Query 021223
Match_columns 316
No_of_seqs 187 out of 1777
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 08:34:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021223.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021223hhsearch_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 1.2E-58 2.6E-63 420.7 17.7 254 26-295 13-271 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 2.6E-49 5.7E-54 354.7 13.0 214 57-314 42-280 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 2E-44 4.4E-49 333.6 23.0 179 130-312 108-293 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 2.3E-41 5E-46 289.3 13.5 172 78-260 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 1.1E-40 2.5E-45 290.6 15.0 178 134-314 101-307 (309)
6 COG5273 Uncharacterized protei 100.0 6.1E-39 1.3E-43 295.7 17.1 220 65-313 58-304 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 2.8E-32 6.1E-37 239.3 10.3 172 65-260 100-291 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 1E-27 2.2E-32 231.2 10.5 140 136-282 421-585 (600)
9 PF01529 zf-DHHC: DHHC palmito 94.2 0.89 1.9E-05 38.2 11.4 56 131-197 58-113 (174)
10 KOG1311 DHHC-type Zn-finger pr 90.5 1.6 3.4E-05 40.4 8.7 42 148-189 112-164 (299)
11 PF13240 zinc_ribbon_2: zinc-r 87.5 0.31 6.7E-06 27.0 1.0 21 137-157 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 84.6 0.54 1.2E-05 30.9 1.2 26 132-157 11-36 (48)
13 COG5273 Uncharacterized protei 83.3 3.8 8.3E-05 38.2 6.8 47 132-189 120-166 (309)
14 KOG1315 Predicted DHHC-type Zn 82.7 6.8 0.00015 36.5 8.1 33 132-164 120-152 (307)
15 PF13248 zf-ribbon_3: zinc-rib 82.1 0.74 1.6E-05 26.2 1.0 22 136-157 3-24 (26)
16 PF06906 DUF1272: Protein of u 80.6 0.84 1.8E-05 31.0 1.0 37 136-175 6-50 (57)
17 KOG0509 Ankyrin repeat and DHH 75.9 1.4 3E-05 44.2 1.4 57 133-190 323-379 (600)
18 PTZ00303 phosphatidylinositol 75.0 1.8 3.8E-05 44.7 1.8 23 135-157 460-489 (1374)
19 PHA02680 ORF090 IMV phosphoryl 71.3 29 0.00062 25.9 6.9 37 220-259 47-83 (91)
20 PF12773 DZR: Double zinc ribb 70.3 3.8 8.3E-05 26.9 2.1 35 134-168 11-48 (50)
21 PF10571 UPF0547: Uncharacteri 67.4 3 6.6E-05 23.8 1.0 21 136-156 1-21 (26)
22 COG1552 RPL40A Ribosomal prote 67.2 1.2 2.6E-05 29.3 -0.8 26 132-157 11-36 (50)
23 PF01363 FYVE: FYVE zinc finge 67.1 2.8 6E-05 29.6 1.0 27 134-160 8-36 (69)
24 PF01020 Ribosomal_L40e: Ribos 64.5 3.7 8.1E-05 27.5 1.1 27 132-158 14-42 (52)
25 PF12773 DZR: Double zinc ribb 61.2 5.8 0.00013 26.0 1.6 25 132-156 26-50 (50)
26 smart00064 FYVE Protein presen 55.8 8.2 0.00018 27.0 1.8 25 135-159 10-36 (68)
27 PF00641 zf-RanBP: Zn-finger i 50.1 5.7 0.00012 23.2 0.1 21 137-157 6-26 (30)
28 KOG3183 Predicted Zn-finger pr 48.6 8 0.00017 34.4 0.9 14 157-170 36-49 (250)
29 PF12172 DUF35_N: Rubredoxin-l 47.3 6.9 0.00015 24.0 0.2 23 133-156 9-32 (37)
30 PF07649 C1_3: C1-like domain; 46.9 7.7 0.00017 22.6 0.4 21 137-157 2-23 (30)
31 PF09297 zf-NADH-PPase: NADH p 44.5 9.7 0.00021 22.6 0.5 23 135-157 3-29 (32)
32 KOG1842 FYVE finger-containing 43.4 7.4 0.00016 37.7 -0.2 27 132-158 177-205 (505)
33 PF07282 OrfB_Zn_ribbon: Putat 42.0 16 0.00034 25.7 1.4 27 132-158 25-55 (69)
34 PF02150 RNA_POL_M_15KD: RNA p 40.4 7.3 0.00016 23.8 -0.5 7 136-142 2-8 (35)
35 KOG1398 Uncharacterized conser 40.3 8.2 0.00018 36.8 -0.4 26 144-175 9-34 (460)
36 cd00065 FYVE FYVE domain; Zinc 39.6 19 0.00041 24.0 1.5 23 136-158 3-27 (57)
37 PF08600 Rsm1: Rsm1-like; Int 35.7 19 0.0004 27.2 1.0 10 164-173 56-65 (91)
38 PF03107 C1_2: C1 domain; Int 35.0 26 0.00056 20.4 1.3 20 137-156 2-22 (30)
39 PRK12286 rpmF 50S ribosomal pr 33.8 30 0.00066 23.7 1.7 23 132-156 24-47 (57)
40 COG2093 DNA-directed RNA polym 33.2 23 0.00051 24.7 1.1 23 135-157 4-26 (64)
41 smart00661 RPOL9 RNA polymeras 33.0 23 0.0005 23.2 1.0 7 137-143 2-8 (52)
42 PRK00432 30S ribosomal protein 32.9 26 0.00056 23.3 1.2 24 134-157 19-45 (50)
43 PRK02935 hypothetical protein; 32.7 1.4E+02 0.0029 23.3 5.2 7 136-142 87-93 (110)
44 PLN00186 ribosomal protein S26 30.7 20 0.00044 27.9 0.5 16 148-163 19-34 (109)
45 PF11023 DUF2614: Protein of u 29.6 2.1E+02 0.0046 22.5 5.9 13 29-41 16-28 (114)
46 KOG1818 Membrane trafficking a 29.5 22 0.00048 36.3 0.6 24 134-157 164-189 (634)
47 PRK09335 30S ribosomal protein 29.3 22 0.00047 27.0 0.4 20 148-167 19-38 (95)
48 KOG1729 FYVE finger containing 29.3 16 0.00036 33.7 -0.3 27 134-160 167-196 (288)
49 PHA02942 putative transposase; 29.2 33 0.00072 33.0 1.8 25 133-157 323-350 (383)
50 KOG1819 FYVE finger-containing 29.1 20 0.00043 35.4 0.2 24 134-157 900-925 (990)
51 PF07010 Endomucin: Endomucin; 28.2 1.2E+02 0.0025 27.0 4.7 23 70-92 201-223 (259)
52 KOG1841 Smad anchor for recept 27.4 49 0.0011 36.0 2.7 40 134-185 556-597 (1287)
53 PTZ00172 40S ribosomal protein 27.3 24 0.00052 27.4 0.4 15 149-163 20-34 (108)
54 TIGR00155 pqiA_fam integral me 26.6 6E+02 0.013 24.6 12.0 33 134-166 214-247 (403)
55 PF03842 Silic_transp: Silicon 26.1 5.5E+02 0.012 25.1 9.1 17 179-195 171-187 (512)
56 PRK03681 hypA hydrogenase nick 26.0 34 0.00075 26.9 1.1 26 132-157 67-95 (114)
57 smart00547 ZnF_RBZ Zinc finger 25.5 35 0.00075 18.8 0.8 21 137-157 4-24 (26)
58 PF00751 DM: DM DNA binding do 25.2 25 0.00054 23.1 0.1 15 156-170 12-28 (47)
59 PRK15103 paraquat-inducible me 25.0 6.5E+02 0.014 24.5 11.8 33 134-166 220-252 (419)
60 COG4640 Predicted membrane pro 24.6 37 0.0008 32.6 1.1 24 135-158 1-24 (465)
61 TIGR01031 rpmF_bact ribosomal 23.8 56 0.0012 22.2 1.6 22 133-156 24-46 (55)
62 PF09889 DUF2116: Uncharacteri 22.0 99 0.0021 21.4 2.6 22 136-157 4-26 (59)
63 PF01283 Ribosomal_S26e: Ribos 21.7 34 0.00073 27.0 0.2 20 148-167 19-38 (113)
64 PF00130 C1_1: Phorbol esters/ 21.4 71 0.0015 20.8 1.8 34 133-166 9-50 (53)
65 PRK14559 putative protein seri 21.1 60 0.0013 33.6 2.0 15 264-278 125-139 (645)
66 PRK13130 H/ACA RNA-protein com 20.6 64 0.0014 22.1 1.4 22 134-157 4-25 (56)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-58 Score=420.74 Aligned_cols=254 Identities=40% Similarity=0.736 Sum_probs=203.5
Q ss_pred HHHHHHHHHHHHhheeeeeeeeeccccccCCcchHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCcccccC
Q 021223 26 SVMILVVLGIIGVSYYAVAVAKYGPALFLGGLDSITALFVLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGG 105 (316)
