Query 022940
Match_columns 289
No_of_seqs 171 out of 1717
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 07:16:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022940hhsearch_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 4.7E-57 1E-61 402.5 15.6 248 26-287 13-263 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 2E-47 4.3E-52 336.3 10.3 197 57-282 42-263 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 7.9E-45 1.7E-49 329.8 20.9 155 130-284 108-268 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 1.2E-42 2.6E-47 291.5 12.9 171 78-260 2-174 (174)
5 COG5273 Uncharacterized protei 100.0 4.3E-39 9.3E-44 290.9 15.7 202 64-287 57-285 (309)
6 KOG1313 DHHC-type Zn-finger pr 100.0 2.1E-39 4.5E-44 277.6 12.7 149 133-281 100-275 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 2.1E-32 4.6E-37 235.7 10.5 167 71-260 106-291 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 3.5E-29 7.5E-34 236.7 6.9 140 136-280 421-583 (600)
9 PF01529 zf-DHHC: DHHC palmito 92.0 1.7 3.7E-05 35.7 9.6 58 131-199 58-115 (174)
10 KOG1311 DHHC-type Zn-finger pr 90.4 1.6 3.4E-05 39.6 8.5 42 148-189 112-164 (299)
11 PRK04136 rpl40e 50S ribosomal 88.6 0.25 5.4E-06 31.8 1.2 26 132-157 11-36 (48)
12 PF13240 zinc_ribbon_2: zinc-r 88.1 0.27 5.9E-06 26.7 1.0 21 137-157 1-21 (23)
13 PF13248 zf-ribbon_3: zinc-rib 83.7 0.61 1.3E-05 26.1 1.1 22 136-157 3-24 (26)
14 COG5273 Uncharacterized protei 82.9 4.1 8.9E-05 37.3 6.7 54 131-195 119-172 (309)
15 PHA02680 ORF090 IMV phosphoryl 82.4 10 0.00023 27.7 7.2 38 220-260 47-84 (91)
16 PTZ00303 phosphatidylinositol 79.5 1.1 2.4E-05 45.3 1.9 23 135-157 460-489 (1374)
17 COG1552 RPL40A Ribosomal prote 79.4 0.52 1.1E-05 30.4 -0.3 26 132-157 11-36 (50)
18 KOG0509 Ankyrin repeat and DHH 77.3 1.3 2.8E-05 43.6 1.6 58 133-191 323-380 (600)
19 PF01363 FYVE: FYVE zinc finge 73.0 1.9 4.1E-05 29.8 1.2 27 134-160 8-36 (69)
20 PF10571 UPF0547: Uncharacteri 72.0 2.1 4.6E-05 24.0 1.0 22 136-157 1-22 (26)
21 PF01020 Ribosomal_L40e: Ribos 70.1 1.8 3.9E-05 28.4 0.4 27 132-158 14-42 (52)
22 PF12773 DZR: Double zinc ribb 69.5 4.2 9.1E-05 26.1 2.2 34 134-167 11-47 (50)
23 PF06906 DUF1272: Protein of u 67.0 2.8 6.1E-05 28.0 0.9 37 136-175 6-50 (57)
24 PF12773 DZR: Double zinc ribb 66.5 4.2 9.1E-05 26.2 1.7 25 132-156 26-50 (50)
25 smart00064 FYVE Protein presen 62.6 5.5 0.00012 27.4 1.8 25 135-159 10-36 (68)
26 KOG3183 Predicted Zn-finger pr 51.9 6.6 0.00014 34.2 0.8 12 159-170 38-49 (250)
27 PF00641 zf-RanBP: Zn-finger i 50.7 4.6 0.0001 23.1 -0.2 20 137-156 6-25 (30)
28 PF12172 DUF35_N: Rubredoxin-l 50.2 5.2 0.00011 24.1 -0.0 24 132-156 8-32 (37)
29 KOG1398 Uncharacterized conser 50.2 4.8 0.0001 37.6 -0.3 25 145-175 10-34 (460)
30 PF09297 zf-NADH-PPase: NADH p 49.0 8.2 0.00018 22.4 0.7 23 135-157 3-29 (32)
31 PF07649 C1_3: C1-like domain; 49.0 7.1 0.00015 22.3 0.4 21 137-157 2-23 (30)
32 KOG1842 FYVE finger-containing 46.2 6.4 0.00014 37.4 -0.1 27 132-158 177-205 (505)
33 PF07010 Endomucin: Endomucin; 45.7 46 0.001 28.9 4.9 25 68-92 199-223 (259)
34 cd00065 FYVE FYVE domain; Zinc 45.1 14 0.0003 24.2 1.4 22 137-158 4-27 (57)
35 PF02150 RNA_POL_M_15KD: RNA p 41.4 6.2 0.00014 23.7 -0.7 7 136-142 2-8 (35)
36 PF07282 OrfB_Zn_ribbon: Putat 40.5 18 0.00038 24.9 1.4 27 132-158 25-55 (69)
37 PRK12286 rpmF 50S ribosomal pr 37.2 22 0.00049 23.9 1.5 24 132-157 24-48 (57)
38 TIGR00155 pqiA_fam integral me 37.2 3.7E+02 0.0081 25.5 12.6 32 134-165 214-246 (403)
39 PRK00432 30S ribosomal protein 36.2 21 0.00045 23.3 1.2 24 134-157 19-45 (50)
40 PF03107 C1_2: C1 domain; Int 35.7 26 0.00057 20.0 1.4 20 137-156 2-22 (30)
41 smart00661 RPOL9 RNA polymeras 35.5 21 0.00045 22.9 1.1 7 137-143 2-8 (52)
42 KOG1818 Membrane trafficking a 35.1 16 0.00034 36.6 0.6 23 135-157 165-189 (634)
43 PLN00186 ribosomal protein S26 35.1 15 0.00033 28.0 0.4 17 148-164 19-35 (109)
44 PF08600 Rsm1: Rsm1-like; Int 34.7 20 0.00043 26.5 1.0 10 164-173 56-65 (91)
45 PRK09335 30S ribosomal protein 34.3 16 0.00035 27.2 0.4 20 148-167 19-38 (95)
46 KOG1819 FYVE finger-containing 34.0 15 0.00032 35.6 0.3 24 134-157 900-925 (990)
47 PF09889 DUF2116: Uncharacteri 33.6 58 0.0013 22.1 3.0 23 135-157 3-26 (59)
48 KOG1729 FYVE finger containing 32.9 11 0.00024 34.1 -0.7 28 134-161 167-197 (288)
49 PTZ00172 40S ribosomal protein 31.9 18 0.0004 27.5 0.4 19 148-166 19-37 (108)
50 COG2093 DNA-directed RNA polym 29.9 28 0.00061 23.8 1.0 23 135-157 4-26 (64)
51 PRK14559 putative protein seri 29.4 34 0.00073 34.7 1.9 22 136-157 28-49 (645)
52 PHA02942 putative transposase; 29.3 34 0.00073 32.3 1.8 25 133-157 323-350 (383)
53 smart00547 ZnF_RBZ Zinc finger 27.7 29 0.00064 18.7 0.7 21 137-157 4-24 (26)
54 PF14803 Nudix_N_2: Nudix N-te 27.3 19 0.00042 21.5 -0.1 11 132-142 19-29 (34)
55 COG0603 Predicted PP-loop supe 26.9 23 0.0005 30.8 0.2 20 144-163 187-206 (222)
56 PF01283 Ribosomal_S26e: Ribos 26.7 25 0.00055 27.1 0.4 20 148-167 19-38 (113)
57 PF01437 PSI: Plexin repeat; 26.5 18 0.00039 23.4 -0.4 16 153-168 6-21 (51)
58 KOG3611 Semaphorins [Signal tr 26.0 28 0.0006 35.8 0.6 39 149-187 491-537 (737)
59 PRK03681 hypA hydrogenase nick 25.9 31 0.00067 26.6 0.7 26 132-157 67-95 (114)
60 PHA02898 virion envelope prote 25.7 2.8E+02 0.006 20.4 7.6 34 220-256 46-80 (92)
61 PRK02935 hypothetical protein; 25.3 2.6E+02 0.0055 21.4 5.5 16 27-42 15-30 (110)
62 TIGR01031 rpmF_bact ribosomal 25.0 45 0.00098 22.2 1.3 23 133-157 24-47 (55)
63 PRK14559 putative protein seri 24.5 40 0.00087 34.1 1.5 41 132-174 12-52 (645)
64 KOG0003 Ubiquitin/60s ribosoma 23.7 14 0.0003 28.1 -1.5 25 133-157 91-115 (128)
65 PF03842 Silic_transp: Silicon 23.4 6.7E+02 0.015 24.1 9.4 17 179-195 171-187 (512)
66 PRK15103 paraquat-inducible me 23.1 6.7E+02 0.015 24.0 13.0 34 133-166 219-252 (419)
67 KOG1841 Smad anchor for recept 22.8 75 0.0016 34.1 3.0 40 134-185 556-597 (1287)
