Query 023152
Match_columns 286
No_of_seqs 151 out of 1692
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 08:48:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023152.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023152hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315 Predicted DHHC-type Zn 100.0 1.9E-60 4E-65 417.9 16.4 267 4-286 3-272 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 4.1E-49 9E-54 341.4 13.6 226 14-272 14-263 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 8.5E-45 1.8E-49 325.4 22.0 167 117-283 106-278 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 1.4E-42 3.1E-47 287.7 13.5 173 69-250 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 2.3E-40 5E-45 278.7 14.5 159 122-280 100-289 (309)
6 COG5273 Uncharacterized protei 100.0 2.3E-39 5E-44 288.5 18.4 204 55-279 57-287 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 5.5E-32 1.2E-36 229.3 11.7 165 65-250 109-291 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 5E-28 1.1E-32 225.4 9.7 140 125-272 421-585 (600)
9 KOG1311 DHHC-type Zn-finger pr 94.7 1.4 3E-05 39.5 14.1 58 137-194 112-180 (299)
10 PF01529 zf-DHHC: DHHC palmito 93.5 1.7 3.6E-05 35.3 11.5 58 121-189 59-116 (174)
11 PF13240 zinc_ribbon_2: zinc-r 87.9 0.31 6.8E-06 25.9 1.2 21 126-146 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 86.7 0.39 8.5E-06 30.3 1.3 25 122-146 12-36 (48)
13 PF13248 zf-ribbon_3: zinc-rib 82.2 0.84 1.8E-05 25.0 1.2 23 124-146 2-24 (26)
14 PTZ00303 phosphatidylinositol 82.0 0.82 1.8E-05 45.5 1.9 23 124-146 460-489 (1374)
15 PF01363 FYVE: FYVE zinc finge 74.9 1.3 2.8E-05 30.3 0.7 27 123-149 8-36 (69)
16 COG1552 RPL40A Ribosomal prote 71.4 0.95 2.1E-05 28.7 -0.6 25 122-146 12-36 (50)
17 KOG0509 Ankyrin repeat and DHH 70.1 2.7 5.8E-05 40.9 1.8 54 122-176 323-376 (600)
18 PF06906 DUF1272: Protein of u 69.8 2.3 4.9E-05 27.9 0.9 36 126-164 7-50 (57)
19 PF10571 UPF0547: Uncharacteri 68.2 3 6.5E-05 22.9 1.0 22 125-146 1-22 (26)
20 smart00064 FYVE Protein presen 68.1 3.9 8.4E-05 27.7 1.8 25 124-148 10-36 (68)
21 COG5273 Uncharacterized protei 66.8 24 0.00052 31.9 7.1 52 122-184 121-172 (309)
22 PF12773 DZR: Double zinc ribb 66.3 5.7 0.00012 25.1 2.2 33 124-156 12-47 (50)
23 PF01020 Ribosomal_L40e: Ribos 64.3 3.2 7E-05 26.7 0.8 25 123-147 16-42 (52)
24 PF12773 DZR: Double zinc ribb 62.5 5.8 0.00013 25.1 1.7 25 121-145 26-50 (50)
25 KOG1842 FYVE finger-containing 57.2 3.3 7.1E-05 38.7 -0.2 27 121-147 177-205 (505)
26 KOG1315 Predicted DHHC-type Zn 54.7 1.7E+02 0.0036 26.5 14.0 28 126-153 125-152 (307)
27 cd00065 FYVE FYVE domain; Zinc 51.9 9.5 0.00021 24.6 1.5 22 126-147 4-27 (57)
28 PF07649 C1_3: C1-like domain; 46.8 7.6 0.00017 21.8 0.3 21 126-146 2-23 (30)
29 KOG3183 Predicted Zn-finger pr 46.2 8.6 0.00019 33.0 0.7 14 146-159 36-49 (250)
30 PF07282 OrfB_Zn_ribbon: Putat 46.1 13 0.00028 25.2 1.4 27 121-147 25-55 (69)
31 PF02150 RNA_POL_M_15KD: RNA p 43.5 5.7 0.00012 23.4 -0.6 8 125-132 2-9 (35)
32 PF00641 zf-RanBP: Zn-finger i 42.8 7.3 0.00016 21.8 -0.2 22 125-146 5-26 (30)
33 PF03107 C1_2: C1 domain; Int 39.8 21 0.00045 20.1 1.4 27 126-155 2-29 (30)
34 TIGR02745 ccoG_rdxA_fixG cytoc 39.3 70 0.0015 30.4 5.7 11 139-149 255-265 (434)
35 PF07010 Endomucin: Endomucin; 39.0 78 0.0017 27.1 5.2 28 57-84 197-224 (259)
36 KOG1818 Membrane trafficking a 37.3 13 0.00029 36.6 0.5 25 122-146 163-189 (634)
37 KOG1313 DHHC-type Zn-finger pr 37.3 2.6E+02 0.0057 24.8 8.3 53 123-186 115-167 (309)
38 PF03842 Silic_transp: Silicon 37.1 3.7E+02 0.008 25.5 9.6 16 168-183 171-186 (512)
39 PLN00186 ribosomal protein S26 34.5 16 0.00034 27.5 0.4 19 137-155 19-37 (109)
40 PF09297 zf-NADH-PPase: NADH p 34.3 15 0.00032 21.0 0.2 22 124-145 3-28 (32)
41 COG2093 DNA-directed RNA polym 33.9 23 0.00049 23.8 1.0 23 124-146 4-26 (64)
42 TIGR00155 pqiA_fam integral me 33.8 4.1E+02 0.0088 25.0 13.2 32 124-155 215-247 (403)
43 PRK00432 30S ribosomal protein 33.4 25 0.00054 22.5 1.2 24 123-146 19-45 (50)
44 PRK15103 paraquat-inducible me 33.4 4.2E+02 0.0092 25.0 11.5 33 123-155 220-252 (419)
45 smart00661 RPOL9 RNA polymeras 32.8 24 0.00052 22.3 1.0 7 126-132 2-8 (52)
46 PF08600 Rsm1: Rsm1-like; Int 32.6 21 0.00045 26.0 0.8 13 150-162 53-65 (91)
47 PHA02942 putative transposase; 32.5 28 0.0006 32.5 1.8 26 121-146 322-350 (383)
48 PRK09335 30S ribosomal protein 32.4 18 0.00038 26.5 0.4 21 137-157 19-39 (95)
49 KOG1819 FYVE finger-containing 32.0 16 0.00036 34.8 0.2 24 123-146 900-925 (990)
50 KOG1729 FYVE finger containing 31.3 17 0.00038 32.4 0.2 28 123-150 167-197 (288)
51 PTZ00172 40S ribosomal protein 30.8 19 0.00041 27.0 0.3 20 137-156 19-38 (108)
52 PRK14559 putative protein seri 29.7 36 0.00077 34.1 2.1 22 125-146 28-49 (645)
53 KOG1841 Smad anchor for recept 27.9 30 0.00065 36.4 1.2 40 123-174 556-597 (1287)
54 COG0603 Predicted PP-loop supe 27.6 21 0.00045 30.6 0.1 19 133-151 187-205 (222)
55 PRK03681 hypA hydrogenase nick 27.6 29 0.00062 26.4 0.8 24 123-146 69-95 (114)
56 PRK12286 rpmF 50S ribosomal pr 27.6 35 0.00077 22.5 1.2 22 122-145 25-47 (57)
57 PHA02680 ORF090 IMV phosphoryl 27.2 2.4E+02 0.0053 20.3 7.0 37 210-249 47-83 (91)
58 KOG1398 Uncharacterized conser 26.9 18 0.00039 33.5 -0.4 26 134-165 10-35 (460)
59 PF13842 Tnp_zf-ribbon_2: DDE_ 26.4 47 0.001 19.0 1.4 6 126-131 18-23 (32)
60 TIGR01031 rpmF_bact ribosomal 25.4 39 0.00085 22.1 1.1 21 123-145 25-46 (55)
61 smart00547 ZnF_RBZ Zinc finger 24.8 38 0.00082 17.9 0.8 21 126-146 4-24 (26)
62 PF01283 Ribosomal_S26e: Ribos 24.2 28 0.00061 26.5 0.2 21 137-157 19-39 (113)
63 PRK02935 hypothetical protein; 23.9 3.2E+02 0.0069 20.5 6.2 17 17-33 14-30 (110)
64 PF01437 PSI: Plexin repeat; 22.7 23 0.0005 22.5 -0.4 16 142-157 6-21 (51)
65 cd07973 Spt4 Transcription elo 22.0 59 0.0013 24.1 1.5 24 124-147 3-26 (98)
66 PF12172 DUF35_N: Rubredoxin-l 21.9 25 0.00055 20.6 -0.3 24 121-145 8-32 (37)
67 PF00130 C1_1: Phorbol esters/ 21.6 49 0.0011 20.9 1.0 26 122-147 9-37 (53)
68 PRK11875 psbT photosystem II r 21.4 1.8E+02 0.0038 16.6 3.6 14 70-83 17-30 (31)
69 CHL00031 psbT photosystem II p 21.2 1.8E+02 0.004 16.8 3.4 15 70-84 17-31 (33)
70 PF14127 DUF4294: Domain of un 21.1 90 0.0019 25.2 2.5 32 238-272 103-134 (157)
71 COG3477 Predicted periplasmic/ 20.7 1.4E+02 0.003 24.2 3.5 38 230-277 117-154 (176)
