probs=11.4
Q ss_pred CCCCCccCccccCC
Q psy6282 66 SHHCSVCGKCVLKM 79 (251)
Q Consensus 66 s~HC~~C~~CV~~~ 79 (251)
.=||..|++||.+=
T Consensus 20 ~V~C~nCgr~vPKD 33 (109)
T PLN00186 20 RIRCSNCGKCVPKD 33 (109)
T ss_pred ceeeCCCccccccc
Confidence 34799999999973
No 56
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.94 E-value=32 Score=21.61 Aligned_cols=23 Identities=35% Similarity=0.957 Sum_probs=14.3
Q ss_pred cccCccccc-ccCC--CCCCCCccCc
Q psy6282 52 TRFCDKCYQ-VKAD--RSHHCSVCGK 74 (251)
Q Consensus 52 ~~~C~~C~~-~kP~--Rs~HC~~C~~ 74 (251)
.++|+.|+. ..-+ ..++|..|+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCC
Confidence 469999987 2222 3456777763
No 57
>KOG3611|consensus
Probab=28.85 E-value=20 Score=35.55 Aligned_cols=27 Identities=33% Similarity=0.893 Sum_probs=21.9
Q ss_pred CCCCC---ccCccccCCcccCcccc---cccch
Q psy6282 66 SHHCS---VCGKCVLKMDHHCPWVN---NCVSF 92 (251)
Q Consensus 66 s~HC~---~C~~CV~~~DHHC~wl~---nCIG~ 92 (251)
-|+|+ .|-.|++..|-||.|-+ .|+-.
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~ 523 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLL 523 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceEC
Confidence 46777 79888888999999998 78633
No 58
>PHA02942 putative transposase; Provisional
Probab=28.19 E-value=33 Score=31.30 Aligned_cols=34 Identities=26% Similarity=0.428 Sum_probs=23.2
Q ss_pred CCcccccCCCCcccCcccccccC---CCCCCCCccCc
Q psy6282 41 LPVLNKSIDGGTRFCDKCYQVKA---DRSHHCSVCGK 74 (251)
Q Consensus 41 ~~~~~~~~~~~~~~C~~C~~~kP---~Rs~HC~~C~~ 74 (251)
..+..-++....+.|..|+...+ .|.+.|..||.
T Consensus 314 ~~Vv~V~p~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 314 MIVEFVNPSYSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CEEEEECCCCCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 33333455556789999986654 37888888886
No 59
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=27.87 E-value=73 Score=22.98 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=15.7
Q ss_pred ccCceeeccccCCCcccCCCCCCCC
Q psy6282 162 AQNKTTLEAIRPPVFSYGPDKQGYN 186 (251)
Q Consensus 162 ~~n~TtiE~~~~~~~~~~~~~npyd 186 (251)
..+++|-|.++...+++....-||+
T Consensus 79 ~~~r~tae~lk~e~~~~~~~~~~Y~ 103 (112)
T PF14015_consen 79 IRYRATAESLKREKWLYLAGAGPYK 103 (112)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 4678888888766555443444554
No 60
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.72 E-value=33 Score=17.87 Aligned_cols=21 Identities=24% Similarity=0.635 Sum_probs=15.4
Q ss_pred cCcccccccCCCCCCCCccCc
Q psy6282 54 FCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 54 ~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
.|..|...-.++...|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477787777777777877763
No 61
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=26.69 E-value=22 Score=29.82 Aligned_cols=19 Identities=32% Similarity=0.840 Sum_probs=16.0
Q ss_pred ccCCCCCCCCccCccccCC
Q psy6282 61 VKADRSHHCSVCGKCVLKM 79 (251)
Q Consensus 61 ~kP~Rs~HC~~C~~CV~~~ 79 (251)
|++.+..||..|..|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 5677777999999999983
No 62
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=26.59 E-value=27 Score=25.17 Aligned_cols=19 Identities=26% Similarity=0.595 Sum_probs=13.8
Q ss_pred CCCCCccCccccCCcccCc
Q psy6282 66 SHHCSVCGKCVLKMDHHCP 84 (251)
Q Consensus 66 s~HC~~C~~CV~~~DHHC~ 84 (251)
.=+|..|++||.+----+.