68 COG4640 Predicted membrane pro 22.2 44 0.00095 31.5 1.1 24 135-158 1-24 (465)
69 PRK15033 tricarballylate utili 21.9 3.8E+02 0.0083 25.4 7.2 15 150-168 67-81 (389)
70 smart00423 PSI domain found in 21.8 35 0.00076 21.4 0.3 10 138-147 7-16 (46)
71 PRK10747 putative protoheme IX 21.5 2.4E+02 0.0053 26.4 6.1 47 43-92 27-73 (398)
72 KOG4017 DNA excision repair pr 21.1 28 0.00062 30.6 -0.3 35 132-166 100-138 (274)
73 TIGR00540 hemY_coli hemY prote 20.7 2.2E+02 0.0047 26.8 5.6 17 76-92 57-73 (409)
74 PF14127 DUF4294: Domain of un 20.6 81 0.0018 25.9 2.2 32 248-282 103-134 (157)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.7e-57 Score=402.46 Aligned_cols=248 Identities=38% Similarity=0.673 Sum_probs=199.2
Q ss_pred hHHHHHHHHHHhhheeeeeeeeeccccccCCCchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCcccccc
Q 022940 26 SVMILVVLGIIGVSYYAVAVAKYGPALFLGGLDSITALFVLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGG 105 (289)
Q Consensus 26 ~i~v~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~l~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~ 105 (289)
+++++++.+.+++.||+++...+.+.... ...+.+.+++++.++++.+|+|++++++|||.+|.++.++.++++..
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~----~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~ 88 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISL----TIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSL 88 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhh----hhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccc
Confidence 89999999999999999999888775532 25677888999999999999999999999999999998877654332
Q ss_pred CCCCCCCCCCCCccccccccccccCcccccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHH
Q 022940 106 AGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFL 185 (289)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl 185 (289)
....... + .......++.+..|+|.||+.+|||||||||+|+|||+||||||||+|||||.+|||+|++|+
T Consensus 89 ~~~~~~~--------~-~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl 159 (307)
T KOG1315|consen 89 ENGSDNE--------R-DLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFL 159 (307)
T ss_pred cccCccc--------c-cceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHH
Confidence 2211100 0 111123456789999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhccCCCCC
Q 022940 186 FYTFLETTLVTVSLLPIFIALFTDDEIPESPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKTSPKW 265 (289)
Q Consensus 186 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~~~~~ 265 (289)
+|+.+++.+..+.....+..++... ...++.....+.+.+++++.+++.+++|+++|++||++|+||+|.++......+
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 9999999998888877777777332 233333445555666778888999999999999999999999999987533333
Q ss_pred CCChhH---HHHHHHhCCCCCcccc
Q 022940 266 RYDLGW---KINFEQVIPSQFLMHA 287 (289)
Q Consensus 266 ~yd~G~---~~N~~~vfG~~~~~~~ 287 (289)
.++.+- ..|++|+||+++..|+
T Consensus 239 ~~~~~~~~~~~n~~~vfg~~~~~wl 263 (307)
T KOG1315|consen 239 LHNKNGFNLYVNFREVFGSNLLYWL 263 (307)
T ss_pred ccccCCcceeecHHHHhCCCceEEe
Confidence 344443 5699999999999986
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2e-47 Score=336.33 Aligned_cols=197 Identities=31% Similarity=0.642 Sum_probs=151.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCccccccCCCCCCCCCCCCccccccccccccCcccccc
Q 022940 57 LDSITALFVLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVR 136 (289)
Q Consensus 57 ~~~~~~~~~~~~~~~l~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 (289)
.++..+...-+.|.+...|++++|+.+++++||++|++|.|+..+ +.....
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 455666777788888899999999999999999999999886432 245678
Q ss_pred cccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHH----HHHh----c
Q 022940 137 FCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIF----IALF----T 208 (289)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~----~~~~----~ 208 (289)
||.+|+.+|+||||||+.|||||++|||||||+|||||..||.||..||++..++|+-..+.+.... ...| .
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 9999999999999999999999999999999999999999999999999999997775543322222 2222 1
Q ss_pred CCCCCCC---CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhcc--------------CCCCCCCChhH
Q 022940 209 DDEIPES---PGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK--------------TSPKWRYDLGW 271 (289)
Q Consensus 209 ~~~~~~~---~~~~~~~~l~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~--------------~~~~~~yd~G~ 271 (289)
....+.. +.+++..++++.++++..+.+..|++.|+..|++|+|.||.+..+ .....|||+|+
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 1222222 223344445555566666777778889999999999999987511 12357999999
Q ss_pred HHHHHHhCCCC
Q 022940 272 KINFEQVIPSQ 282 (289)
Q Consensus 272 ~~N~~~vfG~~ 282 (289)
+.|++|||-.+
T Consensus 253 r~n~r~vf~~~ 263 (414)
T KOG1314|consen 253 RINLREVFFQN 263 (414)
T ss_pred cccHHHHhhhc
Confidence 99999999443
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=7.9e-45 Score=329.79 Aligned_cols=155 Identities=32% Similarity=0.629 Sum_probs=125.2
Q ss_pred CcccccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 022940 130 PKHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTD 209 (289)
Q Consensus 130 ~~~~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~ 209 (289)
+...+.++|.+|+..||||||||+.||+||+||||||||+|||||++|||+|++|++++.+.+++........+.....+
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 55678999999999999999999999999999999999999999999999999999999999888877766665543333
Q ss_pred CCCC----CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhc-cCCCC-CCCChhHHHHHHHhCCCCC
Q 022940 210 DEIP----ESPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEK-KTSPK-WRYDLGWKINFEQVIPSQF 283 (289)
Q Consensus 210 ~~~~----~~~~~~~~~~l~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~~~ 283 (289)
.... ..+......++..++++.+.+.+++|+.+|+++|.+|+||+|..+. +...+ ++||+|..+|++++||.+.
