Query psy9546
Match_columns 385
No_of_seqs 265 out of 1631
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 22:20:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9546hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1311|consensus 100.0 6.6E-40 1.4E-44 320.7 10.6 179 34-217 79-266 (299)
2 KOG1315|consensus 100.0 2.8E-37 6.1E-42 301.4 5.9 203 25-232 60-274 (307)
3 PF01529 zf-DHHC: DHHC palmito 100.0 9.7E-37 2.1E-41 274.3 5.0 161 27-187 3-173 (174)
4 COG5273 Uncharacterized protei 100.0 5.8E-33 1.3E-37 273.2 6.9 164 23-188 68-233 (309)
5 KOG1313|consensus 100.0 6.2E-33 1.3E-37 262.2 5.6 170 61-231 100-293 (309)
6 KOG1314|consensus 100.0 1.2E-32 2.6E-37 267.4 3.9 181 26-216 63-262 (414)
7 KOG0509|consensus 100.0 8.8E-30 1.9E-34 263.3 1.4 186 27-214 384-582 (600)
8 KOG1312|consensus 99.9 4.9E-28 1.1E-32 230.1 7.1 163 24-189 111-292 (341)
9 COG5273 Uncharacterized protei 95.6 0.0088 1.9E-07 59.6 3.2 175 2-187 60-244 (309)
10 PF01529 zf-DHHC: DHHC palmito 91.6 0.15 3.3E-06 45.5 3.0 34 59-92 58-91 (174)
11 KOG1311|consensus 86.0 0.61 1.3E-05 45.8 3.0 41 77-117 113-164 (299)
12 KOG1315|consensus 78.2 6.7 0.00015 39.2 7.0 52 76-127 108-170 (307)
13 PRK04136 rpl40e 50S ribosomal 73.2 2 4.3E-05 31.3 1.3 24 62-85 13-36 (48)
14 KOG0509|consensus 66.0 2.1 4.6E-05 46.1 0.3 62 56-118 318-380 (600)
15 KOG4043|consensus 64.2 2 4.3E-05 39.1 -0.3 20 301-320 171-190 (214)
16 PF13240 zinc_ribbon_2: zinc-r 59.7 5.3 0.00011 24.5 1.1 21 65-85 1-21 (23)
17 KOG1314|consensus 56.7 1 2.3E-05 45.5 -3.7 44 61-115 103-146 (414)
18 PF10278 Med19: Mediator of RN 56.4 3.6 7.8E-05 38.0 -0.1 16 170-185 28-43 (178)
19 KOG4043|consensus 54.4 3 6.5E-05 38.0 -0.9 25 301-325 177-201 (214)
20 PTZ00303 phosphatidylinositol 54.2 7.7 0.00017 43.3 1.9 29 57-85 452-489 (1374)
21 PF12773 DZR: Double zinc ribb 52.2 12 0.00026 26.6 2.1 36 61-96 10-48 (50)
22 PF13248 zf-ribbon_3: zinc-rib 51.7 8.5 0.00018 24.1 1.1 22 64-85 3-24 (26)
23 KOG1842|consensus 50.7 3.2 7E-05 43.2 -1.4 46 43-88 159-207 (505)
24 KOG3045|consensus 50.1 11 0.00024 37.1 2.2 58 297-357 27-85 (325)
25 COG1552 RPL40A Ribosomal prote 48.2 4.7 0.0001 29.5 -0.5 24 62-85 13-36 (50)
26 PF01020 Ribosomal_L40e: Ribos 44.8 13 0.00028 27.6 1.3 25 62-86 16-42 (52)
27 PF06375 BLVR: Bovine leukaemi 35.7 16 0.00035 33.0 0.7 22 183-204 4-25 (154)
28 PF12773 DZR: Double zinc ribb 29.7 37 0.00081 24.0 1.7 25 60-84 26-50 (50)
29 PF10571 UPF0547: Uncharacteri 28.8 32 0.0007 21.7 1.1 22 64-85 1-22 (26)
30 PF00641 zf-RanBP: Zn-finger i 28.7 25 0.00054 22.5 0.6 21 65-85 6-26 (30)
31 PF08600 Rsm1: Rsm1-like; Int 28.3 34 0.00073 28.0 1.4 16 88-103 52-67 (91)
32 PF06906 DUF1272: Protein of u 26.6 35 0.00075 25.8 1.1 36 65-103 7-50 (57)
33 PF01363 FYVE: FYVE zinc finge 25.6 22 0.00048 26.8 -0.1 27 62-88 8-36 (69)
34 KOG3183|consensus 25.5 32 0.0007 33.3 0.9 12 87-98 38-49 (250)
35 KOG3598|consensus 24.0 62 0.0013 38.9 2.9 22 317-338 1818-1839(2220)
