Query 019856
Match_columns 335
No_of_seqs 316 out of 1739
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 05:05:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019856.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019856hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1311 DHHC-type Zn-finger pr 100.0 4.8E-46 1E-50 354.6 19.1 218 11-244 50-277 (299)
2 KOG1315 Predicted DHHC-type Zn 100.0 3.3E-44 7.2E-49 338.8 15.9 219 11-241 43-266 (307)
3 PF01529 zf-DHHC: DHHC palmito 100.0 2.6E-40 5.6E-45 290.3 9.8 169 29-209 2-173 (174)
4 KOG1314 DHHC-type Zn-finger pr 100.0 2E-39 4.4E-44 303.4 7.9 193 10-233 44-263 (414)
5 COG5273 Uncharacterized protei 100.0 1.5E-34 3.2E-39 275.9 12.8 164 24-208 66-231 (309)
6 KOG1313 DHHC-type Zn-finger pr 100.0 6E-35 1.3E-39 265.9 7.6 150 87-236 102-279 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 3.5E-31 7.6E-36 242.5 11.4 174 13-209 97-290 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 2.8E-28 6.1E-33 244.0 5.3 176 28-230 382-582 (600)
9 COG5273 Uncharacterized protei 94.9 0.11 2.4E-06 50.1 8.2 114 86-210 122-245 (309)
10 PF01529 zf-DHHC: DHHC palmito 94.3 0.36 7.8E-06 41.8 9.3 55 84-149 59-113 (174)
11 KOG1311 DHHC-type Zn-finger pr 91.1 0.76 1.7E-05 43.8 7.5 42 100-141 112-164 (299)
12 KOG0509 Ankyrin repeat and DHH 83.0 0.53 1.1E-05 48.9 1.0 61 86-147 324-384 (600)
13 PRK04136 rpl40e 50S ribosomal 78.4 1.2 2.6E-05 30.9 1.3 28 86-113 13-40 (48)
14 PF13240 zinc_ribbon_2: zinc-r 73.7 1.8 4E-05 25.3 1.0 21 89-109 1-21 (23)
15 PTZ00303 phosphatidylinositol 66.8 3 6.5E-05 44.7 1.5 22 88-109 461-489 (1374)
16 KOG1313 DHHC-type Zn-finger pr 66.8 1.2E+02 0.0026 28.9 12.0 45 87-142 116-160 (309)
17 PF13248 zf-ribbon_3: zinc-rib 63.6 3.8 8.2E-05 24.5 0.9 22 88-109 3-24 (26)
18 PF01020 Ribosomal_L40e: Ribos 54.7 8 0.00017 27.3 1.5 24 87-110 17-42 (52)
19 KOG1842 FYVE finger-containing 54.2 3.4 7.4E-05 41.5 -0.6 27 86-112 179-207 (505)
20 PF12773 DZR: Double zinc ribb 52.8 9.9 0.00022 25.9 1.7 34 87-120 12-48 (50)
21 PF10571 UPF0547: Uncharacteri 49.9 9.7 0.00021 22.9 1.1 22 88-109 1-22 (26)
22 COG1552 RPL40A Ribosomal prote 49.3 3.4 7.3E-05 28.8 -1.1 27 87-113 14-40 (50)
23 KOG1315 Predicted DHHC-type Zn 44.0 1.2E+02 0.0027 29.3 8.3 31 100-130 108-138 (307)
24 PF00641 zf-RanBP: Zn-finger i 43.5 10 0.00022 23.2 0.6 21 89-109 6-26 (30)
25 KOG1314 DHHC-type Zn-finger pr 41.7 1.1E+02 0.0025 30.1 7.5 104 4-139 41-146 (414)
26 PF08600 Rsm1: Rsm1-like; Int 41.6 14 0.00031 29.0 1.3 11 116-126 56-66 (91)
27 PF01363 FYVE: FYVE zinc finge 41.0 8.9 0.00019 28.0 -0.0 26 87-112 9-36 (69)
28 PF12773 DZR: Double zinc ribb 38.0 20 0.00044 24.3 1.4 23 86-108 28-50 (50)
29 KOG3183 Predicted Zn-finger pr 35.2 18 0.00039 33.6 1.0 22 101-122 23-49 (250)
30 PF06906 DUF1272: Protein of u 35.2 18 0.0004 25.9 0.8 24 101-127 26-50 (57)
31 PF07649 C1_3: C1-like domain; 33.5 17 0.00037 22.2 0.4 23 89-111 2-25 (30)
32 smart00064 FYVE Protein presen 30.3 24 0.00052 25.6 0.8 25 88-112 11-37 (68)
33 PF07010 Endomucin: Endomucin; 28.5 1.2E+02 0.0025 28.2 5.0 14 30-43 210-223 (259)
34 PF10864 DUF2663: Protein of u 25.5 2E+02 0.0043 24.3 5.5 17 132-148 23-39 (130)
35 PRK15033 tricarballylate utili 25.0 2.2E+02 0.0049 28.5 6.7 14 103-120 68-81 (389)
36 cd00065 FYVE FYVE domain; Zinc 23.7 39 0.00084 23.4 0.9 23 89-111 4-28 (57)
37 smart00661 RPOL9 RNA polymeras 23.1 45 0.00097 22.7 1.1 20 89-108 2-27 (52)
38 PF02150 RNA_POL_M_15KD: RNA p 22.3 30 0.00066 22.2 0.1 7 88-94 2-8 (35)
39 PLN00186 ribosomal protein S26 22.1 39 0.00085 27.6 0.7 15 100-114 19-33 (109)
40 PF01405 PsbT: Photosystem II 22.1 1.7E+02 0.0037 18.2 3.3 11 29-39 16-26 (29)
41 KOG1729 FYVE finger containing 21.3 23 0.0005 33.9 -0.9 12 100-111 184-195 (288)
42 PRK00432 30S ribosomal protein 20.1 74 0.0016 22.2 1.7 23 87-109 20-45 (50)
No 1
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.8e-46 Score=354.59 Aligned_cols=218 Identities=37% Similarity=0.716 Sum_probs=174.4
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHhc---CCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceece
Q 019856 11 FFNYPVLIGGLLLTVLDFTFLFMTSGR---DPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRV 87 (335)
Q Consensus 11 ~~~~~~~~~~~~l~il~l~~l~~t~~~---DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~ 87 (335)
.++..+.+.+.++.++.++.+..++++ |||++|++..+..+.. .+.+++++..++|..++.
