Query 021385
Match_columns 313
No_of_seqs 192 out of 1729
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 02:32:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021385hhsearch_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 2.5E-56 5.4E-61 403.9 15.3 264 5-286 6-272 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 1.3E-45 2.9E-50 329.5 15.3 241 14-294 14-278 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 4.2E-43 9E-48 323.7 22.6 167 117-283 106-278 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 2E-40 4.4E-45 282.5 13.5 173 69-250 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 6.6E-38 1.4E-42 272.2 15.2 162 123-284 101-293 (309)
6 COG5273 Uncharacterized protei 100.0 2.1E-37 4.5E-42 284.4 16.6 206 54-280 56-288 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 5.5E-31 1.2E-35 230.1 11.4 147 18-191 69-215 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 1.3E-26 2.9E-31 222.5 9.5 140 125-272 421-585 (600)
9 KOG1311 DHHC-type Zn-finger pr 95.1 0.63 1.4E-05 42.9 13.4 58 137-194 112-180 (299)
10 PF01529 zf-DHHC: DHHC palmito 93.8 1.4 2.9E-05 36.9 11.6 55 120-185 58-112 (174)
11 PF13240 zinc_ribbon_2: zinc-r 84.9 0.51 1.1E-05 26.0 1.1 21 126-146 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 82.8 0.72 1.6E-05 30.2 1.2 25 122-146 12-36 (48)
13 PF06906 DUF1272: Protein of u 78.0 1.2 2.6E-05 30.2 1.1 36 126-164 7-50 (57)
14 PTZ00303 phosphatidylinositol 78.0 1.3 2.8E-05 45.5 1.8 23 124-146 460-489 (1374)
15 PF13248 zf-ribbon_3: zinc-rib 77.4 1.3 2.7E-05 25.1 1.0 23 124-146 2-24 (26)
16 KOG1315 Predicted DHHC-type Zn 72.0 85 0.0018 29.2 13.5 32 122-153 121-152 (307)
17 PF01363 FYVE: FYVE zinc finge 69.6 2.1 4.5E-05 30.1 0.7 26 123-148 8-35 (69)
18 KOG0509 Ankyrin repeat and DHH 69.6 2.7 5.9E-05 42.0 1.8 55 121-176 322-376 (600)
19 COG5273 Uncharacterized protei 69.1 15 0.00033 34.1 6.6 52 121-183 120-171 (309)
20 PF12773 DZR: Double zinc ribb 65.4 5.7 0.00012 25.9 2.2 35 123-157 11-48 (50)
21 COG1552 RPL40A Ribosomal prote 64.9 1.4 3E-05 28.9 -0.8 24 123-146 13-36 (50)
22 smart00064 FYVE Protein presen 62.5 5.3 0.00011 27.9 1.7 25 124-148 10-36 (68)
23 PF10571 UPF0547: Uncharacteri 60.7 4.9 0.00011 22.8 1.0 22 125-146 1-22 (26)
24 PF01020 Ribosomal_L40e: Ribos 59.3 5.4 0.00012 26.6 1.2 26 122-147 15-42 (52)
25 KOG1842 FYVE finger-containing 58.9 3 6.5E-05 40.1 -0.1 27 122-148 178-206 (505)
26 PF12773 DZR: Double zinc ribb 52.2 10 0.00022 24.7 1.6 25 121-145 26-50 (50)
27 PF07649 C1_3: C1-like domain; 48.6 7.3 0.00016 22.6 0.4 21 126-146 2-23 (30)
28 PF00641 zf-RanBP: Zn-finger i 47.8 7 0.00015 22.7 0.3 23 124-146 4-26 (30)
29 cd00065 FYVE FYVE domain; Zinc 47.7 12 0.00026 24.9 1.5 22 126-147 4-27 (57)
30 KOG3183 Predicted Zn-finger pr 42.8 11 0.00023 33.4 0.7 22 139-160 24-50 (250)
31 PF02150 RNA_POL_M_15KD: RNA p 42.0 7.6 0.00016 23.7 -0.2 8 125-132 2-9 (35)
32 TIGR00155 pqiA_fam integral me 40.8 3.5E+02 0.0075 26.2 12.3 32 124-155 215-247 (403)
33 PF07282 OrfB_Zn_ribbon: Putat 39.8 18 0.0004 25.2 1.5 27 121-147 25-55 (69)
34 PF03842 Silic_transp: Silicon 38.4 3.4E+02 0.0074 26.4 9.9 27 168-194 171-197 (512)
35 PF03107 C1_2: C1 domain; Int 37.9 23 0.00049 20.6 1.4 20 126-145 2-22 (30)
36 PF00751 DM: DM DNA binding do 36.8 12 0.00026 24.5 0.1 22 138-159 2-28 (47)
37 PRK15103 paraquat-inducible me 36.4 4.1E+02 0.0089 25.8 11.7 33 123-155 220-252 (419)
38 KOG1313 DHHC-type Zn-finger pr 33.6 3.7E+02 0.0081 24.6 8.9 54 121-185 113-166 (309)
39 smart00661 RPOL9 RNA polymeras 32.5 24 0.00052 23.0 1.0 6 126-131 2-7 (52)
40 PF00130 C1_1: Phorbol esters/ 30.7 42 0.0009 21.9 2.0 34 122-155 9-50 (53)
41 COG2093 DNA-directed RNA polym 30.6 27 0.00059 24.3 1.0 23 124-146 4-26 (64)
42 KOG1818 Membrane trafficking a 29.0 22 0.00048 36.1 0.6 24 123-146 164-189 (634)
43 PF09297 zf-NADH-PPase: NADH p 28.7 21 0.00047 21.0 0.3 22 124-145 3-28 (32)
44 PRK14559 putative protein seri 28.6 36 0.00078 35.0 2.0 22 125-146 28-49 (645)
45 PRK00432 30S ribosomal protein 28.5 34 0.00074 22.6 1.2 23 124-146 20-45 (50)
46 KOG1841 Smad anchor for recept 28.3 27 0.00059 37.7 1.1 40 123-174 556-597 (1287)
47 PHA02942 putative transposase; 27.2 39 0.00084 32.4 1.8 27 120-146 321-350 (383)
48 KOG1819 FYVE finger-containing 26.2 24 0.00051 34.7 0.2 24 123-146 900-925 (990)
49 PRK03681 hypA hydrogenase nick 25.7 35 0.00077 26.7 1.1 24 123-146 69-95 (114)
50 CHL00031 psbT photosystem II p 24.8 1.6E+02 0.0034 17.7 3.4 16 69-84 16-31 (33)
51 COG0603 Predicted PP-loop supe 24.8 27 0.00058 30.9 0.2 18 133-150 187-204 (222)
52 PLN00186 ribosomal protein S26 24.7 30 0.00064 26.8 0.4 16 137-152 19-34 (109)
53 COG4640 Predicted membrane pro 24.6 36 0.00077 32.6 1.0 24 124-147 1-24 (465)
54 smart00547 ZnF_RBZ Zinc finger 24.6 38 0.00082 18.6 0.8 21 126-146 4-24 (26)
55 PF08600 Rsm1: Rsm1-like; Int 24.3 37 0.00081 25.4 0.9 13 150-162 53-65 (91)
56 PF09889 DUF2116: Uncharacteri 23.8 1.1E+02 0.0023 21.1 3.0 23 124-146 3-26 (59)
57 PF07010 Endomucin: Endomucin; 23.8 1.8E+02 0.0038 25.8 5.0 25 60-84 200-224 (259)
58 PRK11875 psbT photosystem II r 22.8 1.8E+02 0.0039 17.2 3.6 16 69-84 16-31 (31)
59 PRK09335 30S ribosomal protein 22.7 33 0.00073 25.9 0.4 20 137-156 19-38 (95)
60 PF12172 DUF35_N: Rubredoxin-l 22.6 31 0.00067 20.9 0.2 23 122-145 9-32 (37)