36 PF10268 Tmemb_161AB: Predicte 20.7 43 0.00094 35.7 0.9 16 296-311 40-55 (486)
No 1
>KOG1311|consensus
Probab=100.00 E-value=6.6e-40 Score=320.74 Aligned_cols=179 Identities=32% Similarity=0.570 Sum_probs=139.2
Q ss_pred cCCCccccc--CCCC---CCcccccccccCcccccccccccCcccCCCCccCcccCcccccccccCcccccccccccchh
Q psy9546 34 GRGGLATRE--LSPG---EKPLHNFQTLTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRNYRF 108 (385)
Q Consensus 34 ~~pG~~~~~--~~~~---~~p~~kel~~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N~r~ 108 (385)
+|||.+++. ...+ ..++.++..++|..++.+||.+|+.+||+|||||++||+||+||||||||+|||||++||||
T Consensus 79 sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~ 158 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRY 158 (299)
T ss_pred CCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHH
Confidence 599999884 3222 23466788889999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhHHHHHHHHHHhhhceeeEeeeecc--cccc--cccccCcccceeeehhhHHHHHHHHHHHHHHHHHhhCccchhh
Q psy9546 109 FYAFIVSLSFHIVFVFCCSVAHLSILAEG--RLVF--DAVRESPTSVLVVAVTFSSVWSVLGLAGFHTYLAASNQTTNED 184 (385)
Q Consensus 109 F~lFLl~l~l~~~~~~~~~~~~i~~~~~~--~~~~--~~~~~~~~~il~~i~~~~~~~~v~~L~~~hl~lI~~n~TT~E~ 184 (385)
|+.|++++.+++++.++.+..++...... ..+. .........+++++++++.++.+++|+.+|+++|.+|+||+|+
T Consensus 159 F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~ 238 (299)
T KOG1311|consen 159 FVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYES 238 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhh
Confidence 99999999999998888776664321111 1111 1111111223344566677777888999999999999999999
Q ss_pred hcccccccCCCCCCCCCCchhHHHHHHHhcCCC
Q psy9546 185 IKGSFTSRRGRASFNPYSYGNACSNCCNATTSR 217 (385)
Q Consensus 185 ik~~~~~k~~~~~~nPyd~Gs~~~N~~~v~~~r 217 (385)
+++ .. .....+||+.| .++|+.+++|++
T Consensus 239 ~~~-~~---~~~~~~~~~~g-~~~n~~~~~~~~ 266 (299)
T KOG1311|consen 239 IKS-LD---FVSRSNPYDLG-LLKNLQEVFGGP 266 (299)
T ss_pred hhc-cc---cccccCCCchh-HHHHHHHHhCCC
Confidence 986 21 11125999999 999999999994
No 2
>KOG1315|consensus
Probab=100.00 E-value=2.8e-37 Score=301.42 Aligned_cols=203 Identities=28% Similarity=0.429 Sum_probs=142.0
Q ss_pred hHHHHHHhhcCCCcccccCCCCCCc--c---------cccccccCcccccccccccCcccCCCCccCcccCccccccccc
Q psy9546 25 TPLYVIQIVGRGGLATRELSPGEKP--L---------HNFQTLTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHH 93 (385)
Q Consensus 25 ~~~~~~~i~~~pG~~~~~~~~~~~p--~---------~kel~~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHH 93 (385)
.-.|+..++-+||.++....++.-+ . .......+.....++|.+|+.+||+|||||++|+|||+|||||
T Consensus 60 ~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHH 139 (307)
T KOG1315|consen 60 LWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHH 139 (307)
T ss_pred HHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccC
Confidence 3445566667888877655443222 1 1112223444589999999999999999999999999999999
Q ss_pred CcccccccccccchhhHHHhHHHHHHHHHHhhhceeeEeeeecccccccccccCcccceeeehhhHHHHHHHHHHHHHHH