T Consensus 50 ~~~~~~~~~~~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~ 113 (299)
T KOG1311|consen 50 GVSPAVLVLGAIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDP----------------ERAPLYKNVDVNGIQVEW 113 (299)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCc----------------cccccCCCcccCCcccce
Confidence 455667777777777778888888777 9999999752111000 034667888899999999
Q ss_pred eeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccC----Ccc
Q 019856 88 KFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEG----DLS 163 (335)
Q Consensus 88 k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~----~~~ 163 (335)
+||.+|+.+||||||||++||+||+||||||||+|||||+||||+|++|+++.++.+++.+++.++.+..... ...
T Consensus 114 ~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~ 193 (299)
T KOG1311|consen 114 KYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLT 193 (299)
T ss_pred EEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999888777554221 122
Q ss_pred --hhhchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcceeeeee-eccCCCCCCCCHhHHHHHHHhcCCCCCCCCcc
Q 019856 164 --SIMRDDLLSVALIVYCFVAVWFVGGLTVFHFYLICTNQTTYENFR-YRYDKKENPFNRGILKNIKELFFSKIPPSMIN 240 (335)
Q Consensus 164 --~~~~~~~~~~~~~~~~~~~~~~v~~l~~~hlylI~~N~TT~E~~~-~~~~~~~npy~~G~~~N~~~vf~~~~~~~~~~ 240 (335)
.........++++++++++++++++|+.+|+++|.+|+||+|.++ ++...++++|++|.++|++++||.+.++++..
T Consensus 194 ~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~ 273 (299)
T KOG1311|consen 194 PVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWLS 273 (299)
T ss_pred ccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCCCCCccccc
Confidence 122223344566677888888899999999999999999999987 34444469999999999999999998887766
Q ss_pred CCcc
Q 019856 241 FRTW 244 (335)
Q Consensus 241 ~~~~ 244 (335)
....
T Consensus 274 p~~~ 277 (299)
T KOG1311|consen 274 PFAR 277 (299)
T ss_pred cccc
Confidence 5543
No 2
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.3e-44 Score=338.75 Aligned_cols=219 Identities=30% Similarity=0.485 Sum_probs=162.6
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceeceeec
Q 019856 11 FFNYPVLIGGLLLTVLDFTFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRVKFC 90 (335)
Q Consensus 11 ~~~~~~~~~~~~l~il~l~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~k~C 90 (335)
..+...++.+.++.++.+++|+.++++|||.+|..+.++..++...... ...++.+.....+...+.|+|
T Consensus 43 ~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~g~~R~C 112 (307)
T KOG1315|consen 43 IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENG----------SDNERDLPGYTRTSDGAVRYC 112 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCcccccccc----------CcccccceeeEecCCCCceee
Confidence 3456677888888999999999999999999999998865443322111 112233444456667789999
Q ss_pred cccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcch-hhchh
Q 019856 91 DTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGDLSS-IMRDD 169 (335)
Q Consensus 91 ~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 169 (335)
.+|+.+||+|||||++|++||+||||||||+|||||.+|||||++|++|+.+++++.++.....+......... .....
T Consensus 113 ~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~~~~~~~ 192 (307)
T KOG1315|consen 113 DKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAGPSSLLL 192 (307)
T ss_pred cccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCchhHH
Confidence 99999999999999999999999999999999999999999999999999999998887665443322101011 01112
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcceeeeeeec----cCCCCCCCCHhHHHHHHHhcCCCCCCCCccC
Q 019856 170 LLSVALIVYCFVAVWFVGGLTVFHFYLICTNQTTYENFRYR----YDKKENPFNRGILKNIKELFFSKIPPSMINF 241 (335)
Q Consensus 170 ~~~~~~~~~~~~~~~~v~~l~~~hlylI~~N~TT~E~~~~~----~~~~~npy~~G~~~N~~~vf~~~~~~~~~~~ 241 (335)
...+++++.+..+++.+++|+++|++||++|+||+|.++.. .....+.|+. ..|+.++||++.--|+.|.
