Query 019492
Match_columns 340
No_of_seqs 179 out of 1596
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 09:54:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019492hhsearch_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-43 2.5E-48 332.4 15.6 209 97-336 43-272 (307)
2 KOG1313 DHHC-type Zn-finger pr 100.0 1.4E-42 3.1E-47 312.2 14.7 277 4-339 3-298 (309)
3 KOG1311 DHHC-type Zn-finger pr 100.0 4.5E-40 9.7E-45 312.4 18.2 204 105-333 58-278 (299)
4 KOG1314 DHHC-type Zn-finger pr 100.0 1.2E-38 2.7E-43 295.1 7.8 206 91-318 39-260 (414)
5 PF01529 zf-DHHC: DHHC palmito 100.0 1.9E-37 4.1E-42 271.5 10.4 159 115-301 2-174 (174)
6 COG5273 Uncharacterized protei 100.0 1.4E-32 3.1E-37 260.6 15.1 121 99-219 55-181 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 7.8E-30 1.7E-34 231.1 10.5 117 97-214 95-215 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 3.6E-25 7.8E-30 219.9 5.1 105 111-215 379-488 (600)
9 KOG1313 DHHC-type Zn-finger pr 97.6 0.0012 2.5E-08 61.1 11.9 156 145-315 114-273 (309)
10 TIGR01053 LSD1 zinc finger dom 93.5 0.042 9.1E-07 34.2 1.4 28 19-46 2-29 (31)
11 KOG1311 DHHC-type Zn-finger pr 92.0 3.6 7.7E-05 39.0 13.0 41 161-201 113-164 (299)
12 COG5273 Uncharacterized protei 90.1 4.1 8.9E-05 39.1 11.3 61 157-217 105-176 (309)
13 PF01529 zf-DHHC: DHHC palmito 89.3 3.5 7.6E-05 35.4 9.5 64 143-217 58-121 (174)
14 KOG1315 Predicted DHHC-type Zn 86.5 3.6 7.7E-05 39.4 8.3 29 160-188 108-136 (307)
15 PF13240 zinc_ribbon_2: zinc-r 85.3 0.49 1.1E-05 27.2 1.2 21 149-169 1-21 (23)
16 PF06943 zf-LSD1: LSD1 zinc fi 83.3 0.72 1.6E-05 27.2 1.3 25 21-45 1-25 (25)
17 TIGR00155 pqiA_fam integral me 81.2 61 0.0013 32.3 16.3 34 14-47 9-44 (403)
18 PF13248 zf-ribbon_3: zinc-rib 79.0 1.1 2.4E-05 26.4 1.1 22 148-169 3-24 (26)
19 PRK04136 rpl40e 50S ribosomal 70.3 2.8 6.2E-05 28.6 1.5 24 146-169 13-36 (48)
20 PF06906 DUF1272: Protein of u 68.7 2.9 6.2E-05 29.6 1.3 36 149-187 7-50 (57)
21 PF12773 DZR: Double zinc ribb 68.6 4.6 0.0001 27.3 2.3 36 145-180 10-48 (50)
22 PF10571 UPF0547: Uncharacteri 66.0 3.7 8.1E-05 24.4 1.2 22 148-169 1-22 (26)
23 PF11278 DUF3079: Protein of u 61.9 3.8 8.2E-05 28.0 0.8 24 14-41 9-32 (52)
24 PRK00398 rpoP DNA-directed RNA 61.1 5.2 0.00011 26.8 1.4 30 18-47 3-32 (46)
25 KOG1314 DHHC-type Zn-finger pr 59.1 23 0.00051 34.4 5.8 87 116-213 69-160 (414)
26 KOG0509 Ankyrin repeat and DHH 51.3 8.6 0.00019 39.9 1.7 58 148-206 326-383 (600)
27 PF12773 DZR: Double zinc ribb 50.1 13 0.00028 25.1 1.9 24 145-168 27-50 (50)
28 PHA02680 ORF090 IMV phosphoryl 47.6 1.3E+02 0.0028 23.3 7.3 23 279-301 62-84 (91)
29 PTZ00303 phosphatidylinositol 47.4 13 0.00028 39.8 2.2 22 148-169 461-489 (1374)
30 PF09889 DUF2116: Uncharacteri 46.7 29 0.00062 24.9 3.3 23 147-169 3-26 (59)
31 PF01363 FYVE: FYVE zinc finge 46.7 9.2 0.0002 27.7 0.8 25 147-171 9-35 (69)
32 smart00064 FYVE Protein presen 43.3 19 0.00041 25.9 2.1 25 147-171 10-36 (68)
33 PF10749 DUF2534: Protein of u 41.4 1.6E+02 0.0035 22.5 8.5 71 186-280 8-79 (85)
34 PF13719 zinc_ribbon_5: zinc-r 41.1 9.7 0.00021 24.4 0.2 27 19-45 3-34 (37)
35 PF07282 OrfB_Zn_ribbon: Putat 40.5 27 0.00059 25.2 2.5 37 10-46 20-56 (69)
36 COG1552 RPL40A Ribosomal prote 38.6 7 0.00015 26.8 -0.8 26 146-171 13-38 (50)
37 PF01020 Ribosomal_L40e: Ribos 37.1 19 0.0004 25.1 1.1 25 146-170 16-42 (52)
38 PF09151 DUF1936: Domain of un 36.8 11 0.00023 23.3 -0.1 21 20-40 3-28 (36)
39 PF07010 Endomucin: Endomucin; 36.8 76 0.0016 29.1 5.2 31 101-131 195-225 (259)
40 PF09082 DUF1922: Domain of un 36.6 17 0.00037 26.8 0.9 27 20-48 5-31 (68)
41 cd00065 FYVE FYVE domain; Zinc 34.9 27 0.00058 24.0 1.7 23 148-170 3-27 (57)
42 KOG1842 FYVE finger-containing 34.7 13 0.00027 37.2 -0.1 26 146-171 179-206 (505)
43 PRK00432 30S ribosomal protein 31.6 25 0.00054 24.2 1.0 27 18-45 20-46 (50)
44 PRK14873 primosome assembly pr 31.2 22 0.00047 37.9 1.0 31 16-46 390-420 (665)
45 PF07649 C1_3: C1-like domain; 30.1 24 0.00052 21.2 0.7 21 149-169 2-23 (30)
46 PF00641 zf-RanBP: Zn-finger i 28.6 19 0.00041 21.7 -0.0 21 149-169 6-26 (30)
47 PF08271 TF_Zn_Ribbon: TFIIB z 27.3 48 0.001 21.7 1.8 31 20-50 2-33 (43)
48 COG1998 RPS31 Ribosomal protei 26.8 34 0.00074 23.6 1.0 28 18-45 19-46 (51)
49 PHA02893 hypothetical protein; 26.6 39 0.00085 25.9 1.4 22 10-31 26-47 (88)
50 PF03107 C1_2: C1 domain; Int 25.8 54 0.0012 19.8 1.7 20 149-168 2-22 (30)
51 smart00109 C1 Protein kinase C 23.7 71 0.0015 20.7 2.2 31 16-48 9-39 (49)
52 PRK15103 paraquat-inducible me 23.3 7.6E+02 0.017 24.7 15.3 33 145-177 219-251 (419)
53 PF03604 DNA_RNApol_7kD: DNA d 21.4 69 0.0015 19.9 1.5 23 21-44 3-25 (32)
54 KOG3183 Predicted Zn-finger pr 20.8 44 0.00096 30.7 0.8 14 170-183 37-50 (250)
55 PRK11875 psbT photosystem II r 20.7 2.2E+02 0.0049 17.6 3.7 13 116-128 17-29 (31)
56 COG1198 PriA Primosomal protei 20.6 65 0.0014 34.7 2.1 34 16-49 442-475 (730)
57 PF09788 Tmemb_55A: Transmembr 20.6 59 0.0013 30.2 1.6 32 15-46 154-187 (256)
58 TIGR00155 pqiA_fam integral me 20.6 8.5E+02 0.018 24.2 10.6 31 147-177 13-49 (403)
59 COG2093 DNA-directed RNA polym 20.3 56 0.0012 23.7 1.1 23 147-169 4-26 (64)
60 CHL00031 psbT photosystem II p 20.1 2.4E+02 0.0051 17.7 3.7 15 116-130 17-31 (33)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-43 Score=332.41 Aligned_cols=209 Identities=27% Similarity=0.446 Sum_probs=165.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC---CC-------------CCCCCCceeccCCCCCCCCC
Q 019492 97 FCGIFHLVIAICLSVSTLSMFCLAAFHCPGASPLVLWGSYPL---VG-------------KGDLENYTFCHYCSKPKSPR 160 (340)
Q Consensus 97 ~~~~~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~~~~~~~~---~~-------------~~~~~~~~~C~~C~~~kP~R 160 (340)
....+.++++..+.++.+++|++++++|||.+|.....+.+. .+ .+.....++|.+|+.+||+|
T Consensus 43 ~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdR 122 (307)
T KOG1315|consen 43 IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDR 122 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCc
Confidence 457788888999999999999999999999998642211111 11 11223578999999999999
Q ss_pred cccccccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccCCCCCCccCchhhHH
Q 019492 161 THHCRSCGMCVLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLSIRSHAPSNVVGTDLAMR 240 (340)
Q Consensus 161 s~HC~~C~~CV~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (340)
||||++|+|||+||||||||+|||||.+|||+|++|++|+.+++++.++..+..++..+.....
