Query 016042
Match_columns 396
No_of_seqs 324 out of 1657
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 03:15:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016042.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016042hhsearch_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 5.2E-61 1.1E-65 442.7 13.8 287 1-307 1-289 (341)
2 KOG1315 Predicted DHHC-type Zn 100.0 1.9E-40 4.2E-45 318.2 10.3 210 78-313 13-237 (307)
3 KOG1311 DHHC-type Zn-finger pr 100.0 3.1E-39 6.6E-44 314.8 15.1 169 121-307 61-240 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 5.8E-39 1.2E-43 288.4 10.7 161 128-309 2-174 (174)
5 KOG1314 DHHC-type Zn-finger pr 100.0 2E-37 4.4E-42 293.3 12.0 181 106-306 44-224 (414)
6 COG5273 Uncharacterized protei 100.0 4.5E-34 9.8E-39 277.6 12.9 171 117-311 60-235 (309)
7 KOG1313 DHHC-type Zn-finger pr 100.0 3.2E-32 6.9E-37 250.9 14.5 142 161-307 101-244 (309)
8 KOG0509 Ankyrin repeat and DHH 99.9 1.7E-28 3.8E-33 249.2 8.9 110 118-227 373-485 (600)
9 COG5273 Uncharacterized protei 89.6 4.9 0.00011 39.6 11.7 166 116-307 62-243 (309)
10 KOG0509 Ankyrin repeat and DHH 87.8 0.56 1.2E-05 49.5 4.0 89 128-218 292-381 (600)
11 KOG1311 DHHC-type Zn-finger pr 85.3 4.3 9.2E-05 39.6 8.5 33 175-207 112-144 (299)
12 PRK04136 rpl40e 50S ribosomal 80.5 1 2.2E-05 31.5 1.4 25 160-184 12-36 (48)
13 PF01529 zf-DHHC: DHHC palmito 80.4 11 0.00023 33.2 8.4 29 163-191 63-91 (174)
14 PF13240 zinc_ribbon_2: zinc-r 79.7 1.1 2.5E-05 26.3 1.3 21 164-184 1-21 (23)
15 PF13248 zf-ribbon_3: zinc-rib 76.9 1.5 3.3E-05 26.5 1.3 23 162-184 2-24 (26)
16 PF10571 UPF0547: Uncharacteri 65.5 3.9 8.5E-05 24.8 1.3 22 163-184 1-22 (26)
17 PTZ00303 phosphatidylinositol 57.5 5.7 0.00012 43.3 1.6 22 163-184 461-489 (1374)
18 COG1552 RPL40A Ribosomal prote 57.2 2.4 5.1E-05 29.7 -0.8 25 160-184 12-36 (50)
19 PF06906 DUF1272: Protein of u 54.0 6.8 0.00015 28.4 1.0 37 163-202 6-50 (57)
20 PF00641 zf-RanBP: Zn-finger i 50.2 5.5 0.00012 24.7 0.1 22 163-184 5-26 (30)
21 KOG3183 Predicted Zn-finger pr 48.5 8 0.00017 36.3 0.9 13 185-197 37-49 (250)
22 PF12773 DZR: Double zinc ribb 47.6 13 0.00029 25.7 1.7 33 162-194 12-47 (50)
23 PF01020 Ribosomal_L40e: Ribos 47.5 9 0.0002 27.3 0.8 24 162-185 17-42 (52)
24 PF12773 DZR: Double zinc ribb 43.3 17 0.00037 25.1 1.8 22 162-183 29-50 (50)
25 KOG1312 DHHC-type Zn-finger pr 41.1 45 0.00097 32.4 4.6 31 176-206 148-178 (341)
26 KOG1315 Predicted DHHC-type Zn 40.1 1.9E+02 0.0041 28.5 9.0 32 175-206 108-139 (307)
27 PF08600 Rsm1: Rsm1-like; Int 34.5 21 0.00045 28.5 1.2 12 191-202 56-67 (91)
28 smart00547 ZnF_RBZ Zinc finger 33.1 23 0.00051 20.9 1.0 21 164-184 4-24 (26)
29 smart00064 FYVE Protein presen 32.7 28 0.0006 25.7 1.5 24 163-186 11-36 (68)
30 COG2093 DNA-directed RNA polym 32.0 25 0.00055 26.0 1.1 23 162-184 4-26 (64)
31 PRK15103 paraquat-inducible me 30.2 6.2E+02 0.014 26.0 11.6 30 163-192 222-251 (419)
32 KOG1842 FYVE finger-containing 27.8 17 0.00038 37.2 -0.4 25 162-186 180-206 (505)
33 PF01363 FYVE: FYVE zinc finge 27.4 18 0.00038 26.8 -0.4 25 162-186 9-35 (69)
34 PRK00944 hypothetical protein; 26.9 82 0.0018 28.5 3.7 31 4-34 15-45 (195)
35 KOG1710 MYND Zn-finger and ank 26.6 27 0.00058 34.1 0.6 21 162-184 319-339 (396)
36 COG3936 Protein involved in po 25.1 2.1E+02 0.0045 28.0 6.2 19 21-39 176-195 (349)
37 PRK04561 tatA twin arginine tr 24.0 63 0.0014 24.9 2.1 13 15-27 12-24 (75)
38 KOG1398 Uncharacterized conser 23.9 21 0.00045 36.0 -0.6 25 172-202 10-34 (460)
39 PRK03554 tatA twin arginine tr 23.9 59 0.0013 25.9 2.0 15 13-27 10-24 (89)
40 PRK04598 tatA twin arginine tr 23.6 61 0.0013 25.4 2.0 15 13-27 10-24 (81)
41 PRK02958 tatA twin arginine tr 23.3 64 0.0014 24.8 2.0 14 14-27 11-24 (73)
42 PF13842 Tnp_zf-ribbon_2: DDE_ 23.1 55 0.0012 20.8 1.4 20 164-183 2-23 (32)
43 cd01995 ExsB ExsB is a transcr 22.8 30 0.00065 30.3 0.2 23 164-189 142-164 (169)
44 PRK01833 tatA twin arginine tr 22.8 66 0.0014 24.7 2.0 14 14-27 11-24 (74)
45 COG0348 NapH Polyferredoxin [E 22.8 2E+02 0.0043 29.2 6.2 14 178-191 246-259 (386)
46 cd00065 FYVE FYVE domain; Zinc 22.5 55 0.0012 23.0 1.5 24 163-186 3-28 (57)
47 PRK00720 tatA twin arginine tr 22.4 68 0.0015 25.0 2.0 14 13-26 10-23 (78)
48 PRK01614 tatE twin arginine tr 22.0 69 0.0015 25.2 2.0 14 14-27 11-24 (85)
49 PF10112 Halogen_Hydrol: 5-bro 21.5 6E+02 0.013 22.9 10.8 23 309-331 68-90 (199)
50 PF07649 C1_3: C1-like domain; 21.3 34 0.00073 21.1 0.1 21 164-184 2-23 (30)
51 PF12273 RCR: Chitin synthesis 20.8 61 0.0013 27.4 1.7 9 5-13 2-10 (130)
52 PLN00186 ribosomal protein S26 20.5 41 0.00088 27.8 0.5 15 175-189 19-33 (109)
53 PF07423 DUF1510: Protein of u 20.3 92 0.002 29.1 2.8 6 365-370 143-148 (217)
54 PF02150 RNA_POL_M_15KD: RNA p 20.1 32 0.00069 22.3 -0.2 7 163-169 2-8 (35)
No 1
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=5.2e-61 Score=442.65 Aligned_cols=287 Identities=39% Similarity=0.614 Sum_probs=234.7
Q ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCCCccCChhhHHHHHHHhhhhhhHHhhhhhhccchhhhhhhhccceeeccCCCcc