T Consensus 193 ~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~--~~n~~~vfg~~~~~wl~P~ 266 (307)
T KOG1315|consen 193 FFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGFNL--YVNFREVFGSNLLYWLLPI 266 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCcce--eecHHHHhCCCceEEeccc
Confidence 22334444455556667779999999999999999998743 2234566665 7899999999866665554
No 3
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=2.6e-40 Score=290.34 Aligned_cols=169 Identities=34% Similarity=0.707 Sum_probs=121.8
Q ss_pred HHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceeceeeccccccccCCCCccCCCCC
Q 019856 29 TFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRVKFCDTCLLYRPPRASHCSICN 108 (335)
Q Consensus 29 ~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~k~C~tC~~~kP~Rs~HC~~C~ 108 (335)
++|+++.++|||++|+.....+..+... ........+....+...+.++|.+|+..||+|||||+.||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~ 69 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEK------------EEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCN 69 (174)
T ss_pred EEehhhheECCcccCCcccccccccccc------------ccccchhhhhhccccCCCCEECcccCCcCCCcceeccccc
Confidence 4688999999999999822111100000 0001112223334556678999999999999999999999
Q ss_pred cccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCc--chhhchhhh-hHHHHHHHHHHHHH
Q 019856 109 NCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGDL--SSIMRDDLL-SVALIVYCFVAVWF 185 (335)
Q Consensus 109 ~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~ 185 (335)
+||+||||||||+|||||++|||+|++|+++.++.+++.++.++..+....... ......... .+++++++++++++
T Consensus 70 ~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (174)
T PF01529_consen 70 RCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIF 149 (174)
T ss_pred cccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999888876665544332111 100001111 14555666677778
Q ss_pred HHHHHHHHHHHHHhCcceeeeeee
Q 019856 186 VGGLTVFHFYLICTNQTTYENFRY 209 (335)
Q Consensus 186 v~~l~~~hlylI~~N~TT~E~~~~ 209 (335)
+++++++|+++|++|+||+|.+++
T Consensus 150 ~~~l~~~~~~~i~~n~Tt~E~~~~ 173 (174)
T PF01529_consen 150 VGFLLIFQLYLILRNITTYERIKR 173 (174)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHc
Confidence 899999999999999999998864
No 4
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2e-39 Score=303.42 Aligned_cols=193 Identities=27% Similarity=0.531 Sum_probs=140.0
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceeceee
Q 019856 10 PFFNYPVLIGGLLLTVLDFTFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRVKF 89 (335)
Q Consensus 10 ~~~~~~~~~~~~~l~il~l~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~k~ 89 (335)
++.+.+-.+..++.+.+.++.|+++++++||++|++|+|....+ .....|
T Consensus 44 s~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D------------------------------~~~lqf 93 (414)
T KOG1314|consen 44 SFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKD------------------------------EMFLQF 93 (414)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChh------------------------------HHHHHH
Confidence 45566677777888889999999999999999999999854211 123569
Q ss_pred ccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHH---HH--------HHHHHHhc
Q 019856 90 CDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVF---VF--------SWINIIRQ 158 (335)
Q Consensus 90 C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~---~~--------~~~~~~~~ 158 (335)
|.+|+.+|+||||||+.|||||.+|||||||+|||||..||.+|+.||++..+.|+-.. +. .|+.-. .
T Consensus 94 Ck~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~-g 172 (414)
T KOG1314|consen 94 CKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKY-G 172 (414)
T ss_pred HhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhc-c
Confidence 99999999999999999999999999999999999999999999999999887665321 11 121111 1
Q ss_pred cCCcchhh---chhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcceeeeee---------eccC----CCCCCCCHhH
Q 019856 159 EGDLSSIM---RDDLLSVALIVYCFVAVWFVGGLTVFHFYLICTNQTTYENFR---------YRYD----KKENPFNRGI 222 (335)
Q Consensus 159 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~v~~l~~~hlylI~~N~TT~E~~~---------~~~~----~~~npy~~G~ 222 (335)
...+.... ...+..++.+.+.+...+.++.|+..|+..|.+|+|.+|.+- +... ...-|||.|+
T Consensus 173 ~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgW 252 (414)
T KOG1314|consen 173 LRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGW 252 (414)
T ss_pred cccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccc
Confidence 11111111 111222333333344455677889999999999999999873 1111 1135999997
Q ss_pred HHHHHHhcCCC
Q 019856 223 LKNIKELFFSK 233 (335)
Q Consensus 223 ~~N~~~vf~~~ 233 (335)
..|+++||...
T Consensus 253 r~n~r~vf~~~ 263 (414)
T KOG1314|consen 253 RINLREVFFQN 263 (414)
T ss_pred cccHHHHhhhc
Confidence 77999999765
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=1.5e-34 Score=275.87 Aligned_cols=164 Identities=32% Similarity=0.566 Sum_probs=115.9
Q ss_pred HHHHHHHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceeceeeccccccccCCCCcc
Q 019856 24 TVLDFTFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRVKFCDTCLLYRPPRASH 103 (335)
Q Consensus 24 ~il~l~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~k~C~tC~~~kP~Rs~H 103 (335)
..++.+.++.....|||+.+++......++.. +.....|...+.++|.+|+.+||+||||
T Consensus 66 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~C~~C~~~KP~RS~H 125 (309)
T COG5273 66 LVLASFSYLLLLVSDPGYLGENITLSGYRETI--------------------SRLLDDGKFGTENFCSTCNIYKPPRSHH 125 (309)
T ss_pred hhhHHHhhHHHhhcCCCccCccccccchhhhh--------------------hhhhhcCccccceeccccccccCCCCcc
Confidence 33566777888999999999775433222111 1122345566789999999999999999
Q ss_pred CCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchhhchhhhhHHH--HHHHHH
Q 019856 104 CSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGDLSSIMRDDLLSVAL--IVYCFV 181 (335)
Q Consensus 104 C~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 181 (335)
|+.||+||+||||||||+|||||++|||+|++|+++....++.+++..++.+.......... ......++. ..+...