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 2222 2222233334444567777777888999999999999999999884 33334 8999999999999998765
Q ss_pred c
Q 022940 284 L 284 (289)
Q Consensus 284 ~ 284 (289)
.
T Consensus 268 ~ 268 (299)
T KOG1311|consen 268 P 268 (299)
T ss_pred C
Confidence 3
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=1.2e-42 Score=291.55 Aligned_cols=171 Identities=30% Similarity=0.590 Sum_probs=124.1
Q ss_pred HHHHHhhhcCCCCCCCCCCCCCccc-cccCCCCCCCCCCCCccccccccccccCcccccccccccccCCCCCcccCcccc
Q 022940 78 WSYFSVVITDPGGVPPNWIPNLDEE-SGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRCHHCSVCR 156 (289)
Q Consensus 78 ~sy~~~~~~dPG~vp~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RahHC~~C~ 156 (289)
++|+++.++|||++|+....+.+.+ ..++.+.. +.....++...+.++|.+|+..||+|||||+.||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~ 69 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQ------------SIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCN 69 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccch------------hhhhhccccCCCCEECcccCCcCCCcceeccccc
Confidence 5789999999999997622111110 00000000 0111223457889999999999999999999999
Q ss_pred ccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-cchHHHHHHHHHHHHHHHH
Q 022940 157 RCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESP-GNLAASFITFVLNLAFALS 235 (289)
Q Consensus 157 rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~v~~~~~~~~ 235 (289)
+||+||||||||+|||||++|||+|++|+++..+.+++.....+..+............. ......++.+++++++.++
T Consensus 70 ~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (174)
T PF01529_consen 70 RCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIF 149 (174)
T ss_pred cccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999888776666665544332211111 1111114444556677778
Q ss_pred HHHHHHHHHHHHhcCcchhhhhhcc
Q 022940 236 ILGFLIMHISLVAGNTTTIEAFEKK 260 (289)
Q Consensus 236 ~~~l~~~h~~li~~n~TT~E~~~~~ 260 (289)
+++++++|+++|++|+||+|.+|++
T Consensus 150 ~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 150 VGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 8899999999999999999999875
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=4.3e-39 Score=290.90 Aligned_cols=202 Identities=33% Similarity=0.595 Sum_probs=146.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCccccccCCCCCCCCCCCCccccccccccccCccccccccccccc
Q 022940 64 FVLFLFHSLLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQ 143 (289)
Q Consensus 64 ~~~~~~~~l~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 143 (289)
+..+.+.+...+...+|++..++|||+.+++-....-++..+ ....++..+..++|.+|+.
T Consensus 57 ~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~C~~C~~ 117 (309)
T COG5273 57 LFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETIS-------------------RLLDDGKFGTENFCSTCNI 117 (309)
T ss_pred hhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhh-------------------hhhhcCccccceecccccc
Confidence 344556666778888999999999999985432221111111 1133466789999999999
Q ss_pred CCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcch-HHH
Q 022940 144 FKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESPGNL-AAS 222 (289)
Q Consensus 144 ~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 222 (289)
+||||||||+.|||||+||||||||+|||||.+|||+|++||+++.......+......+..... ....+... ..+
T Consensus 118 ~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l 194 (309)
T COG5273 118 YKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFS---IRHDTSLAICFL 194 (309)
T ss_pred ccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---ccCChHHHHHHH
Confidence 99999999999999999999999999999999999999999999987776665554444433221 22233222 212
Q ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhccCC-------------------------CCCCCChhHHHHHH
Q 022940 223 FI-TFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKTS-------------------------PKWRYDLGWKINFE 276 (289)
Q Consensus 223 ~l-~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~~-------------------------~~~~yd~G~~~N~~ 276 (289)
+. ...+++.+.+.+..++.+|.+++..|+||+|..+..+. -..|++.|.-+|++
T Consensus 195 i~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 274 (309)
T COG5273 195 IFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLS 274 (309)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccce
Confidence 22 13444555666778889999999999999998764221 12478888899999
Q ss_pred HhCCCCCcccc
Q 022940 277 QVIPSQFLMHA 287 (289)
Q Consensus 277 ~vfG~~~~~~~ 287 (289)
.++|.+...|.
T Consensus 275 ~i~~~~~~~~~ 285 (309)
T COG5273 275 TIKGSNALYWL 285 (309)
T ss_pred eecCCCceeec
Confidence 99999888774
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2.1e-39 Score=277.56 Aligned_cols=149 Identities=32% Similarity=0.635 Sum_probs=113.5
Q ss_pred cccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-C-
Q 022940 133 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTD-D- 210 (289)
Q Consensus 133 ~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~-~- 210 (289)
....+|.+|..+|||||||||.|||||+||||||||+|||||.+|||||++|++|+.+++.+..+...+...+.... .
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 34589999999999999999999999999999999999999999999999999999999999766544333332111 0
Q ss_pred --CCCC------CCcchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhcc--------CCCCC
Q 022940 211 --EIPE------SPGNLA---------ASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK--------TSPKW 265 (289)
Q Consensus 211 --~~~~------~~~~~~---------~~~l~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~--------~~~~~ 265 (289)
..+. .|..+. -+.-..++++.+.+.++.+..+|.++|.+|.|++|.+... +..+|
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 1111 111110 1122344556666777888999999999999999997431 12378
Q ss_pred CCChhHHHHHHHhCCC
Q 022940 266 RYDLGWKINFEQVIPS 281 (289)
Q Consensus 266 ~yd~G~~~N~~~vfG~ 281 (289)
||+.|.++||+.++|-
T Consensus 260 ~~n~g~k~nWr~fLg~ 275 (309)
T KOG1313|consen 260 PTNFGGKANWRNFLGL 275 (309)
T ss_pred CcccchHHHHHHhhcc
Confidence 9999999999999974
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.98 E-value=2.1e-32 Score=235.66 Aligned_cols=167 Identities=30% Similarity=0.523 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCC-CCCCCCccccccCCCCCCCCCCCCccccccccccccCcccccccccccccCCCCCc
Q 022940 71 SLLVMLVWSYFSVVITDPGGVPP-NWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRC 149 (289)
Q Consensus 71 ~l~~~~~~sy~~~~~~dPG~vp~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Ra 149 (289)
.+..+-..++..++.+|||.+.+ |+....+ +-|.+ +.--.+.+.|++|+..||+|+
T Consensus 106 l~vivp~i~f~ltc~snpg~i~k~n~s~~~~-----~ypYD------------------y~if~k~~kCSTCki~KPARS 162 (341)
T KOG1312|consen 106 LLVIVPLIFFTLTCGSNPGIITKANESLFLH-----VYPYD------------------YVIFPKNVKCSTCKIRKPARS 162 (341)
T ss_pred HHHHHHHHHHhhhhcCCCCccchhhhcccee-----ccCcc------------------ceeecCCCccccccCCCcccc
Confidence 33444455677899999999874 2221111 11111 111234478999999999999
Q ss_pred ccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCC----------CCCcc
Q 022940 150 HHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDD-EIP----------ESPGN 218 (289)
Q Consensus 150 hHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~-~~~----------~~~~~ 218 (289)
+|||.|||||.||||||.|+|||||.+|+|||++||++....+.++++.+.........+. +.. .+...