T Consensus 20 ~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 20 YVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred cEEeCCCCCcCcCCceEEE
Confidence 3479999999998544443
No 63
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=25.66 E-value=5.3e+02 Score=23.71 Aligned_cols=32 Identities=16% Similarity=0.417 Sum_probs=24.2
Q ss_pred cccCccccc-ccCCCCCCCCccCccccCCcccC
Q psy6282 52 TRFCDKCYQ-VKADRSHHCSVCGKCVLKMDHHC 83 (251)
Q Consensus 52 ~~~C~~C~~-~kP~Rs~HC~~C~~CV~~~DHHC 83 (251)
..-|..|.. .+|....+|..|+.-..+..++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 456999997 56666778999998887766544
No 64
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=25.36 E-value=28 Score=25.65 Aligned_cols=14 Identities=50% Similarity=1.049 Sum_probs=11.3
Q ss_pred CCCCCccCccccCC
Q psy6282 66 SHHCSVCGKCVLKM 79 (251)
Q Consensus 66 s~HC~~C~~CV~~~ 79 (251)
.=||..|++||.+=
T Consensus 20 ~V~C~nCgr~vPKD 33 (108)
T PTZ00172 20 PVRCSNCGRCVPKD 33 (108)
T ss_pred cEEeCCcccccccc
Confidence 34799999999973
No 65
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.10 E-value=39 Score=25.06 Aligned_cols=24 Identities=29% Similarity=0.648 Sum_probs=16.8
Q ss_pred CcccCcccccccCCCCCC--CCccCc
Q psy6282 51 GTRFCDKCYQVKADRSHH--CSVCGK 74 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~H--C~~C~~ 74 (251)
..-+|..|+..-+....+ |..|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCCC
Confidence 457899998665554333 888874
No 66
>smart00301 DM Doublesex DNA-binding motif.
Probab=24.77 E-value=44 Score=21.47 Aligned_cols=6 Identities=33% Similarity=1.293 Sum_probs=3.8
Q ss_pred cCcccc
Q psy6282 82 HCPWVN 87 (251)
Q Consensus 82 HC~wl~ 87 (251)
+|+|-+
T Consensus 23 ~C~~r~ 28 (54)
T smart00301 23 ECPFRD 28 (54)
T ss_pred CCCCCC
Confidence 677654
No 67
>PF01437 PSI: Plexin repeat; InterPro: IPR002165 This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin (P70206 from SWISSPROT) []. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein (Q19981 from SWISSPROT) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.; GO: 0016020 membrane; PDB: 3NVQ_B 3NVN_B 3OL2_B 3OKT_A 3AL8_A 3OKW_A 3OKY_B 3AFC_B 1OLZ_B 1SHY_B ....
Probab=24.51 E-value=13 Score=23.24 Aligned_cols=17 Identities=29% Similarity=0.933 Sum_probs=10.5
Q ss_pred CccCccccCCcccCccc
Q psy6282 70 SVCGKCVLKMDHHCPWV 86 (251)
Q Consensus 70 ~~C~~CV~~~DHHC~wl 86 (251)
..|..|+.-.|-+|.|-
T Consensus 6 ~sC~~Cl~~~dp~CgWc 22 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWC 22 (51)
T ss_dssp SSHHHHHHSTCTTEEEE
T ss_pred CcHHHHHcCCCcCcccc
Confidence 45666666666666664
No 68
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=24.12 E-value=45 Score=22.45 Aligned_cols=13 Identities=46% Similarity=1.497 Sum_probs=8.3
Q ss_pred ccCcccccccCCCCCCCCcc
Q psy6282 53 RFCDKCYQVKADRSHHCSVC 72 (251)
Q Consensus 53 ~~C~~C~~~kP~Rs~HC~~C 72 (251)
-||.+| ++||-+|
T Consensus 30 CyCK~C-------cyHCqlC 42 (68)
T PF00539_consen 30 CYCKKC-------CYHCQLC 42 (68)
T ss_dssp SSSTTS-------TSSSSCC
T ss_pred cccCcc-------eeeceee
Confidence 555555 6777766
No 69
>KOG1819|consensus
Probab=23.80 E-value=39 Score=31.82 Aligned_cols=22 Identities=36% Similarity=0.795 Sum_probs=13.7
Q ss_pred ccCcccccc--cCCCCCCCCccCc
Q psy6282 53 RFCDKCYQV--KADRSHHCSVCGK 74 (251)
Q Consensus 53 ~~C~~C~~~--kP~Rs~HC~~C~~ 74 (251)
--|-.|+.. .--|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 446666532 2247788988875
No 70
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=23.40 E-value=98 Score=22.30 Aligned_cols=34 Identities=12% Similarity=0.220 Sum_probs=15.7
Q ss_pred CCCCCCCCCCChhhh----hhhccCCChHHHHHHHHHh
Q psy6282 4 LGTAPKHFKLSPSLQ----HALFTTDNDVERKQILEQF 37 (251)
Q Consensus 4 PG~~p~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~ 37 (251)
++++|..|.++..+. .++....+.++-.++.+++