61 smart00301 DM Doublesex DNA-bi 22.5 44 0.00095 22.6 0.9 6 154-159 23-28 (54)
62 PTZ00172 40S ribosomal protein 21.5 36 0.00078 26.4 0.4 17 137-153 19-35 (108)
63 PF14127 DUF4294: Domain of un 21.0 85 0.0018 26.1 2.5 32 238-272 103-134 (157)
64 KOG3611 Semaphorins [Signal tr 20.3 38 0.00082 35.4 0.3 38 138-175 491-536 (737)
65 KOG1398 Uncharacterized conser 20.3 52 0.0011 31.5 1.2 26 134-165 10-35 (460)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.5e-56 Score=403.90 Aligned_cols=264 Identities=35% Similarity=0.683 Sum_probs=207.8
Q ss_pred cccccccccccchhHHHHHHHHHHhhheeEEeeeeccccccCCccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 021385 5 LFKLCSGLKVLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVPE 84 (313)
Q Consensus 5 ~~~~~~~~r~~g~~~~~~v~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~f~~l~~l~~~sy~~~~~~dPG~vp~ 84 (313)
.+++|+ | +++++++.+++++++|++++..+.+.+- ....+.+.+++++.+++|..|+|++++++|||.+|.
T Consensus 6 ~~~~~~--r---~~~~~~i~~~~~~~yy~~v~~~c~~~i~----~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~ 76 (307)
T KOG1315|consen 6 RFSKCL--R---WIPVLIILLVIGWTYYVYVAVLCILSIS----LTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPD 76 (307)
T ss_pred cchhhh--c---chhheeeeeeEEEEEEEeehhhhHHHHh----hhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCcc
Confidence 345554 6 8999999999999999999999887653 225577888999999999999999999999999999
Q ss_pred CCCCCCcCCCCCcCcccccCCCcCCCCCCCCCCCCCCCCeeeccccccccCCCCccCcccCcccccccccCccccccccc
Q 021385 85 NWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGA 164 (313)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~ 164 (313)
.+.++.++..+. +.+...+ .......++..+..|+|.+|+.+|||||||||+|+|||+||||||||+|||||.
T Consensus 77 ~~~~~~~~~~~~-----~~~~~~~--~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf 149 (307)
T KOG1315|consen 77 SYRPSVEDEDSL-----ENGSDNE--RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGF 149 (307)
T ss_pred ccCCCcCccccc-----cccCccc--ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecc
Confidence 988777633211 1111110 111234457788999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchH
Q 021385 165 RNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSI 244 (313)
Q Consensus 165 ~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~l~~~h~~li~~n~Tt~ 244 (313)
+|||+|++|++|+.+.+++..+..+..+...+.. . ...+......+.+.+++++.+++.+.+++++|+++|++|+||+
T Consensus 150 ~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTi 227 (307)
T KOG1315|consen 150 RNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQG-G-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTI 227 (307)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-c-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhH
Confidence 9999999999999999998888888777777722 1 1112222333444456667788888889999999999999999
Q ss_pred HHHhhcCCCCCCCchhH---HHHHhhhCCCCCcceEEeeeeCCCC
Q 021385 245 EVYEKKRTVRWKYDLGR---KKNFEQVYPVQLHLWLQELQNEQRR 286 (313)
Q Consensus 245 E~~~~~~~~~~~yd~G~---~~N~~~vfG~~~~~W~~P~~~~~~~ 286 (313)
|.++......+.++.+- ..|++|+||+++..|++|+..+.++
T Consensus 228 E~~~~~~~~~~~~~~~~~~~~~n~~~vfg~~~~~wl~P~~~s~~~ 272 (307)
T KOG1315|consen 228 EAYKSPVFRSGLHNKNGFNLYVNFREVFGSNLLYWLLPIDSSWGD 272 (307)
T ss_pred hhhccccccccccccCCcceeecHHHHhCCCceEEeccccCcccc
Confidence 99987633333344433 5699999999999999999988643
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.3e-45 Score=329.49 Aligned_cols=241 Identities=27% Similarity=0.496 Sum_probs=169.4
Q ss_pred ccchhHHHHHHHHHHhhheeEEeeeeccccccCCccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCC
Q 021385 14 VLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSS 93 (313)
Q Consensus 14 ~~g~~~~~~v~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~f~~l~~l~~~sy~~~~~~dPG~vp~~~~~~~~~~ 93 (313)
+.|++.-+.+..++....--.-...|.| ..++.+...-+.|-+...|++++|+.+++++||++|++|.|+...
T Consensus 14 hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~- 86 (414)
T KOG1314|consen 14 HWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK- 86 (414)
T ss_pred ccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh-
Confidence 4455554444444433322222334445 466677888888888999999999999999999999999876552
Q ss_pred CCCcCcccccCCCcCCCCCCCCCCCCCCCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHH
Q 021385 94 SSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLF 173 (313)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~F 173 (313)
+..-.+||.+|+.+|+||||||+.|||||.+|||||||+|||||..||.+|+.|
T Consensus 87 --------------------------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~F 140 (414)
T KOG1314|consen 87 --------------------------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRF 140 (414)
T ss_pred --------------------------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHH
Confidence 234578999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHH----HHHHHhhc--c-CCCC---CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcch
Q 021385 174 LLYTFLETTMDTLVLLP----SFIKFFGK--A-KNHS---SSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTS 243 (313)
Q Consensus 174 l~~~~l~~~~~~~~~~~----~~~~~~~~--~-~~~~---~~~~~~~~~~~~~~l~~~~~l~~~~l~~~h~~li~~n~Tt 243 (313)
|++..+.|+...+++.. .+...|.. + ...+ .+..+++.+++++.+++...+++..+++.|+..|.+|+|.
