Query 024129
Match_columns 272
No_of_seqs 244 out of 1491
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 09:12:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1312 DHHC-type Zn-finger pr 100.0 9.6E-56 2.1E-60 396.2 8.2 248 1-260 1-250 (341)
2 KOG1315 Predicted DHHC-type Zn 100.0 3.3E-35 7.2E-40 271.0 10.5 194 78-272 13-230 (307)
3 PF01529 zf-DHHC: DHHC palmito 100.0 1.2E-35 2.5E-40 252.6 6.4 148 125-272 2-171 (174)
4 KOG1311 DHHC-type Zn-finger pr 100.0 5E-34 1.1E-38 263.5 8.8 156 117-272 60-239 (299)
5 COG5273 Uncharacterized protei 100.0 2.4E-32 5.2E-37 253.7 8.6 157 115-271 61-229 (309)
6 KOG1314 DHHC-type Zn-finger pr 100.0 8.3E-32 1.8E-36 247.6 4.4 161 105-271 43-223 (414)
7 KOG1313 DHHC-type Zn-finger pr 99.9 4.8E-26 1E-30 203.9 8.4 72 158-229 101-172 (309)
8 KOG0509 Ankyrin repeat and DHH 99.9 2.3E-25 4.9E-30 218.0 7.6 110 119-228 377-489 (600)
9 KOG0509 Ankyrin repeat and DHH 85.8 0.72 1.6E-05 46.8 3.4 86 125-212 292-378 (600)
10 PF13240 zinc_ribbon_2: zinc-r 84.5 0.6 1.3E-05 26.9 1.3 21 161-181 1-21 (23)
11 PF13248 zf-ribbon_3: zinc-rib 80.7 1 2.2E-05 26.5 1.3 23 159-181 2-24 (26)
12 PRK04136 rpl40e 50S ribosomal 75.9 1.7 3.7E-05 29.6 1.4 24 158-181 13-36 (48)
13 PF01529 zf-DHHC: DHHC palmito 71.5 6.1 0.00013 32.9 4.2 31 158-188 61-91 (174)
14 KOG1311 DHHC-type Zn-finger pr 70.0 2 4.4E-05 39.6 1.0 41 173-213 113-164 (299)
15 PF10571 UPF0547: Uncharacteri 68.6 3.3 7.2E-05 24.6 1.3 22 160-181 1-22 (26)
16 PTZ00303 phosphatidylinositol 61.5 4.6 0.0001 42.5 1.7 22 160-181 461-489 (1374)
17 PF12773 DZR: Double zinc ribb 61.0 7.1 0.00015 26.0 2.1 33 159-191 12-47 (50)
18 PF06906 DUF1272: Protein of u 55.0 6.3 0.00014 27.8 1.0 37 160-199 6-50 (57)
19 PF12773 DZR: Double zinc ribb 53.4 10 0.00022 25.3 1.8 23 158-180 28-50 (50)
20 PF01363 FYVE: FYVE zinc finge 50.1 6.9 0.00015 27.9 0.6 25 159-183 9-35 (69)
21 smart00064 FYVE Protein presen 47.7 13 0.00028 26.3 1.7 25 159-183 10-36 (68)
22 KOG1842 FYVE finger-containing 47.5 4.9 0.00011 39.5 -0.7 24 159-182 180-205 (505)
23 COG1552 RPL40A Ribosomal prote 45.1 4.5 9.8E-05 27.7 -0.9 25 157-181 12-36 (50)
24 PF00641 zf-RanBP: Zn-finger i 43.5 8.1 0.00018 23.2 0.1 22 160-181 5-26 (30)
25 PF01020 Ribosomal_L40e: Ribos 40.6 14 0.0003 25.7 0.9 24 159-182 17-42 (52)
26 cd00065 FYVE FYVE domain; Zinc 40.4 21 0.00045 24.2 1.8 23 160-182 3-27 (57)
27 KOG3183 Predicted Zn-finger pr 39.3 13 0.00028 33.7 0.8 16 179-194 34-49 (250)
28 COG5273 Uncharacterized protei 33.8 77 0.0017 29.8 5.0 49 158-217 122-170 (309)
29 COG2093 DNA-directed RNA polym 32.8 25 0.00054 25.4 1.2 23 159-181 4-26 (64)
30 KOG1315 Predicted DHHC-type Zn 32.2 91 0.002 29.4 5.2 32 172-203 108-139 (307)
31 PF13842 Tnp_zf-ribbon_2: DDE_ 32.0 34 0.00074 21.1 1.6 20 161-180 2-23 (32)
32 smart00547 ZnF_RBZ Zinc finger 28.0 34 0.00074 19.5 1.0 22 160-181 3-24 (26)
33 PF02150 RNA_POL_M_15KD: RNA p 27.6 22 0.00048 22.4 0.2 22 160-181 2-28 (35)
34 cd01995 ExsB ExsB is a transcr 27.4 22 0.00047 29.5 0.2 23 161-186 142-164 (169)
35 PF07092 DUF1356: Protein of u 27.1 31 0.00066 31.4 1.1 33 132-175 44-76 (238)
36 PF08600 Rsm1: Rsm1-like; Int 26.9 35 0.00075 26.1 1.2 14 186-199 54-67 (91)
37 KOG1819 FYVE finger-containing 25.2 24 0.00051 35.6 -0.0 22 160-181 902-925 (990)
38 PRK00944 hypothetical protein; 23.0 1.2E+02 0.0025 26.7 3.8 31 4-34 15-45 (195)
39 PRK04561 tatA twin arginine tr 22.8 70 0.0015 23.9 2.1 13 15-27 12-24 (75)
40 TIGR00364 exsB protein. This p 22.5 46 0.00099 28.6 1.3 13 173-185 189-201 (201)
41 PRK02958 tatA twin arginine tr 22.4 70 0.0015 23.8 2.0 14 14-27 11-24 (73)
42 PRK01833 tatA twin arginine tr 22.0 72 0.0016 23.8 2.0 14 14-27 11-24 (74)
43 PF09297 zf-NADH-PPase: NADH p 21.7 36 0.00079 20.7 0.3 23 159-181 3-29 (32)
44 PRK04598 tatA twin arginine tr 21.7 73 0.0016 24.2 2.0 15 13-27 10-24 (81)
45 PRK00720 tatA twin arginine tr 21.6 74 0.0016 24.0 2.0 14 13-26 10-23 (78)
46 PRK03554 tatA twin arginine tr 21.5 72 0.0016 24.7 2.0 16 12-27 9-24 (89)
47 COG0348 NapH Polyferredoxin [E 21.5 1.3E+02 0.0029 28.9 4.4 14 175-188 246-259 (386)
48 PRK14559 putative protein seri 21.5 55 0.0012 34.0 1.8 32 159-192 15-46 (645)
49 KOG1710 MYND Zn-finger and ank 21.2 39 0.00085 31.9 0.6 19 160-180 320-338 (396)
50 COG3936 Protein involved in po 20.9 93 0.002 29.3 2.9 20 21-40 176-196 (349)