T Consensus 163 KHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g~~ks~~~ 242 (341)
T KOG1312|consen 163 KHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHGHVKSTVF 242 (341)
T ss_pred ccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeeeecchhhHHH
Confidence 9999999999999999999999999999999999999998877777665544322211111 000 00011
Q ss_pred hH-HHHHHH-----HHHHHHH-HHHHHHHHHHHHHHhcCcchhhhhhcc
Q 022940 219 LA-ASFITF-----VLNLAFA-LSILGFLIMHISLVAGNTTTIEAFEKK 260 (289)
Q Consensus 219 ~~-~~~l~~-----v~~~~~~-~~~~~l~~~h~~li~~n~TT~E~~~~~ 260 (289)
++ ..++++ +++.... -++++...+-+++-.+|+||.|+..++
T Consensus 243 L~~yl~la~~~~v~~l~~~~~~~~~~~Y~~f~~y~~~t~~~~~~W~~~d 291 (341)
T KOG1312|consen 243 LIQYLFLAFPRIVFMLGFVVVLSFLGGYLLFVLYLAATNQTTNEWYRGD 291 (341)
T ss_pred HHHHHHHHhccceeeeehhhhhhHhHHHHHHHHHHHhccCCchhhhccc
Confidence 11 111111 1111111 124556778889999999999998764
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=3.5e-29 Score=236.67 Aligned_cols=140 Identities=26% Similarity=0.385 Sum_probs=93.2
Q ss_pred ccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 022940 136 RFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPES 215 (289)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (289)
++|.+|...||.|++||+.|||||.||||||||++||||.+|||+|+.|++.+...+.+.+..... ++.......+
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~----y~~~~~~~~~ 496 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLY----YIMNLENAST 496 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHH----HHhhcchhHH
Confidence 799999999999999999999999999999999999999999999999999877666555443332 2222111110
Q ss_pred CcchHHHHHHHHHHHH-------HH------HHHHHH-HHHHHHHHhcCcchhhhhhccC---------CCCCCCChhHH
Q 022940 216 PGNLAASFITFVLNLA-------FA------LSILGF-LIMHISLVAGNTTTIEAFEKKT---------SPKWRYDLGWK 272 (289)
Q Consensus 216 ~~~~~~~~l~~v~~~~-------~~------~~~~~l-~~~h~~li~~n~TT~E~~~~~~---------~~~~~yd~G~~ 272 (289)
.....++.+. ++... +. ...... ..-|-..++.+.||+|.++.++ ..++|++.|+.
T Consensus 497 ~~~~~l~~~~-~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g~~ 575 (600)
T KOG0509|consen 497 IYVGFLIAVQ-AFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPGPI 575 (600)
T ss_pred HHHHHHHHHH-HHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCchhh
Confidence 0000111000 00000 00 001111 1123445789999999987543 24789999999
Q ss_pred HHHHHhCC
Q 022940 273 INFEQVIP 280 (289)
Q Consensus 273 ~N~~~vfG 280 (289)
+|+.+++-
T Consensus 576 ~Nl~df~~ 583 (600)
T KOG0509|consen 576 RNLVDFFL 583 (600)
T ss_pred hcchheee
Confidence 99999984
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=91.97 E-value=1.7 Score=35.70 Aligned_cols=58 Identities=26% Similarity=0.447 Sum_probs=43.0
Q ss_pred cccccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHHHHHH
Q 022940 131 KHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSL 199 (289)
Q Consensus 131 ~~~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~~~~~ 199 (289)
+..+.+.|..|+.--..+-|||.--|+||-+--| +-+-.|+++..-..+.........
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~~~ 115 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSLYY 115 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567789999999999999999999999998766 556677777765555555544333
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=90.43 E-value=1.6 Score=39.64 Aligned_cols=42 Identities=24% Similarity=0.569 Sum_probs=33.3
Q ss_pred CcccCccccccccccCccCccccccccccch-----------HHHHHHHHHHH
Q 022940 148 RCHHCSVCRRCILKMDHHCVWVVNCVGAFNY-----------KYFLLFLFYTF 189 (289)
Q Consensus 148 RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~-----------k~FilFl~~~~ 189 (289)
+.++|+.|+.-++..-|||+.=|+||-+.-| |-+-.|+.+++
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 5788888888888888888888888877655 56777886655
No 11
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=88.62 E-value=0.25 Score=31.82 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=23.0
Q ss_pred ccccccccccccCCCCCcccCccccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~r 157 (289)
......|.+|...-|+|+..|+.||.
T Consensus 11 ~~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 11 VFNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hhcccchhcccCCCCccccccccCCC
Confidence 34668999999999999999999885
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.06 E-value=0.27 Score=26.72 Aligned_cols=21 Identities=19% Similarity=0.673 Sum_probs=18.0
Q ss_pred cccccccCCCCCcccCccccc
Q 022940 137 FCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~r 157 (289)
+|+.|...-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588898888899999998874
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.75 E-value=0.61 Score=26.05 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=18.6
Q ss_pred ccccccccCCCCCcccCccccc
Q 022940 136 RFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~r 157 (289)
++|..|...-++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6799999877888999998874
No 14
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=82.93 E-value=4.1 Score=37.28 Aligned_cols=54 Identities=24% Similarity=0.355 Sum_probs=43.0
Q ss_pred cccccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHHHHHH
Q 022940 131 KHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLV 195 (289)
Q Consensus 131 ~~~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~~~~~ 195 (289)
+..+.+.|+.|+.--...-|||.-=|+||-+-.| +=.=.|++++....+...+.
T Consensus 119 KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~ 172 (309)
T COG5273 119 KPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLS 172 (309)
T ss_pred cCCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHH
Confidence 3567789999999999999999999999998766 66778888886555444443
No 15
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=82.44 E-value=10 Score=27.65 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhhhcc
Q 022940 220 AASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK 260 (289)
Q Consensus 220 ~~~~l~~v~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~ 260 (289)
++.+++|++++ +.+++++++..|-=+++.++.|+++..
T Consensus 47 alSii~FIlG~---vl~lGilifs~y~~C~~~~~~~r~n~s 84 (91)
T PHA02680 47 ALSVTCFIVGA---VLLLGLFVFSMYRKCSGSMPYERLNNT 84 (91)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHhcccCCCceeecccCC
Confidence 44555555443 335567788888888888888887653
No 16
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=79.54 E-value=1.1 Score=45.27 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=18.5
Q ss_pred cccccccccCCC-------CCcccCccccc
Q 022940 135 VRFCQKCNQFKP-------PRCHHCSVCRR 157 (289)
Q Consensus 135 ~~~C~~C~~~kP-------~RahHC~~C~r 157 (289)
...|..|+..-. -|-|||+.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999986653 39999999987
No 17
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=79.37 E-value=0.52 Score=30.43 Aligned_cols=26 Identities=27% Similarity=0.770 Sum_probs=22.5
Q ss_pred ccccccccccccCCCCCcccCccccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~r 157 (289)
....+.|.+|...-|+|+..|+.|+.