Q Consensus 26 ~~~v~~v~~li~~~~~~~~~~~~~p~l~~~~~~~~~~~~~~i~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~ 105 (316)
+++++++.++++++||+++...+.+....+ ..+.+.+++++.++++.+|+|++++++|||.+|..+.++.++++..
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~----~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~ 88 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISLT----IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSL 88 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhhh----hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccc
Confidence 899999999999999999998887755322 4667788899999999999999999999999999998876654332
Q ss_pred CCCCCCCCCCCCccccccccccccCCCccceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHH
Q 021223 106 AGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFL 185 (316)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL 185 (316)
+..... | ........+..++.|+|.+|+.+|||||||||+|+|||+||||||||+|||||.+|||+|++|+
T Consensus 89 ~~~~~~-~--------~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl 159 (307)
T KOG1315|consen 89 ENGSDN-E--------RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFL 159 (307)
T ss_pred cccCcc-c--------ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHH
Confidence 211100 0 1111233456789999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhhcCC---
Q 021223 186 FYTFLETTLVTVSLLPIFIALFTDDEIPESPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKTS--- 262 (316)
Q Consensus 186 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~~--- 262 (316)
+|+.+++.+..+.....+..++... ...+......+.+.+++.+.+++.+++|+++|++||++|+||+|.++.+.-
T Consensus 160 ~y~~l~~~~~lv~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~ 238 (307)
T KOG1315|consen 160 FYTNLYSIYVLVTTLIGFTKYFQGG-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSG 238 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhcccccccc
Confidence 9999999988887777777766322 222222334445556677888888889999999999999999999987533
Q ss_pred --CCCCCchhHHHHHHHhcCCCccceeeccccCCC
Q 021223 263 --PKWRYDLGWKINFEQVFGKNKKYWLIPAYSKDD 295 (316)
Q Consensus 263 --~~~~yd~G~~~N~~~vfG~~~~~W~~P~~~~~~ 295 (316)
..+.+++ ..|++|+||+++..|++|+.++.+
T Consensus 239 ~~~~~~~~~--~~n~~~vfg~~~~~wl~P~~~s~~ 271 (307)
T KOG1315|consen 239 LHNKNGFNL--YVNFREVFGSNLLYWLLPIDSSWG 271 (307)
T ss_pred ccccCCcce--eecHHHHhCCCceEEeccccCccc
Confidence 3445554 679999999999999999988765
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.6e-49 Score=354.68 Aligned_cols=214 Identities=31% Similarity=0.622 Sum_probs=162.9
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccCCCccce
Q 021223 57 LDSITALFVLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVR 136 (316)
Q Consensus 57 ~~~~~~~~~~i~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 (316)
.++..+....+.|-+...|++++|+.+++++||++|.+|.|+... +..-.+
T Consensus 42 ~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~-----------------------------D~~~lq 92 (414)
T KOG1314|consen 42 LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK-----------------------------DEMFLQ 92 (414)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh-----------------------------hHHHHH
Confidence 455666777778888899999999999999999999999886533 134578
Q ss_pred ecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHh----c
Q 021223 137 FCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSL----LPIFIALF----T 208 (316)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~----~~~~~~~~----~ 208 (316)
||.+|+.+|+||||||+.|||||++|||||||+|||||..||.||..||++..++|+-..+.+ ...++..| .
T Consensus 93 fCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g 172 (414)
T KOG1314|consen 93 FCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYG 172 (414)
T ss_pred HHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999999999999988766433222 11222222 1
Q ss_pred CCCCCC---CCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhhc--------------CCCCCCCchhH
Q 021223 209 DDEIPE---SPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK--------------TSPKWRYDLGW 271 (316)
Q Consensus 209 ~~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~--------------~~~~~~yd~G~ 271 (316)
....+. +...++..++++.++++..+++..|++.|+..|.+|+|.||.+.-+ .....|||+|+
T Consensus 173 ~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgW 252 (414)
T KOG1314|consen 173 LRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGW 252 (414)
T ss_pred cccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccc
Confidence 111111 1122333444445555566667778889999999999999987511 12357999999
Q ss_pred HHHHHHhcCCCccceeeccccCCCCCCCCCCCceeccCCCCCC
Q 021223 272 KINFEQVFGKNKKYWLIPAYSKDDLEWLPSFQCVEYPTRPDSD 314 (316)
Q Consensus 272 ~~N~~~vfG~~~~~W~~P~~~~~~~~~~p~~dG~~~~~~~~~~ 314 (316)
+.|++|||-.+. .+.|||+.||+.++++
T Consensus 253 r~n~r~vf~~~~---------------~~~gdg~~wPv~~gc~ 280 (414)
T KOG1314|consen 253 RINLREVFFQNK---------------KEEGDGIEWPVVEGCV 280 (414)
T ss_pred cccHHHHhhhcc---------------ccCCCCccccccCccc
Confidence 999999997643 2458999999999875
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2e-44 Score=333.64 Aligned_cols=179 Identities=32% Similarity=0.621 Sum_probs=138.1
Q ss_pred CCCccceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 021223 130 PKHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTD 209 (316)
Q Consensus 130 ~~~~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~~ 209 (316)
+...+.+||.+|+.+||||||||+.||+||+||||||||+|||||++|||+|+.|+++..+.+++........+.....+
T Consensus 108 ~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~ 187 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADN 187 (299)
T ss_pred CcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 45678999999999999999999999999999999999999999999999999999999998888877766655543332
Q ss_pred CCC--C--CCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhh-cCCCC-CCCchhHHHHHHHhcCCCc
Q 021223 210 DEI--P--ESPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEK-KTSPK-WRYDLGWKINFEQVFGKNK 283 (316)
Q Consensus 210 ~~~--~--~~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~~~ 283 (316)
... . ..+......++..++++.+.+.+++++.+|+++|.+|+||+|..++ +.+.+ ++||.|..+|++++||.+.