72 PRK15033 tricarballylate utili 20.6 3.8E+02 0.0082 25.1 6.8 15 139-157 67-81 (389)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.9e-60 Score=417.87 Aligned_cols=267 Identities=34% Similarity=0.660 Sum_probs=212.5
Q ss_pred ccccccccccchhHHHHHHHHHHHHhhheeEEeeeeccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 023152 4 NLFKLCSGLKVLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVP 83 (286)
Q Consensus 4 ~~~~~c~~~~~~g~~~~~~v~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~f~~l~~~~~~~y~~~~~~dPG~vp 83 (286)
++++++...| +++++++.+.++|.||++++..+.+... .+..+.+.+++++.++++.+|+|++++++|||.+|
T Consensus 3 ~~~~~~~~~r---~~~~~~i~~~~~~~yy~~v~~~c~~~i~----~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp 75 (307)
T KOG1315|consen 3 GSRRFSKCLR---WIPVLIILLVIGWTYYVYVAVLCILSIS----LTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVP 75 (307)
T ss_pred Ccccchhhhc---chhheeeeeeEEEEEEEeehhhhHHHHh----hhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCc
Confidence 3455555456 8899999999999999999998877552 22567788899999999999999999999999999
Q ss_pred CCCCCCCcCCCCCcCcccccCCCCCCCCCCCCCCCCCCCCeeccccccCCCCCCCccCcccCccccCccccccccccccc
Q 023152 84 ENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVG 163 (286)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG 163 (286)
..+.++.+..+.... +...+ .......++..+..|+|++|+.+|||||||||.|+|||+||||||||+|||||
T Consensus 76 ~~~~~~~~~~~~~~~-----~~~~~--~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVg 148 (307)
T KOG1315|consen 76 DSYRPSVEDEDSLEN-----GSDNE--RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVG 148 (307)
T ss_pred cccCCCcCccccccc-----cCccc--ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceec
Confidence 999887764322111 11100 11233456788899999999999999999999999999999999999999999
Q ss_pred cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcch
Q 023152 164 ARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTS 243 (286)
Q Consensus 164 ~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l~~~~l~~~h~~li~~n~TT 243 (286)
.+|||+|++|++|+.+++.+..+.....++..+.. . ...++.....+.+.+++++.|++.+++++++|++||++|+||
T Consensus 149 f~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TT 226 (307)
T KOG1315|consen 149 FRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQG-G-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTT 226 (307)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-c-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchh
Confidence 99999999999999999999888888878777722 1 222233344455556677788888888999999999999999
Q ss_pred HHHHhhcCCCCCCCchhH---HHHHhhhCCCCccceEEeccCCCCC
Q 023152 244 IEVYEKKRTVRWKYDLGR---KKNFEQVYPVQLHLWLQELQNEQRR 286 (286)
Q Consensus 244 ~E~~~~~~~~~~~yd~G~---~~N~~~vfG~~~~~W~~P~~~~~~~ 286 (286)
+|.++.+....+.++.+- ..|++|+||+++..|++|+.++..+
T Consensus 227 iE~~~~~~~~~~~~~~~~~~~~~n~~~vfg~~~~~wl~P~~~s~~~ 272 (307)
T KOG1315|consen 227 IEAYKSPVFRSGLHNKNGFNLYVNFREVFGSNLLYWLLPIDSSWGD 272 (307)
T ss_pred HhhhccccccccccccCCcceeecHHHHhCCCceEEeccccCcccc
Confidence 999987633333344443 5699999999999999999988653
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.1e-49 Score=341.36 Aligned_cols=226 Identities=29% Similarity=0.544 Sum_probs=171.6
Q ss_pred chhHHHHHHHHHHHHhhheeEEeeeeccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCC
Q 023152 14 VLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSS 93 (286)
Q Consensus 14 ~~g~~~~~~v~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~ 93 (286)
++|++..+.+..++....-......|.| ..+..+...-+.|-+...|++++|+.+++++||++|++|+|+...
T Consensus 14 hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~- 86 (414)
T KOG1314|consen 14 HWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK- 86 (414)
T ss_pred ccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh-
Confidence 4577777766666655443332334555 466777888888888999999999999999999999999986652
Q ss_pred CCCcCcccccCCCCCCCCCCCCCCCCCCCCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHH
Q 023152 94 SSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLF 173 (286)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilF 173 (286)
+..-.+||++|+.+|+||||||+.|||||.||||||||+|||||..||.||..|
T Consensus 87 --------------------------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~F 140 (414)
T KOG1314|consen 87 --------------------------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRF 140 (414)
T ss_pred --------------------------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHH
Confidence 234578999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHh----hcccc--CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcch
Q 023152 174 LLYTFLETTMDTLVLL----PSFIKFF----GKAKN--HSSSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTS 243 (286)
Q Consensus 174 l~~~~~~~~~~~~~~~----~~~~~~~----~~~~~--~~~~~~~~~~~~l~~~l~~~~~l~~~~l~~~h~~li~~n~TT 243 (286)
|++..+.|+-.++.+. ..++..| ..+.. ...++.+++..++++.++++..++++.|++.|+..|.+|+|.
T Consensus 141 Llf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~ 220 (414)
T KOG1314|consen 141 LLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTG 220 (414)
T ss_pred HHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 9999887765443332 2333333 22111 112234555566666666667777788899999999999999
Q ss_pred HHHHhh------------c--CCCCCCCchhHHHHHhhhCCCC
Q 023152 244 IEVYEK------------K--RTVRWKYDLGRKKNFEQVYPVQ 272 (286)
Q Consensus 244 ~E~~~~------------~--~~~~~~yd~G~~~N~~~vfG~~ 272 (286)
||.+.. + .....|||+|++.|++|||-.+
T Consensus 221 IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~ 263 (414)
T KOG1314|consen 221 IESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQN 263 (414)
T ss_pred hHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhc
Confidence 998741 1 1245699999999999999765
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=8.5e-45 Score=325.43 Aligned_cols=167 Identities=33% Similarity=0.616 Sum_probs=132.4
Q ss_pred CCCCCCCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023152 117 ARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFF 196 (286)
Q Consensus 117 ~~~~~~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~ 196 (286)
.++...+.+||.+|+.+||||||||+.||+||+||||||||+|||||++|||+|+.|++++.+.+++........+....