51 PRK14559 putative protein seri 20.9 57 0.0012 33.9 1.8 26 159-184 27-52 (645)
52 PF07649 C1_3: C1-like domain; 20.6 37 0.0008 20.3 0.2 21 161-181 2-23 (30)
53 KOG1398 Uncharacterized conser 20.3 27 0.00059 34.1 -0.7 25 169-199 10-34 (460)
54 PF01437 PSI: Plexin repeat; 20.3 24 0.00052 23.8 -0.8 17 177-193 6-22 (51)
55 PRK01614 tatE twin arginine tr 20.0 83 0.0018 24.1 2.0 14 14-27 11-24 (85)
No 1
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=9.6e-56 Score=396.21 Aligned_cols=248 Identities=41% Similarity=0.632 Sum_probs=226.5
Q ss_pred CchHHHHHHHHHHHHHHHHHHHhcCCCCccCChhhHHHHHHHhhhhhHHHhhhhhhccccchhhhccccceeeccCCCcc
Q 024129 1 MDVQWLLIIHGLLTLLVVVSFLCGQWPIFEGTPIQRIHYFLTFGAYDYFLRFVGSVFGEKAINAILSVEYFCCDRPNPVL 80 (272)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~lfG~~p~~r~t~i~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~p~~ 80 (272)
||++|++++|+..++++++++++|+.|.|++||+ |.|+++..++|+.+.+.|++.+ .+...++++.+||.+
T Consensus 1 Mdf~wllLf~lai~l~vVlilLcgq~p~lKgt~~-w~~~ff~~~ip~~llr~v~~y~--------~sl~~~~l~~tni~L 71 (341)
T KOG1312|consen 1 MDFLWLLLFYLAIVLGVVLILLCGQTPSLKGTAR-WGAQFFSCIIPECLLRAVHGYL--------RSLLFHTLNHTNIVL 71 (341)
T ss_pred CchhHHHHHHHHHHHHHhhhhhcCCCcccccccc-cceeeEEECccHHHHHHHHHHH--------HHheeeeccCCChhH
Confidence 9999999999999999999999999999999999 9999999999999999998654 456778999999999
Q ss_pred eeeeeeeehhhhhhhhhhhcccccccchhhHHHHHHHHHHHHHHHHHHHHhccCCccccCCCcccccccCCCCCccccc-
Q 024129 81 QIIYLAIIGITYYFIAKSSFSYIPGYYLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNIIYTE- 159 (272)
Q Consensus 81 ~i~~l~l~~~~~~~f~~~~~~~ip~~~~~~~~~~~~~~~~~l~~~~~~~~~~~dPG~i~~~~~~~~~~~~~~d~~~~~~- 159 (272)
+++|.+++.- ...+..+.+.+++..|..+++....+++++.+++.+++.+|||.++++|..+..+++|||.+++.+
T Consensus 72 ~lvy~a~m~~---~~~~esfiy~~~l~lsl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if~k~ 148 (341)
T KOG1312|consen 72 HLVYQAMMYT---EYTWESFIYCQELELSLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIFPKN 148 (341)
T ss_pred HHHHHHHHhh---hhhheeeEeccchhhhHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceeecCC
Confidence 8888877653 344556667888888999999999999999999999999999999999999999999999999888
Q ss_pred cccccCCCCCCCCCccCccCCccccCCCCcccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhcccchh
Q 024129 160 KECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFV-LAGRLKELRVVY 238 (272)
Q Consensus 160 ~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~-l~~~~~~~~~~~ 238 (272)
..|+||+++||+||||||+|||||+||||||.|+|||||++|.|||++||+++..++.|+++..+.+ +.+..+..+...
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ 228 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVY 228 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchhee
Confidence 9999999999999999999999999999999999999999999999999999999999999998887 777788899999
Q ss_pred hhHHhhccccccccchhhhhhh
Q 024129 239 ILTVYYGIENSFRKLAPHVVQV 260 (272)
Q Consensus 239 ~~~~y~~i~~~f~~~~~~v~~~ 260 (272)
+++.+++....+.++++.+++-
T Consensus 229 ilt~~~g~~ks~~~L~~yl~la 250 (341)
T KOG1312|consen 229 ILTLGHGHVKSTVFLIQYLFLA 250 (341)
T ss_pred eeeeeecchhhHHHHHHHHHHH
Confidence 9999999888888777775543
No 2
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.3e-35 Score=270.95 Aligned_cols=194 Identities=26% Similarity=0.418 Sum_probs=136.3
Q ss_pred Ccceeeeeeeehhhhhhhhhhhc-ccccccchhhHHHHHHHHHHHHHHHHHHHHhccCCccccCCCccccccc-------
Q 024129 78 PVLQIIYLAIIGITYYFIAKSSF-SYIPGYYLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSA------- 149 (272)
Q Consensus 78 p~~~i~~l~l~~~~~~~f~~~~~-~~ip~~~~~~~~~~~~~~~~~l~~~~~~~~~~~dPG~i~~~~~~~~~~~------- 149 (272)
++++++++.+++++|++++...- ..+.....+....+....+.++..++|.+++++|||.+|.+...+..+.
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~ 92 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISLTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGS 92 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhhhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccC
Confidence 77778888899999888764331 1111111234444455566677788999999999999996543221111
Q ss_pred -CCCC------CccccccccccCCCCCCCCCccCccCCccccCCCCcccccccccccCChHHHHHHHHHHHHHHHHHHHH
Q 024129 150 -YPYD------NIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVA 222 (272)
Q Consensus 150 -~~~d------~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~ 222 (272)
.+.+ +.....|+|.+|+..||+||||||+|+|||.||||||||+|||||.+|||+|++|++|+.+.+.|.++.