Q psy9546 94 CPWVGNCVGKRNYRFFYAFIVSLSFHIVFVFCCSVAHLSILAEGRLVFDAVRESPTSVLVVAVTFSSVWSVLGLAGFHTY 173 (385)
Q Consensus 94 CpWv~NCIG~~N~r~F~lFLl~l~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~il~~i~~~~~~~~v~~L~~~hl~ 173 (385)
|||+|||||.+|||||++|++|..+.+++.++..+..+......... .......+.++.+++.+...+.+++|+++|++
T Consensus 140 CpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~ 218 (307)
T KOG1315|consen 140 CPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAG-PSSLLLFFIVFLFLVAIAFSISLSGLLCFHTY 218 (307)
T ss_pred CcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc-CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999988877766554322111000 00000112233334444445566678899999
Q ss_pred HHhhCccchhhhcccccccCCCCCCCCCCchhHHHHHHHhcCCCCc-ccccccCCCCCCC
Q psy9546 174 LAASNQTTNEDIKGSFTSRRGRASFNPYSYGNACSNCCNATTSRYS-IKTDFVSLVPDRR 232 (385)
Q Consensus 174 lI~~n~TT~E~ik~~~~~k~~~~~~nPyd~Gs~~~N~~~v~~~rw~-~~~p~~Ps~~~~~ 232 (385)
||++|+||+|.++... ...+....+.|+. ..|+.++++++|. |+.|..-+..+..
T Consensus 219 Li~~N~TTiE~~~~~~-~~~~~~~~~~~~~---~~n~~~vfg~~~~~wl~P~~~s~~~~~ 274 (307)
T KOG1315|consen 219 LILKNKTTIEAYKSPV-FRSGLHNKNGFNL---YVNFREVFGSNLLYWLLPIDSSWGDGV 274 (307)
T ss_pred HHHcCchhHhhhcccc-ccccccccCCcce---eecHHHHhCCCceEEeccccCccccCc
Confidence 9999999999988541 1223345666765 6899999999866 8888876655544
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=9.7e-37 Score=274.26 Aligned_cols=161 Identities=34% Similarity=0.552 Sum_probs=118.0
Q ss_pred HHHHHhhcCCCccccc---------CCCCCCcccccccccCcccccccccccCcccCCCCccCcccCcccccccccCccc
Q psy9546 27 LYVIQIVGRGGLATRE---------LSPGEKPLHNFQTLTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWV 97 (385)
Q Consensus 27 ~~~~~i~~~pG~~~~~---------~~~~~~p~~kel~~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv 97 (385)
.|+.++..|||++++. ..........+....+..++.++|.+|+++||+|||||+.||+||+||||||||+
T Consensus 3 ~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w~ 82 (174)
T PF01529_consen 3 SYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPWL 82 (174)
T ss_pred EehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchhh
Confidence 4667888899999888 1111111334445666788999999999999999999999999999999999999
Q ss_pred ccccccccchhhHHHhHHHHHHHHHHhhhceeeEeeeecccccccccccCcc-cceeeehhhHHHHHHHHHHHHHHHHHh
Q psy9546 98 GNCVGKRNYRFFYAFIVSLSFHIVFVFCCSVAHLSILAEGRLVFDAVRESPT-SVLVVAVTFSSVWSVLGLAGFHTYLAA 176 (385)
Q Consensus 98 ~NCIG~~N~r~F~lFLl~l~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~il~~i~~~~~~~~v~~L~~~hl~lI~ 176 (385)
|||||++|||+|++|++++.+.+++.+...+.++.................. .++.++++++..++++.|+++|+++|+
T Consensus 83 ~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~ 162 (174)
T PF01529_consen 83 GNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLIL 162 (174)
T ss_pred ccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999888777666554322111111110000000 133344455555667788899999999
Q ss_pred hCccchhhhcc
Q psy9546 177 SNQTTNEDIKG 187 (385)
Q Consensus 177 ~n~TT~E~ik~ 187 (385)
+|+||+|.++.