Q 016042 1 MDVQWLLIIHGLLTLLVVVSFLCGQWPIFEGTPIQRIHYFLTFGAYDYFLRFVGSVFGEKAINAILSVEYFCCDRPNPVL 80 (396)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~lfG~~p~~r~t~i~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~p~~ 80 (396)
||++|++++|+..++++|+++|||+.|.|++||+ |.|+++..++|+++.+.|++.+ .+...++++.+||.+
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 457788999999999
Q ss_pred eeehhhhhhhhhhhhHhhhccccccccccccccchhHHHHHHHHHHHHHhHHhhccCCCcccCCCcccccccCCCCcccc
Q 016042 81 QIIYLAIIGITYYFIAKSSFSYIPGYYLSGFHRSSRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNIIY 160 (396)
Q Consensus 81 ~i~yl~l~~~~~~~f~~~~~~~ip~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~DPG~i~~~~~~~~~~~~p~d~~~~ 160 (396)
+++|.+++.. ...+..|-+.|.++++..+ ++....+++++++++.+++.+|||.++++|..+..+.||||..++
T Consensus 72 ~lvy~a~m~~---~~~~esfiy~~~l~lsl~~---~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if 145 (341)
T KOG1312|consen 72 HLVYQAMMYT---EYTWESFIYCQELELSLHY---LILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIF 145 (341)
T ss_pred HHHHHHHHhh---hhhheeeEeccchhhhHHH---HHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceee
Confidence 9999998874 3345566677888888888 888888999999999999999999999999999999999999999
Q ss_pred cc-ccccccCCCCCCCCccccccCccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhh
Q 016042 161 TE-KECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFV-LAGRLKELR 238 (396)
Q Consensus 161 ~~-~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~-l~~~~~~~~ 238 (396)
.+ +.|+||++.||+||||||+|||||.||||||.|+|||||++|+|||++||+++..++.|+.+..+++ +....+..+
T Consensus 146 ~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q 225 (341)
T KOG1312|consen 146 PKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQ 225 (341)
T ss_pred cCCCccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccch
Confidence 88 9999999999999999999999999999999999999999999999999999999999998888776 555555555
Q ss_pred eeeeeeeeecccccccccchhHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccccc
Q 016042 239 VVYILTVYYGIENSFRKLAPHVVQWLLGSYNTQILLMVFLAVVSLLLASFFGYHANLCRTNTTTNETVK 307 (396)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k 307 (396)
...+++.+++...+...+.+. ++......++.+-+....+ ++++...+-+|+-++|+||+|...
T Consensus 226 ~v~ilt~~~g~~ks~~~L~~y----l~la~~~~v~~l~~~~~~~-~~~~Y~~f~~y~~~t~~~~~~W~~ 289 (341)
T KOG1312|consen 226 EVYILTLGHGHVKSTVFLIQY----LFLAFPRIVFMLGFVVVLS-FLGGYLLFVLYLAATNQTTNEWYR 289 (341)
T ss_pred heeeeeeeecchhhHHHHHHH----HHHHhccceeeeehhhhhh-HhHHHHHHHHHHHhccCCchhhhc
Confidence 666666666554443322222 1111111111111222222 256666677788888888887543
No 2
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.9e-40 Score=318.20 Aligned_cols=210 Identities=28% Similarity=0.420 Sum_probs=145.3
Q ss_pred CcceeehhhhhhhhhhhhHhhhc-cccccccccccccchhHHHHHHHHHHHHHhHHhhccCCCcccCCCcccccc-cCCC
Q 016042 78 PVLQIIYLAIIGITYYFIAKSSF-SYIPGYYLSGFHRSSRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQS-AYPY 155 (396)
Q Consensus 78 p~~~i~yl~l~~~~~~~f~~~~~-~~ip~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~DPG~i~~~~~~~~~~-~~p~ 155 (396)
+.++++++.+++++|++++.... ..+. .........+....+.++..++|+.+.++|||.+|.+...+..+ +.+.
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~---~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~ 89 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSIS---LTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLE 89 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHh---hhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCcccccc
Confidence 77778888888899988874421 1110 10111111334445666777889999999999999754332211 1111
Q ss_pred -------Cc------cccccccccccCCCCCCCCccccccCccccccccccccccccccccchhhhHHHHHHHHHHHHHH
Q 016042 156 -------DN------IIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYG 222 (396)
Q Consensus 156 -------d~------~~~~~~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~ 222 (396)
+. .....|+|.+|+.+||+||||||+|+|||+||||||||+|||||.+|||+|++||+|+.+.++|.
T Consensus 90 ~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~ 169 (307)
T KOG1315|consen 90 NGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYV 169 (307)
T ss_pred ccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHH
Confidence 11 11245899999999999999999999999999999999999999999999999999999999888
Q ss_pred HHHHHHHHHHHhhhhheeeeeeeeecccccccccchhHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc
Q 016042 223 IVALGFVLAGRLKELRVVYILTVYYGIENSFRKLAPHVVQWLLGSYNTQILLMVFLAVVSLLLASFFGYHANLCRTNTTT 302 (396)
Q Consensus 223 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~f~~~hl~li~~n~TT 302 (396)
++.....+....+.... +.. .......++.++...+++.+.+|+++|++||++|+||
T Consensus 170 lv~~~~~~~~~~~~~~~------------------~~~-----~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TT 226 (307)
T KOG1315|consen 170 LVTTLIGFTKYFQGGAG------------------PSS-----LLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTT 226 (307)
T ss_pred HHHHHHHHHHHHhcccc------------------Cch-----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchh
Confidence 77665544332211000 000 0011223334444567778888999999999999999
Q ss_pred cccccchhhhH
Q 016042 303 NETVKWQDHMN 313 (396)
Q Consensus 303 ~E~~k~~~~~~ 313 (396)
.|.+++..+..