T Consensus 188 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~ 267 (299)
T KOG1311|consen 188 LKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPL 267 (299)
T ss_pred ccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCCCC
Confidence 211 1 1122222333344566667777788999999999999999999884 33334 8999999999999999984
Q ss_pred -cceeeccccCCCCCCCCCCCceeccCCCC
Q 021223 284 -KYWLIPAYSKDDLEWLPSFQCVEYPTRPD 312 (316)
Q Consensus 284 -~~W~~P~~~~~~~~~~p~~dG~~~~~~~~ 312 (316)
+.|.-|...+. ..| .||-.++....
T Consensus 268 ~~~~~~p~~~~~---~~p-~~~~~~~~~~~ 293 (299)
T KOG1311|consen 268 PLSWLSPFARSG---PLP-HDGEGGPPTPH 293 (299)
T ss_pred CcccccccccCC---CCC-CCCCCCCcccc
Confidence 66998876542 223 57766665543
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=2.3e-41 Score=289.29 Aligned_cols=172 Identities=30% Similarity=0.584 Sum_probs=123.1
Q ss_pred HHHhhhcccCCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccCCCccceecccccccCCCCCccCcccCc
Q 021223 78 WSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 78 ~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RahHC~~C~~ 157 (316)
++|++++++|||++|+....+.+.+. +.... ...+.....++...+.++|.+|+..||+|||||+.||+
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~-~~~~~----------~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~ 70 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQE-EKEEE----------QNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNR 70 (174)
T ss_pred EEehhhheECCcccCCcccccccccc-ccccc----------cchhhhhhccccCCCCEECcccCCcCCCcceecccccc
Confidence 57899999999999976221111110 00000 00011112234577899999999999999999999999
Q ss_pred cccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-cchhHHHHHHHHHHHHHHHH
Q 021223 158 CILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESP-GNLAASFITFVLNLAFALSI 236 (316)
Q Consensus 158 CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~ 236 (316)
||+||||||||+|||||++|||+|++|+++..+.+++.....+..+............. ......++.+++++++++++
T Consensus 71 CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (174)
T PF01529_consen 71 CVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFV 150 (174)
T ss_pred ccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998888776665555544332111111 11111144445566777788
Q ss_pred HHHHHHHHHHHhcCcchHhhhhhc
Q 021223 237 LGFLIMHISLVAGNTTTIEAFEKK 260 (316)
Q Consensus 237 ~~l~~~h~~li~~n~TT~E~~~~~ 260 (316)
+++++.|+++|++|+||+|.+|+|
T Consensus 151 ~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 151 GFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHHHcCCcHHHHHHcC
Confidence 889999999999999999999875
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.1e-40 Score=290.59 Aligned_cols=178 Identities=29% Similarity=0.552 Sum_probs=132.1
Q ss_pred cceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---C-
Q 021223 134 GVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFT---D- 209 (316)
Q Consensus 134 ~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~---~- 209 (316)
...+|.+|..+|||||||||.|||||++|||||||+|||||.+|||||++|++|+.+++.+..+...+...+... +
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ 180 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEI 180 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhc
Confidence 357999999999999999999999999999999999999999999999999999999999987765444433211 1
Q ss_pred CCCCC------CCcchh---------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhhcC--------CCCCC
Q 021223 210 DEIPE------SPGNLA---------ASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKT--------SPKWR 266 (316)
Q Consensus 210 ~~~~~------~~~~~~---------~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~--------~~~~~ 266 (316)
..... .|..+. -+.-..+++..+.++++.+..+|.++|.+|.|++|.+...+ ..+||
T Consensus 181 tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~ 260 (309)
T KOG1313|consen 181 TAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNP 260 (309)
T ss_pred ccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCC
Confidence 01111 111111 01123345555667778888999999999999999874321 23689
Q ss_pred CchhHHHHHHHhcCCC--ccceeeccccCCCCCCCCCCCceeccCCCCCC
Q 021223 267 YDLGWKINFEQVFGKN--KKYWLIPAYSKDDLEWLPSFQCVEYPTRPDSD 314 (316)
Q Consensus 267 yd~G~~~N~~~vfG~~--~~~W~~P~~~~~~~~~~p~~dG~~~~~~~~~~ 314 (316)
|+.|.++||+.++|-. +-.|..-.-|+ .+.|.+.|.+||++|..+
T Consensus 261 ~n~g~k~nWr~fLg~~~~r~~wk~v~lPt---~~~p~~~~~~~~~~da~~ 307 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLFRGRHFWKTVLLPT---IRKPVKYGDSKEKSDAYD 307 (309)
T ss_pred cccchHHHHHHhhccccCCceeEEEeccc---cccccccCCcccccchhh
Confidence 9999999999999976 33576422222 356789999999877644
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=6.1e-39 Score=295.66 Aligned_cols=220 Identities=34% Similarity=0.624 Sum_probs=156.5
Q ss_pred HHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccCCCccceeccccccc
Q 021223 65 VLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQF 144 (316)
Q Consensus 65 ~~i~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 144 (316)
..+.+.+.+.+...+|++.+++|||+.+++-.....++..+ ....++..+..++|.+|+.+
T Consensus 58 ~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~C~~C~~~ 118 (309)
T COG5273 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETIS-------------------RLLDDGKFGTENFCSTCNIY 118 (309)
T ss_pred hhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhh-------------------hhhhcCccccceeccccccc
Confidence 34455566778888999999999999985422111111110 11233557789999999999
Q ss_pred CCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcch-hHHH
Q 021223 145 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESPGNL-AASF 223 (316)
Q Consensus 145 kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 223 (316)
||+|||||+.|||||+||||||||+|||||++|||+|++||+++.....+.+......+...+. ....+... ..++
T Consensus 119 KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~li 195 (309)
T COG5273 119 KPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFS---IRHDTSLAICFLI 195 (309)
T ss_pred cCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---ccCChHHHHHHHH
Confidence 9999999999999999999999999999999999999999999877776665554444433221 22222222 1112
Q ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhhcC-------------C------------CCCCCchhHHHHHHH
Q 021223 224 IT-FVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKT-------------S------------PKWRYDLGWKINFEQ 277 (316)
Q Consensus 224 l~-~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~-------------~------------~~~~yd~G~~~N~~~ 277 (316)
.. ..+.+.+.+.+..++.+|.+++..|+||+|..+..+ . ..+|++.|..+|+..