T Consensus 126 C~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~ 204 (309)
T COG5273 126 CSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDT-SLAICFLIFGCSLLGVV 204 (309)
T ss_pred chhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCh-HHHHHHHHHhhhHHHHH
Confidence 99999999999999999999999999999999999998877777766555443222110000 000011111 122333
Q ss_pred HHHHHHHHHHHHHHHHHhCcceeeeee
Q 019856 182 AVWFVGGLTVFHFYLICTNQTTYENFR 208 (335)
Q Consensus 182 ~~~~v~~l~~~hlylI~~N~TT~E~~~ 208 (335)
.++++..++.+|.+++..|+||+|.+.
T Consensus 205 ~f~~~~~~~~~~~~~~~~~~t~~e~~~ 231 (309)
T COG5273 205 FFIITTLLLLFLIYLILNNLTTIEFIQ 231 (309)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 455667889999999999999999765
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=6e-35 Score=265.93 Aligned_cols=150 Identities=29% Similarity=0.541 Sum_probs=113.2
Q ss_pred eeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHH---HHHHHhcc----
Q 019856 87 VKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFS---WINIIRQE---- 159 (335)
Q Consensus 87 ~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~---~~~~~~~~---- 159 (335)
..+|.+|+.+||||+|||++|++||++|||||||+|||||..||||||+|++|+++.+.|+.+.. |...+...
T Consensus 102 ~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~t 181 (309)
T KOG1313|consen 102 DSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEIT 181 (309)
T ss_pred ccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhcc
Confidence 45999999999999999999999999999999999999999999999999999999999987764 33222111
Q ss_pred ---CC---cch--hhc--hh----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcceeeeeeecc-------CCCCCCC
Q 019856 160 ---GD---LSS--IMR--DD----LLSVALIVYCFVAVWFVGGLTVFHFYLICTNQTTYENFRYRY-------DKKENPF 218 (335)
Q Consensus 160 ---~~---~~~--~~~--~~----~~~~~~~~~~~~~~~~v~~l~~~hlylI~~N~TT~E~~~~~~-------~~~~npy 218 (335)
++ .+. .+. .. ...+.+.+.++.+++.++.++.+|.++|+.|.|++|.....+ ..+.||+
T Consensus 182 ay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~~ 261 (309)
T KOG1313|consen 182 AYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNPT 261 (309)
T ss_pred cccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCCc
Confidence 00 000 000 00 012223444455666788999999999999999999764221 3457899
Q ss_pred CHhHHHHHHHhcCCCCCC
Q 019856 219 NRGILKNIKELFFSKIPP 236 (335)
Q Consensus 219 ~~G~~~N~~~vf~~~~~~ 236 (335)
+.|..+||+.++|-..-+
T Consensus 262 n~g~k~nWr~fLg~~~~r 279 (309)
T KOG1313|consen 262 NFGGKANWRNFLGLFRGR 279 (309)
T ss_pred ccchHHHHHHhhccccCC
Confidence 999999999999765444
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=3.5e-31 Score=242.49 Aligned_cols=174 Identities=36% Similarity=0.623 Sum_probs=115.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceeceeeccc
Q 019856 13 NYPVLIGGLLLTVLDFTFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRVKFCDT 92 (335)
Q Consensus 13 ~~~~~~~~~~l~il~l~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~k~C~t 92 (335)
+....+..+.+.++-++++.+|+.+|||++.+....... -.+|.+.-+. -+.+-|+|
T Consensus 97 sl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~------------------~~ypYDy~if-----~k~~kCST 153 (341)
T KOG1312|consen 97 SLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFL------------------HVYPYDYVIF-----PKNVKCST 153 (341)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccce------------------eccCccceee-----cCCCcccc
Confidence 344445555666677889999999999998764321110 1223322221 23468999
Q ss_pred cccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchh-------
Q 019856 93 CLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGDLSSI------- 165 (335)
Q Consensus 93 C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~------- 165 (335)
|++.||.||+|||+||+||+||||||.|+|||||++|+|||++||++...++.|.+.-.++..+....++...
T Consensus 154 Cki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~ 233 (341)
T KOG1312|consen 154 CKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLG 233 (341)
T ss_pred ccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeee
Confidence 9999999999999999999999999999999999999999999999998888887665444322111110000
Q ss_pred hchhhhhHHHHHH------------HHHH-HHHHHHHHHHHHHHHHhCcceeeeeee
Q 019856 166 MRDDLLSVALIVY------------CFVA-VWFVGGLTVFHFYLICTNQTTYENFRY 209 (335)
Q Consensus 166 ~~~~~~~~~~~~~------------~~~~-~~~v~~l~~~hlylI~~N~TT~E~~~~ 209 (335)
.........++-+ ++.. ..++++-..+-+|+.++|+||.|+.+.
T Consensus 234 ~g~~ks~~~L~~yl~la~~~~v~~l~~~~~~~~~~~Y~~f~~y~~~t~~~~~~W~~~ 290 (341)
T KOG1312|consen 234 HGHVKSTVFLIQYLFLAFPRIVFMLGFVVVLSFLGGYLLFVLYLAATNQTTNEWYRG 290 (341)
T ss_pred ecchhhHHHHHHHHHHHhccceeeeehhhhhhHhHHHHHHHHHHHhccCCchhhhcc
Confidence 0000000111111 1111 224566777888999999999998764
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.94 E-value=2.8e-28 Score=243.96 Aligned_cols=176 Identities=31% Similarity=0.661 Sum_probs=114.0
Q ss_pred HHHHHHHHhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeecCceece-eeccccccccCCCCccCCC
Q 019856 28 FTFLFMTSGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVNGHSVRV-KFCDTCLLYRPPRASHCSI 106 (335)
Q Consensus 28 l~~l~~t~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~g~~~~~-k~C~tC~~~kP~Rs~HC~~ 106 (335)
++.+.++..+|||++|.+.... .+.+ ++...-|..... +||.+|.+.||.||+||++
T Consensus 382 ~~~f~~~~rsDPg~i~~~~~~~--~~tI--------------------s~l~d~gkf~~en~FC~~clirKp~rSkhc~v 439 (600)
T KOG0509|consen 382 FITFGLFLRSDPGFIPTSTEVG--RETI--------------------SQLIDFGKFDLENRFCLTCLIRKPLRSKHCSV 439 (600)
T ss_pred HHHHHHHhccCCCCCCCchhhH--HHHH--------------------HHhhccccccccccceeeeeeecCCccchhhh
Confidence 3344455568999999764321 0111 111122333344 6999999999999999999
Q ss_pred CCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchhhchhhhhHHHHHHHHHH----
Q 019856 107 CNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGDLSSIMRDDLLSVALIVYCFVA---- 182 (335)
Q Consensus 107 C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---- 182 (335)
|||||.||||||||++||||.+||++|+.|++.....+.+.++.....+......- .. ....+.++..+..