T Consensus 227 iE~~~~~~~~~ 237 (307)
T KOG1315|consen 227 IEAYKSPVFRS 237 (307)
T ss_pred Hhhhccccccc
Confidence 99999886543
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=3.1e-39 Score=314.78 Aligned_cols=169 Identities=34% Similarity=0.627 Sum_probs=114.7
Q ss_pred HHHHHHHHHhHHhhcc---CCCcccCCC--cccccccCC------CCccccccccccccCCCCCCCCccccccCcccccc
Q 016042 121 LGVGIGVFFFLLTSFA---DPGTVKAEN--VSQYQSAYP------YDNIIYTEKECSTCKIPKPARSKHCSICNRCVARF 189 (396)
Q Consensus 121 ~~~~l~~~~~~~~~~~---DPG~i~~~~--~~~~~~~~p------~d~~~~~~~~C~tC~~~kP~RSkHC~~C~rCV~rf 189 (396)
+..++.+.....++++ |||.++++. ..+..+.-+ -++...+.++|.+|+..||+|||||++||+||.||
T Consensus 61 if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rf 140 (299)
T KOG1311|consen 61 IFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRF 140 (299)
T ss_pred HHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhccccccc
Confidence 3334444445555555 999999852 111111111 13334457999999999999999999999999999
Q ss_pred ccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeeeeeeeecccccccccchhHHHHHhhhhh
Q 016042 190 DHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVYILTVYYGIENSFRKLAPHVVQWLLGSYN 269 (396)
Q Consensus 190 DHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 (396)
||||||+|||||++|||||+.|+++..+.++|.+......+.......... +..... . ....
T Consensus 141 DHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~------------~~~~~~--~----~~~~ 202 (299)
T KOG1311|consen 141 DHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVN------------LTPVLI--P----AGTF 202 (299)
T ss_pred CCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc------------cccccc--c----hhHH
Confidence 999999999999999999999999999998888777665544322211100 000000 0 0011
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccccc
Q 016042 270 TQILLMVFLAVVSLLLASFFGYHANLCRTNTTTNETVK 307 (396)
Q Consensus 270 ~~~~~~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k 307 (396)
..+++.++.+++...+++++.+|++++.+|+||+|.++
T Consensus 203 ~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~ 240 (299)
T KOG1311|consen 203 LSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIK 240 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhh
Confidence 12233344456666777899999999999999999655
No 4
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=5.8e-39 Score=288.43 Aligned_cols=161 Identities=38% Similarity=0.675 Sum_probs=119.3
Q ss_pred HHhHHhhccCCCcccCCCccc------------ccccCCCCccccccccccccCCCCCCCCccccccCcccccccccccc
Q 016042 128 FFFLLTSFADPGTVKAENVSQ------------YQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGW 195 (396)
Q Consensus 128 ~~~~~~~~~DPG~i~~~~~~~------------~~~~~p~d~~~~~~~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~W 195 (396)
++|++++++|||++|..+.++ .....+.++.....++|.+|+..||+|||||+.||+||.||||||||
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 357899999999999871111 00111223344567999999999999999999999999999999999
Q ss_pred ccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeeeeeeeecccccccccchhHHHHHhhhhhhHHHHH
Q 016042 196 MNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVYILTVYYGIENSFRKLAPHVVQWLLGSYNTQILLM 275 (396)
Q Consensus 196 innCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 (396)
+|||||++|||+|++|+++..+.+++.++.....+........... +. . ......++.+
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~----~------~~~~~~~~~~ 140 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSS-----------FW----I------FSNFSSIFLL 140 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc-----------cc----c------chhhhHHHHH
Confidence 9999999999999999999999999988876665554332211100 00 0 0000113444
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCccccccccch
Q 016042 276 VFLAVVSLLLASFFGYHANLCRTNTTTNETVKWQ 309 (396)
Q Consensus 276 v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k~~ 309 (396)
++.++++++++.++++|++++++|+||+|.+||+
T Consensus 141 ~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 141 IISIFFFIFVGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 4556677888899999999999999999998874
No 5
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2e-37 Score=293.31 Aligned_cols=181 Identities=29% Similarity=0.499 Sum_probs=128.4
Q ss_pred ccccccccchhHHHHHHHHHHHHHhHHhhccCCCcccCCCcccccccCCCCccccccccccccCCCCCCCCccccccCcc
Q 016042 106 YYLSGFHRSSRYTSLLGVGIGVFFFLLTSFADPGTVKAENVSQYQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRC 185 (396)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~DPG~i~~~~~~~~~~~~p~d~~~~~~~~C~tC~~~kP~RSkHC~~C~rC 185 (396)
.+.+..+ .++..+...+.++.|+.|+++.||++|..+.++ .|-|.. -.++|..|+-+||||||||+.||||
T Consensus 44 s~~g~~n---~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe----~~~D~~--~lqfCk~CqgYKapRSHHCrkCnrC 114 (414)
T KOG1314|consen 44 SFLGVPN---QITFLLWTSMILYNYFNAIFTGPGFVPLGWKPE----NPKDEM--FLQFCKKCQGYKAPRSHHCRKCNRC 114 (414)
T ss_pred chhhhHH---HHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCC----CChhHH--HHHHHhhccCcCCCccccchHHHHH
Confidence 3455566 666666777778899999999999999987664 233422 2589999999999999999999999
Q ss_pred ccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeeeeeeeecccccccccchhHHHHHh
Q 016042 186 VARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVYILTVYYGIENSFRKLAPHVVQWLL 265 (396)
Q Consensus 186 V~rfDHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 (396)
|.+|||||||+|||||..||.||+.||++..+.|+-+.++.+..++..+....... ++... .|.+. .-.