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 275 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLST 275 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCcccccee
Confidence 11 234444556667788899999999999999875421 1 124788889999999
Q ss_pred hcCCCccceeeccccCCCCCCCCCCCceeccCCCCC
Q 021223 278 VFGKNKKYWLIPAYSKDDLEWLPSFQCVEYPTRPDS 313 (316)
Q Consensus 278 vfG~~~~~W~~P~~~~~~~~~~p~~dG~~~~~~~~~ 313 (316)
++|.+...|..|..... .++.+++.|.+.
T Consensus 276 i~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~ 304 (309)
T COG5273 276 IKGSNALYWLTPLHTNY-------CNSYDFSLRSDT 304 (309)
T ss_pred ecCCCceeeccccccCC-------CCccCcccchhh
Confidence 99999999999943221 477778777654
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=2.8e-32 Score=239.27 Aligned_cols=172 Identities=30% Similarity=0.496 Sum_probs=108.1
Q ss_pred HHHHHHHHHHHHHHHHhhhcccCCCCCCCC-CCCCCcccccCCCCCCCCCCCCCccccccccccccCCCc-cceeccccc
Q 021223 65 VLFLFHSLLVMLVWSYFSVVITDPGGVPPN-WIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQ-GVRFCQKCN 142 (316)
Q Consensus 65 ~~i~~~~l~~~~~~sy~~~~~tdPG~vp~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~C~~C~ 142 (316)
..+....+.++-.+++..++.+|||.+.+. +.... ++-| .|.... ....|+||+
T Consensus 100 ~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~-----~~yp-------------------YDy~if~k~~kCSTCk 155 (341)
T KOG1312|consen 100 YLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFL-----HVYP-------------------YDYVIFPKNVKCSTCK 155 (341)
T ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccce-----eccC-------------------ccceeecCCCcccccc
Confidence 333333444555566778999999998742 21111 1111 112222 237899999
Q ss_pred ccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC----------
Q 021223 143 QFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEI---------- 212 (316)
Q Consensus 143 ~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~~~~~---------- 212 (316)
..||+||+|||.|||||.||||||.|+|||||.+|+|||++||++....+.++++........-.++...
T Consensus 156 i~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g 235 (341)
T KOG1312|consen 156 IRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHG 235 (341)
T ss_pred CCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeeeec
Confidence 9999999999999999999999999999999999999999999999877777766554432221221100
Q ss_pred -CCCCcchh-HHHHHH-----HHHHHHHH-HHHHHHHHHHHHHhcCcchHhhhhhc
Q 021223 213 -PESPGNLA-ASFITF-----VLNLAFAL-SILGFLIMHISLVAGNTTTIEAFEKK 260 (316)
Q Consensus 213 -~~~~~~~~-~~~l~~-----~~~~~~~~-~~~~l~~~h~~li~~n~TT~E~~~~~ 260 (316)
..+...+. ..++++ +++....+ ++++...+-+|+-++|+||.|+..++
T Consensus 236 ~~ks~~~L~~yl~la~~~~v~~l~~~~~~~~~~~Y~~f~~y~~~t~~~~~~W~~~d 291 (341)
T KOG1312|consen 236 HVKSTVFLIQYLFLAFPRIVFMLGFVVVLSFLGGYLLFVLYLAATNQTTNEWYRGD 291 (341)
T ss_pred chhhHHHHHHHHHHHhccceeeeehhhhhhHhHHHHHHHHHHHhccCCchhhhccc
Confidence 00000111 111111 11111111 13345567778889999999998764
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=1e-27 Score=231.18 Aligned_cols=140 Identities=28% Similarity=0.449 Sum_probs=94.4
Q ss_pred eecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 021223 136 RFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPES 215 (316)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (316)
++|.+|.+.||.|++||+.|||||.||||||||++||||.+|||+|+.|++.+...+.+.+....+. +........
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y----~~~~~~~~~ 496 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYY----IMNLENAST 496 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHH----HhhcchhHH
Confidence 7999999999999999999999999999999999999999999999999998776666554443322 222111100
Q ss_pred CcchhHHHHHHHHHHHH--HH-------------HHHH-HHHHHHHHHhcCcchHhhhhhcC---------CCCCCCchh
Q 021223 216 PGNLAASFITFVLNLAF--AL-------------SILG-FLIMHISLVAGNTTTIEAFEKKT---------SPKWRYDLG 270 (316)
Q Consensus 216 ~~~~~~~~l~~~~~~~~--~~-------------~~~~-l~~~h~~li~~n~TT~E~~~~~~---------~~~~~yd~G 270 (316)
....++..+..+.. .+ .... -..-|...++.+.||+|.++.++ ..++|++.|
T Consensus 497 ---~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g 573 (600)
T KOG0509|consen 497 ---IYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPG 573 (600)
T ss_pred ---HHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCch
Confidence 00011111100000 00 0000 11234446789999999986532 346899999
Q ss_pred HHHHHHHhcCCC
Q 021223 271 WKINFEQVFGKN 282 (316)
Q Consensus 271 ~~~N~~~vfG~~ 282 (316)
+.+|+.+++-.+
T Consensus 574 ~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 574 PIRNLVDFFLCS 585 (600)
T ss_pred hhhcchheeecc
Confidence 999999987544
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=94.22 E-value=0.89 Score=38.17 Aligned_cols=56 Identities=27% Similarity=0.475 Sum_probs=41.7
Q ss_pred CCccceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHHHHHHHHH
Q 021223 131 KHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTV 197 (316)
Q Consensus 131 ~~~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l~~~~~~~ 197 (316)
+..+.+.|+.|+.--..+-|||..-|+||-+--| +-+-.|+++..-..+...+...