T Consensus 440 cnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~---~~--~~~~l~~~~~~~~~~~~ 514 (600)
T KOG0509|consen 440 CNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENAS---TI--YVGFLIAVQAFRIPKPV 514 (600)
T ss_pred hHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhH---HH--HHHHHHHHHHHhCCccc
Confidence 99999999999999999999999999999999988777777665554433222110 00 0001111111100
Q ss_pred ------------HHHHHHHHHHHHHHHHhCcceeeeeeecc--------CCCCCCCCHhHHHHHHHhc
Q 019856 183 ------------VWFVGGLTVFHFYLICTNQTTYENFRYRY--------DKKENPFNRGILKNIKELF 230 (335)
Q Consensus 183 ------------~~~v~~l~~~hlylI~~N~TT~E~~~~~~--------~~~~npy~~G~~~N~~~vf 230 (335)
.|-.+...+.|-..++.+.||+|.++.+. ....+|++.|+.+|+.+++
T Consensus 515 ~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g~~~Nl~df~ 582 (600)
T KOG0509|consen 515 TGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPGPIRNLVDFF 582 (600)
T ss_pred eeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCchhhhcchhee
Confidence 01111223344456889999999886322 1236799999999999998
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=94.90 E-value=0.11 Score=50.08 Aligned_cols=114 Identities=19% Similarity=0.349 Sum_probs=68.3
Q ss_pred ceeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC--cc
Q 019856 86 RVKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFVFSWINIIRQEGD--LS 163 (335)
Q Consensus 86 ~~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~~~~~~~~~~~~~--~~ 163 (335)
+.+.|..|+.--...=|||.-=|+||-+--| |=.=.|++++.+.++..++............... .+
T Consensus 122 RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (309)
T COG5273 122 RSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLA 190 (309)
T ss_pred CCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHH
Confidence 4579999999999999999999999998655 5677888888666555544433322222211111 11
Q ss_pred -h-hh------chhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcceeeeeeec
Q 019856 164 -S-IM------RDDLLSVALIVYCFVAVWFVGGLTVFHFYLICTNQTTYENFRYR 210 (335)
Q Consensus 164 -~-~~------~~~~~~~~~~~~~~~~~~~v~~l~~~hlylI~~N~TT~E~~~~~ 210 (335)
. .+ ....+.+..+++.+....++...+..+.+.+.++.++-|.....
T Consensus 191 ~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~ 245 (309)
T COG5273 191 ICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLC 245 (309)
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchh
Confidence 0 00 01111112222222233344567778888899999998876533
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=94.29 E-value=0.36 Score=41.79 Aligned_cols=55 Identities=20% Similarity=0.482 Sum_probs=42.1
Q ss_pred eeceeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHH
Q 019856 84 SVRVKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYVFV 149 (335)
Q Consensus 84 ~~~~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~~~ 149 (335)
..+.++|..|+.-...+=|||.--|+||.+--| +-+-.|+++.....+..++..+
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~ 113 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSL 113 (174)
T ss_pred CCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999999999998766 4566787776655555554433
No 11
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=91.15 E-value=0.76 Score=43.81 Aligned_cols=42 Identities=14% Similarity=0.300 Sum_probs=35.9
Q ss_pred CCccCCCCCcccccccccCccccccccccc-----------hHHHHHHHHHHH
Q 019856 100 RASHCSICNNCIQKFDHHCPWVGQCIGLRN-----------YVSFIFFISTST 141 (335)
Q Consensus 100 Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N-----------~r~F~lFl~~~~ 141 (335)
+.++|..|+..+...-|||..-|+||-+.- +|-+-.|+.+..
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 389999999999999999999999998874 567778885544
No 12
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=82.96 E-value=0.53 Score=48.86 Aligned_cols=61 Identities=11% Similarity=-0.014 Sum_probs=48.7
Q ss_pred ceeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHHHHHHH
Q 019856 86 RVKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTFLCLYV 147 (335)
Q Consensus 86 ~~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~~~~~~ 147 (335)
-.-.|.+|.+..+.+..+|..|-.++..+++||+|+. ||+.+|-..|.+..+...+...+.