T Consensus 115 vmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~-----~g~~h-----lp~v~-ft~ 183 (414)
T KOG1314|consen 115 VMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIK-----YGLRH-----LPIVF-FTL 183 (414)
T ss_pred HHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhh-----ccccc-----Cceee-ccH
Confidence 99999999999999999999999999999999999888777776666554432110 11110 01100 000
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccccc
Q 016042 266 GSYNTQILLMVFLAVVSLLLASFFGYHANLCRTNTTTNETV 306 (396)
Q Consensus 266 ~~~~~~~~~~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~ 306 (396)
......++.+.+...+.+.++.++..|+..|.+|+|.+|+.
T Consensus 184 ~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~w 224 (414)
T KOG1314|consen 184 SSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESW 224 (414)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHH
Confidence 00001111111222344556678889999999999999963
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=4.5e-34 Score=277.63 Aligned_cols=171 Identities=32% Similarity=0.539 Sum_probs=119.5
Q ss_pred HHHHHHHHHHHHHhHHhhccCCCcccCCCccc----ccccCCCCccccccccccccCCCCCCCCccccccCccccccccc
Q 016042 117 YTSLLGVGIGVFFFLLTSFADPGTVKAENVSQ----YQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHH 192 (396)
Q Consensus 117 ~~~~~~~~l~~~~~~~~~~~DPG~i~~~~~~~----~~~~~p~d~~~~~~~~C~tC~~~kP~RSkHC~~C~rCV~rfDHH 192 (396)
+...++..+...++++..++|||..++++... ..+....++....+++|.+|+.+||+|||||+.|||||+|||||
T Consensus 60 i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHH 139 (309)
T COG5273 60 ILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHH 139 (309)
T ss_pred hhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCcc
Confidence 33344455667789999999999998543221 11122223444568999999999999999999999999999999
Q ss_pred cccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeeeeeeeecccccccccchhHHHHHhhhhhhHH
Q 016042 193 CGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVVYILTVYYGIENSFRKLAPHVVQWLLGSYNTQI 272 (396)
Q Consensus 193 C~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 (396)
|||+|||||.+|||+|++||+++.....+.++.....+........ .+.. +. ...+
T Consensus 140 C~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~--~~----~~li 195 (309)
T COG5273 140 CPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRH------------------DTSL--AI----CFLI 195 (309)
T ss_pred CcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccC------------------ChHH--HH----HHHH
Confidence 9999999999999999999999987777666655554433221110 0000 00 0011
Q ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHhcCccccccccchhh
Q 016042 273 LL-MVFLAVVSLLLASFFGYHANLCRTNTTTNETVKWQDH 311 (396)
Q Consensus 273 ~~-~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k~~~~ 311 (396)
.. ..+..++.+.+..++.+|.+++..|+||.|..+-.+.
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~ 235 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRG 235 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccc
Confidence 11 1223345666778899999999999999998765554
No 7
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.98 E-value=3.2e-32 Score=250.87 Aligned_cols=142 Identities=30% Similarity=0.618 Sum_probs=97.9
Q ss_pred ccccccccCCCCCCCCccccccCccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhee
Q 016042 161 TEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVV 240 (396)
Q Consensus 161 ~~~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~ 240 (396)
...+|.+|+-+||||+||||+||+||++|||||||+|||||.+|||||++|++++.+.+.|.++...+.....+......
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ 180 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEI 180 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhc
Confidence 35799999999999999999999999999999999999999999999999999999999998877665554443322111
Q ss_pred eeeeeeecc-cccccccchhHHHHHhhhhhhHHH-HHHHHHHHHHHHHHHHHHHHHHHhcCcccccccc
Q 016042 241 YILTVYYGI-ENSFRKLAPHVVQWLLGSYNTQIL-LMVFLAVVSLLLASFFGYHANLCRTNTTTNETVK 307 (396)
Q Consensus 241 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k 307 (396)
+.|-+. ..-.. .+.+...--....+.+. +.++++.+.++++++..+|.++|.+|.|.+|..+
T Consensus 181 ---tay~~d~~h~~P--p~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~ 244 (309)
T KOG1313|consen 181 ---TAYASDVAHVAP--PPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLI 244 (309)
T ss_pred ---ccccCcccccCC--ChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHH
Confidence 111010 00000 01111110011112222 2333344666788899999999999999999554
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=1.7e-28 Score=249.20 Aligned_cols=110 Identities=39% Similarity=0.628 Sum_probs=82.7
Q ss_pred HHHHHHHHHHHHhHHhhccCCCcccCCCcccc--cccCCCCcccccc-ccccccCCCCCCCCccccccCccccccccccc
Q 016042 118 TSLLGVGIGVFFFLLTSFADPGTVKAENVSQY--QSAYPYDNIIYTE-KECSTCKIPKPARSKHCSICNRCVARFDHHCG 194 (396)
Q Consensus 118 ~~~~~~~l~~~~~~~~~~~DPG~i~~~~~~~~--~~~~p~d~~~~~~-~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~ 194 (396)
..++.++..++.+.+..-+|||+++....... .+..+.-+....+ ++|.+|.+.||.|||||++|||||+|||||||
T Consensus 373 ~~i~~~l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCP 452 (600)
T KOG0509|consen 373 CFIISVLAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCP 452 (600)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCC
Confidence 33344444555666777799999987543221 1122222222234 69999999999999999999999999999999
Q ss_pred cccccccccchhhhHHHHHHHHHHHHHHHHHHH
Q 016042 195 WMNNCIGERNTRYFMAFLLWHLFLCLYGIVALG 227 (396)
Q Consensus 195 WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~ 227 (396)
|++||||.+|||+|+.|+++....+.+.++...
T Consensus 453 wi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~ 485 (600)
T KOG0509|consen 453 WIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCL 485 (600)
T ss_pred ccccccCccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999998877766655543
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=89.58 E-value=4.9 Score=39.59 Aligned_cols=166 Identities=16% Similarity=0.146 Sum_probs=89.4
Q ss_pred hHHHHHHHHHHHHHhHHhhccCCCccc-----CCCcccccccCCCCcc-------c---cccccccccCCCCCCCCcccc
Q 016042 116 RYTSLLGVGIGVFFFLLTSFADPGTVK-----AENVSQYQSAYPYDNI-------I---YTEKECSTCKIPKPARSKHCS 180 (396)
Q Consensus 116 ~~~~~~~~~l~~~~~~~~~~~DPG~i~-----~~~~~~~~~~~p~d~~-------~---~~~~~C~tC~~~kP~RSkHC~ 180 (396)
.+....++...++..+.+.-.-||.-. ++..++..+..+++.. . .+.+.|++|+.=-...-|||.