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~ 113 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSL 113 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999998889999999999999987655 5566777777655555554433
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=90.48 E-value=1.6 Score=40.40 Aligned_cols=42 Identities=24% Similarity=0.569 Sum_probs=36.5
Q ss_pred CCccCcccCccccccCccCcccccccccccH-----------HHHHHHHHHHH
Q 021223 148 RCHHCSVCRRCILKMDHHCVWVVNCVGAFNY-----------KYFLLFLFYTF 189 (316)
Q Consensus 148 RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~-----------k~FilFL~~~~ 189 (316)
+.++|..|+..+...-|||+.=|+||-+.-| |-+-.|+.+++
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 5889999999999999999999999988766 67888886665
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.47 E-value=0.31 Score=27.02 Aligned_cols=21 Identities=19% Similarity=0.673 Sum_probs=18.1
Q ss_pred ecccccccCCCCCccCcccCc
Q 021223 137 FCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~~ 157 (316)
+|+.|+..-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688999888899999998874
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=84.62 E-value=0.54 Score=30.85 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=22.8
Q ss_pred CccceecccccccCCCCCccCcccCc
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~~ 157 (316)
......|.+|...-|+|+..|+.||.
T Consensus 11 ~~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 11 VFNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hhcccchhcccCCCCccccccccCCC
Confidence 34568999999999999999998875
No 13
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=83.27 E-value=3.8 Score=38.22 Aligned_cols=47 Identities=21% Similarity=0.358 Sum_probs=26.8
Q ss_pred CccceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHH
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTF 189 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~ 189 (316)
..+.+.|+.|+.=-...-|||.-=|+||-+--| +=.-.|++++....
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~ 166 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVA 166 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHH
Confidence 345566666666556666666666666665333 44455555554433
No 14
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=82.67 E-value=6.8 Score=36.49 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=24.2
Q ss_pred CccceecccccccCCCCCccCcccCccccccCc
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDH 164 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DH 164 (316)
..+...|+.|+.=--..-|||..-|+||---++
T Consensus 120 PdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny 152 (307)
T KOG1315|consen 120 PDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNY 152 (307)
T ss_pred CCccccchhhhhhhhccccCCcceeceecccch
Confidence 445667788875556667999999999986554
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.10 E-value=0.74 Score=26.19 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=18.8
Q ss_pred eecccccccCCCCCccCcccCc
Q 021223 136 RFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~~ 157 (316)
++|..|+..-++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6799999987888999998874
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=80.64 E-value=0.84 Score=31.03 Aligned_cols=37 Identities=32% Similarity=0.841 Sum_probs=27.8
Q ss_pred eecccccccCCCCC-------ccCcccCcccccc-CccCccccccccc
Q 021223 136 RFCQKCNQFKPPRC-------HHCSVCRRCILKM-DHHCVWVVNCVGA 175 (316)
Q Consensus 136 ~~C~~C~~~kP~Ra-------hHC~~C~~CV~r~-DHHCpWl~nCIG~ 175 (316)
.-|..|+..-|+-+ +-|..|..|+..+ +++|| ||=|.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 34666666555543 6789999999999 99999 77664
No 17
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=75.86 E-value=1.4 Score=44.19 Aligned_cols=57 Identities=7% Similarity=-0.074 Sum_probs=48.3
Q ss_pred ccceecccccccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHHHHHHH
Q 021223 133 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFL 190 (316)
Q Consensus 133 ~~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL~~~~l 190 (316)
.-...|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-..|-+..+...+
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l 379 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVL 379 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHH
Confidence 34567889999999999999999999999999999999 9999998876665544333
No 18
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=74.95 E-value=1.8 Score=44.72 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=18.5
Q ss_pred ceecccccccCC-------CCCccCcccCc
Q 021223 135 VRFCQKCNQFKP-------PRCHHCSVCRR 157 (316)
Q Consensus 135 ~~~C~~C~~~kP-------~RahHC~~C~~ 157 (316)
...|..|+..-. -|-|||+.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999996653 39999999987
No 19
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=71.30 E-value=29 Score=25.92 Aligned_cols=37 Identities=16% Similarity=0.347 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhhhh
Q 021223 220 AASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEK 259 (316)
Q Consensus 220 ~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~ 259 (316)
++.++.|++.+. .+++++++..|-=+++.++.|+++.
T Consensus 47 alSii~FIlG~v---l~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 47 ALSVTCFIVGAV---LLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHHH---HHHHHHHHHHhcccCCCceeecccC
Confidence 444555555433 3445677777777888888888765
No 20
>PF12773 DZR: Double zinc ribbon
Probab=70.34 E-value=3.8 Score=26.89 Aligned_cols=35 Identities=20% Similarity=0.435 Sum_probs=22.2
Q ss_pred cceecccccccCC---CCCccCcccCccccccCccCcc
Q 021223 134 GVRFCQKCNQFKP---PRCHHCSVCRRCILKMDHHCVW 168 (316)
Q Consensus 134 ~~~~C~~C~~~kP---~RahHC~~C~~CV~r~DHHCpW 168 (316)
+.++|..|...-+ .....|..|+.=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 3567777775554 3356677777766666666653
No 21
>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=67.38 E-value=3 Score=23.79 Aligned_cols=21 Identities=24% Similarity=0.752 Sum_probs=17.5
Q ss_pred eecccccccCCCCCccCcccC
Q 021223 136 RFCQKCNQFKPPRCHHCSVCR 156 (316)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~ 156 (316)
+.|+.|+..-|.-+.-|..||
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG 21 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCG 21 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCC
Confidence 468889888888888888887
No 22
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=67.16 E-value=1.2 Score=29.31 Aligned_cols=26 Identities=27% Similarity=0.770 Sum_probs=22.3
Q ss_pred CccceecccccccCCCCCccCcccCc
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~~ 157 (316)
....+.|.+|...-|+|+..|+.|+.
T Consensus 11 ~~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 11 LFNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred HhhHHHHHHhcCCCCcchhHHhhccC
Confidence 34568899999999999999998864
No 23
>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=67.12 E-value=2.8 Score=29.59 Aligned_cols=27 Identities=30% Similarity=0.600 Sum_probs=13.3
Q ss_pred cceecccccc--cCCCCCccCcccCcccc
Q 021223 134 GVRFCQKCNQ--FKPPRCHHCSVCRRCIL 160 (316)
Q Consensus 134 ~~~~C~~C~~--~kP~RahHC~~C~~CV~ 160 (316)
+...|..|+. ---.|-|||+.||+-|=
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 4567888863 22478999999998543
No 24
>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=64.48 E-value=3.7 Score=27.47 Aligned_cols=27 Identities=30% Similarity=0.733 Sum_probs=18.0
Q ss_pred CccceecccccccCCCCCccCcc--cCcc
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSV--CRRC 158 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~--C~~C 158 (316)
+.+...|.+|...-|+||..|+. ||.+
T Consensus 14 n~~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 14 NCDKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp HTS-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cccceecccccCcCCCCccceecccCCCC
Confidence 34568999999999999999998 7754
No 25
>PF12773 DZR: Double zinc ribbon
Probab=61.23 E-value=5.8 Score=25.98 Aligned_cols=25 Identities=28% Similarity=0.838 Sum_probs=21.9
Q ss_pred CccceecccccccCCCCCccCcccC
Q 021223 132 HQGVRFCQKCNQFKPPRCHHCSVCR 156 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~ 156 (316)
.....+|..|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456899999999999999999986
No 26
>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=50.11 E-value=5.7 Score=23.15 Aligned_cols=21 Identities=24% Similarity=0.735 Sum_probs=13.5
Q ss_pred ecccccccCCCCCccCcccCc
Q 021223 137 FCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~~ 157 (316)
.|..|...-++++.+|..|+.