T Consensus 106 ~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~ 185 (299)
T KOG1311|consen 106 VNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRA 185 (299)
T ss_pred cCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34677889999999999999999999999999999999999999999999999999999998888887776665554433
Q ss_pred hcc-ccCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhh-cCCCC-CCCchhHHHHHhhhCCC
Q 023152 197 GKA-KNHS--SSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK-KRTVR-WKYDLGRKKNFEQVYPV 271 (286)
Q Consensus 197 ~~~-~~~~--~~~~~~~~~~l~~~l~~~~~l~~~~l~~~h~~li~~n~TT~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~ 271 (286)
... .... ..+......++..++++.+...+++|+.+|++++.+|+||+|.+++ +...+ ++||+|.++|++++||.
T Consensus 186 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~ 265 (299)
T KOG1311|consen 186 DNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGG 265 (299)
T ss_pred ccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCC
Confidence 221 1112 2223333344444566666777778999999999999999999874 32334 89999999999999999
Q ss_pred Cc-cceEEeccCC
Q 023152 272 QL-HLWLQELQNE 283 (286)
Q Consensus 272 ~~-~~W~~P~~~~ 283 (286)
+. ..|+-|...+
T Consensus 266 ~~~~~~~~p~~~~ 278 (299)
T KOG1311|consen 266 PLPLSWLSPFARS 278 (299)
T ss_pred CCCcccccccccC
Confidence 74 7898887754
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=1.4e-42 Score=287.67 Aligned_cols=173 Identities=30% Similarity=0.592 Sum_probs=124.6
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCcCCCCCcCcccccCCCCCCCCCCCCCCCCCCCCeeccccccCCCCCCCccCcccCccc
Q 023152 69 WSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCV 148 (286)
Q Consensus 69 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~R~hHC~~C~~CV 148 (286)
++|+++.++|||++|+....+.+... +.+.+.. ......+.+...+.++|.+|+..||+|||||+.||+||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~---~~~~~~~------~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 72 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQE---EKEEEQN------QSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCV 72 (174)
T ss_pred EEehhhheECCcccCCcccccccccc---ccccccc------hhhhhhccccCCCCEECcccCCcCCCcceecccccccc
Confidence 56889999999999986221111110 0000000 01111233567889999999999999999999999999
Q ss_pred cCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 023152 149 LKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLC 228 (286)
Q Consensus 149 ~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l~~~~ 228 (286)
++|||||||+|||||++|||+|++|+++..+.+++.....+..+....................++.++++++++++++.
T Consensus 73 ~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (174)
T PF01529_consen 73 LRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGF 152 (174)
T ss_pred ccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999888877766666554433222111111111113444556667777888
Q ss_pred HHHHHHHHHhcCcchHHHHhhc
Q 023152 229 FIVMHSSLVSSNTTSIEVYEKK 250 (286)
Q Consensus 229 l~~~h~~li~~n~TT~E~~~~~ 250 (286)
+++.|++++++|+||+|.+++|
T Consensus 153 l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 153 LLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHcCCcHHHHHHcC
Confidence 9999999999999999999875
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2.3e-40 Score=278.71 Aligned_cols=159 Identities=33% Similarity=0.662 Sum_probs=118.8
Q ss_pred CCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc--
Q 023152 122 RSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKA-- 199 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~-- 199 (286)
....+|.+|+.+||||+||||.||+||+||||||||+|||||.+|||||++|++|+.+++.+..+...+.+++.....
T Consensus 100 ~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~ 179 (309)
T KOG1313|consen 100 ENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE 179 (309)
T ss_pred ccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh
Confidence 345799999999999999999999999999999999999999999999999999999999997766555454432111
Q ss_pred -ccCCCC------ChhHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHh----hcC----CCCC
Q 023152 200 -KNHSSS------PANLA---------IVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYE----KKR----TVRW 255 (286)
Q Consensus 200 -~~~~~~------~~~~~---------~~~l~~~l~~~~~l~~~~l~~~h~~li~~n~TT~E~~~----~~~----~~~~ 255 (286)
.....+ |..+. -+..+.++++.+.++++.+..||.++|.+|.|++|... +|+ ..+|
T Consensus 180 ~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~ 259 (309)
T KOG1313|consen 180 ITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSN 259 (309)
T ss_pred cccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCC
Confidence 111000 11110 11223345555667777888999999999999999863 221 2478
Q ss_pred CCchhHHHHHhhhCCCC--ccce---EEec
Q 023152 256 KYDLGRKKNFEQVYPVQ--LHLW---LQEL 280 (286)
Q Consensus 256 ~yd~G~~~N~~~vfG~~--~~~W---~~P~ 280 (286)
||+.|.++||+.++|-. +-.| ++|-
T Consensus 260 ~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt 289 (309)
T KOG1313|consen 260 PTNFGGKANWRNFLGLFRGRHFWKTVLLPT 289 (309)
T ss_pred CcccchHHHHHHhhccccCCceeEEEeccc
Confidence 99999999999999964 4456 4554
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=2.3e-39 Score=288.51 Aligned_cols=204 Identities=32% Similarity=0.579 Sum_probs=148.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCcCcccccCCCCCCCCCCCCCCCCCCCCeeccccccCCC
Q 023152 55 SIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGK 134 (286)
Q Consensus 55 ~~~~~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~k 134 (286)
+..+.+.+.+.+...+|++.+++|||+.+++-.....+ +..+ +....+..+..++|.+|+.+|
T Consensus 57 ~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~------~~~~-----------~~~~~~~~~~~~~C~~C~~~K 119 (309)
T COG5273 57 LFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYR------ETIS-----------RLLDDGKFGTENFCSTCNIYK 119 (309)
T ss_pred hhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchh------hhhh-----------hhhhcCccccceecccccccc
Confidence 44556666777888999999999999998642221111 1001 112336778899999999999
Q ss_pred CCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCChhH-HHHH
Q 023152 135 PPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANL-AIVF 213 (286)
Q Consensus 135 P~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 213 (286)
|||||||+.||+||+||||||||+|||||++|||+|++||+++.....+........+...+. ....+... ..++
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~li 195 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFS----IRHDTSLAICFLI 195 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc----ccCChHHHHHHHH
Confidence 999999999999999999999999999999999999999999877776665554444433332 11222222 1122
Q ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhhcCC-------------------------CCCCCchhHHHHHhh
Q 023152 214 LA-FVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEKKRT-------------------------VRWKYDLGRKKNFEQ 267 (286)
Q Consensus 214 l~-~~l~~~~~l~~~~l~~~h~~li~~n~TT~E~~~~~~~-------------------------~~~~yd~G~~~N~~~ 267 (286)
.+ ..+...+.+.+..++.+|.+++..|+|+.|.++..+. ..+|+|.|.-+|++.