T Consensus 62 ~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~ 141 (309)
T COG5273 62 FIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCP 141 (309)
T ss_pred hhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccCc
Confidence 444455566666666666666666331 1222333333333221 1 134799999999999999999
Q ss_pred ccCccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhee-eeeeeeecccccccccchh
Q 016042 181 ICNRCVARFDHHCGWMNNCIGERNTRYFMAFLLWHLFLCLYGIVALGFVLAGRLKELRVV-YILTVYYGIENSFRKLAPH 259 (396)
Q Consensus 181 ~C~rCV~rfDHHC~WinnCVG~~N~r~Fl~fL~~~~~~~~y~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 259 (396)
.=|+||.+-.| +=.-.|++++.+..+..++........+...-...... ..+ .
T Consensus 142 Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---------------i 195 (309)
T COG5273 142 WINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFL---------------I 195 (309)
T ss_pred ccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHH---------------H
Confidence 99999998655 56678888886655544444333332222111111110 000 0
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccccc
Q 016042 260 VVQWLLGSYNTQILLMVFLAVVSLLLASFFGYHANLCRTNTTTNETVK 307 (396)
Q Consensus 260 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~f~~~hl~li~~n~TT~E~~k 307 (396)
...+..+......+.+.+......++.....++.+.+.++.++-|...
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~ 243 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFP 243 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccc
Confidence 000111111111222222233445556677888999999999988654
No 10
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=87.83 E-value=0.56 Score=49.47 Aligned_cols=89 Identities=17% Similarity=-0.011 Sum_probs=63.9
Q ss_pred HHhHHhhccCCCcccCCCcccccccCCCCccccccccccccCCCCCCCCccccccCccccccccccccccccccccchhh
Q 016042 128 FFFLLTSFADPGTVKAENVSQYQSAYPYDNIIYTEKECSTCKIPKPARSKHCSICNRCVARFDHHCGWMNNCIGERNTRY 207 (396)
Q Consensus 128 ~~~~~~~~~DPG~i~~~~~~~~~~~~p~d~~~~~~~~C~tC~~~kP~RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r~ 207 (396)
..++..+.-+||++-.-+..-.... +--+...-...|.+|....+.+-++|..|-.++..+++||+|+. ||+.+|-..
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 3455666789999876554211111 11112234579999999999999999999999999999999999 999999875
Q ss_pred h-HHHHHHHHHH
Q 016042 208 F-MAFLLWHLFL 218 (396)
Q Consensus 208 F-l~fL~~~~~~ 218 (396)
| +.|+++..++
T Consensus 370 ~~~~~i~~~l~~ 381 (600)
T KOG0509|consen 370 FHYCFIISVLAY 381 (600)
T ss_pred hHHHHHHHHHHH
Confidence 4 4455554433
No 11
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=85.31 E-value=4.3 Score=39.55 Aligned_cols=33 Identities=24% Similarity=0.454 Sum_probs=30.4
Q ss_pred CCccccccCccccccccccccccccccccchhh
Q 016042 175 RSKHCSICNRCVARFDHHCGWMNNCIGERNTRY 207 (396)
Q Consensus 175 RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r~ 207 (396)
+.|+|+.|+..+...-|||..=|+||-+.-|+=
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC 144 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHC 144 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCC
Confidence 379999999999999999999999999988863
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=80.53 E-value=1 Score=31.47 Aligned_cols=25 Identities=28% Similarity=0.778 Sum_probs=22.4
Q ss_pred cccccccccCCCCCCCCccccccCc
Q 016042 160 YTEKECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 160 ~~~~~C~tC~~~kP~RSkHC~~C~r 184 (396)
...+.|..|...-|+|+..|+.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3568999999999999999998886
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=80.35 E-value=11 Score=33.24 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=19.2
Q ss_pred ccccccCCCCCCCCccccccCcccccccc
Q 016042 163 KECSTCKIPKPARSKHCSICNRCVARFDH 191 (396)
Q Consensus 163 ~~C~tC~~~kP~RSkHC~~C~rCV~rfDH 191 (396)
+.|+.|+.-...+-|||..-|.||.+--|
T Consensus 63 ~HC~~C~~CV~~~DHHC~w~~~cIG~~N~ 91 (174)
T PF01529_consen 63 HHCRVCNRCVLRFDHHCPWLGNCIGRRNH 91 (174)
T ss_pred eeccccccccccccccchhhccccccccH
Confidence 56666666666666777777777666544
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.74 E-value=1.1 Score=26.33 Aligned_cols=21 Identities=24% Similarity=0.645 Sum_probs=18.8
Q ss_pred cccccCCCCCCCCccccccCc
Q 016042 164 ECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 164 ~C~tC~~~kP~RSkHC~~C~r 184 (396)
+|+.|...-++.++.|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 589999999999999999985
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.86 E-value=1.5 Score=26.46 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=19.9
Q ss_pred cccccccCCCCCCCCccccccCc
Q 016042 162 EKECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 162 ~~~C~tC~~~kP~RSkHC~~C~r 184 (396)
.++|+.|...-++-++.|+.||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 36899999988999999999985
No 16
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=65.47 E-value=3.9 Score=24.84 Aligned_cols=22 Identities=32% Similarity=0.813 Sum_probs=19.2
Q ss_pred ccccccCCCCCCCCccccccCc
Q 016042 163 KECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 163 ~~C~tC~~~kP~RSkHC~~C~r 184 (396)
+.|+.|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4799999999999999998874
No 17
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=57.50 E-value=5.7 Score=43.25 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=18.2
Q ss_pred ccccccCCCCC-------CCCccccccCc
Q 016042 163 KECSTCKIPKP-------ARSKHCSICNR 184 (396)
Q Consensus 163 ~~C~tC~~~kP-------~RSkHC~~C~r 184 (396)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 46999997774 39999999988
No 18
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=57.19 E-value=2.4 Score=29.73 Aligned_cols=25 Identities=28% Similarity=0.808 Sum_probs=22.0
Q ss_pred cccccccccCCCCCCCCccccccCc
Q 016042 160 YTEKECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 160 ~~~~~C~tC~~~kP~RSkHC~~C~r 184 (396)
+..+.|..|...-|+|+.-|+.|+.