T Consensus 5 ~a~IP~~YI~d~~~Rl~~Yrrl~~~~~~~el~~l~~El 42 (101)
T PF03461_consen 5 DAYIPEDYIPDDDERLELYRRLASAESEEELEDLREEL 42 (101)
T ss_dssp --S--TTTS--HHHHHHHHHHHHC--SHHHHHHHHHHH
T ss_pred cccCChHHcCChHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence 789999999987763 2455555555555544444
No 71
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.71 E-value=49 Score=21.44 Aligned_cols=20 Identities=35% Similarity=0.811 Sum_probs=13.7
Q ss_pred cccCcccccccCCCCCC-CCccC
Q psy6282 52 TRFCDKCYQVKADRSHH-CSVCG 73 (251)
Q Consensus 52 ~~~C~~C~~~kP~Rs~H-C~~C~ 73 (251)
...|..|+.++.+ || |..||
T Consensus 27 l~~C~~CG~~~~~--H~vC~~CG 47 (57)
T PRK12286 27 LVECPNCGEPKLP--HRVCPSCG 47 (57)
T ss_pred ceECCCCCCccCC--eEECCCCC
Confidence 4679999877755 44 66665
No 72
>KOG1729|consensus
Probab=22.52 E-value=27 Score=30.59 Aligned_cols=25 Identities=36% Similarity=0.755 Sum_probs=13.4
Q ss_pred cccCccccc---ccCCCCCCCCccCccc
Q psy6282 52 TRFCDKCYQ---VKADRSHHCSVCGKCV 76 (251)
Q Consensus 52 ~~~C~~C~~---~kP~Rs~HC~~C~~CV 76 (251)
...|..|.. ---.|=|||+.||.-|
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~iv 195 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIV 195 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHh
Confidence 345555544 2234667777666543
No 73
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=22.49 E-value=27 Score=27.42 Aligned_cols=23 Identities=30% Similarity=0.858 Sum_probs=16.0
Q ss_pred cCcccccccCCCCCCCCccCccccCC
Q psy6282 54 FCDKCYQVKADRSHHCSVCGKCVLKM 79 (251)
Q Consensus 54 ~C~~C~~~kP~Rs~HC~~C~~CV~~~ 79 (251)
.-.+|... ...||..|..|+.|.
T Consensus 142 ~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 142 LTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred heeeccCC---CCCCCCCCHHHHHHH
Confidence 34555543 227999999999873
No 74
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.33 E-value=50 Score=24.69 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=17.5
Q ss_pred CCcccCcccccccCCCC--C-CCCccCc
Q psy6282 50 GGTRFCDKCYQVKADRS--H-HCSVCGK 74 (251)
Q Consensus 50 ~~~~~C~~C~~~kP~Rs--~-HC~~C~~ 74 (251)
...-+|..|+..-+... + +|..|+.
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCC
Confidence 34688999986666543 2 4888875
No 75
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=22.29 E-value=1.4e+02 Score=28.91 Aligned_cols=59 Identities=15% Similarity=0.326 Sum_probs=34.8
Q ss_pred ChHHHHHHHHHhhccCCcccccCCCCcccCcccccccCCCC-CCCCccCccccCCcccCcccccccch
Q psy6282 26 NDVERKQILEQFSASLPVLNKSIDGGTRFCDKCYQVKADRS-HHCSVCGKCVLKMDHHCPWVNNCVSF 92 (251)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs-~HC~~C~~CV~~~DHHC~wl~nCIG~ 92 (251)
+++.-.++.+...+.- +.-...+....+|..|+. .-.+. ..|+.||. |.|-++...+|+
T Consensus 499 n~eal~~lv~~a~~~~-i~Y~~~n~~~~~C~~CG~-~g~~~~~~CP~Cgs------~~~~~~~Rv~GY 558 (579)
T TIGR02487 499 DPEALKDITKKAMKNG-IGYFGINPPVDVCEDCGY-TGEGLNDKCPKCGS------HDIEVISRITGY 558 (579)
T ss_pred CHHHHHHHHHHHHhcC-CceEEeccCCccCCCCCC-CCCCCCCcCcCCCC------ccceehhhhhhh
Confidence 3445555555544431 223345566789999985 55555 68999986 235555555554
No 76
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=22.21 E-value=49 Score=24.60 Aligned_cols=24 Identities=17% Similarity=0.397 Sum_probs=17.3
Q ss_pred CcccCcccccccCC--CCCCCCccCc
Q psy6282 51 GTRFCDKCYQVKAD--RSHHCSVCGK 74 (251)
Q Consensus 51 ~~~~C~~C~~~kP~--Rs~HC~~C~~ 74 (251)
..-+|..|+..-+. +...|+.|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcC
Confidence 45889999866555 3566888874
No 77
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=21.67 E-value=46 Score=27.09 Aligned_cols=22 Identities=41% Similarity=0.913 Sum_probs=17.6
Q ss_pred CcccCcccccccCCCCCCCCccCc
Q psy6282 51 GTRFCDKCYQVKADRSHHCSVCGK 74 (251)
Q Consensus 51 ~~~~C~~C~~~kP~Rs~HC~~C~~ 74 (251)
...||.+|+..-+-|. |+.|+.