T Consensus 11 ~~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 11 LFNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred HhhHHHHHHhcCCCCcchhHHhhccC
Confidence 34568999999999999999998864
No 18
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=77.29 E-value=1.3 Score=43.59 Aligned_cols=58 Identities=7% Similarity=-0.073 Sum_probs=48.8
Q ss_pred cccccccccccCCCCCcccCccccccccccCccCccccccccccchHHHHHHHHHHHHH
Q 022940 133 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLE 191 (289)
Q Consensus 133 ~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl~~~~l~ 191 (289)
.-...|.+|....+.+..++..+-.++..+++||+|+. +|+.+|...|-+..+...+.
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~ 380 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLA 380 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHH
Confidence 44567888999999999999999999999999999999 99999988766655544333
No 19
>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=72.97 E-value=1.9 Score=29.84 Aligned_cols=27 Identities=30% Similarity=0.600 Sum_probs=13.2
Q ss_pred cccccccccc--CCCCCcccCcccccccc
Q 022940 134 GVRFCQKCNQ--FKPPRCHHCSVCRRCIL 160 (289)
Q Consensus 134 ~~~~C~~C~~--~kP~RahHC~~C~rCV~ 160 (289)
+...|..|+. ---.|-|||+.||+-|=
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 20
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=71.98 E-value=2.1 Score=23.95 Aligned_cols=22 Identities=23% Similarity=0.691 Sum_probs=17.8
Q ss_pred ccccccccCCCCCcccCccccc
Q 022940 136 RFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~r 157 (289)
|.|+.|+..-|.-+.-|..||-
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688898888888888888873
No 21
>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=70.10 E-value=1.8 Score=28.42 Aligned_cols=27 Identities=30% Similarity=0.733 Sum_probs=18.2
Q ss_pred ccccccccccccCCCCCcccCcc--cccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHHCSV--CRRC 158 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~--C~rC 158 (289)
..+...|.+|...-||||..|+. ||.+
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 44678999999999999999998 8764
No 22
>PF12773 DZR: Double zinc ribbon
Probab=69.51 E-value=4.2 Score=26.15 Aligned_cols=34 Identities=21% Similarity=0.483 Sum_probs=20.2
Q ss_pred ccccccccccCCC---CCcccCccccccccccCccCc
Q 022940 134 GVRFCQKCNQFKP---PRCHHCSVCRRCILKMDHHCV 167 (289)
Q Consensus 134 ~~~~C~~C~~~kP---~RahHC~~C~rCV~r~DHHCp 167 (289)
..++|..|...-+ .....|..|+.=+...+.+|+
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 4566666665444 335566666666666666665
No 23
>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=67.01 E-value=2.8 Score=27.97 Aligned_cols=37 Identities=32% Similarity=0.841 Sum_probs=27.5
Q ss_pred ccccccccCCCCCc-------ccCcccccccccc-CccCccccccccc
Q 022940 136 RFCQKCNQFKPPRC-------HHCSVCRRCILKM-DHHCVWVVNCVGA 175 (289)
Q Consensus 136 ~~C~~C~~~kP~Ra-------hHC~~C~rCV~r~-DHHCpWv~nCIG~ 175 (289)
..|..|+.--|+-+ +-|..|..|+..+ +++|| ||=|.
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 34666766555543 6788999999999 99999 67663
No 24
>PF12773 DZR: Double zinc ribbon
Probab=66.54 E-value=4.2 Score=26.15 Aligned_cols=25 Identities=28% Similarity=0.838 Sum_probs=22.1
Q ss_pred ccccccccccccCCCCCcccCcccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHHCSVCR 156 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~ 156 (289)
.....+|.+|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 4567899999999999999999986
No 25
>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 KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=51.87 E-value=6.6 Score=34.23 Aligned_cols=12 Identities=25% Similarity=0.241 Sum_probs=9.8
Q ss_pred ccccCccCcccc
Q 022940 159 ILKMDHHCVWVV 170 (289)
Q Consensus 159 V~r~DHHCpWv~ 170 (289)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 567899999876
No 27
>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=50.70 E-value=4.6 Score=23.10 Aligned_cols=20 Identities=25% Similarity=0.782 Sum_probs=12.3
Q ss_pred cccccccCCCCCcccCcccc
Q 022940 137 FCQKCNQFKPPRCHHCSVCR 156 (289)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~ 156 (289)
.|..|...-++++.+|..|+
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~ 25 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACG 25 (30)
T ss_dssp EETTTTEEEESSSSB-TTT-
T ss_pred cCCCCcCCchHHhhhhhCcC
Confidence 46667766677777777665
No 28
>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=50.22 E-value=5.2 Score=24.08 Aligned_cols=24 Identities=29% Similarity=0.768 Sum_probs=13.2
Q ss_pred ccccccccccccCC-CCCcccCcccc
Q 022940 132 HQGVRFCQKCNQFK-PPRCHHCSVCR 156 (289)
Q Consensus 132 ~~~~~~C~~C~~~k-P~RahHC~~C~ 156 (289)
......|..|..+. ||| ..|..|+
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 34557899999775 777 7787775
No 29
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.20 E-value=4.8 Score=37.63 Aligned_cols=25 Identities=40% Similarity=0.853 Sum_probs=19.0
Q ss_pred CCCCcccCccccccccccCccCccccccccc
Q 022940 145 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGA 175 (289)
Q Consensus 145 kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~ 175 (289)
+-.|..||..|+. +|| +|+.||||.
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga 34 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGA 34 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHH
Confidence 4456667777775 788 899999994
No 30
>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=48.99 E-value=8.2 Score=22.45 Aligned_cols=23 Identities=26% Similarity=0.733 Sum_probs=11.4
Q ss_pred ccccccccc----CCCCCcccCccccc
Q 022940 135 VRFCQKCNQ----FKPPRCHHCSVCRR 157 (289)
Q Consensus 135 ~~~C~~C~~----~kP~RahHC~~C~r 157 (289)
.+||..|.. ....++..|..|+.
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 478888873 23446677777664
No 31
>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=48.95 E-value=7.1 Score=22.32 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=8.8
Q ss_pred cccccccCCCC-CcccCccccc
Q 022940 137 FCQKCNQFKPP-RCHHCSVCRR 157 (289)
Q Consensus 137 ~C~~C~~~kP~-RahHC~~C~r 157 (289)
.|..|+..... ...+|+.|+-
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 7888888873
No 32
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=46.22 E-value=6.4 Score=37.40 Aligned_cols=27 Identities=37% Similarity=0.918 Sum_probs=20.9
Q ss_pred ccccccccccccC--CCCCcccCcccccc
Q 022940 132 HQGVRFCQKCNQF--KPPRCHHCSVCRRC 158 (289)
Q Consensus 132 ~~~~~~C~~C~~~--kP~RahHC~~C~rC 158 (289)
.....+|+.|... --.|-|||+-||+-
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 25789999999983
No 33
>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=45.72 E-value=46 Score=28.95 Aligned_cols=25 Identities=28% Similarity=0.234 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCCC
Q 022940 68 LFHSLLVMLVWSYFSVVITDPGGVP 92 (289)
Q Consensus 68 ~~~~l~~~~~~sy~~~~~~dPG~vp 92 (289)
+..++.+.++-.|.+|.-+|||..-
T Consensus 199 Vitl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 199 VITLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 3344445555567789999999644
No 34
>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=45.06 E-value=14 Score=24.23 Aligned_cols=22 Identities=36% Similarity=0.797 Sum_probs=14.3
Q ss_pred ccccccc--CCCCCcccCcccccc
Q 022940 137 FCQKCNQ--FKPPRCHHCSVCRRC 158 (289)
Q Consensus 137 ~C~~C~~--~kP~RahHC~~C~rC 158 (289)
.|..|+. -.-.|.|||+.||+-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 4555652 225678999998874
No 35
>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=41.36 E-value=6.2 Score=23.68 Aligned_cols=7 Identities=57% Similarity=1.716 Sum_probs=4.0
Q ss_pred ccccccc
Q 022940 136 RFCQKCN 142 (289)
Q Consensus 136 ~~C~~C~ 142 (289)
++|++|.