T Consensus 93 ~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~ 172 (307)
T KOG1315|consen 93 DNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVT 172 (307)
T ss_pred cccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHH
Confidence 1111 112246999999999999999999999999999999999999999999999999999999999999888
Q ss_pred HHHHHHHhhhc-----c--cchhhhHHhhccc--cccccchhhhhhhHhhcCcccccCC
Q 024129 223 LGFVLAGRLKE-----L--RVVYILTVYYGIE--NSFRKLAPHVVQVSISNNLSCFFNM 272 (272)
Q Consensus 223 ~~~~l~~~~~~-----~--~~~~~~~~y~~i~--~~f~~~~~~v~~~l~~~~~~~~~~~ 272 (272)
....+....++ . ...........+. ..+++ +...+.||++.|.||.|.|
T Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~-~l~~h~~Li~~N~TTiE~~ 230 (307)
T KOG1315|consen 173 TLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSG-LLCFHTYLILKNKTTIEAY 230 (307)
T ss_pred HHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHcCchhHhhh
Confidence 77766555422 0 0111111111111 11233 6778899999999999975
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=1.2e-35 Score=252.55 Aligned_cols=148 Identities=37% Similarity=0.659 Sum_probs=113.4
Q ss_pred HHHHHHhccCCccccCCCcccc------------cccCCCCCccccccccccCCCCCCCCCccCccCCccccCCCCcccc
Q 024129 125 FFFLLTSFADPGTVKAENVSQY------------QSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 192 (272)
Q Consensus 125 ~~~~~~~~~dPG~i~~~~~~~~------------~~~~~~d~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~W 192 (272)
++|++++.+|||++|+++.++. ....+.++.....++|++|+..||+|||||+.||+||.|+||||+|
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 3578899999999998711100 0111223444567999999999999999999999999999999999
Q ss_pred cccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccch----------hhhHHhhccccccccchhhhhhhHh
Q 024129 193 MNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVV----------YILTVYYGIENSFRKLAPHVVQVSI 262 (272)
Q Consensus 193 innCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~~~~~~~~~~----------~~~~~y~~i~~~f~~~~~~v~~~l~ 262 (272)
+|||||++|||+|++|+++..+.+++..+.....+.....+.... .+...+..+...+.+.+...+.+++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999998877776554432221 1222333333446777777899999
Q ss_pred hcCcccccCC
Q 024129 263 SNNLSCFFNM 272 (272)
Q Consensus 263 ~~~~~~~~~~ 272 (272)
..|.|++|.+
T Consensus 162 ~~n~Tt~E~~ 171 (174)
T PF01529_consen 162 LRNITTYERI 171 (174)
T ss_pred HcCCcHHHHH
Confidence 9999999964
No 4
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=5e-34 Score=263.55 Aligned_cols=156 Identities=33% Similarity=0.607 Sum_probs=109.2
Q ss_pred HHHHHHHHHHHHHHhcc---CCccccCCC--cccccccCC------CCCccccccccccCCCCCCCCCccCccCCccccC
Q 024129 117 LLGVGIGVFFFLLTSFA---DPGTVKAEN--VSQYQSAYP------YDNIIYTEKECSTCKIPKPARSKHCSICNRCVAR 185 (272)
Q Consensus 117 ~~~~~l~~~~~~~~~~~---dPG~i~~~~--~~~~~~~~~------~d~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~r 185 (272)
.+...+.+.....+..+ |||.+|++. ..+..+..+ .++...+.++|.+|+..||+|||||++||+||.|
T Consensus 60 ~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~r 139 (299)
T KOG1311|consen 60 AIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLR 139 (299)
T ss_pred HHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccc
Confidence 33344444455555555 999999852 111111111 1334456799999999999999999999999999
Q ss_pred CCCcccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccch-------------hhhHHhhcccccccc
Q 024129 186 FDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVV-------------YILTVYYGIENSFRK 252 (272)
Q Consensus 186 ~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~~~~~~~~~~-------------~~~~~y~~i~~~f~~ 252 (272)
|||||||+|||||++|||+|+.|+++..+.++|........+.....+.... .++..+-.....+.+
T Consensus 140 fDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 219 (299)
T KOG1311|consen 140 FDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTS 219 (299)
T ss_pred cCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999888877655433211111 111111112222444
Q ss_pred chhhhhhhHhhcCcccccCC
Q 024129 253 LAPHVVQVSISNNLSCFFNM 272 (272)
Q Consensus 253 ~~~~v~~~l~~~~~~~~~~~ 272 (272)
.+...+.+++.+|+|++|++
T Consensus 220 ~l~~fh~~li~~~~Tt~e~~ 239 (299)
T KOG1311|consen 220 ALLCFHIYLIKSGSTTYESI 239 (299)
T ss_pred HHHHhheeeEecCcchhhhh
Confidence 56667889999999999874
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.97 E-value=2.4e-32 Score=253.75 Aligned_cols=157 Identities=34% Similarity=0.555 Sum_probs=117.2
Q ss_pred HHHHHHHHHHHHHHHHhccCCccccCCCc----ccccccCCCCCccccccccccCCCCCCCCCccCccCCccccCCCCcc
Q 024129 115 TSLLGVGIGVFFFLLTSFADPGTVKAENV----SQYQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHC 190 (272)
Q Consensus 115 ~~~~~~~l~~~~~~~~~~~dPG~i~~~~~----~~~~~~~~~d~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC 190 (272)
...+...+...++++...+|||+.++++. ++..+....++....+++|++|+.+||+|||||+.|||||+||||||
T Consensus 61 ~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC 140 (309)
T COG5273 61 LFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHC 140 (309)
T ss_pred hhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccC
Confidence 33444556677889999999999985532 22222233355666789999999999999999999999999999999
Q ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchhhh--H------HhhccccccccchhhhhhhHh
Q 024129 191 GWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVYIL--T------VYYGIENSFRKLAPHVVQVSI 262 (272)
Q Consensus 191 ~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~~~~~~~~~~~~~--~------~y~~i~~~f~~~~~~v~~~l~ 262 (272)
||+|||||++|||+|+.|++++.....+.++.....+......+...... . ..-.....+...+-...++++
T Consensus 141 ~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~ 220 (309)
T COG5273 141 PWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLI 220 (309)
T ss_pred cccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999888888888887776655322111111 0 111112334556677889999
Q ss_pred hcCcccccC
Q 024129 263 SNNLSCFFN 271 (272)
Q Consensus 263 ~~~~~~~~~ 271 (272)
..|+|++|.