T Consensus 13 ~iyWCe~cNlPl~~~~--c~~cg~ 34 (202)
T COG5270 13 PIYWCEKCNLPLLGRR--CSVCGS 34 (202)
T ss_pred ceeehhhCCCcccccc--ccccCC
Confidence 3689999999888764 888884
No 78
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=21.59 E-value=46 Score=27.01 Aligned_cols=13 Identities=31% Similarity=1.009 Sum_probs=10.9
Q ss_pred CCCCCccCccccC
Q psy6282 66 SHHCSVCGKCVLK 78 (251)
Q Consensus 66 s~HC~~C~~CV~~ 78 (251)
..||..|..|+.|
T Consensus 189 ~~~CG~C~~C~~r 201 (201)
T TIGR00364 189 GEGCGKCPSCMLR 201 (201)
T ss_pred CCCCCCChhhhcc
Confidence 3599999999875
No 79
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.46 E-value=39 Score=18.78 Aligned_cols=22 Identities=36% Similarity=1.004 Sum_probs=9.9
Q ss_pred cccCccccc-ccC---CCCCCCCccC
Q psy6282 52 TRFCDKCYQ-VKA---DRSHHCSVCG 73 (251)
Q Consensus 52 ~~~C~~C~~-~kP---~Rs~HC~~C~ 73 (251)
.+||..|.. -++ .++..|..|+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 478888873 222 3445555554
No 80
>TIGR00811 sit silicon transporter. Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterized member of the family (Sit1) functions in the energy-dependent uptake of either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms which make their "glass houses" out of silicon.
Probab=20.30 E-value=4.7e+02 Score=24.71 Aligned_cols=13 Identities=15% Similarity=0.192 Sum_probs=9.1
Q ss_pred HHHHHhccCceee
Q psy6282 156 YHLYLVAQNKTTL 168 (251)
Q Consensus 156 ~h~~li~~n~Tti 168 (251)
.-+..+..|.|+.
T Consensus 239 Vtl~ALFnG~T~m 251 (545)
T TIGR00811 239 VTIEALFNGQTTM 251 (545)
T ss_pred HHHHHHHCCCcee
Confidence 4555677888886
No 81
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=20.22 E-value=91 Score=26.95 Aligned_cols=17 Identities=35% Similarity=0.638 Sum_probs=11.8
Q ss_pred CCCCC--CCCCCCCChhhh
Q psy6282 2 TPLGT--APKHFKLSPSLQ 18 (251)
Q Consensus 2 ~dPG~--~p~~~~~~~~~~ 18 (251)
-|||. .|+.|.+++...
T Consensus 29 iDpGVsLaPkRy~LPPh~~ 47 (304)
T COG2248 29 IDPGVSLAPKRYGLPPHQR 47 (304)
T ss_pred ECCccccCccccCCCCCHH
Confidence 37774 689898776543
No 82
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.15 E-value=66 Score=19.04 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=17.9
Q ss_pred CcccCcccccccCC--CCCCCCccCccc
Q psy6282 51 GTRFCDKCYQVKAD--RSHHCSVCGKCV 76 (251)
Q Consensus 51 ~~~~C~~C~~~kP~--Rs~HC~~C~~CV 76 (251)
...+|..|+..-+. .+..|+.|+.-+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~ 37 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKC 37 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchH
Confidence 35789999765543 388899885433
Done!