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~~~~~ 384 (600)
T KOG0509|consen 324 LTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLAYFIT 384 (600)
T ss_pred hheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHHHHHH
Confidence 4568999999999999999999999999999999999 999999776554443333333333
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=78.38 E-value=1.2 Score=30.85 Aligned_cols=28 Identities=29% Similarity=0.523 Sum_probs=23.3
Q ss_pred ceeeccccccccCCCCccCCCCCccccc
Q 019856 86 RVKFCDTCLLYRPPRASHCSICNNCIQK 113 (335)
Q Consensus 86 ~~k~C~tC~~~kP~Rs~HC~~C~~CV~r 113 (335)
..+.|..|...-|+|+..|+.||.=-+|
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~~~LR 40 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGYKNLR 40 (48)
T ss_pred cccchhcccCCCCccccccccCCCCCcC
Confidence 3578999999999999999999864333
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.73 E-value=1.8 Score=25.26 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=17.6
Q ss_pred eccccccccCCCCccCCCCCc
Q 019856 89 FCDTCLLYRPPRASHCSICNN 109 (335)
Q Consensus 89 ~C~tC~~~kP~Rs~HC~~C~~ 109 (335)
+|+.|...-++-+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588888888888888888874
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=66.82 E-value=3 Score=44.72 Aligned_cols=22 Identities=32% Similarity=0.584 Sum_probs=18.2
Q ss_pred eeccccccccC-------CCCccCCCCCc
Q 019856 88 KFCDTCLLYRP-------PRASHCSICNN 109 (335)
Q Consensus 88 k~C~tC~~~kP-------~Rs~HC~~C~~ 109 (335)
+.|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 57999987664 39999999987
No 16
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=66.78 E-value=1.2e+02 Score=28.94 Aligned_cols=45 Identities=27% Similarity=0.642 Sum_probs=33.7
Q ss_pred eeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHHHHH
Q 019856 87 VKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFISTSTF 142 (335)
Q Consensus 87 ~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~~~~ 142 (335)
...|+.|+.---.=-|||.--|+||--..| |=.-.|+.++..++.
T Consensus 116 THHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~ 160 (309)
T KOG1313|consen 116 THHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATS 160 (309)
T ss_pred cchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHH
Confidence 347888876555667999999999998777 556778888765443
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.60 E-value=3.8 Score=24.50 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=17.7
Q ss_pred eeccccccccCCCCccCCCCCc
Q 019856 88 KFCDTCLLYRPPRASHCSICNN 109 (335)
Q Consensus 88 k~C~tC~~~kP~Rs~HC~~C~~ 109 (335)
++|+.|...-++-+..|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 4788888877888888888874
No 18
>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=54.66 E-value=8 Score=27.29 Aligned_cols=24 Identities=33% Similarity=0.873 Sum_probs=16.6
Q ss_pred eeeccccccccCCCCccCCC--CCcc
Q 019856 87 VKFCDTCLLYRPPRASHCSI--CNNC 110 (335)
Q Consensus 87 ~k~C~tC~~~kP~Rs~HC~~--C~~C 110 (335)
...|..|...-|+|+-.|+. ||.+
T Consensus 17 k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 17 KMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp -EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred ceecccccCcCCCCccceecccCCCC
Confidence 56899999999999999998 8765
No 19
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=54.20 E-value=3.4 Score=41.47 Aligned_cols=27 Identities=30% Similarity=0.742 Sum_probs=20.8
Q ss_pred ceeecccccccc--CCCCccCCCCCcccc
Q 019856 86 RVKFCDTCLLYR--PPRASHCSICNNCIQ 112 (335)
Q Consensus 86 ~~k~C~tC~~~k--P~Rs~HC~~C~~CV~ 112 (335)
.+.+|+.|...- .-|-|||+.||+-+-
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHH
Confidence 357999997543 458999999998654
No 20
>PF12773 DZR: Double zinc ribbon
Probab=52.77 E-value=9.9 Score=25.93 Aligned_cols=34 Identities=26% Similarity=0.517 Sum_probs=22.9
Q ss_pred eeeccccccccC---CCCccCCCCCcccccccccCcc
Q 019856 87 VKFCDTCLLYRP---PRASHCSICNNCIQKFDHHCPW 120 (335)
Q Consensus 87 ~k~C~tC~~~kP---~Rs~HC~~C~~CV~r~DHHCpW 120 (335)
.+||..|...-+ .....|..|+.=+...+.+|++
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 457777776555 3466777777777777777764
No 21
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=49.88 E-value=9.7 Score=22.94 Aligned_cols=22 Identities=32% Similarity=0.643 Sum_probs=17.7
Q ss_pred eeccccccccCCCCccCCCCCc
Q 019856 88 KFCDTCLLYRPPRASHCSICNN 109 (335)
Q Consensus 88 k~C~tC~~~kP~Rs~HC~~C~~ 109 (335)
|.|+.|...-|.-+.-|..||.
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 22
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=49.25 E-value=3.4 Score=28.77 Aligned_cols=27 Identities=33% Similarity=0.764 Sum_probs=22.7
Q ss_pred eeeccccccccCCCCccCCCCCccccc
Q 019856 87 VKFCDTCLLYRPPRASHCSICNNCIQK 113 (335)
Q Consensus 87 ~k~C~tC~~~kP~Rs~HC~~C~~CV~r 113 (335)
.+.|..|...-|+|+--|+.|+.=-+|
T Consensus 14 kkIC~rC~Arnp~~A~kCRkC~~k~LR 40 (50)
T COG1552 14 KKICRRCYARNPPRATKCRKCGYKNLR 40 (50)
T ss_pred HHHHHHhcCCCCcchhHHhhccCCCcc
Confidence 568999999999999999998764443
No 23
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=43.99 E-value=1.2e+02 Score=29.27 Aligned_cols=31 Identities=19% Similarity=0.439 Sum_probs=27.0
Q ss_pred CCccCCCCCcccccccccCccccccccccch
Q 019856 100 RASHCSICNNCIQKFDHHCPWVGQCIGLRNY 130 (335)
Q Consensus 100 Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~ 130 (335)
+...|..|+.-...--|||.--+.||.+.-|
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDH 138 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDH 138 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhcccc
Confidence 6778999998888888999999999998754
No 24
>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=43.49 E-value=10 Score=23.18 Aligned_cols=21 Identities=29% Similarity=0.833 Sum_probs=15.8
Q ss_pred eccccccccCCCCccCCCCCc
Q 019856 89 FCDTCLLYRPPRASHCSICNN 109 (335)
Q Consensus 89 ~C~tC~~~kP~Rs~HC~~C~~ 109 (335)
.|..|...-+++..+|..|+.