T Consensus 163 ~n~Tt~E~~~~ 173 (174)
T PF01529_consen 163 RNITTYERIKR 173 (174)
T ss_pred cCCcHHHHHHc
Confidence 99999999873
No 4
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.97 E-value=5.8e-33 Score=273.16 Aligned_cols=164 Identities=30% Similarity=0.471 Sum_probs=123.7
Q ss_pred chhHHHHHHhhcCCCcccccCCCCCC-cccccccccCcccccccccccCcccCCCCccCcccCcccccccccCccccccc
Q psy9546 23 HATPLYVIQIVGRGGLATRELSPGEK-PLHNFQTLTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCV 101 (385)
Q Consensus 23 ~g~~~~~~~i~~~pG~~~~~~~~~~~-p~~kel~~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCI 101 (385)
.+...|+.++.+|||..+++...... ..++.....++.+..+||.+|+.+||+|||||+.||+||+||||||||+||||
T Consensus 68 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCV 147 (309)
T COG5273 68 LASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCV 147 (309)
T ss_pred hHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccCccccccc
Confidence 55777888999999998866554443 46788888999999999999999999999999999999999999999999999
Q ss_pred ccccchhhHHHhHHHHHHHHHHhhhceeeEeeeecccccccccccCccccee-eehhhHHHHHHHHHHHHHHHHHhhCcc
Q psy9546 102 GKRNYRFFYAFIVSLSFHIVFVFCCSVAHLSILAEGRLVFDAVRESPTSVLV-VAVTFSSVWSVLGLAGFHTYLAASNQT 180 (385)
Q Consensus 102 G~~N~r~F~lFLl~l~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~il~-~i~~~~~~~~v~~L~~~hl~lI~~n~T 180 (385)
|++|||+|++|++++...++++++...+++............. .. +.++. ..+.....+.+.+++.++.+++..|+|
T Consensus 148 G~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t 225 (309)
T COG5273 148 GFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLA-IC-FLIFGCSLLGVVFFIITTLLLLFLIYLILNNLT 225 (309)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHH-HH-HHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 9999999999999998888887777776664322111111100 00 00111 112222234455678999999999999
Q ss_pred chhhhccc
Q psy9546 181 TNEDIKGS 188 (385)
Q Consensus 181 T~E~ik~~ 188 (385)
++|.....
T Consensus 226 ~~e~~~~~ 233 (309)
T COG5273 226 TIEFIQIS 233 (309)
T ss_pred HHHHHHhc
Confidence 99998744
No 5
>KOG1313|consensus
Probab=99.97 E-value=6.2e-33 Score=262.19 Aligned_cols=170 Identities=26% Similarity=0.459 Sum_probs=119.4
Q ss_pred cccccccccCcccCCCCccCcccCcccccccccCcccccccccccchhhHHHhHHHHHHHHHHhhhceeeE----eeeec
Q psy9546 61 LHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRNYRFFYAFIVSLSFHIVFVFCCSVAHL----SILAE 136 (385)
Q Consensus 61 ~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N~r~F~lFLl~l~l~~~~~~~~~~~~i----~~~~~ 136 (385)
....||.+|.-+||||+|||++||+||++|||||||+|||||..||||||+|++|+++++.|+.+...+.. .....