T Consensus 221 ~~~~t~~e~ 229 (309)
T COG5273 221 LNNLTTIEF 229 (309)
T ss_pred HhhHHHHHH
Confidence 999999885
No 6
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=99.97 E-value=8.3e-32 Score=247.60 Aligned_cols=161 Identities=27% Similarity=0.490 Sum_probs=122.5
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHhccCCccccCCCcccccccCCCCCccccccccccCCCCCCCCCccCccCCcccc
Q 024129 105 GYYLSGFHRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVA 184 (272)
Q Consensus 105 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~dPG~i~~~~~~~~~~~~~~d~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~ 184 (272)
..+.+..+.++..+...+.+..|+.++++.||++|.+..+|. |.|.. -.++|..|+.+|++||||||.|||||.
T Consensus 43 ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~----~~D~~--~lqfCk~CqgYKapRSHHCrkCnrCvm 116 (414)
T KOG1314|consen 43 SSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPEN----PKDEM--FLQFCKKCQGYKAPRSHHCRKCNRCVM 116 (414)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCC----ChhHH--HHHHHhhccCcCCCccccchHHHHHHH
Confidence 344567777777778888889999999999999999887753 33421 248999999999999999999999999
Q ss_pred CCCCcccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchh---------------hhHHhhccccc
Q 024129 185 RFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVY---------------ILTVYYGIENS 249 (272)
Q Consensus 185 r~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~~~~~~~~~~~---------------~~~~y~~i~~~ 249 (272)
+|||||||+|||||..||-+|+.||++..+.|+.++++...+++..+..+..+. +...-++++..
T Consensus 117 kMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla 196 (414)
T KOG1314|consen 117 KMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLA 196 (414)
T ss_pred hhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHH
Confidence 999999999999999999999999999999999998887777766554432111 11222233221
Q ss_pred -----cccchhhhhhhHhhcCcccccC
Q 024129 250 -----FRKLAPHVVQVSISNNLSCFFN 271 (272)
Q Consensus 250 -----f~~~~~~v~~~l~~~~~~~~~~ 271 (272)
-.+++.-.+...+..|||--|+
T Consensus 197 ~gv~la~t~Lf~~qlk~Il~nrt~IE~ 223 (414)
T KOG1314|consen 197 IGVVLALTMLFFIQLKQILNNRTGIES 223 (414)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcchHH
Confidence 1233344455578889987775
No 7
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.93 E-value=4.8e-26 Score=203.94 Aligned_cols=72 Identities=40% Similarity=1.011 Sum_probs=66.7
Q ss_pred cccccccCCCCCCCCCccCccCCccccCCCCcccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024129 158 TEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAG 229 (272)
Q Consensus 158 ~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~~ 229 (272)
...+|.+|..+||||+|||+.|||||.||||||||+|||||..|||||++|++++.+.+.|..+...+....
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~ 172 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWID 172 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999999999999999999999999999999999999999999988887665543
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.92 E-value=2.3e-25 Score=218.05 Aligned_cols=110 Identities=39% Similarity=0.639 Sum_probs=84.7
Q ss_pred HHHHHHHHHHHHhccCCccccCCCccc--ccccCCCCCccccc-cccccCCCCCCCCCccCccCCccccCCCCccccccc
Q 024129 119 GVGIGVFFFLLTSFADPGTVKAENVSQ--YQSAYPYDNIIYTE-KECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNN 195 (272)
Q Consensus 119 ~~~l~~~~~~~~~~~dPG~i~~~~~~~--~~~~~~~d~~~~~~-~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~Winn 195 (272)
.++..++.+.+..-+|||+++.+.... .....+..+....+ ++|.+|.++||.|||||++|||||+||||||||++|
T Consensus 377 ~~l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~n 456 (600)
T KOG0509|consen 377 SVLAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGN 456 (600)
T ss_pred HHHHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCcccc
Confidence 333445566666679999998764322 11122222233334 799999999999999999999999999999999999
Q ss_pred ccccCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024129 196 CIGERNTRYFMAFLLWHLFLCLYGIVALGFVLA 228 (272)
Q Consensus 196 CIG~~N~r~F~lFL~~~~i~~~y~~~~~~~~l~ 228 (272)
|||.+|||+|+.|++.....+.+.++...+.+.
T Consensus 457 cVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~ 489 (600)
T KOG0509|consen 457 CVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIM 489 (600)
T ss_pred ccCccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999998888877777655543
No 9
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=85.79 E-value=0.72 Score=46.76 Aligned_cols=86 Identities=16% Similarity=-0.033 Sum_probs=62.2
Q ss_pred HHHHHHhccCCccccCCCcccccccCCCCCccccccccccCCCCCCCCCccCccCCccccCCCCcccccccccccCChHH
Q 024129 125 FFFLLTSFADPGTVKAENVSQYQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRY 204 (272)
Q Consensus 125 ~~~~~~~~~dPG~i~~~~~~~~~~~~~~d~~~~~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r~ 204 (272)
..++..+..+||++-..+..-.... +--+...-...|.+|....+.+-.++..+-.+...+++||+|+. +|+.+|...
T Consensus 292 ~~~~~~~~~~~g~i~~~~~~w~i~~-~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~ 369 (600)
T KOG0509|consen 292 GLFYFISSWLPGVIFLINSLWLIKG-LALGKLVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFD 369 (600)
T ss_pred HHHHHHHhhccchhhhhhhHHHHhh-hhhhhhhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhh
Confidence 3445567789999976553111111 11122334578999999999999999999999999999999999 999999875
Q ss_pred HHH-HHHHH
Q 024129 205 FMA-FLLWH 212 (272)
Q Consensus 205 F~l-FL~~~ 212 (272)
+-. |+++.