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 275 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLST 275 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCcccccee
Confidence 22 2334444556667888999999999999998764321 124778888999999
Q ss_pred hCCCCccceEEe
Q 023152 268 VYPVQLHLWLQE 279 (286)
Q Consensus 268 vfG~~~~~W~~P 279 (286)
++|.....|..|
T Consensus 276 i~~~~~~~~~~~ 287 (309)
T COG5273 276 IKGSNALYWLTP 287 (309)
T ss_pred ecCCCceeeccc
Confidence 999999999998
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=5.5e-32 Score=229.26 Aligned_cols=165 Identities=26% Similarity=0.438 Sum_probs=103.6
Q ss_pred HHHHHHHHHHhhcCCCCCCCC-CCCCCcCCCCCcCcccccCCCCCCCCCCCCCCCCCCCCeeccccccCCCCCCCccCcc
Q 023152 65 VMLVWSYVMVVFWDPGSVPEN-WRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSV 143 (286)
Q Consensus 65 ~~~~~~y~~~~~~dPG~vp~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~R~hHC~~ 143 (286)
++=..++..+..+|||.+.+. +....+ .-|.+ ...-.+...|++|+..||.|++|||.
T Consensus 109 ivp~i~f~ltc~snpg~i~k~n~s~~~~-----------~ypYD----------y~if~k~~kCSTCki~KPARSKHCsi 167 (341)
T KOG1312|consen 109 IVPLIFFTLTCGSNPGIITKANESLFLH-----------VYPYD----------YVIFPKNVKCSTCKIRKPARSKHCSI 167 (341)
T ss_pred HHHHHHHhhhhcCCCCccchhhhcccee-----------ccCcc----------ceeecCCCccccccCCCccccccchH
Confidence 334455677899999998752 211111 11111 01112337899999999999999999
Q ss_pred cCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCC--CC--------ChhHH-HH
Q 023152 144 CQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHS--SS--------PANLA-IV 212 (286)
Q Consensus 144 C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--------~~~~~-~~ 212 (286)
|||||.|+||||.|+|||||.+|.|||++||++...++.+++..+........++..... .+ ...++ .+
T Consensus 168 CNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g~~ks~~~L~~yl 247 (341)
T KOG1312|consen 168 CNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHGHVKSTVFLIQYL 247 (341)
T ss_pred HHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeeeecchhhHHHHHHHH
Confidence 999999999999999999999999999999999877777766555433222222211100 00 01111 11
Q ss_pred HHHHH-----HHHHH-HHHHHHHHHHHHHHHhcCcchHHHHhhc
Q 023152 213 FLAFV-----INLAF-ALSLLCFIVMHSSLVSSNTTSIEVYEKK 250 (286)
Q Consensus 213 ~l~~~-----l~~~~-~l~~~~l~~~h~~li~~n~TT~E~~~~~ 250 (286)
++++. ++... ..++++...+-+++-++|+||.|...++
T Consensus 248 ~la~~~~v~~l~~~~~~~~~~~Y~~f~~y~~~t~~~~~~W~~~d 291 (341)
T KOG1312|consen 248 FLAFPRIVFMLGFVVVLSFLGGYLLFVLYLAATNQTTNEWYRGD 291 (341)
T ss_pred HHHhccceeeeehhhhhhHhHHHHHHHHHHHhccCCchhhhccc
Confidence 11110 11111 1123445667788889999999998654
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=5e-28 Score=225.42 Aligned_cols=140 Identities=30% Similarity=0.525 Sum_probs=93.3
Q ss_pred eccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCC
Q 023152 125 GFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSS 204 (286)
Q Consensus 125 ~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (286)
++|.+|...||.|+|||+.|||||.++||||||++||||.+|||+|+.|++.+...+.+...... .++...+.. .
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~----~y~~~~~~~-~ 495 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCL----YYIMNLENA-S 495 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHH----HHHhhcchh-H
Confidence 79999999999999999999999999999999999999999999999999887665554443322 222221110 0
Q ss_pred CChhHHHHHHHHHHHHHH---------H-------HHHHHHHHHHHHHHhcCcchHHHHhhcC---------CCCCCCch
Q 023152 205 SPANLAIVFLAFVINLAF---------A-------LSLLCFIVMHSSLVSSNTTSIEVYEKKR---------TVRWKYDL 259 (286)
Q Consensus 205 ~~~~~~~~~l~~~l~~~~---------~-------l~~~~l~~~h~~li~~n~TT~E~~~~~~---------~~~~~yd~ 259 (286)
... ..++.++..+.. . ......-..|-..++.+.||+|.++.++ ..+.|++.
T Consensus 496 --~~~-~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~ 572 (600)
T KOG0509|consen 496 --TIY-VGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSP 572 (600)
T ss_pred --HHH-HHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCc
Confidence 000 011111110000 0 0000011234445788999999987543 24679999
Q ss_pred hHHHHHhhhCCCC
Q 023152 260 GRKKNFEQVYPVQ 272 (286)
Q Consensus 260 G~~~N~~~vfG~~ 272 (286)
|+++|+.+++=.+
T Consensus 573 g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 573 GPIRNLVDFFLCS 585 (600)
T ss_pred hhhhcchheeecc
Confidence 9999999998654
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=94.66 E-value=1.4 Score=39.54 Aligned_cols=58 Identities=24% Similarity=0.359 Sum_probs=36.4
Q ss_pred CCccCcccCccccCccccccccccccccC-----------cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023152 137 RCHHCSVCQRCVLKMDHHCVWVVNCVGAR-----------NYKSFLLFLLYTFLETTMDTLVLLPSFIK 194 (286)
Q Consensus 137 R~hHC~~C~~CV~~~DHHCpwi~nCIG~~-----------N~r~FilFl~~~~~~~~~~~~~~~~~~~~ 194 (286)
+.++|..|+.-+...-|||+.=|+||-+. -+|-+-.|+.+++...+.........++.
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~ 180 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYE 180 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777777777778888778877665 35677777766553333333333333333
No 10
>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=93.55 E-value=1.7 Score=35.33 Aligned_cols=58 Identities=26% Similarity=0.412 Sum_probs=40.4
Q ss_pred CCCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHH
Q 023152 121 SRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLL 189 (286)
Q Consensus 121 ~~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~~~~ 189 (286)
..+.+.|+.|+.--..+-|||.--|.||-+--| +.+=.|+++..-..+.........+
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~~~~ 116 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSLYYL 116 (174)
T ss_pred CCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678999998888999999999999887666 3444677766555555544433333
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.93 E-value=0.31 Score=25.95 Aligned_cols=21 Identities=19% Similarity=0.683 Sum_probs=17.9
Q ss_pred ccccccCCCCCCCccCcccCc
Q 023152 126 FCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 126 ~C~~C~~~kP~R~hHC~~C~~ 146 (286)
||.+|...-++.+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688899888889999988875
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=86.74 E-value=0.39 Score=30.32 Aligned_cols=25 Identities=28% Similarity=0.630 Sum_probs=22.3
Q ss_pred CCeeccccccCCCCCCCccCcccCc
Q 023152 122 RSVGFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
.....|.+|...-|+|+..|+.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3567899999999999999999875
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.16 E-value=0.84 Score=24.97 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=18.8
Q ss_pred eeccccccCCCCCCCccCcccCc
Q 023152 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 124 ~~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
.++|..|...-++.++.|..||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 36789999887888888888874
No 14
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=81.97 E-value=0.82 Score=45.53 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=18.5
Q ss_pred eeccccccCCCC-------CCCccCcccCc
Q 023152 124 VGFCDRCQNGKP-------PRCHHCSVCQR 146 (286)
Q Consensus 124 ~~~C~~C~~~kP-------~R~hHC~~C~~ 146 (286)
...|..|+..-. -|-||||.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999997664 39999999987
No 15
>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=74.91 E-value=1.3 Score=30.26 Aligned_cols=27 Identities=33% Similarity=0.591 Sum_probs=13.2
Q ss_pred CeeccccccCC--CCCCCccCcccCcccc
Q 023152 123 SVGFCDRCQNG--KPPRCHHCSVCQRCVL 149 (286)
Q Consensus 123 ~~~~C~~C~~~--kP~R~hHC~~C~~CV~ 149 (286)
+...|..|+.. --.|-|||+.||+-|=
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 34577777733 3478999999998653
No 16
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=71.41 E-value=0.95 Score=28.68 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=21.7
Q ss_pred CCeeccccccCCCCCCCccCcccCc
Q 023152 122 RSVGFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
...+.|.+|...-|+|+-.|+.|+.