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 477777777777777777763
No 28
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=48.57 E-value=8 Score=34.36 Aligned_cols=14 Identities=21% Similarity=0.185 Sum_probs=11.0
Q ss_pred ccccccCccCcccc
Q 021223 157 RCILKMDHHCVWVV 170 (316)
Q Consensus 157 ~CV~r~DHHCpWl~ 170 (316)
.=..+.+|||||..
T Consensus 36 eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 36 EHRSYESHHCPKGL 49 (250)
T ss_pred ccchHhhcCCCccc
Confidence 34678899999974
No 29
>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=47.29 E-value=6.9 Score=24.00 Aligned_cols=23 Identities=30% Similarity=0.793 Sum_probs=13.1
Q ss_pred ccceecccccccC-CCCCccCcccC
Q 021223 133 QGVRFCQKCNQFK-PPRCHHCSVCR 156 (316)
Q Consensus 133 ~~~~~C~~C~~~k-P~RahHC~~C~ 156 (316)
...+.|..|..+. ||| ..|..|+
T Consensus 9 l~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEEEE-TTT--EEES---SEETTTT
T ss_pred EEEEEcCCCCCEecCCC-cCCCCcC
Confidence 3467899999875 777 7777765
No 30
>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=46.87 E-value=7.7 Score=22.61 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=8.9
Q ss_pred ecccccccCCC-CCccCcccCc
Q 021223 137 FCQKCNQFKPP-RCHHCSVCRR 157 (316)
Q Consensus 137 ~C~~C~~~kP~-RahHC~~C~~ 157 (316)
.|..|+..... ..++|+.|+-
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 57778776665 7888888873
No 31
>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=44.52 E-value=9.7 Score=22.58 Aligned_cols=23 Identities=26% Similarity=0.712 Sum_probs=10.9
Q ss_pred ceeccccccc----CCCCCccCcccCc
Q 021223 135 VRFCQKCNQF----KPPRCHHCSVCRR 157 (316)
Q Consensus 135 ~~~C~~C~~~----kP~RahHC~~C~~ 157 (316)
.+||..|... .-.++..|..|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 4788888742 3345666666653
No 32
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=43.37 E-value=7.4 Score=37.70 Aligned_cols=27 Identities=37% Similarity=0.918 Sum_probs=21.0
Q ss_pred Cccceeccccccc--CCCCCccCcccCcc
Q 021223 132 HQGVRFCQKCNQF--KPPRCHHCSVCRRC 158 (316)
Q Consensus 132 ~~~~~~C~~C~~~--kP~RahHC~~C~~C 158 (316)
.....+|+.|... --.|-|||+.||+-
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 3467899999743 36789999999983
No 33
>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=41.98 E-value=16 Score=25.67 Aligned_cols=27 Identities=19% Similarity=0.451 Sum_probs=19.9
Q ss_pred CccceecccccccC----CCCCccCcccCcc
Q 021223 132 HQGVRFCQKCNQFK----PPRCHHCSVCRRC 158 (316)
Q Consensus 132 ~~~~~~C~~C~~~k----P~RahHC~~C~~C 158 (316)
....+.|+.|+... ..|.++|..||.-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCE
Confidence 34678899998654 4578889988764
No 34
>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=40.36 E-value=7.3 Score=23.84 Aligned_cols=7 Identities=57% Similarity=1.716 Sum_probs=3.9
Q ss_pred eeccccc
Q 021223 136 RFCQKCN 142 (316)
Q Consensus 136 ~~C~~C~ 142 (316)
++|++|+
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 4666665
No 35
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.28 E-value=8.2 Score=36.82 Aligned_cols=26 Identities=38% Similarity=0.779 Sum_probs=19.7
Q ss_pred cCCCCCccCcccCccccccCccCccccccccc
Q 021223 144 FKPPRCHHCSVCRRCILKMDHHCVWVVNCVGA 175 (316)
Q Consensus 144 ~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~ 175 (316)
.+-.|..||.+|+. +|| +|..||||.
T Consensus 9 ~sl~~p~l~~tC~e----~~h--~w~~~c~ga 34 (460)
T KOG1398|consen 9 RSLARPSLAETCDE----ADH--SWVANCIGA 34 (460)
T ss_pred hhhcCchHhhhhhh----ccC--CcccchhHH
Confidence 34556678888775 688 899999994
No 36
>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=39.61 E-value=19 Score=24.01 Aligned_cols=23 Identities=35% Similarity=0.759 Sum_probs=14.9
Q ss_pred eecccccc--cCCCCCccCcccCcc
Q 021223 136 RFCQKCNQ--FKPPRCHHCSVCRRC 158 (316)
Q Consensus 136 ~~C~~C~~--~kP~RahHC~~C~~C 158 (316)
+-|..|+. -.-.|.|||+.||+-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCCccccccCcCcCC
Confidence 34566652 235678999998874
No 37
>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=35.66 E-value=19 Score=27.18 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=8.0
Q ss_pred ccCccccccc
Q 021223 164 HHCVWVVNCV 173 (316)
Q Consensus 164 HHCpWl~nCI 173 (316)
.||||++.-.
T Consensus 56 ~~CPwv~~~~ 65 (91)
T PF08600_consen 56 EYCPWVNPST 65 (91)
T ss_pred ccCCccCCcc
Confidence 6899998754
No 38
>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=35.00 E-value=26 Score=20.43 Aligned_cols=20 Identities=30% Similarity=0.680 Sum_probs=13.1
Q ss_pred ecccccccCCCC-CccCcccC
Q 021223 137 FCQKCNQFKPPR-CHHCSVCR 156 (316)
Q Consensus 137 ~C~~C~~~kP~R-ahHC~~C~ 156 (316)
.|..|...-... .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 466676555555 77887776
No 39
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.81 E-value=30 Score=23.68 Aligned_cols=23 Identities=35% Similarity=0.868 Sum_probs=16.3
Q ss_pred CccceecccccccCCCCCcc-CcccC
Q 021223 132 HQGVRFCQKCNQFKPPRCHH-CSVCR 156 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahH-C~~C~ 156 (316)
......|+.|+..+.+ || |..||
T Consensus 24 ~~~l~~C~~CG~~~~~--H~vC~~CG 47 (57)
T PRK12286 24 APGLVECPNCGEPKLP--HRVCPSCG 47 (57)
T ss_pred CCcceECCCCCCccCC--eEECCCCC
Confidence 3456789999977644 66 77776
No 40
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.18 E-value=23 Score=24.69 Aligned_cols=23 Identities=26% Similarity=0.845 Sum_probs=20.2
Q ss_pred ceecccccccCCCCCccCcccCc
Q 021223 135 VRFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 135 ~~~C~~C~~~kP~RahHC~~C~~ 157 (316)
.+-|..|+..-|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 36699999999999999999986
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.00 E-value=23 Score=23.16 Aligned_cols=7 Identities=57% Similarity=1.621 Sum_probs=3.8
Q ss_pred ecccccc
Q 021223 137 FCQKCNQ 143 (316)
Q Consensus 137 ~C~~C~~ 143 (316)
+|+.|+.