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccC
Confidence 4568999999999999999998864
No 19
>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=53.99 E-value=6.8 Score=28.36 Aligned_cols=37 Identities=32% Similarity=0.838 Sum_probs=29.1
Q ss_pred ccccccCCCCCCCC-------ccccccCcccccc-ccccccccccccc
Q 016042 163 KECSTCKIPKPARS-------KHCSICNRCVARF-DHHCGWMNNCIGE 202 (396)
Q Consensus 163 ~~C~tC~~~kP~RS-------kHC~~C~rCV~rf-DHHC~WinnCVG~ 202 (396)
..|..|+..-|+-| .-|..|..|+... +++|| ||=|+
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 46777877777654 4588899999887 99999 88775
No 20
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=50.18 E-value=5.5 Score=24.72 Aligned_cols=22 Identities=27% Similarity=0.809 Sum_probs=16.1
Q ss_pred ccccccCCCCCCCCccccccCc
Q 016042 163 KECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 163 ~~C~tC~~~kP~RSkHC~~C~r 184 (396)
=.|.+|...-++++.+|..|+.
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 3688899888999999988874
No 21
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=48.51 E-value=8 Score=36.32 Aligned_cols=13 Identities=23% Similarity=0.118 Sum_probs=10.4
Q ss_pred ccccccccccccc
Q 016042 185 CVARFDHHCGWMN 197 (396)
Q Consensus 185 CV~rfDHHC~Win 197 (396)
=..+.+|||||..
T Consensus 37 Hrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 37 HRSYESHHCPKGL 49 (250)
T ss_pred cchHhhcCCCccc
Confidence 4578899999973
No 22
>PF12773 DZR: Double zinc ribbon
Probab=47.62 E-value=13 Score=25.70 Aligned_cols=33 Identities=27% Similarity=0.567 Sum_probs=20.5
Q ss_pred cccccccCCCCC---CCCccccccCccccccccccc
Q 016042 162 EKECSTCKIPKP---ARSKHCSICNRCVARFDHHCG 194 (396)
Q Consensus 162 ~~~C~tC~~~kP---~RSkHC~~C~rCV~rfDHHC~ 194 (396)
.++|..|...-+ ...+.|..|+.=+...+.+|+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 466777766555 234567777776666666665
No 23
>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=47.46 E-value=9 Score=27.26 Aligned_cols=24 Identities=25% Similarity=0.707 Sum_probs=16.6
Q ss_pred cccccccCCCCCCCCccccc--cCcc
Q 016042 162 EKECSTCKIPKPARSKHCSI--CNRC 185 (396)
Q Consensus 162 ~~~C~tC~~~kP~RSkHC~~--C~rC 185 (396)
...|..|...-|+|+..|+. ||++
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 57999999999999999998 8765
No 24
>PF12773 DZR: Double zinc ribbon
Probab=43.31 E-value=17 Score=25.11 Aligned_cols=22 Identities=32% Similarity=0.869 Sum_probs=20.2
Q ss_pred cccccccCCCCCCCCccccccC
Q 016042 162 EKECSTCKIPKPARSKHCSICN 183 (396)
Q Consensus 162 ~~~C~tC~~~kP~RSkHC~~C~ 183 (396)
..+|..|....++.++.|..||
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCCCcCCcCccCccc
Confidence 4799999999999999999986
No 25
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=41.12 E-value=45 Score=32.42 Aligned_cols=31 Identities=23% Similarity=0.524 Sum_probs=26.7
Q ss_pred CccccccCccccccccccccccccccccchh
Q 016042 176 SKHCSICNRCVARFDHHCGWMNNCIGERNTR 206 (396)
Q Consensus 176 SkHC~~C~rCV~rfDHHC~WinnCVG~~N~r 206 (396)
.+-||.|+---.-...||.--|-||-+-.|+
T Consensus 148 ~~kCSTCki~KPARSKHCsiCNrCV~rfDHH 178 (341)
T KOG1312|consen 148 NVKCSTCKIRKPARSKHCSICNRCVHRFDHH 178 (341)
T ss_pred CCccccccCCCccccccchHHHHHHHHhccc
Confidence 4679999987777899999999999887776
No 26
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=40.05 E-value=1.9e+02 Score=28.49 Aligned_cols=32 Identities=22% Similarity=0.514 Sum_probs=28.0
Q ss_pred CCccccccCccccccccccccccccccccchh
Q 016042 175 RSKHCSICNRCVARFDHHCGWMNNCIGERNTR 206 (396)
Q Consensus 175 RSkHC~~C~rCV~rfDHHC~WinnCVG~~N~r 206 (396)
+.+.|..|+.-....-|||.--+.||.+.-|+
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHH 139 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHH 139 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccC
Confidence 77889999988888889999999999988776
No 27
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=34.45 E-value=21 Score=28.49 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=9.3
Q ss_pred cccccccccccc
Q 016042 191 HHCGWMNNCIGE 202 (396)
Q Consensus 191 HHC~WinnCVG~ 202 (396)
.||||+|.-...