T Consensus 141 Llf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~ 220 (414)
T KOG1314|consen 141 LLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTG 220 (414)
T ss_pred HHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 99998877654433322 22222311 1 1111 1123333344444444555566666788899999999999
Q ss_pred HHHHhhc--------------CCCCCCCchhHHHHHhhhCCCCCcceEEeeeeCCCCceeccCCC
Q 021385 244 IEVYEKK--------------RTVRWKYDLGRKKNFEQVYPVQLHLWLQELQNEQRRFLVQTRHY 294 (313)
Q Consensus 244 ~E~~~~~--------------~~~~~~yd~G~~~N~~~vfG~~~~~W~~P~~~~~~~~~~~~~~~ 294 (313)
||.+..+ .....|||+|++.|+++||-...- ...++..|+..++
T Consensus 221 IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~~-------~~gdg~~wPv~~g 278 (414)
T KOG1314|consen 221 IESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNKK-------EEGDGIEWPVVEG 278 (414)
T ss_pred hHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhccc-------cCCCCccccccCc
Confidence 9986411 124579999999999999976521 4445555655543
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.2e-43 Score=323.68 Aligned_cols=167 Identities=32% Similarity=0.603 Sum_probs=131.4
Q ss_pred CCCCCCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 021385 117 ARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFF 196 (313)
Q Consensus 117 ~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~ 196 (313)
.++...+.+||.+|+.+||||||||+.||+||+||||||||+|||||++|||+|+.|++++.+.+++........+....
T Consensus 106 ~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~ 185 (299)
T KOG1311|consen 106 VNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRA 185 (299)
T ss_pred cCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34677889999999999999999999999999999999999999999999999999999998888888777666555433
Q ss_pred hcc-CCCC--CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhh-cCCCC-CCCchhHHHHHhhhCCC
Q 021385 197 GKA-KNHS--SSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK-KRTVR-WKYDLGRKKNFEQVYPV 271 (313)
Q Consensus 197 ~~~-~~~~--~~~~~~~~~~~~~~l~~~~~l~~~~l~~~h~~li~~n~Tt~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~ 271 (313)
... .... ..+......++..++++.+...++.++.+|++++.+|+||+|..++ +...+ ++||.|.++|++++||.
T Consensus 186 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~ 265 (299)
T KOG1311|consen 186 DNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGG 265 (299)
T ss_pred ccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCC
Confidence 221 1111 1122222333333556666666777899999999999999999874 32334 79999999999999998
Q ss_pred C-CcceEEeeeeC
Q 021385 272 Q-LHLWLQELQNE 283 (313)
Q Consensus 272 ~-~~~W~~P~~~~ 283 (313)
+ ...|+-|...+
T Consensus 266 ~~~~~~~~p~~~~ 278 (299)
T KOG1311|consen 266 PLPLSWLSPFARS 278 (299)
T ss_pred CCCcccccccccC
Confidence 7 57899888854
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=2e-40 Score=282.47 Aligned_cols=173 Identities=30% Similarity=0.592 Sum_probs=122.9
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCcCCCCCcCcccccCCCcCCCCCCCCCCCCCCCCeeeccccccccCCCCccCcccCccc
Q 021385 69 WSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCV 148 (313)
Q Consensus 69 ~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV 148 (313)
++|++++++|||++|+....+.+.. .+.+.+.. ......+.+..++.++|.+|+..||+|||||+.||+||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~---~~~~~~~~------~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 72 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQ---EEKEEEQN------QSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCV 72 (174)
T ss_pred EEehhhheECCcccCCccccccccc---cccccccc------hhhhhhccccCCCCEECcccCCcCCCcceecccccccc
Confidence 5788999999999998622111100 00000000 01112233567889999999999999999999999999
Q ss_pred ccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHH
Q 021385 149 LKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLC 228 (313)
Q Consensus 149 ~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~ 228 (313)
+||||||||+|||||++|||+|++|+++..+.+++.....+..+....................++.++++++++++++.
T Consensus 73 ~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (174)
T PF01529_consen 73 LRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGF 152 (174)
T ss_pred ccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998888777666655554433211111111111113344555666777778
Q ss_pred HHHHHHHHHhcCcchHHHHhhc
Q 021385 229 FIVMHSSLVSSNTTSIEVYEKK 250 (313)
Q Consensus 229 l~~~h~~li~~n~Tt~E~~~~~ 250 (313)
+++.|++++++|+||+|.++++
T Consensus 153 l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 153 LLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHcCCcHHHHHHcC
Confidence 8999999999999999999864
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=6.6e-38 Score=272.15 Aligned_cols=162 Identities=31% Similarity=0.634 Sum_probs=119.3
Q ss_pred CeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q 021385 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNH 202 (313)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 202 (313)
...+|.+|..+||||+||||.||+||++|||||||+|||||.+|||||++|++|+.+++.++.+...+.+++.....++.
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ 180 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEI 180 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhc
Confidence 45799999999999999999999999999999999999999999999999999999999998777655554432111000
Q ss_pred C---CC------Cchh-------H--HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhhc--------CCCCCC
Q 021385 203 S---SS------PANL-------A--IVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEKK--------RTVRWK 256 (313)
Q Consensus 203 ~---~~------~~~~-------~--~~~~~~~l~~~~~l~~~~l~~~h~~li~~n~Tt~E~~~~~--------~~~~~~ 256 (313)
. .. |... . -+.-+.++++.+.++++.+..||.++|.+|.|++|.+... +..++|
T Consensus 181 tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~ 260 (309)
T KOG1313|consen 181 TAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNP 260 (309)
T ss_pred ccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCC
Confidence 0 00 1000 0 0111334455556667778889999999999999986422 123689
Q ss_pred CchhHHHHHhhhCCCC--Ccce---EEeeeeCC
Q 021385 257 YDLGRKKNFEQVYPVQ--LHLW---LQELQNEQ 284 (313)
Q Consensus 257 yd~G~~~N~~~vfG~~--~~~W---~~P~~~~~ 284 (313)
++.|.++||+.++|-. +-.| ++|...++
T Consensus 261 ~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p 293 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLFRGRHFWKTVLLPTIRKP 293 (309)
T ss_pred cccchHHHHHHhhccccCCceeEEEeccccccc
Confidence 9999999999999954 3356 55655443
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=2.1e-37 Score=284.35 Aligned_cols=206 Identities=33% Similarity=0.583 Sum_probs=147.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCcCcccccCCCcCCCCCCCCCCCCCCCCeeeccccccc
Q 021385 54 FSIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNG 133 (313)
Q Consensus 54 ~~~~~~f~~l~~l~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 133 (313)
.+..+.+.+...+...+|++.+++|||+.+++-..... .+..+ .....+..+..++|.+|+.+
T Consensus 56 ~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~------~~~~~-----------~~~~~~~~~~~~~C~~C~~~ 118 (309)
T COG5273 56 VLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGY------RETIS-----------RLLDDGKFGTENFCSTCNIY 118 (309)
T ss_pred hhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccch------hhhhh-----------hhhhcCccccceeccccccc
Confidence 34455566677788889999999999999864221111 00011 11223567889999999999
Q ss_pred cCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCchh-H-H
Q 021385 134 KPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANL-A-I 211 (313)
Q Consensus 134 kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~ 211 (313)
||+|||||+.||+||+||||||||+|||||.+|||+|++|++++....+.........+...+.. ...+... . +
T Consensus 119 KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~l 194 (309)
T COG5273 119 KPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSI----RHDTSLAICFL 194 (309)
T ss_pred cCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc----cCChHHHHHHH
Confidence 99999999999999999999999999999999999999999998777766655544444433322 1222222 1 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhhcCC-------------------------CCCCCchhHHHHHh
Q 021385 212 VFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEKKRT-------------------------VRWKYDLGRKKNFE 266 (313)
Q Consensus 212 ~~~~~~l~~~~~l~~~~l~~~h~~li~~n~Tt~E~~~~~~~-------------------------~~~~yd~G~~~N~~ 266 (313)
+.....+++++.+.++.++..+.+++..|+|+.|..+..+. ..+|++.|.-+|++
T Consensus 195 i~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 274 (309)
T COG5273 195 IFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLS 274 (309)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccce
Confidence 22112344445556667788999999999999998654321 12467888889999
Q ss_pred hhCCCCCcceEEee
Q 021385 267 QVYPVQLHLWLQEL 280 (313)
Q Consensus 267 ~vfG~~~~~W~~P~ 280 (313)
.++|.....|..|.