T Consensus 370 ~~~~~i~~~ 378 (600)
T KOG0509|consen 370 FHYCFIISV 378 (600)
T ss_pred hHHHHHHHH
Confidence 444 44443
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.46 E-value=0.6 Score=26.90 Aligned_cols=21 Identities=24% Similarity=0.645 Sum_probs=18.8
Q ss_pred ccccCCCCCCCCCccCccCCc
Q 024129 161 ECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 161 ~C~tC~~~kP~RskHC~~C~~ 181 (272)
+|+.|...-++.++.|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999985
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=80.73 E-value=1 Score=26.54 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=19.8
Q ss_pred ccccccCCCCCCCCCccCccCCc
Q 024129 159 EKECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 159 ~~~C~tC~~~kP~RskHC~~C~~ 181 (272)
.++|+.|...-++.++.|..||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 36899999988999999999885
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=75.89 E-value=1.7 Score=29.65 Aligned_cols=24 Identities=29% Similarity=0.740 Sum_probs=21.8
Q ss_pred cccccccCCCCCCCCCccCccCCc
Q 024129 158 TEKECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 158 ~~~~C~tC~~~kP~RskHC~~C~~ 181 (272)
....|..|...-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 457899999999999999999886
No 13
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=71.47 E-value=6.1 Score=32.91 Aligned_cols=31 Identities=23% Similarity=0.565 Sum_probs=25.8
Q ss_pred cccccccCCCCCCCCCccCccCCccccCCCC
Q 024129 158 TEKECSTCKIPKPARSKHCSICNRCVARFDH 188 (272)
Q Consensus 158 ~~~~C~tC~~~kP~RskHC~~C~~CV~r~DH 188 (272)
+.++|+.|+.-...+-|||..-|.||.+.-|
T Consensus 61 Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~ 91 (174)
T PF01529_consen 61 RSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH 91 (174)
T ss_pred cceeccccccccccccccchhhccccccccH
Confidence 3478888888888888999999999988766
No 14
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=69.98 E-value=2 Score=39.63 Aligned_cols=41 Identities=27% Similarity=0.532 Sum_probs=33.2
Q ss_pred CccCccCCccccCCCCcccccccccccCCh-----------HHHHHHHHHHH
Q 024129 173 SKHCSICNRCVARFDHHCGWMNNCIGERNT-----------RYFMAFLLWHL 213 (272)
Q Consensus 173 skHC~~C~~CV~r~DHHC~WinnCIG~~N~-----------r~F~lFL~~~~ 213 (272)
-|+|..|+..+.+.-|||..=|+||-+.=| |-+-.|+.+..
T Consensus 113 ~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred eEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 789999999999999999999999988765 34667885444
No 15
>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=68.61 E-value=3.3 Score=24.58 Aligned_cols=22 Identities=32% Similarity=0.813 Sum_probs=19.3
Q ss_pred cccccCCCCCCCCCccCccCCc
Q 024129 160 KECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~kP~RskHC~~C~~ 181 (272)
+.|+.|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4699999999999999998875
No 16
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=61.50 E-value=4.6 Score=42.50 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=17.9
Q ss_pred cccccCCCCCC-------CCCccCccCCc
Q 024129 160 KECSTCKIPKP-------ARSKHCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~kP-------~RskHC~~C~~ 181 (272)
+.|..|+..-. .|-||||.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 46999998764 38999999876
No 17
>PF12773 DZR: Double zinc ribbon
Probab=61.00 E-value=7.1 Score=26.04 Aligned_cols=33 Identities=27% Similarity=0.567 Sum_probs=21.9
Q ss_pred ccccccCCCCCC---CCCccCccCCccccCCCCccc
Q 024129 159 EKECSTCKIPKP---ARSKHCSICNRCVARFDHHCG 191 (272)
Q Consensus 159 ~~~C~tC~~~kP---~RskHC~~C~~CV~r~DHHC~ 191 (272)
.++|..|...-+ ...+.|..|+.=+...+.+|+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 467777777655 335567777776666666665
No 18
>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=54.96 E-value=6.3 Score=27.83 Aligned_cols=37 Identities=32% Similarity=0.838 Sum_probs=29.4
Q ss_pred cccccCCCCCCCCC-------ccCccCCccccCC-CCccccccccccc
Q 024129 160 KECSTCKIPKPARS-------KHCSICNRCVARF-DHHCGWMNNCIGE 199 (272)
Q Consensus 160 ~~C~tC~~~kP~Rs-------kHC~~C~~CV~r~-DHHC~WinnCIG~ 199 (272)
..|..|...-|+-| .-|..|..|+... +++|| ||=|+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 46888888777765 4588999999998 99998 77665
No 19
>PF12773 DZR: Double zinc ribbon
Probab=53.35 E-value=10 Score=25.25 Aligned_cols=23 Identities=30% Similarity=0.853 Sum_probs=20.5
Q ss_pred cccccccCCCCCCCCCccCccCC
Q 024129 158 TEKECSTCKIPKPARSKHCSICN 180 (272)
Q Consensus 158 ~~~~C~tC~~~kP~RskHC~~C~ 180 (272)
...+|+.|....++.+++|..||
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 34789999999999999999986
No 20
>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=50.12 E-value=6.9 Score=27.87 Aligned_cols=25 Identities=32% Similarity=0.684 Sum_probs=12.1
Q ss_pred ccccccCCCC--CCCCCccCccCCccc
Q 024129 159 EKECSTCKIP--KPARSKHCSICNRCV 183 (272)
Q Consensus 159 ~~~C~tC~~~--kP~RskHC~~C~~CV 183 (272)
...|..|+.. --.|-|||+.||+-|
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 4678888764 346888999998844
No 21
>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 KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=47.51 E-value=4.9 Score=39.55 Aligned_cols=24 Identities=29% Similarity=0.769 Sum_probs=19.6
Q ss_pred ccccccCCCC--CCCCCccCccCCcc
Q 024129 159 EKECSTCKIP--KPARSKHCSICNRC 182 (272)
Q Consensus 159 ~~~C~tC~~~--kP~RskHC~~C~~C 182 (272)
..+|+.|... --.|-||||.||+-
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchH
Confidence 4799999875 35689999999983
No 23
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=45.09 E-value=4.5 Score=27.74 Aligned_cols=25 Identities=28% Similarity=0.808 Sum_probs=21.8
Q ss_pred ccccccccCCCCCCCCCccCccCCc
Q 024129 157 YTEKECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 157 ~~~~~C~tC~~~kP~RskHC~~C~~ 181 (272)
+..+.|..|...-|+|+.-|+.|+.