T Consensus 123 aHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~---------------- 186 (307)
T KOG1315|consen 123 AHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAG---------------- 186 (307)
T ss_pred cccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc----------------
Confidence 9999999999999999999999999999999999999999999999999998888877622100
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCC--CChhh---HHHHH
Q 019492 241 FVKEIIIALLNSALLMSSRGLLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNSQGGDG--ADQKD---CQNIL 315 (340)
Q Consensus 241 ~~~~~~~~~~~~~~~~s~~~~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~~~~~~--~~~~~---~~Nl~ 315 (340)
..+.....++++++.+..+++.++.|+++|++||++|+||+|..+.+.... ++++. ..|++
T Consensus 187 --------------~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~~~n~~ 252 (307)
T KOG1315|consen 187 --------------PSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGFNLYVNFR 252 (307)
T ss_pred --------------CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCcceeecHH
Confidence 000011244566677777888888999999999999999999988763221 23333 46999
Q ss_pred hhcCCCCceeEEeeccCCCcc
Q 019492 316 RFFGCPYSVSRYLPVVRDSEK 336 (340)
Q Consensus 316 ~vFG~~~~~~w~~P~~~~~~~ 336 (340)
|+||..+ ..|++|+.++.++
T Consensus 253 ~vfg~~~-~~wl~P~~~s~~~ 272 (307)
T KOG1315|consen 253 EVFGSNL-LYWLLPIDSSWGD 272 (307)
T ss_pred HHhCCCc-eEEeccccCcccc
Confidence 9999886 9999999988766
No 2
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.4e-42 Score=312.24 Aligned_cols=277 Identities=36% Similarity=0.557 Sum_probs=196.3
Q ss_pred CCCcceeeeccCCCCccccccccccccCCCCCccceeeccceecCCCCCcccccchhhhccCceeEeeehhhHHHHhhhh
Q 019492 4 SPNEHYVTTIDKDNEPTCWGCGLHLVLPSYTPTFKCGWCGAITSLNLQKHESKWFKWRRLRDRCFVCVLFGFMGFVICGG 83 (340)
Q Consensus 4 ~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~v~~~~ 83 (340)
+.|...|-++ |..||+| +-|++|||.+.++|+|||+++..+..+++.+.+..++.+|. ...+.+++..
T Consensus 3 ~~~~sl~~~i----~~~c~~p-l~~~l~s~~~~~g~~~~~~V~~~~~~~~~t~~fi~~~f~~~----~~~~~~~f~~--- 70 (309)
T KOG1313|consen 3 HSQGSLVATI----EDICLGP-LNLVLPSYARCFGPFLVGAVTNQNTVRVETKSFILRPFRDV----ILAVFMLFLL--- 70 (309)
T ss_pred cchhhhhcch----hhhhhhH-HHHhcccccccCCCeEEEEEEeeccchhhhhhhccccHHHH----HHHHHHHHHH---
Confidence 3455556555 8899999 99999999999999999999999999998888877766661 0111111110
Q ss_pred eeeehhhhcchhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCceeccCCCCCCCCCccc
Q 019492 84 VWAVHPVVFSVSYFCGIFHLVIAICLSVSTLSMFCLAAFHCPGASPLVLWGSYPLVGKGDLENYTFCHYCSKPKSPRTHH 163 (340)
Q Consensus 84 ~~~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~H 163 (340)
......+....++.|+++..+.| +.+...+...+|.+|+.+||||+||
T Consensus 71 -------------------~~l~i~~l~nvi~hy~ka~t~pP-------------vgn~~~~~~SfC~KC~~pK~prTHH 118 (309)
T KOG1313|consen 71 -------------------ATLAIYLLSNVIFHYYKARTKPP-------------VGNPGLENDSFCNKCNYPKSPRTHH 118 (309)
T ss_pred -------------------HHHHHHHHHHHHHhheeecccCC-------------cCCCCCccccHHhhcCCCCCCCcch
Confidence 12223444566677777765543 2244566788999999999999999
Q ss_pred ccccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccCCCCC-----CccCchhh
Q 019492 164 CRSCGMCVLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLSIRSHAPS-----NVVGTDLA 238 (340)
Q Consensus 164 C~~C~~CV~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~ 238 (340)
|+.|||||+||||||||+|||||..|||||++|++|+.+++.|+.++..|..++....... ...+ +...+.+.
T Consensus 119 CsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~--~tay~~d~~h~~Pp~~i 196 (309)
T KOG1313|consen 119 CSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE--ITAYASDVAHVAPPPSI 196 (309)
T ss_pred hhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh--cccccCcccccCCChhh
Confidence 9999999999999999999999999999999999999999999999988776655433221 1111 11111111
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEecccC----------CCCCCCh
Q 019492 239 MRFVKEIIIALLNSALLMSSRGLLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNSQ----------GGDGADQ 308 (340)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~s~~~~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~~----------~~~~~~~ 308 (340)
-+.... +....+..+.+++..++++++.+..+|.++|.+|+|++|+++.. +.++++.