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 36
>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=40.48 E-value=18 Score=24.88 Aligned_cols=27 Identities=19% Similarity=0.451 Sum_probs=19.9
Q ss_pred ccccccccccccCC----CCCcccCcccccc
Q 022940 132 HQGVRFCQKCNQFK----PPRCHHCSVCRRC 158 (289)
Q Consensus 132 ~~~~~~C~~C~~~k----P~RahHC~~C~rC 158 (289)
....+.|+.|.... ..|.++|..||.-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCE
Confidence 34678899998543 5578889998864
No 37
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=37.21 E-value=22 Score=23.85 Aligned_cols=24 Identities=33% Similarity=0.807 Sum_probs=16.7
Q ss_pred ccccccccccccCCCCCccc-Cccccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHH-CSVCRR 157 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahH-C~~C~r 157 (289)
......|+.|...+.+ || |..||-
T Consensus 24 ~~~l~~C~~CG~~~~~--H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP--HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC--eEECCCCCc
Confidence 4556779999977644 66 777763
No 38
>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=37.19 E-value=3.7e+02 Score=25.55 Aligned_cols=32 Identities=19% Similarity=0.497 Sum_probs=20.7
Q ss_pred cccccccccc-CCCCCcccCccccccccccCcc
Q 022940 134 GVRFCQKCNQ-FKPPRCHHCSVCRRCILKMDHH 165 (289)
Q Consensus 134 ~~~~C~~C~~-~kP~RahHC~~C~rCV~r~DHH 165 (289)
...-|+.|+. .+|....||..||.-..+..++
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~ 246 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVRRRN 246 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCCCCC
Confidence 3456999997 4555566777777665554443
No 39
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=36.22 E-value=21 Score=23.29 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=15.3
Q ss_pred cccccccccc-CC--CCCcccCccccc
Q 022940 134 GVRFCQKCNQ-FK--PPRCHHCSVCRR 157 (289)
Q Consensus 134 ~~~~C~~C~~-~k--P~RahHC~~C~r 157 (289)
..++|++|.. .- -....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 4569999976 22 223567887763
No 40
>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=35.72 E-value=26 Score=19.97 Aligned_cols=20 Identities=30% Similarity=0.680 Sum_probs=13.0
Q ss_pred cccccccCCCCC-cccCcccc
Q 022940 137 FCQKCNQFKPPR-CHHCSVCR 156 (289)
Q Consensus 137 ~C~~C~~~kP~R-ahHC~~C~ 156 (289)
.|..|+..-... ..||+.|+
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 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.54 E-value=21 Score=22.89 Aligned_cols=7 Identities=57% Similarity=1.621 Sum_probs=3.9
Q ss_pred ccccccc
Q 022940 137 FCQKCNQ 143 (289)
Q Consensus 137 ~C~~C~~ 143 (289)
+|+.|+.
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 5666653
No 42
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=35.14 E-value=16 Score=36.62 Aligned_cols=23 Identities=30% Similarity=0.684 Sum_probs=17.5
Q ss_pred cccccccccC--CCCCcccCccccc
Q 022940 135 VRFCQKCNQF--KPPRCHHCSVCRR 157 (289)
Q Consensus 135 ~~~C~~C~~~--kP~RahHC~~C~r 157 (289)
..-|.+|... ---|.|||+.||+
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccceeeeeeeeccccccccccch
Confidence 3679999742 1349999999998
No 43
>PLN00186 ribosomal protein S26; Provisional
Probab=35.08 E-value=15 Score=27.96 Aligned_cols=17 Identities=29% Similarity=0.702 Sum_probs=13.1
Q ss_pred CcccCccccccccccCc
Q 022940 148 RCHHCSVCRRCILKMDH 164 (289)
Q Consensus 148 RahHC~~C~rCV~r~DH 164 (289)
+.-||..|++||++---
T Consensus 19 ~~V~C~nCgr~vPKDKA 35 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKA 35 (109)
T ss_pred cceeeCCCcccccccce
Confidence 35589999999998443
No 44
>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=34.72 E-value=20 Score=26.51 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=8.0
Q ss_pred ccCccccccc
Q 022940 164 HHCVWVVNCV 173 (289)
Q Consensus 164 HHCpWv~nCI 173 (289)
.||||++.-.
T Consensus 56 ~~CPwv~~~~ 65 (91)
T PF08600_consen 56 EYCPWVNPST 65 (91)
T ss_pred ccCCccCCcc
Confidence 4899999754
No 45
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=34.26 E-value=16 Score=27.21 Aligned_cols=20 Identities=25% Similarity=0.561 Sum_probs=15.1
Q ss_pred CcccCccccccccccCccCc
Q 022940 148 RCHHCSVCRRCILKMDHHCV 167 (289)
Q Consensus 148 RahHC~~C~rCV~r~DHHCp 167 (289)
+.-+|..||+||++----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 35589999999998655443
No 46
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=34.04 E-value=15 Score=35.57 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=16.7
Q ss_pred ccccccccccCC--CCCcccCccccc
Q 022940 134 GVRFCQKCNQFK--PPRCHHCSVCRR 157 (289)
Q Consensus 134 ~~~~C~~C~~~k--P~RahHC~~C~r 157 (289)
.-..|..|+..- -.|-|||+.||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 345677777532 357899999987
No 47
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=33.64 E-value=58 Score=22.08 Aligned_cols=23 Identities=35% Similarity=0.839 Sum_probs=16.7
Q ss_pred cccccccccCCCCCcccCc-cccc
Q 022940 135 VRFCQKCNQFKPPRCHHCS-VCRR 157 (289)
Q Consensus 135 ~~~C~~C~~~kP~RahHC~-~C~r 157 (289)
.+-|..|+..-|+--..|| .|+.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 4678888877777777775 6654
No 48
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=32.92 E-value=11 Score=34.05 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=15.7
Q ss_pred cccccccccc-CC--CCCcccCccccccccc
Q 022940 134 GVRFCQKCNQ-FK--PPRCHHCSVCRRCILK 161 (289)
Q Consensus 134 ~~~~C~~C~~-~k--P~RahHC~~C~rCV~r 161 (289)
+..-|..|.. .. -.|-|||+.||+-|-.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 3455666654 22 3566777777764443
No 49
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=31.88 E-value=18 Score=27.55 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=13.8
Q ss_pred CcccCccccccccccCccC
Q 022940 148 RCHHCSVCRRCILKMDHHC 166 (289)
Q Consensus 148 RahHC~~C~rCV~r~DHHC 166 (289)
+.-||..|++||++----+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIK 37 (108)
T ss_pred ccEEeCCccccccccceEE
Confidence 3558999999999844333
No 50
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=29.92 E-value=28 Score=23.84 Aligned_cols=23 Identities=26% Similarity=0.845 Sum_probs=20.3
Q ss_pred cccccccccCCCCCcccCccccc
Q 022940 135 VRFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 135 ~~~C~~C~~~kP~RahHC~~C~r 157 (289)
.+-|.+|...-|+-+.-|..||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999986
No 51
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.36 E-value=34 Score=34.68 Aligned_cols=22 Identities=27% Similarity=0.686 Sum_probs=13.0
Q ss_pred ccccccccCCCCCcccCccccc
Q 022940 136 RFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 136 ~~C~~C~~~kP~RahHC~~C~r 157 (289)
+.|.+|...-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 4566666666666666666654
No 52
>PHA02942 putative transposase; Provisional
Probab=29.29 E-value=34 Score=32.34 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=19.1
Q ss_pred cccccccccccCCC---CCcccCccccc
Q 022940 133 QGVRFCQKCNQFKP---PRCHHCSVCRR 157 (289)
Q Consensus 133 ~~~~~C~~C~~~kP---~RahHC~~C~r 157 (289)
...+.|+.|....+ .|.+.|..||-
T Consensus 323 yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 323 YSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 46688999996644 47888988885
No 53
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.67 E-value=29 Score=18.75 Aligned_cols=21 Identities=19% Similarity=0.515 Sum_probs=14.1
Q ss_pred cccccccCCCCCcccCccccc
Q 022940 137 FCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 137 ~C~~C~~~kP~RahHC~~C~r 157 (289)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 366777777777777777653
No 54
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.28 E-value=19 Score=21.47 Aligned_cols=11 Identities=18% Similarity=0.601 Sum_probs=4.5
Q ss_pred ccccccccccc
Q 022940 132 HQGVRFCQKCN 142 (289)
Q Consensus 132 ~~~~~~C~~C~ 142 (289)
..++..|..|.