T Consensus 100 ~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~ 179 (309)
T KOG1313|consen 100 ENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE 179 (309)
T ss_pred ccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh
Confidence 35689999999999999999999999999999999999999999999999999999999999776644321 11111
Q ss_pred ccccccc---------cccCc--c---c-ceeeehhhHHHHHHHHHHHHHHHHHhhCccchhhhcccccccC--CCCCCC
Q psy9546 137 GRLVFDA---------VRESP--T---S-VLVVAVTFSSVWSVLGLAGFHTYLAASNQTTNEDIKGSFTSRR--GRASFN 199 (385)
Q Consensus 137 ~~~~~~~---------~~~~~--~---~-il~~i~~~~~~~~v~~L~~~hl~lI~~n~TT~E~ik~~~~~k~--~~~~~n 199 (385)
.....+. +.+.. + . +.+.++++..+++++.|..+|.++|++|.|.+|+......+++ .+...|
T Consensus 180 ~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~ 259 (309)
T KOG1313|consen 180 ITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSN 259 (309)
T ss_pred cccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCC
Confidence 0111000 00000 0 0 1123344555667778999999999999999999765544432 234589
Q ss_pred CCCchhHHHHHHHhcCC---CCcccccccCCCCCC
Q psy9546 200 PYSYGNACSNCCNATTS---RYSIKTDFVSLVPDR 231 (385)
Q Consensus 200 Pyd~Gs~~~N~~~v~~~---rw~~~~p~~Ps~~~~ 231 (385)
|++.| ..+||+.+++= |=.|.+-+.|+....
T Consensus 260 ~~n~g-~k~nWr~fLg~~~~r~~wk~v~lPt~~~p 293 (309)
T KOG1313|consen 260 PTNFG-GKANWRNFLGLFRGRHFWKTVLLPTIRKP 293 (309)
T ss_pred Ccccc-hHHHHHHhhccccCCceeEEEeccccccc
Confidence 99999 88899888743 323444344444333
No 6
>KOG1314|consensus
Probab=99.97 E-value=1.2e-32 Score=267.36 Aligned_cols=181 Identities=22% Similarity=0.371 Sum_probs=123.3
Q ss_pred HHHHHHhhcCCCcccccCCCCCCcccccccccCcccccccccccCcccCCCCccCcccCcccccccccCccccccccccc
Q psy9546 26 PLYVIQIVGRGGLATRELSPGEKPLHNFQTLTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRN 105 (385)
Q Consensus 26 ~~~~~~i~~~pG~~~~~~~~~~~p~~kel~~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N 105 (385)
.-|+.+++-.||+++...-|+..+ ....++||..|+-+|+||||||+.|||||.+|||||||+|||||..|
T Consensus 63 ~ny~~A~~~gPG~vp~~wkPe~~~---------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aN 133 (414)
T KOG1314|consen 63 YNYFNAIFTGPGFVPLGWKPENPK---------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWAN 133 (414)
T ss_pred HHHHHHHhcCCCCCCCCCCCCCCh---------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccc
Confidence 356677788899988777664432 12457899999999999999999999999999999999999999999
Q ss_pred chhhHHHhHHHHHHHHHHh---hhcee----eEeeeecccccccccc----cCcccceeeehhhHHHHHHHHHHHHHHHH
Q psy9546 106 YRFFYAFIVSLSFHIVFVF---CCSVA----HLSILAEGRLVFDAVR----ESPTSVLVVAVTFSSVWSVLGLAGFHTYL 174 (385)
Q Consensus 106 ~r~F~lFLl~l~l~~~~~~---~~~~~----~i~~~~~~~~~~~~~~----~~~~~il~~i~~~~~~~~v~~L~~~hl~l 174 (385)
|.||+.||+...++++-.. .+..+ ..+.+..+......+. ...+.++.+.+++..++.+..|++.|+.+
T Consensus 134 h~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~ 213 (414)
T KOG1314|consen 134 HAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQ 213 (414)
T ss_pred cHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999887654321 11111 1111111100000000 00111222333344455666788899999