T Consensus 197 ~r~~~~-------------i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~~n~ 263 (309)
T KOG1313|consen 197 LRVYKN-------------ITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNPTNF 263 (309)
T ss_pred hhhhhh-------------hhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCCccc
Confidence 111111 11122344667777788889999999999999999999976443 3345666
Q ss_pred hhHHHHHhhcC---CC-CceeEEeeccCCCccccC
Q 019492 309 KDCQNILRFFG---CP-YSVSRYLPVVRDSEKRHT 339 (340)
Q Consensus 309 ~~~~Nl~~vFG---~~-~~~~w~~P~~~~~~~~~~ 339 (340)
|..+||+.++| .+ .+..-++|......+.+|
T Consensus 264 g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p~~~~~ 298 (309)
T KOG1313|consen 264 GGKANWRNFLGLFRGRHFWKTVLLPTIRKPVKYGD 298 (309)
T ss_pred chHHHHHHhhccccCCceeEEEeccccccccccCC
Confidence 66555555554 55 335568999888877665
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.5e-40 Score=312.45 Aligned_cols=204 Identities=26% Similarity=0.454 Sum_probs=152.3
Q ss_pred HHHHHHHHHHHHHHHHHhc---CCCCCCCCCCCCCC----------CCCCCCCCCceeccCCCCCCCCCcccccccCccc
Q 019492 105 IAICLSVSTLSMFCLAAFH---CPGASPLVLWGSYP----------LVGKGDLENYTFCHYCSKPKSPRTHHCRSCGMCV 171 (340)
Q Consensus 105 ~~~~l~~~~~~~y~~~~~~---dPG~~~~~~~~~~~----------~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV 171 (340)
...++.+..+.+...+.++ |||.+|+....+.+ ...++...+.+||.+|+..||+|||||+.||+||
T Consensus 58 ~~~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV 137 (299)
T KOG1311|consen 58 LGAIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCV 137 (299)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccc
Confidence 3334444444555555555 99999984211111 1123344568999999999999999999999999
Q ss_pred ccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccCCCCCCccCchhhHHHHHHHHHHHHH
Q 019492 172 LDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLSIRSHAPSNVVGTDLAMRFVKEIIIALLN 251 (340)
Q Consensus 172 ~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (340)
.||||||||+|||||++|||+|+.|+++.++++++.++...+.+.....+.... +. +
T Consensus 138 ~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~-------------~~---~------- 194 (299)
T KOG1311|consen 138 LRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVN-------------LT---P------- 194 (299)
T ss_pred cccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc-------------cc---c-------
Confidence 999999999999999999999999999999999999999888766554433211 11 0
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEeccc----CCCCCCChhhHHHHHhhcCCCCceeEE
Q 019492 252 SALLMSSRGLLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNS----QGGDGADQKDCQNILRFFGCPYSVSRY 327 (340)
Q Consensus 252 ~~~~~s~~~~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~----~~~~~~~~~~~~Nl~~vFG~~~~~~w~ 327 (340)
..........+++.++++.+.+.++.|+.+|++++.+|+||+|++++ .+.+++++|.++|++++||.+....|+
T Consensus 195 --~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~ 272 (299)
T KOG1311|consen 195 --VLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWL 272 (299)
T ss_pred --cccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCCCCCcccc
Confidence 00000112334445667777788889999999999999999999875 223688889899999999999999999
Q ss_pred eeccCC
Q 019492 328 LPVVRD 333 (340)
Q Consensus 328 ~P~~~~ 333 (340)
-|....
T Consensus 273 ~p~~~~ 278 (299)
T KOG1311|consen 273 SPFARS 278 (299)
T ss_pred cccccC
Confidence 998865
No 4
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-38 Score=295.10 Aligned_cols=206 Identities=32% Similarity=0.456 Sum_probs=151.3
Q ss_pred hcchhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCceeccCCCCCCCCCcccccccCcc
Q 019492 91 VFSVSYFCGIFHLVIAICLSVSTLSMFCLAAFHCPGASPLVLWGSYPLVGKGDLENYTFCHYCSKPKSPRTHHCRSCGMC 170 (340)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~C 170 (340)
.++.++..+..+.+.+.....+.++||+.+++++||.+|..-. |.. ..+..-.+||..|+.+|+||||||+.||||
T Consensus 39 w~p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wk---Pe~-~~D~~~lqfCk~CqgYKapRSHHCrkCnrC 114 (414)
T KOG1314|consen 39 WFPLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWK---PEN-PKDEMFLQFCKKCQGYKAPRSHHCRKCNRC 114 (414)
T ss_pred hccccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC---CCC-ChhHHHHHHHhhccCcCCCccccchHHHHH
Confidence 4567788999999999999999999999999999999997422 211 122234689999999999999999999999
Q ss_pred cccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccCCCCCCccCchhhHHHHHHHHHHHH
Q 019492 171 VLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLSIRSHAPSNVVGTDLAMRFVKEIIIALL 250 (340)
Q Consensus 171 V~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 (340)
|.+|||||||+|||||.+||.||+.||++..++|+-..++...++++......+...+.-+.
T Consensus 115 vmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hl------------------ 176 (414)
T KOG1314|consen 115 VMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHL------------------ 176 (414)
T ss_pred HHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccC------------------
Confidence 99999999999999999999999999999999887766655444433222211100000010
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEecccC--------------C--CCCCChhhHHHH
Q 019492 251 NSALLMSSRGLLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNSQ--------------G--GDGADQKDCQNI 314 (340)
Q Consensus 251 ~~~~~~s~~~~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~~--------------~--~~~~~~~~~~Nl 314 (340)
...++.-...+++++.+-+++.+.+++++||+.|+..|.+|+|.+|.+... + .-+||.|...|+
T Consensus 177 p~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~ 256 (414)
T KOG1314|consen 177 PIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINL 256 (414)
T ss_pred ceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccH
Confidence 000011112234556666677778899999999999999999999976511 0 125677744599
Q ss_pred Hhhc
Q 019492 315 LRFF 318 (340)
Q Consensus 315 ~~vF 318 (340)
++||
T Consensus 257 r~vf 260 (414)
T KOG1314|consen 257 REVF 260 (414)
T ss_pred HHHh
Confidence 9998
No 5
>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=1.9e-37 Score=271.50 Aligned_cols=159 Identities=32% Similarity=0.596 Sum_probs=124.0
Q ss_pred HHHHHHHhcCCCCCCCCC-C--------C-----CCCCCCCCCCCCceeccCCCCCCCCCcccccccCcccccccccCcc
Q 019492 115 SMFCLAAFHCPGASPLVL-W--------G-----SYPLVGKGDLENYTFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPF 180 (340)
Q Consensus 115 ~~y~~~~~~dPG~~~~~~-~--------~-----~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~W 180 (340)
++|++++++|||++|... . . .....+.+...+.++|.+|+..||+|||||+.||+||.||||||+|
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 468899999999999871 0 0 0111223445668999999999999999999999999999999999
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccCCCCCCccCchhhHHHHHHHHHHHHHHHHHHhHHH
Q 019492 181 IGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLSIRSHAPSNVVGTDLAMRFVKEIIIALLNSALLMSSRG 260 (340)
Q Consensus 181 i~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 260 (340)
+|||||++|||+|++|+++..+++++.+...++.+............ +.. ..