T Consensus 56 ~~CPwv~~~~q~ 67 (91)
T PF08600_consen 56 EYCPWVNPSTQS 67 (91)
T ss_pred ccCCccCCcccc
Confidence 689999986643
No 28
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=33.15 E-value=23 Score=20.85 Aligned_cols=21 Identities=29% Similarity=0.719 Sum_probs=17.9
Q ss_pred cccccCCCCCCCCccccccCc
Q 016042 164 ECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 164 ~C~tC~~~kP~RSkHC~~C~r 184 (396)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 688999988999989988874
No 29
>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 COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.04 E-value=25 Score=26.04 Aligned_cols=23 Identities=35% Similarity=0.920 Sum_probs=20.6
Q ss_pred cccccccCCCCCCCCccccccCc
Q 016042 162 EKECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 162 ~~~C~tC~~~kP~RSkHC~~C~r 184 (396)
.+-|..|+..-|.-++-|.+|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999986
No 31
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=30.21 E-value=6.2e+02 Score=26.02 Aligned_cols=30 Identities=23% Similarity=0.440 Sum_probs=23.1
Q ss_pred ccccccCCCCCCCCccccccCccccccccc
Q 016042 163 KECSTCKIPKPARSKHCSICNRCVARFDHH 192 (396)
Q Consensus 163 ~~C~tC~~~kP~RSkHC~~C~rCV~rfDHH 192 (396)
..|+.|+..-|....||..|+.-..+..++
T Consensus 222 ~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~ 251 (419)
T PRK15103 222 RSCSCCTAILPADQPVCPRCHTKGYVRRRN 251 (419)
T ss_pred CcCCCCCCCCCCCCCCCCCCCCcCcCCCCC
Confidence 569999998887777888888877555443
No 32
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=27.82 E-value=17 Score=37.16 Aligned_cols=25 Identities=28% Similarity=0.744 Sum_probs=19.2
Q ss_pred cccccccCCCC--CCCCccccccCccc
Q 016042 162 EKECSTCKIPK--PARSKHCSICNRCV 186 (396)
Q Consensus 162 ~~~C~tC~~~k--P~RSkHC~~C~rCV 186 (396)
..+|+.|...= --|-|||+.||+-+
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchHH
Confidence 47999997533 34889999999844
No 33
>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=27.42 E-value=18 Score=26.85 Aligned_cols=25 Identities=32% Similarity=0.668 Sum_probs=11.7
Q ss_pred cccccccCCCC--CCCCccccccCccc
Q 016042 162 EKECSTCKIPK--PARSKHCSICNRCV 186 (396)
Q Consensus 162 ~~~C~tC~~~k--P~RSkHC~~C~rCV 186 (396)
...|..|+..= -.|-|||+.||+.|
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 36787786422 35889999999865
No 34
>PRK00944 hypothetical protein; Provisional
Probab=26.94 E-value=82 Score=28.55 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCCCCccCChh
Q 016042 4 QWLLIIHGLLTLLVVVSFLCGQWPIFEGTPI 34 (396)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~lfG~~p~~r~t~i 34 (396)
.|++++.+++++.++.++.+||.|...=+.|
T Consensus 15 ~w~~~~~~~~~~~a~~L~~mGR~pIC~CG~v 45 (195)
T PRK00944 15 FWLLAALAVLALQALILYAMGRVPICECGYV 45 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccccCcce
Confidence 6899999999999999999999998887776
No 35
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=26.63 E-value=27 Score=34.07 Aligned_cols=21 Identities=43% Similarity=0.844 Sum_probs=16.3
Q ss_pred cccccccCCCCCCCCccccccCc
Q 016042 162 EKECSTCKIPKPARSKHCSICNR 184 (396)
Q Consensus 162 ~~~C~tC~~~kP~RSkHC~~C~r 184 (396)
-++|+||...+| +|.|+.|+-
T Consensus 319 ~~fCstCG~~ga--~KrCs~CKa 339 (396)
T KOG1710|consen 319 CQFCSTCGHPGA--KKRCSQCKA 339 (396)
T ss_pred cccccccCCCCc--cchhhhhHH
Confidence 379999998776 567888873
No 36
>COG3936 Protein involved in polysaccharide intercellular adhesin (PIA) synthesis/biofilm formation [Carbohydrate transport and metabolism]
Probab=25.08 E-value=2.1e+02 Score=27.97 Aligned_cols=19 Identities=21% Similarity=0.301 Sum_probs=10.3
Q ss_pred HHhcCCCCccCChh-hHHHH
Q 016042 21 FLCGQWPIFEGTPI-QRIHY 39 (396)
Q Consensus 21 ~lfG~~p~~r~t~i-~~~~~ 39 (396)
.++|--|.|.++|+ ||+..
T Consensus 176 ~~~~~fp~f~~~if~GW~fy 195 (349)
T COG3936 176 LLFLTFPYFFAMIFMGWYFY 195 (349)
T ss_pred HHHhhhHHHHHHHHHHHHHH
Confidence 34555666666654 44444
No 37
>PRK04561 tatA twin arginine translocase protein A; Provisional
Probab=23.96 E-value=63 Score=24.90 Aligned_cols=13 Identities=31% Similarity=0.483 Sum_probs=8.7
Q ss_pred HHHHHHHHhcCCC
Q 016042 15 LLVVVSFLCGQWP 27 (396)
Q Consensus 15 ~~~~~~~lfG~~p 27 (396)
.++|++++||...
T Consensus 12 IlvIvlLlFG~~K 24 (75)
T PRK04561 12 VLVIVLLVFGTKR 24 (75)
T ss_pred HHHHHHHHhCCcc
Confidence 3446688899754
No 38
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.89 E-value=21 Score=36.01 Aligned_cols=25 Identities=40% Similarity=0.905 Sum_probs=18.8
Q ss_pred CCCCCccccccCccccccccccccccccccc
Q 016042 172 KPARSKHCSICNRCVARFDHHCGWMNNCIGE 202 (396)
Q Consensus 172 kP~RSkHC~~C~rCV~rfDHHC~WinnCVG~ 202 (396)
+-.|-.||..|+. +|| +|+.||||.
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 3455667777765 688 799999997
No 39
>PRK03554 tatA twin arginine translocase protein A; Provisional
Probab=23.86 E-value=59 Score=25.88 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=9.1
Q ss_pred HHHHHHHHHHhcCCC
Q 016042 13 LTLLVVVSFLCGQWP 27 (396)
Q Consensus 13 ~~~~~~~~~lfG~~p 27 (396)
++.++|+++|||...
T Consensus 10 lIIlvIvLLlFG~kK 24 (89)
T PRK03554 10 LIIAVIVVLLFGTKK 24 (89)
T ss_pred HHHHHHHHHHhCcch
Confidence 344556677888653
No 40
>PRK04598 tatA twin arginine translocase protein A; Provisional
Probab=23.61 E-value=61 Score=25.42 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=8.7
Q ss_pred HHHHHHHHHHhcCCC
Q 016042 13 LTLLVVVSFLCGQWP 27 (396)
Q Consensus 13 ~~~~~~~~~lfG~~p 27 (396)
++.++|+++|||...
T Consensus 10 liIlvivlllFG~kK 24 (81)
T PRK04598 10 LIIAVIVVLLFGTKK 24 (81)
T ss_pred HHHHHHHHHHhCcch
Confidence 334456667788643
No 41
>PRK02958 tatA twin arginine translocase protein A; Provisional
Probab=23.33 E-value=64 Score=24.77 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=9.1
Q ss_pred HHHHHHHHHhcCCC
Q 016042 14 TLLVVVSFLCGQWP 27 (396)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (396)
+.++|++++||...
T Consensus 11 iIl~IvlllFG~kK 24 (73)
T PRK02958 11 IVLVIVVLVFGTKK 24 (73)
T ss_pred HHHHHHHHHhCcch
Confidence 34456777888754
No 42
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=23.10 E-value=55 Score=20.80 Aligned_cols=20 Identities=30% Similarity=0.876 Sum_probs=10.6
Q ss_pred cccccCCCCCCC-Ccc-ccccC
Q 016042 164 ECSTCKIPKPAR-SKH-CSICN 183 (396)
Q Consensus 164 ~C~tC~~~kP~R-SkH-C~~C~ 183 (396)
.|.-|...+..+ ++. |+.|+
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~ 23 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCD 23 (32)
T ss_pred CCeECCcCCccceeEEEccCCC
Confidence 355555555544 333 66665
No 43
>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=22.84 E-value=30 Score=30.28 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=16.8
Q ss_pred cccccCCCCCCCCccccccCcccccc
Q 016042 164 ECSTCKIPKPARSKHCSICNRCVARF 189 (396)
Q Consensus 164 ~C~tC~~~kP~RSkHC~~C~rCV~rf 189 (396)
...+|+.. ..+||-.|..|+.|.