T Consensus 275 ~i~~~~~~~~~~~~ 288 (309)
T COG5273 275 TIKGSNALYWLTPL 288 (309)
T ss_pred eecCCCceeecccc
Confidence 99999999999883
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=5.5e-31 Score=230.15 Aligned_cols=147 Identities=28% Similarity=0.480 Sum_probs=96.1
Q ss_pred hHHHHHHHHHHhhheeEEeeeeccccccCCccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCc
Q 021385 18 FMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSSSSSS 97 (313)
Q Consensus 18 ~~~~~v~~~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~f~~l~~l~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~ 97 (313)
+..-++...++++.++.-.+.+.+.+. .+....+....+.++=..++..++.+|||.+.++....
T Consensus 69 i~L~lvy~a~m~~~~~~esfiy~~~l~-------lsl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~-------- 133 (341)
T KOG1312|consen 69 IVLHLVYQAMMYTEYTWESFIYCQELE-------LSLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESL-------- 133 (341)
T ss_pred hhHHHHHHHHHhhhhhheeeEeccchh-------hhHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhcc--------
Confidence 333344444444444444444445432 12233333333333444556788999999998631110
Q ss_pred CcccccCCCcCCCCCCCCCCCCCCCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHH
Q 021385 98 GVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYT 177 (313)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~ 177 (313)
-.+.-|.+ ...-.....|++|+..||.||+|||.||+||+|+||||.|+|||||.+|.|||++|+++.
T Consensus 134 --~~~~ypYD----------y~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~ 201 (341)
T KOG1312|consen 134 --FLHVYPYD----------YVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTL 201 (341)
T ss_pred --ceeccCcc----------ceeecCCCccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHH
Confidence 11111211 012223478999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHHH
Q 021385 178 FLETTMDTLVLLPS 191 (313)
Q Consensus 178 ~l~~~~~~~~~~~~ 191 (313)
..++.++++.+...
T Consensus 202 i~l~~yaivrlgfi 215 (341)
T KOG1312|consen 202 ISLATYAIVRLGFI 215 (341)
T ss_pred HHHHHHHHHHHHhe
Confidence 77777776555443
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.93 E-value=1.3e-26 Score=222.52 Aligned_cols=140 Identities=30% Similarity=0.502 Sum_probs=93.1
Q ss_pred eeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCC
Q 021385 125 GFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSS 204 (313)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (313)
++|.+|...||.|||||++|||||.+|||||||++||||.+|||+|+.|++.+...+.+.+.... .++...++..
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~----~y~~~~~~~~- 495 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCL----YYIMNLENAS- 495 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHH----HHHhhcchhH-
Confidence 79999999999999999999999999999999999999999999999999886665554433322 2232211110
Q ss_pred CCchhHHHHHHHHHHHHH----HH-----------HHHH-HHHHHHHHHhcCcchHHHHhhcCC---------CCCCCch
Q 021385 205 SPANLAIVFLAFVINLAF----AL-----------SLLC-FIVMHSSLVSSNTTSIEVYEKKRT---------VRWKYDL 259 (313)
Q Consensus 205 ~~~~~~~~~~~~~l~~~~----~l-----------~~~~-l~~~h~~li~~n~Tt~E~~~~~~~---------~~~~yd~ 259 (313)
.....++.++..+.. .. .... --..|-..++.+.||+|.++..+. .++|++.
T Consensus 496 ---~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~ 572 (600)
T KOG0509|consen 496 ---TIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSP 572 (600)
T ss_pred ---HHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCc
Confidence 000111111111000 00 0000 112234457889999999875432 3679999
Q ss_pred hHHHHHhhhCCCC
Q 021385 260 GRKKNFEQVYPVQ 272 (313)
Q Consensus 260 G~~~N~~~vfG~~ 272 (313)
|+.+|+.+++-.+
T Consensus 573 g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 573 GPIRNLVDFFLCS 585 (600)
T ss_pred hhhhcchheeecc
Confidence 9999999997554
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=95.06 E-value=0.63 Score=42.94 Aligned_cols=58 Identities=24% Similarity=0.369 Sum_probs=39.8
Q ss_pred CCccCcccCcccccccccCccccccccccc-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 021385 137 RCHHCSVCQRCVLKMDHHCVWVVNCVGARN-----------YKSFLLFLLYTFLETTMDTLVLLPSFIK 194 (313)
Q Consensus 137 RshHC~~C~~CV~~~DHHCpwi~nCIG~~N-----------~r~F~~Fl~~~~l~~~~~~~~~~~~~~~ 194 (313)
+.++|..|+.-+..+-|||+.-|+||-+.= +|-+-.|+.+++...+.....+......
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~ 180 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYE 180 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888888888888888887763 4677888866664444433333333333
No 10
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=93.76 E-value=1.4 Score=36.92 Aligned_cols=55 Identities=24% Similarity=0.390 Sum_probs=39.3
Q ss_pred CCCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHH
Q 021385 120 PSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDT 185 (313)
Q Consensus 120 ~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~ 185 (313)
...+.++|+.|+.--..+-|||.--|+||.+.-| +..=.|+++..-..+..+...