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~-----------------~~ 133 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSF-----------WIF-----------------SN 133 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc-----------ccc-----------------hh
Confidence 99999999999999999999999999999888877766543321100 000 00
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEecccC
Q 019492 261 LLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNSQ 301 (340)
Q Consensus 261 ~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~~ 301 (340)
...+++++++++++++++.++++|++++++|+||+|.++++
T Consensus 134 ~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 134 FSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 01245556667788888999999999999999999998864
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=1.4e-32 Score=260.57 Aligned_cols=121 Identities=31% Similarity=0.609 Sum_probs=98.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC-CC-----CCCCCCCCCCCCceeccCCCCCCCCCcccccccCcccc
Q 019492 99 GIFHLVIAICLSVSTLSMFCLAAFHCPGASPLVL-WG-----SYPLVGKGDLENYTFCHYCSKPKSPRTHHCRSCGMCVL 172 (340)
Q Consensus 99 ~~~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~~-~~-----~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~ 172 (340)
.....+...+.......+|+...+.|||.++... .. ..+..+.+.....++|.+|+.+||+|||||+.||+||+
T Consensus 55 ~~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~ 134 (309)
T COG5273 55 VVLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVL 134 (309)
T ss_pred hhhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhh
Confidence 3444455556667888899999999999998431 11 11223445566789999999999999999999999999
Q ss_pred cccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 019492 173 DMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIW 219 (340)
Q Consensus 173 ~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~ 219 (340)
||||||+|+|||||.+|||+|++|+++.....++++..+.+.+....
T Consensus 135 k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~ 181 (309)
T COG5273 135 KFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIF 181 (309)
T ss_pred ccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999888888877766554
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.96 E-value=7.8e-30 Score=231.12 Aligned_cols=117 Identities=30% Similarity=0.541 Sum_probs=99.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCC----CCCCCCCCCCCceeccCCCCCCCCCcccccccCcccc
Q 019492 97 FCGIFHLVIAICLSVSTLSMFCLAAFHCPGASPLVLWGS----YPLVGKGDLENYTFCHYCSKPKSPRTHHCRSCGMCVL 172 (340)
Q Consensus 97 ~~~~~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~~~~~----~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~ 172 (340)
..+..+.+....+.+.-.+++..++.+|||.....++.. ||. +.........|++|+.+||+||||||.||+||.
T Consensus 95 ~lsl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypY-Dy~if~k~~kCSTCki~KPARSKHCsiCNrCV~ 173 (341)
T KOG1312|consen 95 ELSLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPY-DYVIFPKNVKCSTCKIRKPARSKHCSICNRCVH 173 (341)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCc-cceeecCCCccccccCCCccccccchHHHHHHH
Confidence 467788888888888889999999999999998766533 332 223345568999999999999999999999999
Q ss_pred cccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhh
Q 019492 173 DMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTA 214 (340)
Q Consensus 173 ~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~ 214 (340)
||||||.|+|||||++|+|||++|+++...++.|+..-..+.
T Consensus 174 rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi 215 (341)
T KOG1312|consen 174 RFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFI 215 (341)
T ss_pred HhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHhe
Confidence 999999999999999999999999999988888877665554
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.91 E-value=3.6e-25 Score=219.94 Aligned_cols=105 Identities=32% Similarity=0.638 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCC----CCCCCCCCCCc-eeccCCCCCCCCCcccccccCcccccccccCccccccc
Q 019492 111 VSTLSMFCLAAFHCPGASPLVLWGSY----PLVGKGDLENY-TFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPFIGNCV 185 (340)
Q Consensus 111 ~~~~~~y~~~~~~dPG~~~~~~~~~~----~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCI 185 (340)
+..++.+.+..-+|||.+|....... +..+.+..+.. +||.+|..+||.|||||+.||+||.||||||||++|||
T Consensus 379 l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncV 458 (600)
T KOG0509|consen 379 LAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCV 458 (600)
T ss_pred HHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCcccccc
Confidence 33444455555699999987543221 12334444444 79999999999999999999999999999999999999
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019492 186 GAANHRYFILFLISAVVSTIYVAIMSVTAG 215 (340)
Q Consensus 186 G~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~ 215 (340)
|.+|||+|+.|++.....+.+.+....+++
T Consensus 459 G~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~ 488 (600)
T KOG0509|consen 459 GLKNHRLFVFFLLTLLTVIVFYLYLCLYYI 488 (600)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999988888777766654
No 9
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=97.56 E-value=0.0012 Score=61.08 Aligned_cols=156 Identities=21% Similarity=0.238 Sum_probs=97.7
Q ss_pred CCceeccCCCCCCCCCcccccccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccc-
Q 019492 145 ENYTFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLHIWSPLS- 223 (340)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~- 223 (340)
++...|+.|+.-.-.=-|||..=|.||.-..| +=.-.|+.++.-+..++.+............+....
T Consensus 114 prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ta 182 (309)
T KOG1313|consen 114 PRTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEITA 182 (309)
T ss_pred CCcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhccc
Confidence 34568888887767778999999999998877 455678888876666666554433332222221111
Q ss_pred c--cCCCCCCccCchhhHHHHH-HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEeccc
Q 019492 224 I--RSHAPSNVVGTDLAMRFVK-EIIIALLNSALLMSSRGLLLVYLFVSSISVNLGLSVLLWQQLFYIYEGKTYLSHLNS 300 (340)
Q Consensus 224 ~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~s~~~~~li~l~v~~~~~~i~~~~Ll~~hl~li~~n~Tt~E~~~~ 300 (340)
+ +.....+...-....+.+. ..+. ...+++.+..+++..+......+|..+...+.|+.++..++++..+.++
T Consensus 183 y~~d~~h~~Pp~~i~r~~~~i~~t~~~----~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~ 258 (309)
T KOG1313|consen 183 YASDVAHVAPPPSILRVYKNITRTSIA----NLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRS 258 (309)
T ss_pred ccCcccccCCChhhhhhhhhhhHHHHH----HHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccC
Confidence 0 1001101100011111111 1111 1334555555666666666677788899999999999999999999999
Q ss_pred CCCCCCChhhHHHHH
Q 019492 301 QGGDGADQKDCQNIL 315 (340)
Q Consensus 301 ~~~~~~~~~~~~Nl~ 315 (340)
+..+...+..|+|+.
T Consensus 259 ~~~n~g~k~nWr~fL 273 (309)
T KOG1313|consen 259 NPTNFGGKANWRNFL 273 (309)
T ss_pred CCcccchHHHHHHhh
Confidence 888888888888864
No 10
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=93.51 E-value=0.042 Score=34.17 Aligned_cols=28 Identities=25% Similarity=0.713 Sum_probs=25.8
Q ss_pred ccccccccccccCCCCCccceeecccee
Q 019492 19 PTCWGCGLHLVLPSYTPTFKCGWCGAIT 46 (340)
Q Consensus 19 ~~c~~c~~~~~~~~~~~~~~c~~~~~~~ 46 (340)
..|-+||..|..|.-++.++|.-|..+|
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCCeEe
Confidence 3699999999999999999999998876
No 11
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=92.00 E-value=3.6 Score=39.04 Aligned_cols=41 Identities=22% Similarity=0.466 Sum_probs=33.6
Q ss_pred cccccccCcccccccccCcccccccccc-----------cHHHHHHHHHHHH
Q 019492 161 THHCRSCGMCVLDMDHHCPFIGNCVGAA-----------NHRYFILFLISAV 201 (340)
Q Consensus 161 s~HC~~C~~CV~~~DHHC~Wi~nCIG~~-----------N~r~Fi~fl~~~~ 201 (340)
.++|..|+..+.++-|||..-|+||-+. -+|-+-.|+.+++
T Consensus 113 ~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred eEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 7889999999999999999999999776 3467888885554
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=90.06 E-value=4.1 Score=39.11 Aligned_cols=61 Identities=16% Similarity=0.379 Sum_probs=33.5
Q ss_pred CCCCcccccccCcccccccccCcccccccccc-----------cHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019492 157 KSPRTHHCRSCGMCVLDMDHHCPFIGNCVGAA-----------NHRYFILFLISAVVSTIYVAIMSVTAGLH 217 (340)
Q Consensus 157 kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~-----------N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~ 217 (340)
+-.+.+.|+.|+.-.+..-|||.--|.||-+- ..|-.=.|..++.......+.+.+...+.