Q ss_pred HhhCccchhhhccc--------ccccCCCCCCCCCCchhHHHHHHHhcCC
Q psy9546 175 AASNQTTNEDIKGS--------FTSRRGRASFNPYSYGNACSNCCNATTS 216 (385)
Q Consensus 175 I~~n~TT~E~ik~~--------~~~k~~~~~~nPyd~Gs~~~N~~~v~~~ 216 (385)
|.+|+|.+|..--. +..+-.+....|||.| +..|+++|+++
T Consensus 214 Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlg-Wr~n~r~vf~~ 262 (414)
T KOG1314|consen 214 ILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLG-WRINLREVFFQ 262 (414)
T ss_pred HHcCCcchHHHHHHHHHHHHHhhccCCCCceeeecccc-ccccHHHHhhh
Confidence 99999999985311 1111124578999999 77899999988
No 7
>KOG0509|consensus
Probab=99.95 E-value=8.8e-30 Score=263.28 Aligned_cols=186 Identities=27% Similarity=0.478 Sum_probs=135.0
Q ss_pred HHHHHhhcCCCcccccCCCCCCcccccccccCccccc-ccccccCcccCCCCccCcccCcccccccccCccccccccccc
Q psy9546 27 LYVIQIVGRGGLATRELSPGEKPLHNFQTLTSSPLHL-KYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRN 105 (385)
Q Consensus 27 ~~~~~i~~~pG~~~~~~~~~~~p~~kel~~~g~~~~~-k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N 105 (385)
.+.+...+|||+++.+.+.. +..+.++...|+++.. +||.+|.++||+|||||++|||||+||||||||++||||.+|
T Consensus 384 ~f~~~~rsDPg~i~~~~~~~-~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kN 462 (600)
T KOG0509|consen 384 TFGLFLRSDPGFIPTSTEVG-RETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKN 462 (600)
T ss_pred HHHHHhccCCCCCCCchhhH-HHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccc
Confidence 34456669999999888877 5578999999999999 599999999999999999999999999999999999999999
Q ss_pred chhhHHHhHHHHHHHHHHhhhceeeEeeeeccccccc----cc----ccCcccceeee-hhhHHHHHHHHHHHHHHHHHh
Q psy9546 106 YRFFYAFIVSLSFHIVFVFCCSVAHLSILAEGRLVFD----AV----RESPTSVLVVA-VTFSSVWSVLGLAGFHTYLAA 176 (385)
Q Consensus 106 ~r~F~lFLl~l~l~~~~~~~~~~~~i~~~~~~~~~~~----~~----~~~~~~il~~i-~~~~~~~~v~~L~~~hl~lI~ 176 (385)
||+|+.|++++...+.++++.+.+|+.........+. .+ ...+++..++. .-+-..|........|...++
T Consensus 463 h~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c 542 (600)
T KOG0509|consen 463 HRLFVFFLLTLLTVIVFYLYLCLYYIMNLENASTIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCAC 542 (600)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceee
Confidence 9999999999999999988888877743322111111 00 11111111111 011112222333344556789
Q ss_pred hCccchhhhcccccc---cCCCCCCCCCCchhHHHHHHHhc
Q psy9546 177 SNQTTNEDIKGSFTS---RRGRASFNPYSYGNACSNCCNAT 214 (385)
Q Consensus 177 ~n~TT~E~ik~~~~~---k~~~~~~nPyd~Gs~~~N~~~v~ 214 (385)
.++||+|.++..... .+.....+|++.| +.+|+.+++
T Consensus 543 ~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g-~~~Nl~df~ 582 (600)
T KOG0509|consen 543 LHLTTNEQINVKRYEHLGIKRGPTRSPFSPG-PIRNLVDFF 582 (600)
T ss_pred ecccHHHHHHHHHhhccccccCcCCCCCCch-hhhcchhee
Confidence 999999998743211 1223468899999 999998886
No 8
>KOG1312|consensus
Probab=99.94 E-value=4.9e-28 Score=230.10 Aligned_cols=163 Identities=31% Similarity=0.504 Sum_probs=105.3
Q ss_pred hhHHHHHHhhcCCCcccccCCCCCCcccccccccC-cccccccccccCcccCCCCccCcccCcccccccccCcccccccc
Q psy9546 24 ATPLYVIQIVGRGGLATRELSPGEKPLHNFQTLTS-SPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVG 102 (385)