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 5556653
No 42
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=32.86 E-value=26 Score=23.31 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=15.3
Q ss_pred cceecccccc-cC--CCCCccCcccCc
Q 021223 134 GVRFCQKCNQ-FK--PPRCHHCSVCRR 157 (316)
Q Consensus 134 ~~~~C~~C~~-~k--P~RahHC~~C~~ 157 (316)
..++|+.|.. .. -....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 4579999986 22 223567777763
No 43
>PRK02935 hypothetical protein; Provisional
Probab=32.74 E-value=1.4e+02 Score=23.28 Aligned_cols=7 Identities=43% Similarity=1.132 Sum_probs=3.0
Q ss_pred eeccccc
Q 021223 136 RFCQKCN 142 (316)
Q Consensus 136 ~~C~~C~ 142 (316)
..|-.|+
T Consensus 87 D~CM~C~ 93 (110)
T PRK02935 87 DACMHCN 93 (110)
T ss_pred eecCcCC
Confidence 3444444
No 44
>PLN00186 ribosomal protein S26; Provisional
Probab=30.72 E-value=20 Score=27.87 Aligned_cols=16 Identities=31% Similarity=0.762 Sum_probs=12.5
Q ss_pred CCccCcccCccccccC
Q 021223 148 RCHHCSVCRRCILKMD 163 (316)
Q Consensus 148 RahHC~~C~~CV~r~D 163 (316)
+.-||..|++||.+=-
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (109)
T PLN00186 19 KRIRCSNCGKCVPKDK 34 (109)
T ss_pred cceeeCCCcccccccc
Confidence 3458999999999733
No 45
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=29.61 E-value=2.1e+02 Score=22.51 Aligned_cols=13 Identities=15% Similarity=0.148 Sum_probs=5.6
Q ss_pred HHHHHHHHHhhee
Q 021223 29 ILVVLGIIGVSYY 41 (316)
Q Consensus 29 v~~v~~li~~~~~ 41 (316)
..++++.++..|-
T Consensus 16 l~lif~g~~vmy~ 28 (114)
T PF11023_consen 16 LSLIFIGMIVMYI 28 (114)
T ss_pred HHHHHHHHHHHhh
Confidence 3444444444443
No 46
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.47 E-value=22 Score=36.26 Aligned_cols=24 Identities=29% Similarity=0.657 Sum_probs=17.7
Q ss_pred cceeccccccc--CCCCCccCcccCc
Q 021223 134 GVRFCQKCNQF--KPPRCHHCSVCRR 157 (316)
Q Consensus 134 ~~~~C~~C~~~--kP~RahHC~~C~~ 157 (316)
...-|.+|... ---|.|||+.||+
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccccceeeeeeeeccccccccccch
Confidence 34678888732 1349999999998
No 47
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=29.30 E-value=22 Score=27.04 Aligned_cols=20 Identities=25% Similarity=0.561 Sum_probs=15.1
Q ss_pred CCccCcccCccccccCccCc
Q 021223 148 RCHHCSVCRRCILKMDHHCV 167 (316)
Q Consensus 148 RahHC~~C~~CV~r~DHHCp 167 (316)
+.-+|..|++||++---.+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 35589999999998555554
No 48
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=29.30 E-value=16 Score=33.66 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=15.9
Q ss_pred cceecccccc-cC--CCCCccCcccCcccc
Q 021223 134 GVRFCQKCNQ-FK--PPRCHHCSVCRRCIL 160 (316)
Q Consensus 134 ~~~~C~~C~~-~k--P~RahHC~~C~~CV~ 160 (316)
+..-|..|.. .. -.|-|||+.||+-|-
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC 196 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVC 196 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhh
Confidence 3455666654 22 456777777776443
No 49
>PHA02942 putative transposase; Provisional
Probab=29.16 E-value=33 Score=33.03 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=19.2
Q ss_pred ccceecccccccCC---CCCccCcccCc
Q 021223 133 QGVRFCQKCNQFKP---PRCHHCSVCRR 157 (316)
Q Consensus 133 ~~~~~C~~C~~~kP---~RahHC~~C~~ 157 (316)
...+.|+.|+...+ .|.+.|..||-
T Consensus 323 yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 323 YSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 46789999996654 47888988875
No 50
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=29.11 E-value=20 Score=35.37 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=17.3
Q ss_pred cceecccccccC--CCCCccCcccCc
Q 021223 134 GVRFCQKCNQFK--PPRCHHCSVCRR 157 (316)
Q Consensus 134 ~~~~C~~C~~~k--P~RahHC~~C~~ 157 (316)
....|..|+..- -.|-|||+.||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 345688887542 457899999986
No 51
>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=28.17 E-value=1.2e+02 Score=27.02 Aligned_cols=23 Identities=30% Similarity=0.213 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHhhhcccCCCCCC
Q 021223 70 HSLLVMLVWSYFSVVITDPGGVP 92 (316)
Q Consensus 70 ~~l~~~~~~sy~~~~~tdPG~vp 92 (316)
.++.+.++-.|..|.-+|||...
T Consensus 201 tl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 201 TLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHhhcCCCCCcc
Confidence 33444444557789999999643
No 52
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=27.35 E-value=49 Score=35.99 Aligned_cols=40 Identities=30% Similarity=0.478 Sum_probs=26.9
Q ss_pred cceeccccc--ccCCCCCccCcccCccccccCccCcccccccccccHHHHHHHH
Q 021223 134 GVRFCQKCN--QFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFL 185 (316)
Q Consensus 134 ~~~~C~~C~--~~kP~RahHC~~C~~CV~r~DHHCpWl~nCIG~~N~k~FilFL 185 (316)
...-|..|. ..--.|-|||+.||+- =|-.--|-|.+.-|+
T Consensus 556 e~pncm~clqkft~ikrrhhcRacgkV------------lcgvccnek~~leyl 597 (1287)
T KOG1841|consen 556 EAPNCMDCLQKFTPIKRRHHCRACGKV------------LCGVCCNEKSALEYL 597 (1287)
T ss_pred cCchHHHHHhhcccccccccchhccce------------eehhhcchhhhhhhc
Confidence 345566666 4557799999999982 122335677777776
No 53
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=27.33 E-value=24 Score=27.42 Aligned_cols=15 Identities=40% Similarity=0.782 Sum_probs=12.1
Q ss_pred CccCcccCccccccC
Q 021223 149 CHHCSVCRRCILKMD 163 (316)
Q Consensus 149 ahHC~~C~~CV~r~D 163 (316)
.-||..|++||.+=-
T Consensus 20 ~V~C~nCgr~vPKDK 34 (108)
T PTZ00172 20 PVRCSNCGRCVPKDK 34 (108)
T ss_pred cEEeCCccccccccc
Confidence 458999999999733
No 54
>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=26.61 E-value=6e+02 Score=24.64 Aligned_cols=33 Identities=18% Similarity=0.483 Sum_probs=21.6
Q ss_pred cceecccccc-cCCCCCccCcccCccccccCccC
Q 021223 134 GVRFCQKCNQ-FKPPRCHHCSVCRRCILKMDHHC 166 (316)
Q Consensus 134 ~~~~C~~C~~-~kP~RahHC~~C~~CV~r~DHHC 166 (316)
...-|+.|+. .+|....||..|+.-..+..++.