T Consensus 105 ~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~ 176 (309)
T COG5273 105 KFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYY 176 (309)
T ss_pred ccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445666666666666666666666666444 23445555555555444444444444433
No 13
>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=89.33 E-value=3.5 Score=35.39 Aligned_cols=64 Identities=17% Similarity=0.330 Sum_probs=46.1
Q ss_pred CCCCceeccCCCCCCCCCcccccccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019492 143 DLENYTFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIYVAIMSVTAGLH 217 (340)
Q Consensus 143 ~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~~~~~~~~~~~~ 217 (340)
..++.++|..|+.-...+-|||..-+.||.+.-| +..-.|+.+..-..+...+.....+.....
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~ 121 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSLYYLVRYIP 121 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4456789999998899999999999999998666 455677777666666666655555554443
No 14
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=86.49 E-value=3.6 Score=39.44 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=16.5
Q ss_pred CcccccccCcccccccccCcccccccccc
Q 019492 160 RTHHCRSCGMCVLDMDHHCPFIGNCVGAA 188 (340)
Q Consensus 160 Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~ 188 (340)
+.+.|..|+.-.++.-|||.--+.||.+-
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKm 136 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKM 136 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhcc
Confidence 44555555555555555555555555554
No 15
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.32 E-value=0.49 Score=27.24 Aligned_cols=21 Identities=24% Similarity=0.830 Sum_probs=18.5
Q ss_pred eccCCCCCCCCCcccccccCc
Q 019492 149 FCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
+|+.|....++.++.|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688999999999999999885
No 16
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=83.29 E-value=0.72 Score=27.18 Aligned_cols=25 Identities=32% Similarity=0.902 Sum_probs=22.4
Q ss_pred ccccccccccCCCCCccceeeccce
Q 019492 21 CWGCGLHLVLPSYTPTFKCGWCGAI 45 (340)
Q Consensus 21 c~~c~~~~~~~~~~~~~~c~~~~~~ 45 (340)
|-||+..|..|.-++.-+|.-|..+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 7899999999999999999998653
No 17
>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=81.24 E-value=61 Score=32.30 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=25.5
Q ss_pred cCCCCccccccccccccCCCCCc--cceeeccceec
Q 019492 14 DKDNEPTCWGCGLHLVLPSYTPT--FKCGWCGAITS 47 (340)
Q Consensus 14 ~~~~~~~c~~c~~~~~~~~~~~~--~~c~~~~~~~~ 47 (340)
+++.-..|-.|++-...|...+. -+|..||+.-.
T Consensus 9 ~~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 9 PAAKHILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred CCCCeeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 34445569999999988876554 46999988773
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=78.99 E-value=1.1 Score=26.43 Aligned_cols=22 Identities=32% Similarity=0.940 Sum_probs=18.8
Q ss_pred eeccCCCCCCCCCcccccccCc
Q 019492 148 TFCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
++|+.|....++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 5789999988888999998875
No 19
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=70.34 E-value=2.8 Score=28.59 Aligned_cols=24 Identities=33% Similarity=0.809 Sum_probs=21.9
Q ss_pred CceeccCCCCCCCCCcccccccCc
Q 019492 146 NYTFCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
+.+.|..|...-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 467999999999999999999886
No 20
>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=68.74 E-value=2.9 Score=29.56 Aligned_cols=36 Identities=36% Similarity=0.900 Sum_probs=28.4
Q ss_pred eccCCCCCCCCCc-------ccccccCcccccc-cccCccccccccc
Q 019492 149 FCHYCSKPKSPRT-------HHCRSCGMCVLDM-DHHCPFIGNCVGA 187 (340)
Q Consensus 149 ~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHHC~Wi~nCIG~ 187 (340)
-|..|+..-|+-| +-|..|..|+..+ +++|| ||=|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 4777777766664 6688999999999 99999 77665
No 21
>PF12773 DZR: Double zinc ribbon
Probab=68.59 E-value=4.6 Score=27.35 Aligned_cols=36 Identities=25% Similarity=0.636 Sum_probs=25.5
Q ss_pred CCceeccCCCCCCC---CCcccccccCcccccccccCcc
Q 019492 145 ENYTFCHYCSKPKS---PRTHHCRSCGMCVLDMDHHCPF 180 (340)
Q Consensus 145 ~~~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHHC~W 180 (340)
++.++|..|....+ .....|..|++=+...+.+|+.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 44678888877655 3466788888877777777764
No 22
>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=65.96 E-value=3.7 Score=24.35 Aligned_cols=22 Identities=23% Similarity=0.667 Sum_probs=18.9
Q ss_pred eeccCCCCCCCCCcccccccCc
Q 019492 148 TFCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
+.|+.|....|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4689999999999999988875
No 23
>PF11278 DUF3079: Protein of unknown function (DUF3079); InterPro: IPR021430 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=61.90 E-value=3.8 Score=28.00 Aligned_cols=24 Identities=33% Similarity=0.803 Sum_probs=16.2
Q ss_pred cCCCCccccccccccccCCCCCccceee
Q 019492 14 DKDNEPTCWGCGLHLVLPSYTPTFKCGW 41 (340)
Q Consensus 14 ~~~~~~~c~~c~~~~~~~~~~~~~~c~~ 41 (340)
+.--|.+||||-..-- +..-.||-
T Consensus 9 P~hPERiCWGCD~YC~----a~~l~CGN 32 (52)
T PF11278_consen 9 PKHPERICWGCDRYCP----ADSLACGN 32 (52)
T ss_pred CCCccceeeccccccC----hhhhcccC
Confidence 5667999999987433 34556664
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=61.15 E-value=5.2 Score=26.83 Aligned_cols=30 Identities=30% Similarity=0.672 Sum_probs=24.2
Q ss_pred CccccccccccccCCCCCccceeeccceec
Q 019492 18 EPTCWGCGLHLVLPSYTPTFKCGWCGAITS 47 (340)
Q Consensus 18 ~~~c~~c~~~~~~~~~~~~~~c~~~~~~~~ 47 (340)
+-.|-.||..+.+.+.....+|..||....
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 457999999988877766899999987553
No 25
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=59.09 E-value=23 Score=34.42 Aligned_cols=87 Identities=20% Similarity=0.236 Sum_probs=56.5
Q ss_pred HHHHHHhcCCCCCCCCCCC----CCCCC-CCCCCCCceeccCCCCCCCCCcccccccCcccccccccCcccccccccccH
Q 019492 116 MFCLAAFHCPGASPLVLWG----SYPLV-GKGDLENYTFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPFIGNCVGAANH 190 (340)
Q Consensus 116 ~y~~~~~~dPG~~~~~~~~----~~~~~-~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~N~ 190 (340)
.+.--=+..+|.-|..... ++=.. +.-..++...|.+|+.-.-.=-|||..-+.||.-..| .-.