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 588999888899999988874
No 25
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=41.68 E-value=1.1e+02 Score=30.14 Aligned_cols=104 Identities=17% Similarity=0.234 Sum_probs=64.3
Q ss_pred ccccCCCCchhhHHHHHHHHHHHHHHHHHHH--HhcCCcccCCCCCCCCccccccCCCCchhhcccCCCCCCcccceeec
Q 019856 4 MIKQENPFFNYPVLIGGLLLTVLDFTFLFMT--SGRDPGIIPRNAQPPELDESVDLNTPSIEWISNKDVKLPRTKDLIVN 81 (335)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~l~il~l~~l~~t--~~~DPG~vPr~~~~~~~~e~~~~~~~~~~~~~~~~~~~p~~k~~~v~ 81 (335)
.....-+..+.+.+.+-..++++.++.=.++ -+.-||.-|.+......-.-.. .=...+.||
T Consensus 41 p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~lqfCk---------~CqgYKapR------- 104 (414)
T KOG1314|consen 41 PLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDEMFLQFCK---------KCQGYKAPR------- 104 (414)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHh---------hccCcCCCc-------
Confidence 3445556667666666666666666554444 4778999998765422211110 000123443
Q ss_pred CceeceeeccccccccCCCCccCCCCCcccccccccCccccccccccchHHHHHHHHH
Q 019856 82 GHSVRVKFCDTCLLYRPPRASHCSICNNCIQKFDHHCPWVGQCIGLRNYVSFIFFIST 139 (335)
Q Consensus 82 g~~~~~k~C~tC~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCIG~~N~r~F~lFl~~ 139 (335)
...|++|+.-.-.=-|||.--++||---.| --.-+|++|.+.
T Consensus 105 -----SHHCrkCnrCvmkMDHHCPWinnCVG~aNh-----------~~F~~FLlf~iv 146 (414)
T KOG1314|consen 105 -----SHHCRKCNRCVMKMDHHCPWINNCVGWANH-----------AYFLRFLLFSIV 146 (414)
T ss_pred -----cccchHHHHHHHhhccCCcchhhccccccc-----------HHHHHHHHHHHH
Confidence 357999987666677999999999976554 235778888665
No 26
>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=41.58 E-value=14 Score=28.97 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=8.8
Q ss_pred ccCcccccccc
Q 019856 116 HHCPWVGQCIG 126 (335)
Q Consensus 116 HHCpWi~nCIG 126 (335)
.||||++.-..
T Consensus 56 ~~CPwv~~~~q 66 (91)
T PF08600_consen 56 EYCPWVNPSTQ 66 (91)
T ss_pred ccCCccCCccc
Confidence 58999997653
No 27
>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=40.97 E-value=8.9 Score=28.00 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=12.5
Q ss_pred eeecccccccc--CCCCccCCCCCcccc
Q 019856 87 VKFCDTCLLYR--PPRASHCSICNNCIQ 112 (335)
Q Consensus 87 ~k~C~tC~~~k--P~Rs~HC~~C~~CV~ 112 (335)
...|..|...= -.|-|||+.||+.|=
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 35788786432 368999999998654
No 28
>PF12773 DZR: Double zinc ribbon
Probab=38.01 E-value=20 Score=24.35 Aligned_cols=23 Identities=35% Similarity=0.811 Sum_probs=20.6
Q ss_pred ceeeccccccccCCCCccCCCCC
Q 019856 86 RVKFCDTCLLYRPPRASHCSICN 108 (335)
Q Consensus 86 ~~k~C~tC~~~kP~Rs~HC~~C~ 108 (335)
..++|..|....++.+.+|..||
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 45799999999999999999986
No 29
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=35.19 E-value=18 Score=33.60 Aligned_cols=22 Identities=27% Similarity=0.453 Sum_probs=14.9
Q ss_pred CccCCCCC-----cccccccccCcccc
Q 019856 101 ASHCSICN-----NCIQKFDHHCPWVG 122 (335)
Q Consensus 101 s~HC~~C~-----~CV~r~DHHCpWi~ 122 (335)
..||..|+ .=..+.+|||||..
T Consensus 23 Pf~Cd~C~~~FC~eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 23 PFKCDGCSGIFCLEHRSYESHHCPKGL 49 (250)
T ss_pred ceeeCCccchhhhccchHhhcCCCccc
Confidence 34555554 34567899999975
No 30
>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=35.17 E-value=18 Score=25.95 Aligned_cols=24 Identities=29% Similarity=0.966 Sum_probs=19.9
Q ss_pred CccCCCCCcccccc-cccCccccccccc
Q 019856 101 ASHCSICNNCIQKF-DHHCPWVGQCIGL 127 (335)
Q Consensus 101 s~HC~~C~~CV~r~-DHHCpWi~nCIG~ 127 (335)
|+-|..|..|+..+ +++|| ||=|.