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccC
Confidence 3457899999999999999998865
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=43.54 E-value=8.1 Score=23.19 Aligned_cols=22 Identities=27% Similarity=0.809 Sum_probs=15.1
Q ss_pred cccccCCCCCCCCCccCccCCc
Q 024129 160 KECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~kP~RskHC~~C~~ 181 (272)
-.|..|...-++++.+|..|+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--
T ss_pred ccCCCCcCCchHHhhhhhCcCC
Confidence 4588888888888888888763
No 25
>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=40.64 E-value=14 Score=25.69 Aligned_cols=24 Identities=25% Similarity=0.707 Sum_probs=16.4
Q ss_pred ccccccCCCCCCCCCccCcc--CCcc
Q 024129 159 EKECSTCKIPKPARSKHCSI--CNRC 182 (272)
Q Consensus 159 ~~~C~tC~~~kP~RskHC~~--C~~C 182 (272)
...|..|...-|+|+..|+. ||++
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 46899999999999999998 8764
No 26
>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=40.37 E-value=21 Score=24.18 Aligned_cols=23 Identities=35% Similarity=0.836 Sum_probs=15.2
Q ss_pred cccccCCCC--CCCCCccCccCCcc
Q 024129 160 KECSTCKIP--KPARSKHCSICNRC 182 (272)
Q Consensus 160 ~~C~tC~~~--kP~RskHC~~C~~C 182 (272)
+.|..|+.. .-.|.+||+.||+-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCCccccccCcCcCC
Confidence 456666642 35578889888774
No 27
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=39.28 E-value=13 Score=33.74 Aligned_cols=16 Identities=25% Similarity=0.281 Sum_probs=11.9
Q ss_pred CCccccCCCCcccccc
Q 024129 179 CNRCVARFDHHCGWMN 194 (272)
Q Consensus 179 C~~CV~r~DHHC~Win 194 (272)
|-.=..+.+|||||..
T Consensus 34 C~eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 34 CLEHRSYESHHCPKGL 49 (250)
T ss_pred hhccchHhhcCCCccc
Confidence 3445678899999975
No 28
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=33.75 E-value=77 Score=29.77 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=36.8
Q ss_pred cccccccCCCCCCCCCccCccCCccccCCCCcccccccccccCChHHHHHHHHHHHHHHH
Q 024129 158 TEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCL 217 (272)
Q Consensus 158 ~~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r~F~lFL~~~~i~~~ 217 (272)
+.+.|+.|+.=-...-|||..=|+||.+--| |=.-.|++++...+.+.+
T Consensus 122 RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~ 170 (309)
T COG5273 122 RSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVL 170 (309)
T ss_pred CCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHH
Confidence 3478999998888889999999999998665 556667777655544433
No 29
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.79 E-value=25 Score=25.43 Aligned_cols=23 Identities=35% Similarity=0.920 Sum_probs=20.4
Q ss_pred ccccccCCCCCCCCCccCccCCc
Q 024129 159 EKECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 159 ~~~C~tC~~~kP~RskHC~~C~~ 181 (272)
.+-|..|+...|..++-|..||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 36799999999999999999986
No 30
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=32.19 E-value=91 Score=29.42 Aligned_cols=32 Identities=22% Similarity=0.514 Sum_probs=19.5
Q ss_pred CCccCccCCccccCCCCcccccccccccCChH
Q 024129 172 RSKHCSICNRCVARFDHHCGWMNNCIGERNTR 203 (272)
Q Consensus 172 RskHC~~C~~CV~r~DHHC~WinnCIG~~N~r 203 (272)
+.+.|..|+.-....-|||.--+.||.+.-|+
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHH 139 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHH 139 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccC
Confidence 55566666666666666666666666665443
No 31
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=32.03 E-value=34 Score=21.12 Aligned_cols=20 Identities=30% Similarity=0.876 Sum_probs=10.6
Q ss_pred ccccCCCCCCCC-Ccc-CccCC
Q 024129 161 ECSTCKIPKPAR-SKH-CSICN 180 (272)
Q Consensus 161 ~C~tC~~~kP~R-skH-C~~C~ 180 (272)
.|..|...+..+ +++ |+.|+
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~ 23 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCD 23 (32)
T ss_pred CCeECCcCCccceeEEEccCCC
Confidence 355555544444 443 66665
No 32
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.97 E-value=34 Score=19.49 Aligned_cols=22 Identities=27% Similarity=0.634 Sum_probs=17.6
Q ss_pred cccccCCCCCCCCCccCccCCc
Q 024129 160 KECSTCKIPKPARSKHCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~kP~RskHC~~C~~ 181 (272)
-.|..|.....+++..|..|+.
T Consensus 3 W~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 3 WECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred ccCCCCCCcChhhhccccccCC
Confidence 3588888888888888888864
No 33
>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=27.63 E-value=22 Score=22.41 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=10.7
Q ss_pred cccccCCCC---CCCCCc--cCccCCc
Q 024129 160 KECSTCKIP---KPARSK--HCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~---kP~Rsk--HC~~C~~ 181 (272)
++|++|+.. +.++.+ .|+.|+.
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 467777764 222222 3666654
No 34
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=27.44 E-value=22 Score=29.54 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=16.3
Q ss_pred ccccCCCCCCCCCccCccCCccccCC
Q 024129 161 ECSTCKIPKPARSKHCSICNRCVARF 186 (272)
Q Consensus 161 ~C~tC~~~kP~RskHC~~C~~CV~r~ 186 (272)
...+|... +.+||..|..|+.|.
T Consensus 142 ~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 142 LTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred heeeccCC---CCCCCCCCHHHHHHH
Confidence 45566643 338999999998873
No 35
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=27.11 E-value=31 Score=31.40 Aligned_cols=33 Identities=27% Similarity=0.409 Sum_probs=24.3
Q ss_pred ccCCccccCCCcccccccCCCCCccccccccccCCCCCCCCCcc
Q 024129 132 FADPGTVKAENVSQYQSAYPYDNIIYTEKECSTCKIPKPARSKH 175 (272)
Q Consensus 132 ~~dPG~i~~~~~~~~~~~~~~d~~~~~~~~C~tC~~~kP~RskH 175 (272)
...-|.||++..++.....|+.+. ..||.|+|-
T Consensus 44 CqGtGrIP~eqe~qLVALIPy~Dq-----------RLKPrRTkl 76 (238)
T PF07092_consen 44 CQGTGRIPREQENQLVALIPYSDQ-----------RLKPRRTKL 76 (238)
T ss_pred CcCCccCCccchhcEEEEEecccc-----------ccCCceeEE
Confidence 467788888888888888888642 348888763
No 36
>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=26.90 E-value=35 Score=26.13 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=10.3
Q ss_pred CCCccccccccccc
Q 024129 186 FDHHCGWMNNCIGE 199 (272)
Q Consensus 186 ~DHHC~WinnCIG~ 199 (272)
+-.||||+|.-...