T Consensus 69 ~~~gPG~vp~~wkPe~~~D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh-----------~~F 137 (414)
T KOG1314|consen 69 IFTGPGFVPLGWKPENPKDEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANH-----------AYF 137 (414)
T ss_pred HhcCCCCCCCCCCCCCChhHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhccccccc-----------HHH
Confidence 3333448899988754322 11001 1123456789999987777778999999999986655 356
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 019492 191 RYFILFLISAVVSTIYVAIMSVT 213 (340)
Q Consensus 191 r~Fi~fl~~~~~~~~~~~~~~~~ 213 (340)
-+|++|.+.+.+-...++....+
T Consensus 138 ~~FLlf~ivG~ih~tiI~~~~~~ 160 (414)
T KOG1314|consen 138 LRFLLFSIVGCIHGTIILVCAQY 160 (414)
T ss_pred HHHHHHHHHhcccceeeehhHHH
Confidence 89999999866555444444433
No 26
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=51.27 E-value=8.6 Score=39.88 Aligned_cols=58 Identities=9% Similarity=-0.128 Sum_probs=45.3
Q ss_pred eeccCCCCCCCCCcccccccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHH
Q 019492 148 TFCHYCSKPKSPRTHHCRSCGMCVLDMDHHCPFIGNCVGAANHRYFILFLISAVVSTIY 206 (340)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~Wi~nCIG~~N~r~Fi~fl~~~~~~~~~ 206 (340)
..|..+....+.+..++..+-.++..+++||.|.. +|+.+|...|-...+..++..++
T Consensus 326 ~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~~~~ 383 (600)
T KOG0509|consen 326 CLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLAYFI 383 (600)
T ss_pred eeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHHHHH
Confidence 46677777788889999999999999999999999 99999988654444433333333
No 27
>PF12773 DZR: Double zinc ribbon
Probab=50.08 E-value=13 Score=25.12 Aligned_cols=24 Identities=25% Similarity=0.852 Sum_probs=21.1
Q ss_pred CCceeccCCCCCCCCCcccccccC
Q 019492 145 ENYTFCHYCSKPKSPRTHHCRSCG 168 (340)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~C~ 168 (340)
....+|..|....++.+++|..||
T Consensus 27 ~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 27 QSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCCcCCcCCCcCCcCccCccc
Confidence 346799999999999999999886
No 28
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=47.57 E-value=1.3e+02 Score=23.29 Aligned_cols=23 Identities=17% Similarity=0.203 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhCCeeEEecccC
Q 019492 279 VLLWQQLFYIYEGKTYLSHLNSQ 301 (340)
Q Consensus 279 ~Ll~~hl~li~~n~Tt~E~~~~~ 301 (340)
+++++.+|--+++.+..|++++.
T Consensus 62 Gilifs~y~~C~~~~~~~r~n~s 84 (91)
T PHA02680 62 GLFVFSMYRKCSGSMPYERLNNT 84 (91)
T ss_pred HHHHHHHhcccCCCceeecccCC
Confidence 46666777678888888988654
No 29
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=47.45 E-value=13 Score=39.84 Aligned_cols=22 Identities=45% Similarity=1.088 Sum_probs=18.0
Q ss_pred eeccCCCCCCC-------CCcccccccCc
Q 019492 148 TFCHYCSKPKS-------PRTHHCRSCGM 169 (340)
Q Consensus 148 ~~C~~C~~~kP-------~Rs~HC~~C~~ 169 (340)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999987764 38999999987
No 30
>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=46.73 E-value=29 Score=24.90 Aligned_cols=23 Identities=30% Similarity=0.795 Sum_probs=17.5
Q ss_pred ceeccCCCCCCCCCccccc-ccCc
Q 019492 147 YTFCHYCSKPKSPRTHHCR-SCGM 169 (340)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~-~C~~ 169 (340)
-+.|..|+..-|+.-..|| .|++
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 4678888888888888886 5555
No 31
>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=46.68 E-value=9.2 Score=27.69 Aligned_cols=25 Identities=44% Similarity=0.903 Sum_probs=12.7
Q ss_pred ceeccCCCCC--CCCCcccccccCccc
Q 019492 147 YTFCHYCSKP--KSPRTHHCRSCGMCV 171 (340)
Q Consensus 147 ~~~C~~C~~~--kP~Rs~HC~~C~~CV 171 (340)
...|..|+.. .-.|-|||+.||+.|
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 4678888754 457899999999854
No 32
>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 PF10749 DUF2534: Protein of unknown function (DUF2534); InterPro: IPR019685 This entry represents proteins with unknown function, and appear to be restricted to Enterobacteriaceae.
Probab=41.35 E-value=1.6e+02 Score=22.53 Aligned_cols=71 Identities=17% Similarity=0.206 Sum_probs=34.9
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHH-HHhhhhhhcccccccCCCCCCccCchhhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 019492 186 GAANHRYFILFLISAVVSTIYVAIM-SVTAGLHIWSPLSIRSHAPSNVVGTDLAMRFVKEIIIALLNSALLMSSRGLLLV 264 (340)
Q Consensus 186 G~~N~r~Fi~fl~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~li 264 (340)
-.+|-|.|+.-+.-+.+...-+..= .+-..+..+ +. +.++|..-+-+++. ..+++
T Consensus 8 k~~~~kkFl~~l~~vfiia~~Vv~rAt~gGVi~qY-----------ni--P~s~WttsMf~~Q~-----------ami~v 63 (85)
T PF10749_consen 8 KTKEGKKFLLALAIVFIIAATVVGRATIGGVIEQY-----------NI--PFSEWTTSMFILQG-----------AMILV 63 (85)
T ss_pred cChhhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHh-----------CC--ChhhhhHHHHHHHH-----------HHHHH
Confidence 3578888887765554432222211 111111111 11 35778765444433 23456
Q ss_pred HHHHHHHHHHHHHHHH
Q 019492 265 YLFVSSISVNLGLSVL 280 (340)
Q Consensus 265 ~l~v~~~~~~i~~~~L 280 (340)
+..++++.+.+.++..