T Consensus 26 SfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 26 SFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred eEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 47789999999998 99998 66653
No 31
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=33.52 E-value=17 Score=22.20 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=9.2
Q ss_pred eccccccccCC-CCccCCCCCccc
Q 019856 89 FCDTCLLYRPP-RASHCSICNNCI 111 (335)
Q Consensus 89 ~C~tC~~~kP~-Rs~HC~~C~~CV 111 (335)
.|..|+..... ..++|..|+--+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 57788777666 788999887543
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 PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=28.46 E-value=1.2e+02 Score=28.24 Aligned_cols=14 Identities=29% Similarity=0.316 Sum_probs=9.0
Q ss_pred HHHHHHhcCCcccC
Q 019856 30 FLFMTSGRDPGIIP 43 (335)
Q Consensus 30 ~l~~t~~~DPG~vP 43 (335)
+|.+|--+|||..-
T Consensus 210 Lyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 210 LYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHhhcCCCCCcc
Confidence 34456668999543
No 34
>PF10864 DUF2663: Protein of unknown function (DUF2663); InterPro: IPR020210 This entry represents a group of uncharacterised transmembrane proteins.
Probab=25.46 E-value=2e+02 Score=24.35 Aligned_cols=17 Identities=12% Similarity=0.344 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHH
Q 019856 132 SFIFFISTSTFLCLYVF 148 (335)
Q Consensus 132 ~F~lFl~~~~~~~~~~~ 148 (335)
+..+++++.+++++|+.
T Consensus 23 ~~~~~l~~~~~~~~y~~ 39 (130)
T PF10864_consen 23 WQWLFLFSLFLFFIYFY 39 (130)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45556666666555554
No 35
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=25.05 E-value=2.2e+02 Score=28.48 Aligned_cols=14 Identities=36% Similarity=1.262 Sum_probs=11.8
Q ss_pred cCCCCCcccccccccCcc
Q 019856 103 HCSICNNCIQKFDHHCPW 120 (335)
Q Consensus 103 HC~~C~~CV~r~DHHCpW 120 (335)
.|..|+.|. |+||-
T Consensus 68 ~C~~Cg~C~----~~CP~ 81 (389)
T PRK15033 68 LCHNCGACL----HACQY 81 (389)
T ss_pred hCcCccccc----ccCcC
Confidence 799999995 58997
No 36
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=23.71 E-value=39 Score=23.41 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=15.4
Q ss_pred ecccccc--ccCCCCccCCCCCccc
Q 019856 89 FCDTCLL--YRPPRASHCSICNNCI 111 (335)
Q Consensus 89 ~C~tC~~--~kP~Rs~HC~~C~~CV 111 (335)
-|..|.. -.-.|.|||+.||+-+
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred cCcccCccccCCccccccCcCcCCc
Confidence 4566643 2246889999998754
No 37
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.13 E-value=45 Score=22.67 Aligned_cols=20 Identities=30% Similarity=0.717 Sum_probs=10.0
Q ss_pred eccccccccCCC------CccCCCCC
Q 019856 89 FCDTCLLYRPPR------ASHCSICN 108 (335)
Q Consensus 89 ~C~tC~~~kP~R------s~HC~~C~ 108 (335)
||+.|.....++ -..|+.||
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg 27 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC
Confidence 666665433221 24466666
No 38
>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=22.30 E-value=30 Score=22.20 Aligned_cols=7 Identities=43% Similarity=1.307 Sum_probs=4.3
Q ss_pred eeccccc
Q 019856 88 KFCDTCL 94 (335)
Q Consensus 88 k~C~tC~ 94 (335)
+||++|.
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 5777775
No 39
>PLN00186 ribosomal protein S26; Provisional
Probab=22.12 E-value=39 Score=27.55 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=12.2
Q ss_pred CCccCCCCCcccccc
Q 019856 100 RASHCSICNNCIQKF 114 (335)
Q Consensus 100 Rs~HC~~C~~CV~r~ 114 (335)
+.-||..|++||.+=
T Consensus 19 ~~V~C~nCgr~vPKD 33 (109)
T PLN00186 19 KRIRCSNCGKCVPKD 33 (109)
T ss_pred cceeeCCCccccccc
Confidence 456899999999973
No 40
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=22.10 E-value=1.7e+02 Score=18.18 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=5.8
Q ss_pred HHHHHHHhcCC
Q 019856 29 TFLFMTSGRDP 39 (335)
Q Consensus 29 ~~l~~t~~~DP 39 (335)
+.++...++||
T Consensus 16 ilffAI~FReP 26 (29)
T PF01405_consen 16 ILFFAIFFREP 26 (29)
T ss_dssp HHHHHHHSS--
T ss_pred HHHhhhhccCC
Confidence 34566678888
No 41
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=21.31 E-value=23 Score=33.92 Aligned_cols=12 Identities=33% Similarity=0.958 Sum_probs=6.6
Q ss_pred CCccCCCCCccc
Q 019856 100 RASHCSICNNCI 111 (335)
Q Consensus 100 Rs~HC~~C~~CV 111 (335)
|=|||+.||.-|
T Consensus 184 RRHHCR~CG~iv 195 (288)
T KOG1729|consen 184 RRHHCRNCGDIV 195 (288)
T ss_pred HHHHHHhcchHh
Confidence 556665555543
No 42
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.06 E-value=74 Score=22.15 Aligned_cols=23 Identities=30% Similarity=0.683 Sum_probs=14.8
Q ss_pred eeecccccc-ccC--CCCccCCCCCc
Q 019856 87 VKFCDTCLL-YRP--PRASHCSICNN 109 (335)
Q Consensus 87 ~k~C~tC~~-~kP--~Rs~HC~~C~~ 109 (335)
.++|+.|.. ..- .-..+|..|+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCC
Confidence 569999976 222 23567777764
Done!