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~ 112 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILS 112 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHH
Confidence 4457889999999999999999999999988665 445566666555444444433
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.92 E-value=0.51 Score=26.01 Aligned_cols=21 Identities=19% Similarity=0.683 Sum_probs=17.6
Q ss_pred eccccccccCCCCccCcccCc
Q 021385 126 FCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 126 ~C~~C~~~kP~RshHC~~C~~ 146 (313)
+|..|...-++.+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588888888888888888875
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=82.84 E-value=0.72 Score=30.15 Aligned_cols=25 Identities=28% Similarity=0.630 Sum_probs=22.3
Q ss_pred CCeeeccccccccCCCCccCcccCc
Q 021385 122 RSVGFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~C~~ 146 (313)
...+.|.+|...-|+|+..|+.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3567899999999999999999876
No 13
>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=78.03 E-value=1.2 Score=30.18 Aligned_cols=36 Identities=33% Similarity=0.923 Sum_probs=27.7
Q ss_pred eccccccccCCCC-------ccCcccCcccccc-cccCccccccccc
Q 021385 126 FCDRCQNGKPPRC-------HHCSVCQRCVLKM-DHHCVWVVNCVGA 164 (313)
Q Consensus 126 ~C~~C~~~kP~Rs-------hHC~~C~~CV~~~-DHHCpwi~nCIG~ 164 (313)
-|..|+.--|+-+ +-|..|..|+..+ +++|| ||=|.
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 4666666666554 7799999999998 99999 77664
No 14
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=77.97 E-value=1.3 Score=45.46 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=18.8
Q ss_pred eeeccccccccC-------CCCccCcccCc
Q 021385 124 VGFCDRCQNGKP-------PRCHHCSVCQR 146 (313)
Q Consensus 124 ~~~C~~C~~~kP-------~RshHC~~C~~ 146 (313)
...|..|+..-. -|.||||.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999997764 39999999977
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=77.40 E-value=1.3 Score=25.10 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=18.4
Q ss_pred eeeccccccccCCCCccCcccCc
Q 021385 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~ 146 (313)
.++|..|...-++.++.|..||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 35788888887888888888874
No 16
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=72.01 E-value=85 Score=29.18 Aligned_cols=32 Identities=22% Similarity=0.374 Sum_probs=21.9
Q ss_pred CCeeeccccccccCCCCccCcccCcccccccc
Q 021385 122 RSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDH 153 (313)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DH 153 (313)
.+...|+.|+.=--..-|||.-=|+||.-.++
T Consensus 121 dRaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny 152 (307)
T KOG1315|consen 121 DRAHHCSVCNRCVLKMDHHCPWINNCVGFRNY 152 (307)
T ss_pred CccccchhhhhhhhccccCCcceeceecccch
Confidence 45557777766666667888888888865444
No 17
>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=69.58 E-value=2.1 Score=30.13 Aligned_cols=26 Identities=35% Similarity=0.632 Sum_probs=12.9
Q ss_pred Ceeeccccccc--cCCCCccCcccCccc
Q 021385 123 SVGFCDRCQNG--KPPRCHHCSVCQRCV 148 (313)
Q Consensus 123 ~~~~C~~C~~~--kP~RshHC~~C~~CV 148 (313)
+...|..|+.. --.|-|||+.||+.|
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 34577777743 347899999999855
No 18
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=69.58 E-value=2.7 Score=42.04 Aligned_cols=55 Identities=5% Similarity=-0.138 Sum_probs=47.6
Q ss_pred CCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHH
Q 021385 121 SRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLY 176 (313)
Q Consensus 121 ~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~ 176 (313)
-.....|.+|....+.+..++..+-.++..+++||+|+. +|+.+|...+....+.
T Consensus 322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~ 376 (600)
T KOG0509|consen 322 LVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFII 376 (600)
T ss_pred hhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHH
Confidence 345678999999999999999999999999999999999 9999998866554433
No 19
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=69.06 E-value=15 Score=34.09 Aligned_cols=52 Identities=23% Similarity=0.388 Sum_probs=34.6
Q ss_pred CCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHH
Q 021385 121 SRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTM 183 (313)
Q Consensus 121 ~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~ 183 (313)
..+.+.|+.|+.=-...-|||.-=|+||-+.-| +=.=.|++++...++..++
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~ 171 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLL 171 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHH
Confidence 346677888887777788888888888876544 4455666666544444333
No 20
>PF12773 DZR: Double zinc ribbon
Probab=65.39 E-value=5.7 Score=25.91 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=22.6
Q ss_pred CeeeccccccccC---CCCccCcccCcccccccccCcc
Q 021385 123 SVGFCDRCQNGKP---PRCHHCSVCQRCVLKMDHHCVW 157 (313)
Q Consensus 123 ~~~~C~~C~~~kP---~RshHC~~C~~CV~~~DHHCpw 157 (313)
..++|..|...-+ .....|..|+.=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 3567777776655 3356677777766666666653
No 21
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=64.90 E-value=1.4 Score=28.88 Aligned_cols=24 Identities=33% Similarity=0.879 Sum_probs=21.4
Q ss_pred CeeeccccccccCCCCccCcccCc
Q 021385 123 SVGFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~C~~ 146 (313)
..+.|.+|...-|+|+-.|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 457899999999999999998865
No 22
>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 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=60.74 E-value=4.9 Score=22.83 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=17.6
Q ss_pred eeccccccccCCCCccCcccCc
Q 021385 125 GFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~ 146 (313)
+.|+.|...-|.-+.-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688888888888888888874
No 24
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=59.30 E-value=5.4 Score=26.56 Aligned_cols=26 Identities=27% Similarity=0.724 Sum_probs=17.4
Q ss_pred CCeeeccccccccCCCCccCcc--cCcc
Q 021385 122 RSVGFCDRCQNGKPPRCHHCSV--CQRC 147 (313)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~--C~~C 147 (313)
-....|.+|...-|+|+..|+. ||.+
T Consensus 15 ~~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 15 CDKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp TS-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred ccceecccccCcCCCCccceecccCCCC
Confidence 3467899999999999999998 8754
No 25
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=58.93 E-value=3 Score=40.10 Aligned_cols=27 Identities=44% Similarity=0.982 Sum_probs=21.4
Q ss_pred CCeeeccccccc--cCCCCccCcccCccc
Q 021385 122 RSVGFCDRCQNG--KPPRCHHCSVCQRCV 148 (313)
Q Consensus 122 ~~~~~C~~C~~~--kP~RshHC~~C~~CV 148 (313)
....+|+.|... ---|-|||+.||+-+
T Consensus 178 s~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred CcccccccccchhhhHHHhhhhhhcchHH
Confidence 467899999954 556899999999843
No 26
>PF12773 DZR: Double zinc ribbon
Probab=52.17 E-value=10 Score=24.67 Aligned_cols=25 Identities=28% Similarity=0.805 Sum_probs=21.7
Q ss_pred CCCeeeccccccccCCCCccCcccC
Q 021385 121 SRSVGFCDRCQNGKPPRCHHCSVCQ 145 (313)
Q Consensus 121 ~~~~~~C~~C~~~kP~RshHC~~C~ 145 (313)
.....+|..|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456799999999999999999886
No 27
>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=48.63 E-value=7.3 Score=22.62 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=9.1
Q ss_pred eccccccccCC-CCccCcccCc
Q 021385 126 FCDRCQNGKPP-RCHHCSVCQR 146 (313)
Q Consensus 126 ~C~~C~~~kP~-RshHC~~C~~ 146 (313)
.|..|+..... ..++|..|+-
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 57788877666 7888888874
No 28
>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=47.83 E-value=7 Score=22.68 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=16.2
Q ss_pred eeeccccccccCCCCccCcccCc
Q 021385 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~ 146 (313)
.-.|..|...-+++..+|..|+.