T Consensus 64 YS~VFT~L~sIPlg~~ 79 (85)
T PF10749_consen 64 YSIVFTILLSIPLGFY 79 (85)
T ss_pred HHHHHHHHHHHHHHhe
Confidence 6666666666665543
No 34
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=41.13 E-value=9.7 Score=24.40 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=21.8
Q ss_pred ccccccccccccCC-----CCCccceeeccce
Q 019492 19 PTCWGCGLHLVLPS-----YTPTFKCGWCGAI 45 (340)
Q Consensus 19 ~~c~~c~~~~~~~~-----~~~~~~c~~~~~~ 45 (340)
.+|-.|+....+|. .....+|+.|+.+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 57999999998885 3558899999764
No 35
>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=40.50 E-value=27 Score=25.16 Aligned_cols=37 Identities=24% Similarity=0.347 Sum_probs=27.3
Q ss_pred eeeccCCCCccccccccccccCCCCCccceeecccee
Q 019492 10 VTTIDKDNEPTCWGCGLHLVLPSYTPTFKCGWCGAIT 46 (340)
Q Consensus 10 ~~~~~~~~~~~c~~c~~~~~~~~~~~~~~c~~~~~~~ 46 (340)
+.+.+...-.+|..||...--+.....+.|.-||..-
T Consensus 20 ~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 20 VEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred EEECCCCCccCccCcccccccccccceEEcCCCCCEE
Confidence 3344444556799999987765567799999998876
No 36
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=38.61 E-value=7 Score=26.79 Aligned_cols=26 Identities=35% Similarity=0.833 Sum_probs=22.2
Q ss_pred CceeccCCCCCCCCCcccccccCccc
Q 019492 146 NYTFCHYCSKPKSPRTHHCRSCGMCV 171 (340)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~C~~CV 171 (340)
+.+.|..|+..-|+|+.-|+.|+.=-
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~k~ 38 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGYKN 38 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccCCC
Confidence 46789999999999999999887633
No 37
>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=37.14 E-value=19 Score=25.09 Aligned_cols=25 Identities=32% Similarity=0.854 Sum_probs=16.9
Q ss_pred CceeccCCCCCCCCCcccccc--cCcc
Q 019492 146 NYTFCHYCSKPKSPRTHHCRS--CGMC 170 (340)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 170 (340)
+...|..|...-|+|+..|+. ||.+
T Consensus 16 ~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 16 DKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp S-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cceecccccCcCCCCccceecccCCCC
Confidence 457899999999999999998 8764
No 38
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=36.84 E-value=11 Score=23.35 Aligned_cols=21 Identities=33% Similarity=0.947 Sum_probs=15.0
Q ss_pred cccccccccccCCCCC-----cccee
Q 019492 20 TCWGCGLHLVLPSYTP-----TFKCG 40 (340)
Q Consensus 20 ~c~~c~~~~~~~~~~~-----~~~c~ 40 (340)
-|-.||..++.|-|.+ +|+|+
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcs 28 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCS 28 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES
T ss_pred cCCccCceEEEEeecCCCcEEEEEcC
Confidence 4889999999987754 66765
No 39
>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=36.82 E-value=76 Score=29.08 Aligned_cols=31 Identities=10% Similarity=0.151 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 019492 101 FHLVIAICLSVSTLSMFCLAAFHCPGASPLV 131 (340)
Q Consensus 101 ~~~~~~~~l~~~~~~~y~~~~~~dPG~~~~~ 131 (340)
+.+++..++.+..+..|.++.-+|||.+.+.
T Consensus 195 IaliVitl~vf~LvgLyr~C~k~dPg~p~~g 225 (259)
T PF07010_consen 195 IALIVITLSVFTLVGLYRMCWKTDPGTPENG 225 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCcccC
Confidence 3344445555666667777778999987664
No 40
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=36.56 E-value=17 Score=26.76 Aligned_cols=27 Identities=33% Similarity=0.635 Sum_probs=19.5
Q ss_pred cccccccccccCCCCCccceeeccceecC
Q 019492 20 TCWGCGLHLVLPSYTPTFKCGWCGAITSL 48 (340)
Q Consensus 20 ~c~~c~~~~~~~~~~~~~~c~~~~~~~~~ 48 (340)
.| .||.+|.-...+...+| -||...+=
T Consensus 5 rC-~Cgr~lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 5 RC-DCGRYLYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp EE-TTS--EEEETT-SEEEE-TTTEEEE-
T ss_pred Ee-cCCCEEEecCCcceeEe-cCCCeeee
Confidence 58 89999998888889999 99987743
No 41
>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=34.89 E-value=27 Score=24.01 Aligned_cols=23 Identities=48% Similarity=1.086 Sum_probs=15.7
Q ss_pred eeccCCCCC--CCCCcccccccCcc
Q 019492 148 TFCHYCSKP--KSPRTHHCRSCGMC 170 (340)
Q Consensus 148 ~~C~~C~~~--kP~Rs~HC~~C~~C 170 (340)
+.|..|+.. .-.|.|||+.|++-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCCccccccCcCcCC
Confidence 456666542 46678899988874
No 42
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=34.75 E-value=13 Score=37.23 Aligned_cols=26 Identities=38% Similarity=0.966 Sum_probs=20.8
Q ss_pred CceeccCCCCC--CCCCcccccccCccc
Q 019492 146 NYTFCHYCSKP--KSPRTHHCRSCGMCV 171 (340)
Q Consensus 146 ~~~~C~~C~~~--kP~Rs~HC~~C~~CV 171 (340)
...+|+.|... --.|-|||+.||+-+
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHH
Confidence 46899999865 567899999999843
No 43
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=31.61 E-value=25 Score=24.22 Aligned_cols=27 Identities=26% Similarity=0.634 Sum_probs=21.3
Q ss_pred CccccccccccccCCCCCccceeeccce
Q 019492 18 EPTCWGCGLHLVLPSYTPTFKCGWCGAI 45 (340)
Q Consensus 18 ~~~c~~c~~~~~~~~~~~~~~c~~~~~~ 45 (340)
...|.-||.. ++..-..-+.|+-||..
T Consensus 20 ~~fCP~Cg~~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCPRCGSG-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCcCCCcc-hheccCCcEECCCcCCE
Confidence 4589999998 66666688999999753
No 44
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.23 E-value=22 Score=37.90 Aligned_cols=31 Identities=35% Similarity=0.712 Sum_probs=25.9
Q ss_pred CCCccccccccccccCCCCCccceeecccee
Q 019492 16 DNEPTCWGCGLHLVLPSYTPTFKCGWCGAIT 46 (340)
Q Consensus 16 ~~~~~c~~c~~~~~~~~~~~~~~c~~~~~~~ 46 (340)
.+...|-.|+..|.+.+....-+|+|||...
T Consensus 390 g~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 390 RTPARCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred cCeeECCCCCCceeEecCCCeeECCCCcCCC
Confidence 4567899999999988877889999999854
No 45
>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=30.14 E-value=24 Score=21.25 Aligned_cols=21 Identities=29% Similarity=0.719 Sum_probs=9.0
Q ss_pred eccCCCCCCCC-CcccccccCc
Q 019492 149 FCHYCSKPKSP-RTHHCRSCGM 169 (340)
Q Consensus 149 ~C~~C~~~kP~-Rs~HC~~C~~ 169 (340)
.|..|+..... ..++|..|+-
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 57888877666 7888888875
No 46
>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=28.56 E-value=19 Score=21.69 Aligned_cols=21 Identities=24% Similarity=0.667 Sum_probs=13.6
Q ss_pred eccCCCCCCCCCcccccccCc
Q 019492 149 FCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
.|..|...-++++.+|..|+.
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 577777777777777777764
No 47
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=27.31 E-value=48 Score=21.72 Aligned_cols=31 Identities=26% Similarity=0.545 Sum_probs=17.7
Q ss_pred ccccccccc-ccCCCCCccceeeccceecCCC
Q 019492 20 TCWGCGLHL-VLPSYTPTFKCGWCGAITSLNL 50 (340)
Q Consensus 20 ~c~~c~~~~-~~~~~~~~~~c~~~~~~~~~~~ 50 (340)
.|..||..- +.....--+-|.-||.+.+...