T Consensus 54 Hr~~CPwv~~~~q~ 67 (91)
T PF08600_consen 54 HREYCPWVNPSTQS 67 (91)
T ss_pred ccccCCccCCcccc
Confidence 44689999987643
No 37
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=25.17 E-value=24 Score=35.59 Aligned_cols=22 Identities=32% Similarity=0.901 Sum_probs=16.0
Q ss_pred cccccCCCCC--CCCCccCccCCc
Q 024129 160 KECSTCKIPK--PARSKHCSICNR 181 (272)
Q Consensus 160 ~~C~tC~~~k--P~RskHC~~C~~ 181 (272)
..|..|..+- -.|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 4688887653 237889998876
No 38
>PRK00944 hypothetical protein; Provisional
Probab=23.00 E-value=1.2e+02 Score=26.73 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCccCChh
Q 024129 4 QWLLIIHGLLTLLVVVSFLCGQWPIFEGTPI 34 (272)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~lfG~~p~~r~t~i 34 (272)
.|++++.+++++.++.++.+||.|...=+.|
T Consensus 15 ~w~~~~~~~~~~~a~~L~~mGR~pIC~CG~v 45 (195)
T PRK00944 15 FWLLAALAVLALQALILYAMGRVPICECGYV 45 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccccCcce
Confidence 6889999999999999999999999887776
No 39
>PRK04561 tatA twin arginine translocase protein A; Provisional
Probab=22.78 E-value=70 Score=23.94 Aligned_cols=13 Identities=31% Similarity=0.483 Sum_probs=8.8
Q ss_pred HHHHHHHHhcCCC
Q 024129 15 LLVVVSFLCGQWP 27 (272)
Q Consensus 15 ~~~~~~~lfG~~p 27 (272)
.+++++++||...
T Consensus 12 IlvIvlLlFG~~K 24 (75)
T PRK04561 12 VLVIVLLVFGTKR 24 (75)
T ss_pred HHHHHHHHhCCcc
Confidence 3446688899764
No 40
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=22.48 E-value=46 Score=28.61 Aligned_cols=13 Identities=31% Similarity=0.948 Sum_probs=11.1
Q ss_pred CccCccCCccccC
Q 024129 173 SKHCSICNRCVAR 185 (272)
Q Consensus 173 skHC~~C~~CV~r 185 (272)
.+||..|..|+.|
T Consensus 189 ~~~CG~C~~C~~r 201 (201)
T TIGR00364 189 GEGCGKCPSCMLR 201 (201)
T ss_pred CCCCCCChhhhcc
Confidence 4699999999876
No 41
>PRK02958 tatA twin arginine translocase protein A; Provisional
Probab=22.44 E-value=70 Score=23.79 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=9.5
Q ss_pred HHHHHHHHHhcCCC
Q 024129 14 TLLVVVSFLCGQWP 27 (272)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (272)
+.+++++++||...
T Consensus 11 iIl~IvlllFG~kK 24 (73)
T PRK02958 11 IVLVIVVLVFGTKK 24 (73)
T ss_pred HHHHHHHHHhCcch
Confidence 34566778899764
No 42
>PRK01833 tatA twin arginine translocase protein A; Provisional
Probab=21.99 E-value=72 Score=23.77 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=9.2
Q ss_pred HHHHHHHHHhcCCC
Q 024129 14 TLLVVVSFLCGQWP 27 (272)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (272)
+.+++++++||...
T Consensus 11 iIl~i~lllFG~kK 24 (74)
T PRK01833 11 IIVAIIVLLFGTKK 24 (74)
T ss_pred HHHHHHHHHhCcch
Confidence 34456678899653
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=21.75 E-value=36 Score=20.67 Aligned_cols=23 Identities=35% Similarity=0.966 Sum_probs=10.5
Q ss_pred ccccccCCCC-CCC---CCccCccCCc
Q 024129 159 EKECSTCKIP-KPA---RSKHCSICNR 181 (272)
Q Consensus 159 ~~~C~tC~~~-kP~---RskHC~~C~~ 181 (272)
.+||..|..+ ++. +++.|..|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 5789999875 233 4555655553
No 44
>PRK04598 tatA twin arginine translocase protein A; Provisional
Probab=21.66 E-value=73 Score=24.16 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=9.8
Q ss_pred HHHHHHHHHHhcCCC
Q 024129 13 LTLLVVVSFLCGQWP 27 (272)
Q Consensus 13 ~~~~~~~~~lfG~~p 27 (272)
++.+++++++||...
T Consensus 10 liIlvivlllFG~kK 24 (81)
T PRK04598 10 LIIAVIVVLLFGTKK 24 (81)
T ss_pred HHHHHHHHHHhCcch
Confidence 344556778899653
No 45
>PRK00720 tatA twin arginine translocase protein A; Provisional
Probab=21.58 E-value=74 Score=23.98 Aligned_cols=14 Identities=43% Similarity=0.555 Sum_probs=9.1
Q ss_pred HHHHHHHHHHhcCC
Q 024129 13 LTLLVVVSFLCGQW 26 (272)
Q Consensus 13 ~~~~~~~~~lfG~~ 26 (272)
++.+++++++||..
T Consensus 10 lIIlvIvlllFG~k 23 (78)
T PRK00720 10 LIVLAVVLLLFGRG 23 (78)
T ss_pred HHHHHHHHHHhCcc
Confidence 34455677889954
No 46
>PRK03554 tatA twin arginine translocase protein A; Provisional
Probab=21.55 E-value=72 Score=24.66 Aligned_cols=16 Identities=38% Similarity=0.534 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHhcCCC
Q 024129 12 LLTLLVVVSFLCGQWP 27 (272)
Q Consensus 12 ~~~~~~~~~~lfG~~p 27 (272)
+++.+++++++||...