T Consensus 4 ~W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 4 DWKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp SEEETTTTEEEESSSSB-TTT--
T ss_pred CccCCCCcCCchHHhhhhhCcCC
Confidence 35688888888888888888864
No 29
>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=47.68 E-value=12 Score=24.91 Aligned_cols=22 Identities=36% Similarity=0.753 Sum_probs=14.6
Q ss_pred ecccccc--ccCCCCccCcccCcc
Q 021385 126 FCDRCQN--GKPPRCHHCSVCQRC 147 (313)
Q Consensus 126 ~C~~C~~--~kP~RshHC~~C~~C 147 (313)
-|..|+. -.-.|.|||+.|++-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 4555553 145678999999874
No 30
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=42.77 E-value=11 Score=33.45 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=14.9
Q ss_pred ccCcccCc-----ccccccccCccccc
Q 021385 139 HHCSVCQR-----CVLKMDHHCVWVVN 160 (313)
Q Consensus 139 hHC~~C~~-----CV~~~DHHCpwi~n 160 (313)
.||..|+. =..+.+|||||...
T Consensus 24 f~Cd~C~~~FC~eHrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 24 FKCDGCSGIFCLEHRSYESHHCPKGLR 50 (250)
T ss_pred eeeCCccchhhhccchHhhcCCCcccc
Confidence 45555543 35788999999754
No 31
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=41.98 E-value=7.6 Score=23.66 Aligned_cols=8 Identities=50% Similarity=1.310 Sum_probs=4.7
Q ss_pred eecccccc
Q 021385 125 GFCDRCQN 132 (313)
Q Consensus 125 ~~C~~C~~ 132 (313)
++|.+|+.
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 56777773
No 32
>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=40.77 E-value=3.5e+02 Score=26.19 Aligned_cols=32 Identities=16% Similarity=0.393 Sum_probs=23.3
Q ss_pred eeecccccc-ccCCCCccCcccCcccccccccC
Q 021385 124 VGFCDRCQN-GKPPRCHHCSVCQRCVLKMDHHC 155 (313)
Q Consensus 124 ~~~C~~C~~-~kP~RshHC~~C~~CV~~~DHHC 155 (313)
..-|..|+. .+|....||.+|+.-..+..++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 456999997 46666778888888776655544
No 33
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=39.75 E-value=18 Score=25.19 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=20.0
Q ss_pred CCCeeecccccccc----CCCCccCcccCcc
Q 021385 121 SRSVGFCDRCQNGK----PPRCHHCSVCQRC 147 (313)
Q Consensus 121 ~~~~~~C~~C~~~k----P~RshHC~~C~~C 147 (313)
....+.|+.|.... ..|.++|..||.-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCE
Confidence 34678899998664 4477889988875
No 34
>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=38.35 E-value=3.4e+02 Score=26.40 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 021385 168 KSFLLFLLYTFLETTMDTLVLLPSFIK 194 (313)
Q Consensus 168 r~F~~Fl~~~~l~~~~~~~~~~~~~~~ 194 (313)
.||.+|.+|+....=...++....+++
T Consensus 171 nyFalFTlyvam~IEfsGvmHssYLIq 197 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFSGVMHSSYLIQ 197 (512)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence 389999999877654444443333333
No 35
>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=37.87 E-value=23 Score=20.59 Aligned_cols=20 Identities=35% Similarity=0.771 Sum_probs=13.9
Q ss_pred eccccccccCCC-CccCcccC
Q 021385 126 FCDRCQNGKPPR-CHHCSVCQ 145 (313)
Q Consensus 126 ~C~~C~~~kP~R-shHC~~C~ 145 (313)
+|..|+..-... .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776666666 78887776
No 36
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=36.79 E-value=12 Score=24.52 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=8.7
Q ss_pred CccCccc---Ccccccccc--cCcccc
Q 021385 138 CHHCSVC---QRCVLKMDH--HCVWVV 159 (313)
Q Consensus 138 shHC~~C---~~CV~~~DH--HCpwi~ 159 (313)
..+|..| |.=+..-+| .|||-+
T Consensus 2 ~p~C~RCrnHG~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 2 SPTCARCRNHGVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp -SS-HHHHTTT---TTTT-GGG-TTTT
T ss_pred CCcCcchhcCCcccchhhhccccCcCC
Confidence 3445555 445566666 688764
No 37
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=36.45 E-value=4.1e+02 Score=25.82 Aligned_cols=33 Identities=15% Similarity=0.298 Sum_probs=25.3
Q ss_pred CeeeccccccccCCCCccCcccCcccccccccC
Q 021385 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHC 155 (313)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHC 155 (313)
...-|..|+..-|....||..|+.-..+..++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 455699999887777778999988776655544
No 38
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=33.59 E-value=3.7e+02 Score=24.64 Aligned_cols=54 Identities=24% Similarity=0.411 Sum_probs=39.4
Q ss_pred CCCeeeccccccccCCCCccCcccCcccccccccCcccccccccccHHHHHHHHHHHHHHHHHHH
Q 021385 121 SRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDT 185 (313)
Q Consensus 121 ~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl~~~~l~~~~~~ 185 (313)
..+...|+.|+.---.=-|||.-=|+||--..| +-.=.|+.++.-......++.