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE-TT
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEeeccc
Confidence 477777764 3333334457888888876554
No 48
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.75 E-value=34 Score=23.60 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=22.7
Q ss_pred CccccccccccccCCCCCccceeeccce
Q 019492 18 EPTCWGCGLHLVLPSYTPTFKCGWCGAI 45 (340)
Q Consensus 18 ~~~c~~c~~~~~~~~~~~~~~c~~~~~~ 45 (340)
...|..||-..+|+.-.+-..||-||-.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccce
Confidence 4579999988888777778889999743
No 49
>PHA02893 hypothetical protein; Provisional
Probab=26.64 E-value=39 Score=25.88 Aligned_cols=22 Identities=36% Similarity=0.446 Sum_probs=19.1
Q ss_pred eeeccCCCCccccccccccccC
Q 019492 10 VTTIDKDNEPTCWGCGLHLVLP 31 (340)
Q Consensus 10 ~~~~~~~~~~~c~~c~~~~~~~ 31 (340)
-|.+++|.-++|.-|++.|+.=
T Consensus 26 ~T~~~~d~C~TCSsC~SKLV~~ 47 (88)
T PHA02893 26 ETAIPEDACTTCQICQSKLVMF 47 (88)
T ss_pred ceecCCCCCcchhhhhcceeee
Confidence 3667999999999999999864
No 50
>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=25.75 E-value=54 Score=19.77 Aligned_cols=20 Identities=25% Similarity=0.733 Sum_probs=14.5
Q ss_pred eccCCCCCCCCC-cccccccC
Q 019492 149 FCHYCSKPKSPR-THHCRSCG 168 (340)
Q Consensus 149 ~C~~C~~~kP~R-s~HC~~C~ 168 (340)
.|..|+...... .++|+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477777766666 78887776
No 51
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=23.70 E-value=71 Score=20.66 Aligned_cols=31 Identities=16% Similarity=0.484 Sum_probs=23.3
Q ss_pred CCCccccccccccccCCCCCccceeeccceecC
Q 019492 16 DNEPTCWGCGLHLVLPSYTPTFKCGWCGAITSL 48 (340)
Q Consensus 16 ~~~~~c~~c~~~~~~~~~~~~~~c~~~~~~~~~ 48 (340)
...+.|-.|+..+.... +.++|.||+....+
T Consensus 9 ~~~~~C~~C~~~i~~~~--~~~~C~~C~~~~H~ 39 (49)
T smart00109 9 KKPTKCCVCRKSIWGSF--QGLRCSWCKVKCHK 39 (49)
T ss_pred CCCCCccccccccCcCC--CCcCCCCCCchHHH
Confidence 44567999999876433 68999999876643
No 52
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=23.29 E-value=7.6e+02 Score=24.72 Aligned_cols=33 Identities=12% Similarity=0.262 Sum_probs=24.6
Q ss_pred CCceeccCCCCCCCCCcccccccCccccccccc
Q 019492 145 ENYTFCHYCSKPKSPRTHHCRSCGMCVLDMDHH 177 (340)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHH 177 (340)
++..-|+.|+...|....+|..|+.-..+..++
T Consensus 219 ~~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~ 251 (419)
T PRK15103 219 QGLRSCSCCTAILPADQPVCPRCHTKGYVRRRN 251 (419)
T ss_pred cCCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCC
Confidence 345679999988777777899888877665543
No 53
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=21.41 E-value=69 Score=19.94 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=10.0
Q ss_pred ccccccccccCCCCCccceeeccc
Q 019492 21 CWGCGLHLVLPSYTPTFKCGWCGA 44 (340)
Q Consensus 21 c~~c~~~~~~~~~~~~~~c~~~~~ 44 (340)
|-.||...-+.... .-+|--||.
T Consensus 3 C~~Cg~~~~~~~~~-~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPGD-PIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred CCcCCCeeEcCCCC-cEECCcCCC
Confidence 44555555544332 235555553
No 54
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=20.85 E-value=44 Score=30.75 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=10.9
Q ss_pred ccccccccCccccc
Q 019492 170 CVLDMDHHCPFIGN 183 (340)
Q Consensus 170 CV~~~DHHC~Wi~n 183 (340)
=..+.+|||||...
T Consensus 37 Hrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 37 HRSYESHHCPKGLR 50 (250)
T ss_pred cchHhhcCCCcccc
Confidence 46788999998764
No 55
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=20.67 E-value=2.2e+02 Score=17.58 Aligned_cols=13 Identities=31% Similarity=0.452 Sum_probs=8.0
Q ss_pred HHHHHHhcCCCCC
Q 019492 116 MFCLAAFHCPGAS 128 (340)
Q Consensus 116 ~y~~~~~~dPG~~ 128 (340)
.|+...++||...
T Consensus 17 iFFAIfFRepPri 29 (31)
T PRK11875 17 LFFAIAFRDPPKI 29 (31)
T ss_pred HHHhhhccCCCCC
Confidence 3445568888644
No 56
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.62 E-value=65 Score=34.72 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=28.4
Q ss_pred CCCccccccccccccCCCCCccceeeccceecCC
Q 019492 16 DNEPTCWGCGLHLVLPSYTPTFKCGWCGAITSLN 49 (340)
Q Consensus 16 ~~~~~c~~c~~~~~~~~~~~~~~c~~~~~~~~~~ 49 (340)
+|-..|-.|...|.+......-+|+|||+-.+.+
T Consensus 442 g~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 442 GYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred CCcccCCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 4667899999999988899999999999985444
No 57
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=20.59 E-value=59 Score=30.23 Aligned_cols=32 Identities=19% Similarity=0.514 Sum_probs=20.7
Q ss_pred CCCCccccccccccccCCCC-Ccc-ceeecccee
Q 019492 15 KDNEPTCWGCGLHLVLPSYT-PTF-KCGWCGAIT 46 (340)
Q Consensus 15 ~~~~~~c~~c~~~~~~~~~~-~~~-~c~~~~~~~ 46 (340)
.....+|-.|...-+.+... ... +|--|..++
T Consensus 154 ~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvS 187 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVS 187 (256)
T ss_pred CceeEECCCCCCcEeccCCCCCccccCCCCceec
Confidence 44556788888887777655 333 777775544
No 58
>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=20.58 E-value=8.5e+02 Score=24.23 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=20.4
Q ss_pred ceeccCCCCCC--C----CCcccccccCccccccccc
Q 019492 147 YTFCHYCSKPK--S----PRTHHCRSCGMCVLDMDHH 177 (340)
Q Consensus 147 ~~~C~~C~~~k--P----~Rs~HC~~C~~CV~~~DHH 177 (340)
..-|+.|+... | ...-+|..||.-..+.+++
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~ 49 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLTVGWDW 49 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCcCCCCC
Confidence 45699998532 2 3344688888877765554
No 59
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.34 E-value=56 Score=23.68 Aligned_cols=23 Identities=26% Similarity=0.645 Sum_probs=19.9
Q ss_pred ceeccCCCCCCCCCcccccccCc
Q 019492 147 YTFCHYCSKPKSPRTHHCRSCGM 169 (340)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~ 169 (340)
.+-|..|+...|+.+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46689999999999999999886
No 60
>CHL00031 psbT photosystem II protein T
Probab=20.10 E-value=2.4e+02 Score=17.74 Aligned_cols=15 Identities=27% Similarity=0.443 Sum_probs=9.0
Q ss_pred HHHHHHhcCCCCCCC
Q 019492 116 MFCLAAFHCPGASPL 130 (340)
Q Consensus 116 ~y~~~~~~dPG~~~~ 130 (340)
.|+...++||...++
T Consensus 17 lFFAI~FRePPri~k 31 (33)
T CHL00031 17 IFFAIFFREPPKVPT 31 (33)
T ss_pred HHHhheecCCCCCCC
Confidence 344456899865543
Done!