T Consensus 9 LlIIlvIvLLlFG~kK 24 (89)
T PRK03554 9 LLIIAVIVVLLFGTKK 24 (89)
T ss_pred HHHHHHHHHHHhCcch
Confidence 3444566678899753
No 47
>COG0348 NapH Polyferredoxin [Energy production and conversion]
Probab=21.48 E-value=1.3e+02 Score=28.94 Aligned_cols=14 Identities=36% Similarity=0.956 Sum_probs=11.6
Q ss_pred cCccCCccccCCCC
Q 024129 175 HCSICNRCVARFDH 188 (272)
Q Consensus 175 HC~~C~~CV~r~DH 188 (272)
-|-.|++|+.--||
T Consensus 246 ~CI~C~~CidaCd~ 259 (386)
T COG0348 246 ECIGCGRCIDACDD 259 (386)
T ss_pred ccccHhhHhhhCCH
Confidence 39999999998665
No 48
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.48 E-value=55 Score=34.03 Aligned_cols=32 Identities=25% Similarity=0.539 Sum_probs=19.6
Q ss_pred ccccccCCCCCCCCCccCccCCccccCCCCcccc
Q 024129 159 EKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 192 (272)
Q Consensus 159 ~~~C~tC~~~kP~RskHC~~C~~CV~r~DHHC~W 192 (272)
.++|..|...-+ .+.|..||.=+..-..+|+=
T Consensus 15 akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~ 46 (645)
T PRK14559 15 NRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPN 46 (645)
T ss_pred CccccccCCCCC--CCcCCCCCCCCCcccccccc
Confidence 467777765432 35677776666666666653
No 49
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=21.24 E-value=39 Score=31.94 Aligned_cols=19 Identities=47% Similarity=0.996 Sum_probs=15.1
Q ss_pred cccccCCCCCCCCCccCccCC
Q 024129 160 KECSTCKIPKPARSKHCSICN 180 (272)
Q Consensus 160 ~~C~tC~~~kP~RskHC~~C~ 180 (272)
++|+||..++| +|-|+.|+
T Consensus 320 ~fCstCG~~ga--~KrCs~CK 338 (396)
T KOG1710|consen 320 QFCSTCGHPGA--KKRCSQCK 338 (396)
T ss_pred ccccccCCCCc--cchhhhhH
Confidence 79999998776 46777776
No 50
>COG3936 Protein involved in polysaccharide intercellular adhesin (PIA) synthesis/biofilm formation [Carbohydrate transport and metabolism]
Probab=20.91 E-value=93 Score=29.28 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=10.4
Q ss_pred HHhcCCCCccCChh-hHHHHH
Q 024129 21 FLCGQWPIFEGTPI-QRIHYF 40 (272)
Q Consensus 21 ~lfG~~p~~r~t~i-~~~~~~ 40 (272)
.++|.-|.|.++|+ ||+..+
T Consensus 176 ~~~~~fp~f~~~if~GW~fyF 196 (349)
T COG3936 176 LLFLTFPYFFAMIFMGWYFYF 196 (349)
T ss_pred HHHhhhHHHHHHHHHHHHHHH
Confidence 34555566665554 444443
No 51
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.90 E-value=57 Score=33.90 Aligned_cols=26 Identities=27% Similarity=0.689 Sum_probs=22.5
Q ss_pred ccccccCCCCCCCCCccCccCCcccc
Q 024129 159 EKECSTCKIPKPARSKHCSICNRCVA 184 (272)
Q Consensus 159 ~~~C~tC~~~kP~RskHC~~C~~CV~ 184 (272)
.+.|+.|....|+.+++|..||.=..
T Consensus 27 ~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 27 HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCcCCCCCCCCCcccccccccCCccc
Confidence 36899999999999999999998443
No 52
>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=20.63 E-value=37 Score=20.27 Aligned_cols=21 Identities=29% Similarity=0.670 Sum_probs=8.0
Q ss_pred ccccCCCCCCC-CCccCccCCc
Q 024129 161 ECSTCKIPKPA-RSKHCSICNR 181 (272)
Q Consensus 161 ~C~tC~~~kP~-RskHC~~C~~ 181 (272)
.|..|+..... ...+|..|+-
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 47777766655 6667887764
No 53
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.34 E-value=27 Score=34.06 Aligned_cols=25 Identities=40% Similarity=0.905 Sum_probs=18.1
Q ss_pred CCCCCccCccCCccccCCCCccccccccccc
Q 024129 169 KPARSKHCSICNRCVARFDHHCGWMNNCIGE 199 (272)
Q Consensus 169 kP~RskHC~~C~~CV~r~DHHC~WinnCIG~ 199 (272)
+-.|-.||..|+. +|| +|..||||.
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga 34 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGA 34 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHH
Confidence 3445557777764 788 799999996
No 54
>PF01437 PSI: Plexin repeat; InterPro: IPR002165 This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin (P70206 from SWISSPROT) []. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein (Q19981 from SWISSPROT) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.; GO: 0016020 membrane; PDB: 3NVQ_B 3NVN_B 3OL2_B 3OKT_A 3AL8_A 3OKW_A 3OKY_B 3AFC_B 1OLZ_B 1SHY_B ....
Probab=20.27 E-value=24 Score=23.76 Aligned_cols=17 Identities=35% Similarity=1.091 Sum_probs=10.6
Q ss_pred ccCCccccCCCCccccc
Q 024129 177 SICNRCVARFDHHCGWM 193 (272)
Q Consensus 177 ~~C~~CV~r~DHHC~Wi 193 (272)
..|+.|+.-.|-+|.|=
T Consensus 6 ~sC~~Cl~~~dp~CgWc 22 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWC 22 (51)
T ss_dssp SSHHHHHHSTCTTEEEE
T ss_pred CcHHHHHcCCCcCcccc
Confidence 45666666666666664
No 55
>PRK01614 tatE twin arginine translocase protein A; Validated
Probab=20.01 E-value=83 Score=24.07 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=9.1
Q ss_pred HHHHHHHHHhcCCC
Q 024129 14 TLLVVVSFLCGQWP 27 (272)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (272)
+.+++++++||...
T Consensus 11 IIlvIvLLLFG~kK 24 (85)
T PRK01614 11 VVGILIVLLFGTSK 24 (85)
T ss_pred HHHHHHHHHhCcch
Confidence 34456678899753
Done!