T Consensus 113 ~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~~ 166 (309)
T KOG1313|consen 113 SPRTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIMC 166 (309)
T ss_pred CCCcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHHH
Confidence 345667888886666667999999999998777 556678888766555555443
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.50 E-value=24 Score=22.96 Aligned_cols=6 Identities=50% Similarity=1.719 Sum_probs=2.9
Q ss_pred eccccc
Q 021385 126 FCDRCQ 131 (313)
Q Consensus 126 ~C~~C~ 131 (313)
+|+.|+
T Consensus 2 FCp~Cg 7 (52)
T smart00661 2 FCPKCG 7 (52)
T ss_pred CCCCCC
Confidence 455554
No 40
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=30.74 E-value=42 Score=21.88 Aligned_cols=34 Identities=26% Similarity=0.597 Sum_probs=22.5
Q ss_pred CCeeecccccccc---CCCCccCcccCc-----ccccccccC
Q 021385 122 RSVGFCDRCQNGK---PPRCHHCSVCQR-----CVLKMDHHC 155 (313)
Q Consensus 122 ~~~~~C~~C~~~k---P~RshHC~~C~~-----CV~~~DHHC 155 (313)
..+.+|..|+..- .....+|+.|+. |..+.+.-|
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 4567999999776 667889999965 555444444
No 41
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=30.63 E-value=27 Score=24.26 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=20.0
Q ss_pred eeeccccccccCCCCccCcccCc
Q 021385 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~ 146 (313)
.+-|.+|+...|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 35699999999999999999986
No 42
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=28.99 E-value=22 Score=36.10 Aligned_cols=24 Identities=33% Similarity=0.678 Sum_probs=18.1
Q ss_pred Ceeeccccccc--cCCCCccCcccCc
Q 021385 123 SVGFCDRCQNG--KPPRCHHCSVCQR 146 (313)
Q Consensus 123 ~~~~C~~C~~~--kP~RshHC~~C~~ 146 (313)
...-|.+|... ---|.|||+.||+
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccccceeeeeeeeccccccccccch
Confidence 34578888843 3349999999998
No 43
>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=28.68 E-value=21 Score=20.95 Aligned_cols=22 Identities=36% Similarity=0.931 Sum_probs=9.1
Q ss_pred eeeccccccc-cCC---CCccCcccC
Q 021385 124 VGFCDRCQNG-KPP---RCHHCSVCQ 145 (313)
Q Consensus 124 ~~~C~~C~~~-kP~---RshHC~~C~ 145 (313)
.+||..|... ++. ++..|..|+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 4678888744 333 444444444
No 44
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.64 E-value=36 Score=35.02 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=11.6
Q ss_pred eeccccccccCCCCccCcccCc
Q 021385 125 GFCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~ 146 (313)
+.|..|...-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 4455555555555555555554
No 45
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.52 E-value=34 Score=22.61 Aligned_cols=23 Identities=30% Similarity=0.650 Sum_probs=14.6
Q ss_pred eeecccccc-c--cCCCCccCcccCc
Q 021385 124 VGFCDRCQN-G--KPPRCHHCSVCQR 146 (313)
Q Consensus 124 ~~~C~~C~~-~--kP~RshHC~~C~~ 146 (313)
.++|+.|.. . .-....+|..|+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCC
Confidence 568999986 2 2223567777764
No 46
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=28.27 E-value=27 Score=37.69 Aligned_cols=40 Identities=33% Similarity=0.521 Sum_probs=26.8
Q ss_pred Ceeeccccc--cccCCCCccCcccCcccccccccCcccccccccccHHHHHHHH
Q 021385 123 SVGFCDRCQ--NGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFL 174 (313)
Q Consensus 123 ~~~~C~~C~--~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~~Fl 174 (313)
...-|..|+ ..--.|-||||.||+- .-+.| -|.|.++-|+
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 344566666 4567899999999993 22334 3567777766
No 47
>PHA02942 putative transposase; Provisional
Probab=27.17 E-value=39 Score=32.43 Aligned_cols=27 Identities=33% Similarity=0.650 Sum_probs=20.4
Q ss_pred CCCCeeeccccccccC---CCCccCcccCc
Q 021385 120 PSRSVGFCDRCQNGKP---PRCHHCSVCQR 146 (313)
Q Consensus 120 ~~~~~~~C~~C~~~kP---~RshHC~~C~~ 146 (313)
.....+.|+.|....+ .|.+.|..||.
T Consensus 321 p~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 321 PSYSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 3346789999997654 47888988886
No 48
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=26.22 E-value=24 Score=34.73 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=17.6
Q ss_pred Ceeeccccccc--cCCCCccCcccCc
Q 021385 123 SVGFCDRCQNG--KPPRCHHCSVCQR 146 (313)
Q Consensus 123 ~~~~C~~C~~~--kP~RshHC~~C~~ 146 (313)
.-..|..|+.+ ---|-|||+.||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 44578888865 3357899999987
No 49
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.66 E-value=35 Score=26.68 Aligned_cols=24 Identities=21% Similarity=0.598 Sum_probs=17.7
Q ss_pred CeeeccccccccCCCCcc---CcccCc
Q 021385 123 SVGFCDRCQNGKPPRCHH---CSVCQR 146 (313)
Q Consensus 123 ~~~~C~~C~~~kP~RshH---C~~C~~ 146 (313)
..-+|..|+..-|...++ |..||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 456899999887765554 888774
No 50
>CHL00031 psbT photosystem II protein T
Probab=24.85 E-value=1.6e+02 Score=17.71 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=12.2
Q ss_pred HHHHHHhhcCCCCCCC
Q 021385 69 WSYVMVVFWDPGSVPE 84 (313)
Q Consensus 69 ~sy~~~~~~dPG~vp~ 84 (313)
..++...+.||-.+++
T Consensus 16 ilFFAI~FRePPri~k 31 (33)
T CHL00031 16 IIFFAIFFREPPKVPT 31 (33)
T ss_pred HHHHhheecCCCCCCC
Confidence 3466788999988875
No 51
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=24.83 E-value=27 Score=30.87 Aligned_cols=18 Identities=33% Similarity=0.796 Sum_probs=14.8
Q ss_pred ccCCCCccCcccCccccc
Q 021385 133 GKPPRCHHCSVCQRCVLK 150 (313)
Q Consensus 133 ~kP~RshHC~~C~~CV~~ 150 (313)
|++.+..||..|..|++|
T Consensus 187 Y~g~~~~~CG~C~sC~~R 204 (222)
T COG0603 187 YNGGEGDHCGECESCVLR 204 (222)
T ss_pred eCCCCCCCCCCCHHHHHH
Confidence 466666699999999988
No 52
>PLN00186 ribosomal protein S26; Provisional
Probab=24.67 E-value=30 Score=26.84 Aligned_cols=16 Identities=38% Similarity=0.769 Sum_probs=12.4
Q ss_pred CCccCcccCccccccc
Q 021385 137 RCHHCSVCQRCVLKMD 152 (313)
Q Consensus 137 RshHC~~C~~CV~~~D 152 (313)
+.-||..|++||.+--
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (109)
T PLN00186 19 KRIRCSNCGKCVPKDK 34 (109)
T ss_pred cceeeCCCcccccccc
Confidence 3457999999999833
No 53
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.61 E-value=36 Score=32.57 Aligned_cols=24 Identities=25% Similarity=0.693 Sum_probs=20.5
Q ss_pred eeeccccccccCCCCccCcccCcc
Q 021385 124 VGFCDRCQNGKPPRCHHCSVCQRC 147 (313)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~C 147 (313)
+++|..|...+-.-+..|..||.=
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~ 24 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHK 24 (465)
T ss_pred CCcccccccccccccccccccCCc
Confidence 478999999999999888888874
No 54
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.57 E-value=38 Score=18.59 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=15.5
Q ss_pred eccccccccCCCCccCcccCc
Q 021385 126 FCDRCQNGKPPRCHHCSVCQR 146 (313)
Q Consensus 126 ~C~~C~~~kP~RshHC~~C~~ 146 (313)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477787777777777777764
No 55
>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=24.31 E-value=37 Score=25.41 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=9.2
Q ss_pred cccccCccccccc
Q 021385 150 KMDHHCVWVVNCV 162 (313)
Q Consensus 150 ~~DHHCpwi~nCI 162 (313)
.+=.||||++.-.