T Consensus 19 ~r~R~vC~~Cg 29 (34)
T PF14803_consen 19 DRERLVCPACG 29 (34)
T ss_dssp SS-EEEETTTT
T ss_pred CccceECCCCC
Confidence 34444454443
No 55
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=26.95 E-value=23 Score=30.79 Aligned_cols=20 Identities=25% Similarity=0.803 Sum_probs=15.4
Q ss_pred CCCCCcccCccccccccccC
Q 022940 144 FKPPRCHHCSVCRRCILKMD 163 (289)
Q Consensus 144 ~kP~RahHC~~C~rCV~r~D 163 (289)
+++.+..||..|+.|++|..
T Consensus 187 Y~g~~~~~CG~C~sC~~R~~ 206 (222)
T COG0603 187 YNGGEGDHCGECESCVLRER 206 (222)
T ss_pred eCCCCCCCCCCCHHHHHHHH
Confidence 35566569999999999843
No 56
>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=26.69 E-value=25 Score=27.12 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=12.7
Q ss_pred CcccCccccccccccCccCc
Q 022940 148 RCHHCSVCRRCILKMDHHCV 167 (289)
Q Consensus 148 RahHC~~C~rCV~r~DHHCp 167 (289)
+.-||..|++||++----..
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 45689999999998654443
No 57
>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=26.47 E-value=18 Score=23.36 Aligned_cols=16 Identities=31% Similarity=0.958 Sum_probs=10.1
Q ss_pred ccccccccccCccCcc
Q 022940 153 SVCRRCILKMDHHCVW 168 (289)
Q Consensus 153 ~~C~rCV~r~DHHCpW 168 (289)
..|+.|+.-.|-+|.|
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 4566666666666666
No 58
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=25.99 E-value=28 Score=35.83 Aligned_cols=39 Identities=26% Similarity=0.525 Sum_probs=31.0
Q ss_pred cccCc---cccccccccCccCcccc---ccc--cccchHHHHHHHHH
Q 022940 149 CHHCS---VCRRCILKMDHHCVWVV---NCV--GAFNYKYFLLFLFY 187 (289)
Q Consensus 149 ahHC~---~C~rCV~r~DHHCpWv~---nCI--G~~N~k~FilFl~~ 187 (289)
-|+|+ .|-.|++.-|-||.|-+ .|+ +..|.|.+.+=+-.
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~~ 537 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVSS 537 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhcc
Confidence 57888 89888888999999977 797 55577888776553
No 59
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.87 E-value=31 Score=26.61 Aligned_cols=26 Identities=19% Similarity=0.678 Sum_probs=18.4
Q ss_pred ccccccccccccCCCCCccc---Cccccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHH---CSVCRR 157 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahH---C~~C~r 157 (289)
.+..-+|..|+..-|...++ |..||.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 45567899998777665444 888874
No 60
>PHA02898 virion envelope protein; Provisional
Probab=25.65 E-value=2.8e+02 Score=20.45 Aligned_cols=34 Identities=32% Similarity=0.506 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCcchhhh
Q 022940 220 AASFITFVLNLAFALSILGFLIMHISL-VAGNTTTIEA 256 (289)
Q Consensus 220 ~~~~l~~v~~~~~~~~~~~l~~~h~~l-i~~n~TT~E~ 256 (289)
++.+++|++++ +.+++++++..|. =+++.++.|.
T Consensus 46 alSii~FIlgi---vl~lG~~ifs~y~r~C~~~~~~e~ 80 (92)
T PHA02898 46 SISIISFILAI---ILILGIIFFKGYNMFCGGNTTDEV 80 (92)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHhhhcCCCccccc
Confidence 44455555433 3356777788887 5777777753
No 61
>PRK02935 hypothetical protein; Provisional
Probab=25.30 E-value=2.6e+02 Score=21.38 Aligned_cols=16 Identities=19% Similarity=0.108 Sum_probs=6.5
Q ss_pred HHHHHHHHHHhhheee
Q 022940 27 VMILVVLGIIGVSYYA 42 (289)
Q Consensus 27 i~v~~v~~~i~~~~~~ 42 (289)
+...++++-+++.|-.
T Consensus 15 ~aL~lvfiG~~vMy~G 30 (110)
T PRK02935 15 FALSLVFIGFIVMYLG 30 (110)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3334444444444433
No 62
>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=25.04 E-value=45 Score=22.17 Aligned_cols=23 Identities=26% Similarity=0.748 Sum_probs=15.7
Q ss_pred cccccccccccCCCCCccc-Cccccc
Q 022940 133 QGVRFCQKCNQFKPPRCHH-CSVCRR 157 (289)
Q Consensus 133 ~~~~~C~~C~~~kP~RahH-C~~C~r 157 (289)
.....|+.|..+ -++|| |..||.
T Consensus 24 p~l~~C~~cG~~--~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEF--KLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCc--ccCeeECCccCe
Confidence 455678888864 45666 777763
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.51 E-value=40 Score=34.15 Aligned_cols=41 Identities=27% Similarity=0.489 Sum_probs=29.4
Q ss_pred ccccccccccccCCCCCcccCccccccccccCccCcccccccc
Q 022940 132 HQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVG 174 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG 174 (289)
....++|.+|...-+ ...|..||.=+..-..+||==|.=.|
T Consensus 12 ~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 12 PNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCccc
Confidence 456789999986543 35799998888888888885554444
No 64
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=23.70 E-value=14 Score=28.14 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=21.0
Q ss_pred cccccccccccCCCCCcccCccccc
Q 022940 133 QGVRFCQKCNQFKPPRCHHCSVCRR 157 (289)
Q Consensus 133 ~~~~~C~~C~~~kP~RahHC~~C~r 157 (289)
..--.|.+|-..-|||+..|+.|..