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccC
Confidence 3467899999999999999998865
No 17
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=70.09 E-value=2.7 Score=40.93 Aligned_cols=54 Identities=6% Similarity=-0.128 Sum_probs=46.6
Q ss_pred CCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHH
Q 023152 122 RSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLY 176 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~ 176 (286)
.-...|.+|....+.+..++..+-.+...+++||+|+. +|+..|-..|-...+.
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~ 376 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFII 376 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHH
Confidence 34567899999999999999999999999999999999 9999998866555443
No 18
>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=69.80 E-value=2.3 Score=27.89 Aligned_cols=36 Identities=33% Similarity=0.923 Sum_probs=26.4
Q ss_pred ccccccCCCCCC-------CccCcccCccccCc-ccccccccccccc
Q 023152 126 FCDRCQNGKPPR-------CHHCSVCQRCVLKM-DHHCVWVVNCVGA 164 (286)
Q Consensus 126 ~C~~C~~~kP~R-------~hHC~~C~~CV~~~-DHHCpwi~nCIG~ 164 (286)
-|..|+.--|+- ++-|..|..|+..+ +++|| ||=|.
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 366666555544 37799999999999 99998 66553
No 19
>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=68.25 E-value=3 Score=22.88 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=17.9
Q ss_pred eccccccCCCCCCCccCcccCc
Q 023152 125 GFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 125 ~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
+.|..|...-|.-+.-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688899888888888888874
No 20
>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 COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=66.75 E-value=24 Score=31.87 Aligned_cols=52 Identities=23% Similarity=0.388 Sum_probs=39.8
Q ss_pred CCeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHH
Q 023152 122 RSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMD 184 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~ 184 (286)
.+...|+.|+.=-...-|||.--|+||-+--| +=.=.|++++....+..++.
T Consensus 121 ~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~ 172 (309)
T COG5273 121 PRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLS 172 (309)
T ss_pred CCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999999988665 55667888875555444433
No 22
>PF12773 DZR: Double zinc ribbon
Probab=66.33 E-value=5.7 Score=25.11 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=18.7
Q ss_pred eeccccccCCCC---CCCccCcccCccccCcccccc
Q 023152 124 VGFCDRCQNGKP---PRCHHCSVCQRCVLKMDHHCV 156 (286)
Q Consensus 124 ~~~C~~C~~~kP---~R~hHC~~C~~CV~~~DHHCp 156 (286)
.++|..|...-+ .....|..|+.=+...+.+|+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 456666665544 334556666665555555554
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=64.28 E-value=3.2 Score=26.71 Aligned_cols=25 Identities=28% Similarity=0.782 Sum_probs=17.0
Q ss_pred CeeccccccCCCCCCCccCcc--cCcc
Q 023152 123 SVGFCDRCQNGKPPRCHHCSV--CQRC 147 (286)
Q Consensus 123 ~~~~C~~C~~~kP~R~hHC~~--C~~C 147 (286)
....|.+|...-|+|+-.|+. ||.+
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 467899999999999999998 8754
No 24
>PF12773 DZR: Double zinc ribbon
Probab=62.45 E-value=5.8 Score=25.07 Aligned_cols=25 Identities=28% Similarity=0.805 Sum_probs=21.8
Q ss_pred CCCeeccccccCCCCCCCccCcccC
Q 023152 121 SRSVGFCDRCQNGKPPRCHHCSVCQ 145 (286)
Q Consensus 121 ~~~~~~C~~C~~~kP~R~hHC~~C~ 145 (286)
.....+|..|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 4456899999999999999999986
No 25
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=57.25 E-value=3.3 Score=38.75 Aligned_cols=27 Identities=44% Similarity=0.968 Sum_probs=21.4
Q ss_pred CCCeeccccccCC--CCCCCccCcccCcc
Q 023152 121 SRSVGFCDRCQNG--KPPRCHHCSVCQRC 147 (286)
Q Consensus 121 ~~~~~~C~~C~~~--kP~R~hHC~~C~~C 147 (286)
.....+|+.|... ---|-||||-||+-
T Consensus 177 Ds~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 177 DSSVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred CCcccccccccchhhhHHHhhhhhhcchH
Confidence 3467899999944 45689999999984
No 26
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=54.70 E-value=1.7e+02 Score=26.53 Aligned_cols=28 Identities=25% Similarity=0.449 Sum_probs=16.0
Q ss_pred ccccccCCCCCCCccCcccCccccCccc
Q 023152 126 FCDRCQNGKPPRCHHCSVCQRCVLKMDH 153 (286)
Q Consensus 126 ~C~~C~~~kP~R~hHC~~C~~CV~~~DH 153 (286)
-|+.|+.=--..-|||.--++||--.++
T Consensus 125 HCsvC~rCvLKmDHHCpWi~nCVgf~Ny 152 (307)
T KOG1315|consen 125 HCSVCNRCVLKMDHHCPWINNCVGFRNY 152 (307)
T ss_pred cchhhhhhhhccccCCcceeceecccch
Confidence 4555554444455777777777664443
No 27
>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=51.90 E-value=9.5 Score=24.65 Aligned_cols=22 Identities=36% Similarity=0.745 Sum_probs=14.4
Q ss_pred ccccccCC--CCCCCccCcccCcc
Q 023152 126 FCDRCQNG--KPPRCHHCSVCQRC 147 (286)
Q Consensus 126 ~C~~C~~~--kP~R~hHC~~C~~C 147 (286)
-|..|... .-.|.|||+.||+-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 45555521 35678999998874
No 28
>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=46.81 E-value=7.6 Score=21.77 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=8.5
Q ss_pred ccccccCCCCC-CCccCcccCc
Q 023152 126 FCDRCQNGKPP-RCHHCSVCQR 146 (286)
Q Consensus 126 ~C~~C~~~kP~-R~hHC~~C~~ 146 (286)
.|..|+..... ..++|..|+-
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 57777766655 7788888764
No 29
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=46.24 E-value=8.6 Score=33.04 Aligned_cols=14 Identities=21% Similarity=0.195 Sum_probs=10.6
Q ss_pred ccccCccccccccc
Q 023152 146 RCVLKMDHHCVWVV 159 (286)
Q Consensus 146 ~CV~~~DHHCpwi~ 159 (286)
.=..+.+|||||..
T Consensus 36 eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 36 EHRSYESHHCPKGL 49 (250)
T ss_pred ccchHhhcCCCccc
Confidence 34678899999864
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=46.10 E-value=13 Score=25.19 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=19.9
Q ss_pred CCCeeccccccCCC----CCCCccCcccCcc
Q 023152 121 SRSVGFCDRCQNGK----PPRCHHCSVCQRC 147 (286)
Q Consensus 121 ~~~~~~C~~C~~~k----P~R~hHC~~C~~C 147 (286)
....+.|+.|.... ..|.++|..||.-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCE
Confidence 34678899998664 4477889988874
No 31
>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=43.46 E-value=5.7 Score=23.42 Aligned_cols=8 Identities=50% Similarity=1.310 Sum_probs=4.9
Q ss_pred eccccccC
Q 023152 125 GFCDRCQN 132 (286)
Q Consensus 125 ~~C~~C~~ 132 (286)
++|.+|+.