T Consensus 53 eHr~~CPwv~~~~ 65 (91)
T PF08600_consen 53 EHREYCPWVNPST 65 (91)
T ss_pred cccccCCccCCcc
Confidence 3346899998754
No 56
>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=23.81 E-value=1.1e+02 Score=21.10 Aligned_cols=23 Identities=30% Similarity=0.727 Sum_probs=14.8
Q ss_pred eeeccccccccCCCCccCc-ccCc
Q 021385 124 VGFCDRCQNGKPPRCHHCS-VCQR 146 (313)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~-~C~~ 146 (313)
-+.|..|+..-|+--..|| .|+.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 3567777777776666664 5544
No 57
>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=23.77 E-value=1.8e+02 Score=25.83 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCC
Q 021385 60 FHILLVMLVWSYVMVVFWDPGSVPE 84 (313)
Q Consensus 60 f~~l~~l~~~sy~~~~~~dPG~vp~ 84 (313)
..++.+.++..|..|--+|||....
T Consensus 200 itl~vf~LvgLyr~C~k~dPg~p~~ 224 (259)
T PF07010_consen 200 ITLSVFTLVGLYRMCWKTDPGTPEN 224 (259)
T ss_pred HHHHHHHHHHHHHHhhcCCCCCccc
Confidence 3344455556677888899997443
No 58
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=22.77 E-value=1.8e+02 Score=17.21 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=11.5
Q ss_pred HHHHHHhhcCCCCCCC
Q 021385 69 WSYVMVVFWDPGSVPE 84 (313)
Q Consensus 69 ~sy~~~~~~dPG~vp~ 84 (313)
..++...+.||-.+++
T Consensus 16 iiFFAIfFRepPri~k 31 (31)
T PRK11875 16 TLFFAIAFRDPPKIDK 31 (31)
T ss_pred HHHHhhhccCCCCCCC
Confidence 3466788999987763
No 59
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=22.71 E-value=33 Score=25.92 Aligned_cols=20 Identities=30% Similarity=0.565 Sum_probs=14.7
Q ss_pred CCccCcccCcccccccccCc
Q 021385 137 RCHHCSVCQRCVLKMDHHCV 156 (313)
Q Consensus 137 RshHC~~C~~CV~~~DHHCp 156 (313)
+.-+|..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 34579999999998555443
No 60
>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=22.59 E-value=31 Score=20.91 Aligned_cols=23 Identities=30% Similarity=0.587 Sum_probs=13.2
Q ss_pred CCeeeccccccc-cCCCCccCcccC
Q 021385 122 RSVGFCDRCQNG-KPPRCHHCSVCQ 145 (313)
Q Consensus 122 ~~~~~C~~C~~~-kP~RshHC~~C~ 145 (313)
...+.|..|..+ -||| ..|..|+
T Consensus 9 l~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEEEE-TTT--EEES---SEETTTT
T ss_pred EEEEEcCCCCCEecCCC-cCCCCcC
Confidence 456789999987 5566 7787775
No 61
>smart00301 DM Doublesex DNA-binding motif.
Probab=22.48 E-value=44 Score=22.58 Aligned_cols=6 Identities=17% Similarity=0.490 Sum_probs=3.4
Q ss_pred cCcccc
Q 021385 154 HCVWVV 159 (313)
Q Consensus 154 HCpwi~ 159 (313)
+|||-+
T Consensus 23 ~C~~r~ 28 (54)
T smart00301 23 ECPFRD 28 (54)
T ss_pred CCCCCC
Confidence 566653
No 62
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=21.46 E-value=36 Score=26.35 Aligned_cols=17 Identities=41% Similarity=0.733 Sum_probs=12.8
Q ss_pred CCccCcccCcccccccc
Q 021385 137 RCHHCSVCQRCVLKMDH 153 (313)
Q Consensus 137 RshHC~~C~~CV~~~DH 153 (313)
+.-||..|++||.+---
T Consensus 19 ~~V~C~nCgr~vPKDKA 35 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKA 35 (108)
T ss_pred ccEEeCCccccccccce
Confidence 34579999999998433
No 63
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=21.04 E-value=85 Score=26.14 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=27.6
Q ss_pred hcCcchHHHHhhcCCCCCCCchhHHHHHhhhCCCC
Q 021385 238 SSNTTSIEVYEKKRTVRWKYDLGRKKNFEQVYPVQ 272 (313)
Q Consensus 238 ~~n~Tt~E~~~~~~~~~~~yd~G~~~N~~~vfG~~ 272 (313)
-+|.|+.|..+.-+ .++.-|+++.+..+||.+
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 48999999987654 488899999999999987
No 64
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=20.32 E-value=38 Score=35.41 Aligned_cols=38 Identities=29% Similarity=0.586 Sum_probs=28.9
Q ss_pred CccCc---ccCcccccccccCcccc---cccc--cccHHHHHHHHH
Q 021385 138 CHHCS---VCQRCVLKMDHHCVWVV---NCVG--ARNYKSFLLFLL 175 (313)
Q Consensus 138 shHC~---~C~~CV~~~DHHCpwi~---nCIG--~~N~r~F~~Fl~ 175 (313)
-|+|+ .|..|++..|-||-|-+ .|+- ..|.|.+.+=+-
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~ 536 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVS 536 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhc
Confidence 37888 89888888999999998 7873 346666666543
No 65
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.27 E-value=52 Score=31.47 Aligned_cols=26 Identities=38% Similarity=0.808 Sum_probs=18.8
Q ss_pred cCCCCccCcccCcccccccccCcccccccccc
Q 021385 134 KPPRCHHCSVCQRCVLKMDHHCVWVVNCVGAR 165 (313)
Q Consensus 134 kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~ 165 (313)
+-.|..||..|+. .|| +|+.||||.-
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHHH
Confidence 3445667777764 677 8999999973
Done!