T Consensus 91 ~D~lICRkCYAR~g~~Ae~CRK~~~ 115 (128)
T KOG0003|consen 91 CDKLICRKCYARLGPRAENCRKKKC 115 (128)
T ss_pred cchHHHHHHHHhcCcHHHHhHHhhc
Confidence 4456899999999999999998863
No 65
>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=23.45 E-value=6.7e+02 Score=24.12 Aligned_cols=17 Identities=29% Similarity=0.680 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 022940 179 KYFLLFLFYTFLETTLV 195 (289)
Q Consensus 179 k~FilFl~~~~l~~~~~ 195 (289)
-||.+|.+|+.+..=+.
T Consensus 171 nyFalFTlyvam~IEfs 187 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFS 187 (512)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 48999999987765443
No 66
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=23.06 E-value=6.7e+02 Score=23.98 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=23.4
Q ss_pred cccccccccccCCCCCcccCccccccccccCccC
Q 022940 133 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHC 166 (289)
Q Consensus 133 ~~~~~C~~C~~~kP~RahHC~~C~rCV~r~DHHC 166 (289)
....-|+.|+..-|....||..||.-..+.+++.
T Consensus 219 ~~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 219 QGLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred cCCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 3456799999887776668888877665544433
No 67
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=22.82 E-value=75 Score=34.08 Aligned_cols=40 Identities=30% Similarity=0.502 Sum_probs=26.3
Q ss_pred ccccccccc--cCCCCCcccCccccccccccCccCccccccccccchHHHHHHH
Q 022940 134 GVRFCQKCN--QFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFL 185 (289)
Q Consensus 134 ~~~~C~~C~--~~kP~RahHC~~C~rCV~r~DHHCpWv~nCIG~~N~k~FilFl 185 (289)
...-|..|+ ..--.|-|||+.||+- .-+.| -|-|.++.|+
T Consensus 556 e~pncm~clqkft~ikrrhhcRacgkV---------lcgvc---cnek~~leyl 597 (1287)
T KOG1841|consen 556 EAPNCMDCLQKFTPIKRRHHCRACGKV---------LCGVC---CNEKSALEYL 597 (1287)
T ss_pred cCchHHHHHhhcccccccccchhccce---------eehhh---cchhhhhhhc
Confidence 345566665 3446789999999982 11333 5677777776
No 68
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.23 E-value=44 Score=31.53 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=20.3
Q ss_pred cccccccccCCCCCcccCcccccc
Q 022940 135 VRFCQKCNQFKPPRCHHCSVCRRC 158 (289)
Q Consensus 135 ~~~C~~C~~~kP~RahHC~~C~rC 158 (289)
.++|.+|...+-+-+..|..||.=
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~ 24 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHK 24 (465)
T ss_pred CCcccccccccccccccccccCCc
Confidence 378999999998888889888873
No 69
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=21.92 E-value=3.8e+02 Score=25.44 Aligned_cols=15 Identities=33% Similarity=1.001 Sum_probs=12.6
Q ss_pred ccCccccccccccCccCcc
Q 022940 150 HHCSVCRRCILKMDHHCVW 168 (289)
Q Consensus 150 hHC~~C~rCV~r~DHHCpW 168 (289)
..|..||.| +|+||-
T Consensus 67 ~~C~~Cg~C----~~~CP~ 81 (389)
T PRK15033 67 NLCHNCGAC----LHACQY 81 (389)
T ss_pred HhCcCcccc----cccCcC
Confidence 389999999 469998
No 70
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=21.75 E-value=35 Score=21.36 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=4.8
Q ss_pred ccccccCCCC
Q 022940 138 CQKCNQFKPP 147 (289)
Q Consensus 138 C~~C~~~kP~ 147 (289)
|..|...+++
T Consensus 7 C~~C~~~~~~ 16 (46)
T smart00423 7 CSECLLARDP 16 (46)
T ss_pred HHHHHcCCCC
Confidence 4455444444
No 71
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=21.46 E-value=2.4e+02 Score=26.37 Aligned_cols=47 Identities=6% Similarity=0.104 Sum_probs=22.5
Q ss_pred eeeeeeccccccCCCchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCC
Q 022940 43 VAVAKYGPALFLGGLDSITALFVLFLFHSLLVMLVWSYFSVVITDPGGVP 92 (289)
Q Consensus 43 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~l~~~~~~sy~~~~~~dPG~vp 92 (289)
++...|.++-+. .+....+++++..++.+.+++-.+..++.-|+.+-
T Consensus 27 yv~i~~~~~~ie---~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~ 73 (398)
T PRK10747 27 YVLIQTDNYNIE---TSVTGLAIILILAMVVLFAIEWLLRRIFRTGARTR 73 (398)
T ss_pred eEEEEECCEEEE---ehHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhh
Confidence 344444444332 23333333333333333344556677788888754
No 72
>KOG4017 consensus DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair]
Probab=21.07 E-value=28 Score=30.56 Aligned_cols=35 Identities=23% Similarity=0.450 Sum_probs=26.3
Q ss_pred ccccccccccccCCCC----CcccCccccccccccCccC
Q 022940 132 HQGVRFCQKCNQFKPP----RCHHCSVCRRCILKMDHHC 166 (289)
Q Consensus 132 ~~~~~~C~~C~~~kP~----RahHC~~C~rCV~r~DHHC 166 (289)
......|..|+..--+ -..+|++|+.|...+|-|=
T Consensus 100 i~~~~~C~eC~~i~mDs~L~~~F~~~VCd~CRd~~ekyk 138 (274)
T KOG4017|consen 100 IALAPKCEECDKIEMDSYLFDTFGCSVCDSCRDKDEKYK 138 (274)
T ss_pred hhhchhHHHhcCccchHHHHHhcCChhhhHhhhhhhhhh
Confidence 3456789999844322 3789999999999998754
No 73
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=20.67 E-value=2.2e+02 Score=26.79 Aligned_cols=17 Identities=0% Similarity=-0.396 Sum_probs=11.2
Q ss_pred HHHHHHHhhhcCCCCCC
Q 022940 76 LVWSYFSVVITDPGGVP 92 (289)
Q Consensus 76 ~~~sy~~~~~~dPG~vp 92 (289)
.++-.+..++.-|+.+-
T Consensus 57 ~~~~l~~~~~~~p~~~~ 73 (409)
T TIGR00540 57 AFEWGLRRFFRLGAHSR 73 (409)
T ss_pred HHHHHHHHHHHccHHHH
Confidence 44556677788887653
No 74
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=20.57 E-value=81 Score=25.89 Aligned_cols=32 Identities=13% Similarity=0.154 Sum_probs=26.6
Q ss_pred hcCcchhhhhhccCCCCCCCChhHHHHHHHhCCCC
Q 022940 248 AGNTTTIEAFEKKTSPKWRYDLGWKINFEQVIPSQ 282 (289)
Q Consensus 248 ~~n~TT~E~~~~~~~~~~~yd~G~~~N~~~vfG~~ 282 (289)
=+|+|++|.++.-+ .++.-|+++.+..+||-+
T Consensus 103 etg~TsyelIK~~r---gg~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 103 ETGSTSYELIKELR---GGWRAFWYQTFAWLFGIS 134 (157)
T ss_pred hcCCcHHHHHHHhh---CChhHHHHHHHHHHhCcc
Confidence 47999999987654 588899999999999864
Done!