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 338999999999873
No 44
>PRK01833 tatA twin arginine translocase protein A; Provisional
Probab=22.82 E-value=66 Score=24.75 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=8.8
Q ss_pred HHHHHHHHHhcCCC
Q 016042 14 TLLVVVSFLCGQWP 27 (396)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (396)
+.++|++++||...
T Consensus 11 iIl~i~lllFG~kK 24 (74)
T PRK01833 11 IIVAIIVLLFGTKK 24 (74)
T ss_pred HHHHHHHHHhCcch
Confidence 34456678898653
No 45
>COG0348 NapH Polyferredoxin [Energy production and conversion]
Probab=22.81 E-value=2e+02 Score=29.18 Aligned_cols=14 Identities=36% Similarity=0.956 Sum_probs=11.1
Q ss_pred cccccCcccccccc
Q 016042 178 HCSICNRCVARFDH 191 (396)
Q Consensus 178 HC~~C~rCV~rfDH 191 (396)
-|-.|++|+.--||
T Consensus 246 ~CI~C~~CidaCd~ 259 (386)
T COG0348 246 ECIGCGRCIDACDD 259 (386)
T ss_pred ccccHhhHhhhCCH
Confidence 38889999887666
No 46
>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=22.45 E-value=55 Score=22.98 Aligned_cols=24 Identities=29% Similarity=0.699 Sum_probs=15.5
Q ss_pred ccccccCC--CCCCCCccccccCccc
Q 016042 163 KECSTCKI--PKPARSKHCSICNRCV 186 (396)
Q Consensus 163 ~~C~tC~~--~kP~RSkHC~~C~rCV 186 (396)
+.|..|+. -.-.|.+||+.||+-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 45666653 2345788999888753
No 47
>PRK00720 tatA twin arginine translocase protein A; Provisional
Probab=22.38 E-value=68 Score=24.96 Aligned_cols=14 Identities=43% Similarity=0.555 Sum_probs=8.6
Q ss_pred HHHHHHHHHHhcCC
Q 016042 13 LTLLVVVSFLCGQW 26 (396)
Q Consensus 13 ~~~~~~~~~lfG~~ 26 (396)
++.++|+++|||..
T Consensus 10 lIIlvIvlllFG~k 23 (78)
T PRK00720 10 LIVLAVVLLLFGRG 23 (78)
T ss_pred HHHHHHHHHHhCcc
Confidence 34455667778853
No 48
>PRK01614 tatE twin arginine translocase protein A; Validated
Probab=22.02 E-value=69 Score=25.24 Aligned_cols=14 Identities=14% Similarity=0.294 Sum_probs=9.0
Q ss_pred HHHHHHHHHhcCCC
Q 016042 14 TLLVVVSFLCGQWP 27 (396)
Q Consensus 14 ~~~~~~~~lfG~~p 27 (396)
+.++|+++|||...
T Consensus 11 IIlvIvLLLFG~kK 24 (85)
T PRK01614 11 VVGILIVLLFGTSK 24 (85)
T ss_pred HHHHHHHHHhCcch
Confidence 33456678899754
No 49
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=21.54 E-value=6e+02 Score=22.85 Aligned_cols=23 Identities=9% Similarity=0.105 Sum_probs=12.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHhh
Q 016042 309 QDHMNWLRKVNEARASAAALKAS 331 (396)
Q Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~ 331 (396)
+|+.+.++.+++++...+.+++.
T Consensus 68 ~e~~~~~~~l~ea~~~i~~i~~~ 90 (199)
T PF10112_consen 68 REYEYIREILEEAKEKIRRIEKA 90 (199)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555556666665555444443
No 50
>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=21.28 E-value=34 Score=21.09 Aligned_cols=21 Identities=29% Similarity=0.670 Sum_probs=8.2
Q ss_pred cccccCCCCCC-CCccccccCc
Q 016042 164 ECSTCKIPKPA-RSKHCSICNR 184 (396)
Q Consensus 164 ~C~tC~~~kP~-RSkHC~~C~r 184 (396)
.|..|+..... ...+|+.|+-
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 57777766666 6677887764
No 51
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=20.79 E-value=61 Score=27.40 Aligned_cols=9 Identities=22% Similarity=0.671 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 016042 5 WLLIIHGLL 13 (396)
Q Consensus 5 ~~~~~~~~~ 13 (396)
|+|++.+++
T Consensus 2 W~l~~iii~ 10 (130)
T PF12273_consen 2 WVLFAIIIV 10 (130)
T ss_pred eeeHHHHHH
Confidence 344433333
No 52
>PLN00186 ribosomal protein S26; Provisional
Probab=20.45 E-value=41 Score=27.77 Aligned_cols=15 Identities=33% Similarity=0.886 Sum_probs=12.1
Q ss_pred CCccccccCcccccc
Q 016042 175 RSKHCSICNRCVARF 189 (396)
Q Consensus 175 RSkHC~~C~rCV~rf 189 (396)
+.-||..|++||.+=
T Consensus 19 ~~V~C~nCgr~vPKD 33 (109)
T PLN00186 19 KRIRCSNCGKCVPKD 33 (109)
T ss_pred cceeeCCCccccccc
Confidence 345899999999873
No 53
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=20.35 E-value=92 Score=29.10 Aligned_cols=6 Identities=50% Similarity=0.911 Sum_probs=2.8
Q ss_pred CCCCHh
Q 016042 365 NIYDKG 370 (396)
Q Consensus 365 N~YD~G 370 (396)
+-||.|
T Consensus 143 ~~y~~~ 148 (217)
T PF07423_consen 143 MTYDSG 148 (217)
T ss_pred ccccCC
Confidence 335554
No 54
>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=20.11 E-value=32 Score=22.33 Aligned_cols=7 Identities=29% Similarity=0.999 Sum_probs=4.1
Q ss_pred ccccccC
Q 016042 163 KECSTCK 169 (396)
Q Consensus 163 ~~C~tC~ 169 (396)
++|++|+
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 4677775
Done!