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 3556999997 45555667777777655544443
No 55
>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=26.13 E-value=5.5e+02 Score=25.13 Aligned_cols=17 Identities=29% Similarity=0.680 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 021223 179 KYFLLFLFYTFLETTLV 195 (316)
Q Consensus 179 k~FilFL~~~~l~~~~~ 195 (316)
-||.+|.+|+.+..=+.
T Consensus 171 nyFalFTlyvam~IEfs 187 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFS 187 (512)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 48999999987765543
No 56
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.97 E-value=34 Score=26.87 Aligned_cols=26 Identities=19% Similarity=0.678 Sum_probs=18.4
Q ss_pred CccceecccccccCCCCCcc---CcccCc
Q 021223 132 HQGVRFCQKCNQFKPPRCHH---CSVCRR 157 (316)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahH---C~~C~~ 157 (316)
....-+|..|+..-|...++ |..||.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 34567899999877665444 888874
No 57
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.52 E-value=35 Score=18.84 Aligned_cols=21 Identities=19% Similarity=0.515 Sum_probs=14.6
Q ss_pred ecccccccCCCCCccCcccCc
Q 021223 137 FCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~~ 157 (316)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477777777777777777753
No 58
>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=25.24 E-value=25 Score=23.14 Aligned_cols=15 Identities=13% Similarity=0.124 Sum_probs=5.9
Q ss_pred CccccccCc--cCcccc
Q 021223 156 RRCILKMDH--HCVWVV 170 (316)
Q Consensus 156 ~~CV~r~DH--HCpWl~ 170 (316)
|.=+..-+| .|||-+
T Consensus 12 G~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 12 GVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp T---TTTT-GGG-TTTT
T ss_pred CcccchhhhccccCcCC
Confidence 344555566 688754
No 59
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=25.04 E-value=6.5e+02 Score=24.54 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=23.6
Q ss_pred cceecccccccCCCCCccCcccCccccccCccC
Q 021223 134 GVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHC 166 (316)
Q Consensus 134 ~~~~C~~C~~~kP~RahHC~~C~~CV~r~DHHC 166 (316)
...-|+.|+..-|....||..|+.-..+..++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 456799999887777778888877665544443
No 60
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.56 E-value=37 Score=32.62 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=20.5
Q ss_pred ceecccccccCCCCCccCcccCcc
Q 021223 135 VRFCQKCNQFKPPRCHHCSVCRRC 158 (316)
Q Consensus 135 ~~~C~~C~~~kP~RahHC~~C~~C 158 (316)
.++|.+|+..+-+-+..|..||.=
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~ 24 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHK 24 (465)
T ss_pred CCcccccccccccccccccccCCc
Confidence 378999999999999889988863
No 61
>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=23.85 E-value=56 Score=22.16 Aligned_cols=22 Identities=32% Similarity=0.866 Sum_probs=15.3
Q ss_pred ccceecccccccCCCCCcc-CcccC
Q 021223 133 QGVRFCQKCNQFKPPRCHH-CSVCR 156 (316)
Q Consensus 133 ~~~~~C~~C~~~kP~RahH-C~~C~ 156 (316)
.....|+.|+.++ ++|| |..||
T Consensus 24 p~l~~C~~cG~~~--~~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFK--LPHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCcc--cCeeECCccC
Confidence 4556799998644 5666 77776
No 62
>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=22.00 E-value=99 Score=21.38 Aligned_cols=22 Identities=36% Similarity=0.907 Sum_probs=15.6
Q ss_pred eecccccccCCCCCccCc-ccCc
Q 021223 136 RFCQKCNQFKPPRCHHCS-VCRR 157 (316)
Q Consensus 136 ~~C~~C~~~kP~RahHC~-~C~~ 157 (316)
+.|..|+..-|+--..|| .|+.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 568888877777777775 5554
No 63
>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=21.71 E-value=34 Score=26.95 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=12.6
Q ss_pred CCccCcccCccccccCccCc
Q 021223 148 RCHHCSVCRRCILKMDHHCV 167 (316)
Q Consensus 148 RahHC~~C~~CV~r~DHHCp 167 (316)
+.-||..|++||++---...
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKR 38 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEE
T ss_pred cCEeeCcccccCcCCceEEE
Confidence 35689999999998555443
No 64
>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=21.42 E-value=71 Score=20.80 Aligned_cols=34 Identities=26% Similarity=0.714 Sum_probs=22.5
Q ss_pred ccceecccccccC---CCCCccCcccCc-----cccccCccC
Q 021223 133 QGVRFCQKCNQFK---PPRCHHCSVCRR-----CILKMDHHC 166 (316)
Q Consensus 133 ~~~~~C~~C~~~k---P~RahHC~~C~~-----CV~r~DHHC 166 (316)
..+.+|..|+..- .....+|+.|+. |..+.+.-|
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 4578999998654 667888999974 555555444
No 65
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.14 E-value=60 Score=33.57 Aligned_cols=15 Identities=0% Similarity=-0.398 Sum_probs=8.9
Q ss_pred CCCCchhHHHHHHHh
Q 021223 264 KWRYDLGWKINFEQV 278 (316)
Q Consensus 264 ~~~yd~G~~~N~~~v 278 (316)
..|+.....+++.+-
T Consensus 125 ~~p~~~s~~~~~~~~ 139 (645)
T PRK14559 125 CQPLQPSPLEALLEQ 139 (645)
T ss_pred cCCCccCHHHHHHHH
Confidence 456666666666444
No 66
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=20.57 E-value=64 Score=22.06 Aligned_cols=22 Identities=32% Similarity=0.779 Sum_probs=15.5
Q ss_pred cceecccccccCCCCCccCcccCc
Q 021223 134 GVRFCQKCNQFKPPRCHHCSVCRR 157 (316)
Q Consensus 134 ~~~~C~~C~~~kP~RahHC~~C~~ 157 (316)
..+.|..|+.+-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4678888887666 566777764
Done!