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 57777773
No 32
>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=42.76 E-value=7.3 Score=21.84 Aligned_cols=22 Identities=23% Similarity=0.537 Sum_probs=13.7
Q ss_pred eccccccCCCCCCCccCcccCc
Q 023152 125 GFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 125 ~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
-.|..|...-+++..+|..|+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--
T ss_pred ccCCCCcCCchHHhhhhhCcCC
Confidence 4577777777777777777763
No 33
>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=39.77 E-value=21 Score=20.06 Aligned_cols=27 Identities=30% Similarity=0.762 Sum_probs=15.5
Q ss_pred ccccccCCCCCC-CccCcccCccccCccccc
Q 023152 126 FCDRCQNGKPPR-CHHCSVCQRCVLKMDHHC 155 (286)
Q Consensus 126 ~C~~C~~~kP~R-~hHC~~C~~CV~~~DHHC 155 (286)
+|..|...-... .+||+.|+ ..+|-.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~---f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC---FTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC---CeEcCcc
Confidence 466666555555 67777666 4444443
No 34
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=39.33 E-value=70 Score=30.40 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=6.4
Q ss_pred ccCcccCcccc
Q 023152 139 HHCSVCQRCVL 149 (286)
Q Consensus 139 hHC~~C~~CV~ 149 (286)
..|..|++|+.
T Consensus 255 ~~Ci~Cg~Cid 265 (434)
T TIGR02745 255 LECINCGLCID 265 (434)
T ss_pred hhChhhhHHHH
Confidence 34666666654
No 35
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=39.02 E-value=78 Score=27.15 Aligned_cols=28 Identities=29% Similarity=0.386 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 023152 57 IILFHILLVMLVWSYVMVVFWDPGSVPE 84 (286)
Q Consensus 57 ~~~f~~l~~~~~~~y~~~~~~dPG~vp~ 84 (286)
+++..++.+.++..|..|--+|||....
T Consensus 197 liVitl~vf~LvgLyr~C~k~dPg~p~~ 224 (259)
T PF07010_consen 197 LIVITLSVFTLVGLYRMCWKTDPGTPEN 224 (259)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCccc
Confidence 3444556666667788899999997443
No 36
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=37.35 E-value=13 Score=36.61 Aligned_cols=25 Identities=32% Similarity=0.619 Sum_probs=18.7
Q ss_pred CCeeccccccCC--CCCCCccCcccCc
Q 023152 122 RSVGFCDRCQNG--KPPRCHHCSVCQR 146 (286)
Q Consensus 122 ~~~~~C~~C~~~--kP~R~hHC~~C~~ 146 (286)
....-|.+|... ---|.|||+.||+
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccccceeeeeeeeccccccccccch
Confidence 344678999833 3349999999998
No 37
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=37.32 E-value=2.6e+02 Score=24.84 Aligned_cols=53 Identities=23% Similarity=0.422 Sum_probs=38.6
Q ss_pred CeeccccccCCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHHHHHHHHHHHHHH
Q 023152 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTL 186 (286)
Q Consensus 123 ~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl~~~~~~~~~~~~ 186 (286)
...-|+.|+.---.=-|||.--|.||--..| +=.=.|+.++.-...+..++..
T Consensus 115 rTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~~~ 167 (309)
T KOG1313|consen 115 RTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIMCV 167 (309)
T ss_pred CcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHHHH
Confidence 3456888875545556999999999998887 4566788888776666665544
No 38
>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=37.08 E-value=3.7e+02 Score=25.45 Aligned_cols=16 Identities=31% Similarity=0.575 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 023152 168 KSFLLFLLYTFLETTM 183 (286)
Q Consensus 168 r~FilFl~~~~~~~~~ 183 (286)
.||.+|-+|+.+..=.
T Consensus 171 nyFalFTlyvam~IEf 186 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEF 186 (512)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4899999998776543
No 39
>PLN00186 ribosomal protein S26; Provisional
Probab=34.46 E-value=16 Score=27.45 Aligned_cols=19 Identities=32% Similarity=0.546 Sum_probs=14.3
Q ss_pred CCccCcccCccccCccccc
Q 023152 137 RCHHCSVCQRCVLKMDHHC 155 (286)
Q Consensus 137 R~hHC~~C~~CV~~~DHHC 155 (286)
+.-||..|++||.+----+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIK 37 (109)
T ss_pred cceeeCCCcccccccceEE
Confidence 3457999999999855544
No 40
>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=34.34 E-value=15 Score=20.96 Aligned_cols=22 Identities=36% Similarity=0.931 Sum_probs=9.5
Q ss_pred eeccccccCC-CCC---CCccCcccC
Q 023152 124 VGFCDRCQNG-KPP---RCHHCSVCQ 145 (286)
Q Consensus 124 ~~~C~~C~~~-kP~---R~hHC~~C~ 145 (286)
.+||.+|... ++. ++..|..|+
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 4688888854 333 444455444
No 41
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.89 E-value=23 Score=23.84 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=20.1
Q ss_pred eeccccccCCCCCCCccCcccCc
Q 023152 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 124 ~~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
.+-|.+|+..-|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 35699999999999999999986
No 42
>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=33.77 E-value=4.1e+02 Score=24.99 Aligned_cols=32 Identities=16% Similarity=0.393 Sum_probs=22.9
Q ss_pred eeccccccC-CCCCCCccCcccCccccCccccc
Q 023152 124 VGFCDRCQN-GKPPRCHHCSVCQRCVLKMDHHC 155 (286)
Q Consensus 124 ~~~C~~C~~-~kP~R~hHC~~C~~CV~~~DHHC 155 (286)
..-|..|+. .+|....||..|+.-..+..++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 456999997 46666678888888766655544
No 43
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=33.44 E-value=25 Score=22.53 Aligned_cols=24 Identities=29% Similarity=0.624 Sum_probs=15.0
Q ss_pred CeeccccccC-C--CCCCCccCcccCc
Q 023152 123 SVGFCDRCQN-G--KPPRCHHCSVCQR 146 (286)
Q Consensus 123 ~~~~C~~C~~-~--kP~R~hHC~~C~~ 146 (286)
..++|++|.. . .-....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3468999986 3 2223567777764
No 44
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=33.38 E-value=4.2e+02 Score=25.04 Aligned_cols=33 Identities=15% Similarity=0.298 Sum_probs=24.7
Q ss_pred CeeccccccCCCCCCCccCcccCccccCccccc
Q 023152 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHC 155 (286)
Q Consensus 123 ~~~~C~~C~~~kP~R~hHC~~C~~CV~~~DHHC 155 (286)
...-|..|+..-|....||..||.-..+.+++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 456799999887777778888888766655544
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.81 E-value=24 Score=22.25 Aligned_cols=7 Identities=57% Similarity=1.654 Sum_probs=3.5
Q ss_pred ccccccC
Q 023152 126 FCDRCQN 132 (286)
Q Consensus 126 ~C~~C~~ 132 (286)
+|.+|..
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 4555543
No 46
>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=32.61 E-value=21 Score=25.98 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=9.1
Q ss_pred Ccccccccccccc
Q 023152 150 KMDHHCVWVVNCV 162 (286)
Q Consensus 150 ~~DHHCpwi~nCI 162 (286)
.+-.||||++.-.
T Consensus 53 eHr~~CPwv~~~~ 65 (91)
T PF08600_consen 53 EHREYCPWVNPST 65 (91)
T ss_pred cccccCCccCCcc
Confidence 3446899998743
No 47
>PHA02942 putative transposase; Provisional
Probab=32.48 E-value=28 Score=32.49 Aligned_cols=26 Identities=31% Similarity=0.577 Sum_probs=20.0
Q ss_pred CCCeeccccccCCCC---CCCccCcccCc
Q 023152 121 SRSVGFCDRCQNGKP---PRCHHCSVCQR 146 (286)
Q Consensus 121 ~~~~~~C~~C~~~kP---~R~hHC~~C~~ 146 (286)
....+.|+.|....+ .|.+.|..||.
T Consensus 322 ~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 322 SYSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 346789999997644 47888988886
No 48
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=32.40 E-value=18 Score=26.55 Aligned_cols=21 Identities=29% Similarity=0.483 Sum_probs=16.0
Q ss_pred CCccCcccCccccCccccccc
Q 023152 137 RCHHCSVCQRCVLKMDHHCVW 157 (286)
Q Consensus 137 R~hHC~~C~~CV~~~DHHCpw 157 (286)
+.-+|..|++||.+----+.+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEE
Confidence 455799999999987665543
No 49
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=32.02 E-value=16 Score=34.79 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=16.9
Q ss_pred CeeccccccCC--CCCCCccCcccCc
Q 023152 123 SVGFCDRCQNG--KPPRCHHCSVCQR 146 (286)
Q Consensus 123 ~~~~C~~C~~~--kP~R~hHC~~C~~ 146 (286)
.-..|..|+.+ ---|-|||+.||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 44567777754 2237899999987
No 50
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=31.25 E-value=17 Score=32.40 Aligned_cols=28 Identities=29% Similarity=0.494 Sum_probs=18.2
Q ss_pred CeeccccccC---CCCCCCccCcccCccccC
Q 023152 123 SVGFCDRCQN---GKPPRCHHCSVCQRCVLK 150 (286)
Q Consensus 123 ~~~~C~~C~~---~kP~R~hHC~~C~~CV~~ 150 (286)
+..-|..|.. ---.|=|||+.||+-|-.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 3455666664 234577999999886554
No 51
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=30.81 E-value=19 Score=27.00 Aligned_cols=20 Identities=35% Similarity=0.507 Sum_probs=14.7
Q ss_pred CCccCcccCccccCcccccc
Q 023152 137 RCHHCSVCQRCVLKMDHHCV 156 (286)
Q Consensus 137 R~hHC~~C~~CV~~~DHHCp 156 (286)
+.-||..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIKR 38 (108)
T ss_pred ccEEeCCccccccccceEEE
Confidence 34579999999998555443
No 52
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.67 E-value=36 Score=34.11 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=15.8
Q ss_pred eccccccCCCCCCCccCcccCc
Q 023152 125 GFCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 125 ~~C~~C~~~kP~R~hHC~~C~~ 146 (286)
+.|.+|...-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 5677777777777777777766
No 53
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=27.91 E-value=30 Score=36.43 Aligned_cols=40 Identities=35% Similarity=0.555 Sum_probs=27.4
Q ss_pred Ceecccccc--CCCCCCCccCcccCccccCccccccccccccccCcHHHHHHHH
Q 023152 123 SVGFCDRCQ--NGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFL 174 (286)
Q Consensus 123 ~~~~C~~C~--~~kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~FilFl 174 (286)
+..-|..|+ ..--.|-||||.||+- + |-.--|.|.++.|+
T Consensus 556 e~pncm~clqkft~ikrrhhcRacgkV-l-----------cgvccnek~~leyl 597 (1287)
T KOG1841|consen 556 EAPNCMDCLQKFTPIKRRHHCRACGKV-L-----------CGVCCNEKSALEYL 597 (1287)
T ss_pred cCchHHHHHhhcccccccccchhccce-e-----------ehhhcchhhhhhhc
Confidence 445677776 5566799999999983 1 22234777887777
No 54
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=27.62 E-value=21 Score=30.59 Aligned_cols=19 Identities=32% Similarity=0.719 Sum_probs=15.1
Q ss_pred CCCCCCccCcccCccccCc
Q 023152 133 GKPPRCHHCSVCQRCVLKM 151 (286)
Q Consensus 133 ~kP~R~hHC~~C~~CV~~~ 151 (286)
+++.+..||..|+.|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 4566666999999999874
No 55
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.60 E-value=29 Score=26.39 Aligned_cols=24 Identities=21% Similarity=0.598 Sum_probs=17.3
Q ss_pred CeeccccccCCCCCCCcc---CcccCc
Q 023152 123 SVGFCDRCQNGKPPRCHH---CSVCQR 146 (286)
Q Consensus 123 ~~~~C~~C~~~kP~R~hH---C~~C~~ 146 (286)
..-+|..|+..-|...++ |..||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 456899999877665444 887774
No 56
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.59 E-value=35 Score=22.51 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=14.9
Q ss_pred CCeeccccccCCCCCCCcc-CcccC
Q 023152 122 RSVGFCDRCQNGKPPRCHH-CSVCQ 145 (286)
Q Consensus 122 ~~~~~C~~C~~~kP~R~hH-C~~C~ 145 (286)
.....|+.|..++. +|| |..||
T Consensus 25 ~~l~~C~~CG~~~~--~H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKL--PHRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccC--CeEECCCCC
Confidence 34567999996654 466 77776
No 57
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=27.22 E-value=2.4e+02 Score=20.34 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhh
Q 023152 210 AIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK 249 (286)
Q Consensus 210 ~~~~l~~~l~~~~~l~~~~l~~~h~~li~~n~TT~E~~~~ 249 (286)
++.+++|++.+ +.+++++++..|--+++.++.|.++.
T Consensus 47 alSii~FIlG~---vl~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 47 ALSVTCFIVGA---VLLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHhcccCCCceeecccC
Confidence 44555555543 33445677777776777777777654
No 58
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.93 E-value=18 Score=33.47 Aligned_cols=26 Identities=38% Similarity=0.808 Sum_probs=19.3
Q ss_pred CCCCCccCcccCccccCccccccccccccccC
Q 023152 134 KPPRCHHCSVCQRCVLKMDHHCVWVVNCVGAR 165 (286)
Q Consensus 134 kP~R~hHC~~C~~CV~~~DHHCpwi~nCIG~~ 165 (286)
+-.|..||..|+. .|| +|..||||.-
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHHH
Confidence 4456667777765 688 8999999964
No 59
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=26.37 E-value=47 Score=19.05 Aligned_cols=6 Identities=33% Similarity=1.592 Sum_probs=2.6
Q ss_pred cccccc
Q 023152 126 FCDRCQ 131 (286)
Q Consensus 126 ~C~~C~ 131 (286)
+|.+|+
T Consensus 18 ~C~~C~ 23 (32)
T PF13842_consen 18 MCSKCD 23 (32)
T ss_pred EccCCC
Confidence 444443
No 60
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=25.39 E-value=39 Score=22.07 Aligned_cols=21 Identities=24% Similarity=0.649 Sum_probs=14.5
Q ss_pred CeeccccccCCCCCCCcc-CcccC
Q 023152 123 SVGFCDRCQNGKPPRCHH-CSVCQ 145 (286)
Q Consensus 123 ~~~~C~~C~~~kP~R~hH-C~~C~ 145 (286)
....|..|.. +-++|| |..||
T Consensus 25 ~l~~C~~cG~--~~~~H~vc~~cG 46 (55)
T TIGR01031 25 TLVVCPNCGE--FKLPHRVCPSCG 46 (55)
T ss_pred cceECCCCCC--cccCeeECCccC
Confidence 4556888885 446677 77776
No 61
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.77 E-value=38 Score=17.94 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=14.3
Q ss_pred ccccccCCCCCCCccCcccCc
Q 023152 126 FCDRCQNGKPPRCHHCSVCQR 146 (286)
Q Consensus 126 ~C~~C~~~kP~R~hHC~~C~~ 146 (286)
.|..|.....++...|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477777777777777777653
No 62
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=24.23 E-value=28 Score=26.45 Aligned_cols=21 Identities=29% Similarity=0.494 Sum_probs=13.3
Q ss_pred CCccCcccCccccCccccccc
Q 023152 137 RCHHCSVCQRCVLKMDHHCVW 157 (286)
Q Consensus 137 R~hHC~~C~~CV~~~DHHCpw 157 (286)
+.-||..|++||.+----..+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKRF 39 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEEE
T ss_pred cCEeeCcccccCcCCceEEEE
Confidence 456899999999986655543
No 63
>PRK02935 hypothetical protein; Provisional
Probab=23.94 E-value=3.2e+02 Score=20.54 Aligned_cols=17 Identities=29% Similarity=0.303 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHhhhee
Q 023152 17 YFMILLVAAIIAVSYYA 33 (286)
Q Consensus 17 ~~~~~~v~~~i~~~~~~ 33 (286)
.+...++++.++.+|-+
T Consensus 14 t~aL~lvfiG~~vMy~G 30 (110)
T PRK02935 14 TFALSLVFIGFIVMYLG 30 (110)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444444555555544
No 64
>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=22.69 E-value=23 Score=22.48 Aligned_cols=16 Identities=31% Similarity=0.945 Sum_probs=11.0
Q ss_pred cccCccccCccccccc
Q 023152 142 SVCQRCVLKMDHHCVW 157 (286)
Q Consensus 142 ~~C~~CV~~~DHHCpw 157 (286)
..|+.|+...|-+|.|
T Consensus 6 ~sC~~Cl~~~dp~CgW 21 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGW 21 (51)
T ss_dssp SSHHHHHHSTCTTEEE
T ss_pred CcHHHHHcCCCcCccc
Confidence 5666777777767776
No 65
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=21.98 E-value=59 Score=24.08 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=16.7
Q ss_pred eeccccccCCCCCCCccCcccCcc
Q 023152 124 VGFCDRCQNGKPPRCHHCSVCQRC 147 (286)
Q Consensus 124 ~~~C~~C~~~kP~R~hHC~~C~~C 147 (286)
.+-|..|+..++.....=..|..|
T Consensus 3 lrAC~~C~~I~~~~qf~~~gCpnC 26 (98)
T cd07973 3 LRACLLCSLIKTEDQFERDGCPNC 26 (98)
T ss_pred CchhccCCcccccccccCCCCCCC
Confidence 467999999999776544444444
No 66
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=21.92 E-value=25 Score=20.61 Aligned_cols=24 Identities=29% Similarity=0.560 Sum_probs=13.3
Q ss_pred CCCeeccccccCC-CCCCCccCcccC
Q 023152 121 SRSVGFCDRCQNG-KPPRCHHCSVCQ 145 (286)
Q Consensus 121 ~~~~~~C~~C~~~-kP~R~hHC~~C~ 145 (286)
....+.|..|..+ -||| ..|..|+
T Consensus 8 ~l~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp -EEEEE-TTT--EEES---SEETTTT
T ss_pred EEEEEEcCCCCCEecCCC-cCCCCcC
Confidence 3456789999977 6666 7777775
No 67
>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=21.59 E-value=49 Score=20.87 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=17.9
Q ss_pred CCeeccccccCCC---CCCCccCcccCcc
Q 023152 122 RSVGFCDRCQNGK---PPRCHHCSVCQRC 147 (286)
Q Consensus 122 ~~~~~C~~C~~~k---P~R~hHC~~C~~C 147 (286)
..+.+|..|+..- .....+|+.|+.-
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 4567999999665 5667889998643
No 68
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=21.35 E-value=1.8e+02 Score=16.63 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=10.3
Q ss_pred HHHHHhhcCCCCCC
Q 023152 70 SYVMVVFWDPGSVP 83 (286)
Q Consensus 70 ~y~~~~~~dPG~vp 83 (286)
.++...++||-.++
T Consensus 17 iFFAIfFRepPri~ 30 (31)
T PRK11875 17 LFFAIAFRDPPKID 30 (31)
T ss_pred HHHhhhccCCCCCC
Confidence 35677889997765
No 69
>CHL00031 psbT photosystem II protein T
Probab=21.23 E-value=1.8e+02 Score=16.82 Aligned_cols=15 Identities=27% Similarity=0.689 Sum_probs=11.4
Q ss_pred HHHHHhhcCCCCCCC
Q 023152 70 SYVMVVFWDPGSVPE 84 (286)
Q Consensus 70 ~y~~~~~~dPG~vp~ 84 (286)
.++...++||=.+++
T Consensus 17 lFFAI~FRePPri~k 31 (33)
T CHL00031 17 IFFAIFFREPPKVPT 31 (33)
T ss_pred HHHhheecCCCCCCC
Confidence 356788899988765
No 70
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=21.15 E-value=90 Score=25.24 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=27.3
Q ss_pred hcCcchHHHHhhcCCCCCCCchhHHHHHhhhCCCC
Q 023152 238 SSNTTSIEVYEKKRTVRWKYDLGRKKNFEQVYPVQ 272 (286)
Q Consensus 238 ~~n~TT~E~~~~~~~~~~~yd~G~~~N~~~vfG~~ 272 (286)
-+|.|+.|.++.- +.++.-|+++.+..+||.+
T Consensus 103 etg~TsyelIK~~---rgg~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 103 ETGSTSYELIKEL---RGGWRAFWYQTFAWLFGIS 134 (157)
T ss_pred hcCCcHHHHHHHh---hCChhHHHHHHHHHHhCcc
Confidence 4899999998654 4588999999999999975
No 71
>COG3477 Predicted periplasmic/secreted protein [Function unknown]
Probab=20.69 E-value=1.4e+02 Score=24.19 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCcchHHHHhhcCCCCCCCchhHHHHHhhhCCCCccceE
Q 023152 230 IVMHSSLVSSNTTSIEVYEKKRTVRWKYDLGRKKNFEQVYPVQLHLWL 277 (286)
Q Consensus 230 ~~~h~~li~~n~TT~E~~~~~~~~~~~yd~G~~~N~~~vfG~~~~~W~ 277 (286)
+++|+.++=-+.|+ .-++|+-..||+.|+||-=.|.|-
T Consensus 117 ~~~H~ilmP~~~~v----------pplw~~p~~Eh~SEifGHivW~ws 154 (176)
T COG3477 117 LFVHMILMPLMGTV----------PPLWDLPFYEHLSEIFGHIVWFWS 154 (176)
T ss_pred HHHHHHHHHhhccC----------CCcccCcHHHHHHHHHHHHHHHHH
Confidence 45677766444332 236788888999999997666553
No 72
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=20.60 E-value=3.8e+02 Score=25.15 Aligned_cols=15 Identities=33% Similarity=1.001 Sum_probs=12.7
Q ss_pred ccCcccCccccCccccccc
Q 023152 139 HHCSVCQRCVLKMDHHCVW 157 (286)
Q Consensus 139 hHC~~C~~CV~~~DHHCpw 157 (286)
..|..|+.| +|+||.
T Consensus 67 ~~C~~Cg~C----~~~CP~ 81 (389)
T PRK15033 67 NLCHNCGAC----LHACQY 81 (389)
T ss_pred HhCcCcccc----cccCcC
Confidence 489999999 569998
Done!