Q Consensus 24 g~~~~~~~i~~~pG~~~~~~~~~~~p~~kel~~~g-~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG 102 (385)
+...+.++..++||.++.+...+... +...+. .+-+.+-|.||+++||.||||||+|||||+||||||.|+|||||
T Consensus 111 p~i~f~ltc~snpg~i~k~n~s~~~~---~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG 187 (341)
T KOG1312|consen 111 PLIFFTLTCGSNPGIITKANESLFLH---VYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIG 187 (341)
T ss_pred HHHHHhhhhcCCCCccchhhhcccee---ccCccceeecCCCccccccCCCccccccchHHHHHHHHhccceEeeecccc
Confidence 34455577888999998887766543 222222 23455889999999999999999999999999999999999999
Q ss_pred cccchhhHHHhHHHHHHHHHHhhhceee-Eeeeecc-------cccccccc-------cCcccc--eeeehhhHHHHH-H
Q psy9546 103 KRNYRFFYAFIVSLSFHIVFVFCCSVAH-LSILAEG-------RLVFDAVR-------ESPTSV--LVVAVTFSSVWS-V 164 (385)
Q Consensus 103 ~~N~r~F~lFLl~l~l~~~~~~~~~~~~-i~~~~~~-------~~~~~~~~-------~~~~~i--l~~i~~~~~~~~-v 164 (385)
.+|+|||++|+++....+.+.+....+. +....+. ...+...+ ....++ ..+.+++...|. +
T Consensus 188 ~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g~~ks~~~L~~yl~la~~~~v~~l~~~~~~~~~ 267 (341)
T KOG1312|consen 188 AWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHGHVKSTVFLIQYLFLAFPRIVFMLGFVVVLSFL 267 (341)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeeeecchhhHHHHHHHHHHHhccceeeeehhhhhhHh
Confidence 9999999999999866665543322221 1111100 00111110 000011 123333433322 3
Q ss_pred HHHHHHHHHHHhhCccchhhhcccc
Q psy9546 165 LGLAGFHTYLAASNQTTNEDIKGSF 189 (385)
Q Consensus 165 ~~L~~~hl~lI~~n~TT~E~ik~~~ 189 (385)
++-..+-.|+.+.|+||.|+.++.+
T Consensus 268 ~~Y~~f~~y~~~t~~~~~~W~~~d~ 292 (341)
T KOG1312|consen 268 GGYLLFVLYLAATNQTTNEWYRGDW 292 (341)
T ss_pred HHHHHHHHHHHhccCCchhhhccch
Confidence 3445667788899999999987643
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=95.62 E-value=0.0088 Score=59.60 Aligned_cols=175 Identities=15% Similarity=0.132 Sum_probs=95.0
Q ss_pred EEEEeehhHHHHHHHhhhhccchhHHHHHHhhcCCCcccccCCCC--CCcccccccccCcccccccccccCcccCCCCcc
Q psy9546 2 LLYIIVNTCTKLVSALHLELDHATPLYVIQIVGRGGLATRELSPG--EKPLHNFQTLTSSPLHLKYCFTCKIFRPPRASH 79 (385)
Q Consensus 2 i~~v~l~~~~~~~~~l~~~v~~g~~~~~~~i~~~pG~~~~~~~~~--~~p~~kel~~~g~~~~~k~C~tC~i~kP~RS~H 79 (385)
+.++++.......+...+..+||.+..-...........+..+.+ ..+..=.--...+..+.+.|..|+.=-.-.=||
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 344455556666677777778887753211111111112211111 111110111335678999999999888888999
Q ss_pred CcccCcccccccccCcccccccccccchhhHHHhHHHHHHHHHHhhhceeeEe-eeeccccc-cccccc------Ccccc
Q psy9546 80 CSICDNCVDHFDHHCPWVGNCVGKRNYRFFYAFIVSLSFHIVFVFCCSVAHLS-ILAEGRLV-FDAVRE------SPTSV 151 (385)
Q Consensus 80 C~~C~rCV~rfDHHCpWv~NCIG~~N~r~F~lFLl~l~l~~~~~~~~~~~~i~-~~~~~~~~-~~~~~~------~~~~i 151 (385)
|..=|+||-+--| +=.-.|++++.+..+..++....-+..+. ........ +..+.. ..+.+
T Consensus 140 C~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~~ 208 (309)
T COG5273 140 CPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFII 208 (309)
T ss_pred CcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHhhhHHHHHHHHH
Confidence 9999999988655 55667888876665555544333322222 11111111 111111 11111
Q ss_pred eeeehhhHHHHHHHHHHHHHHHHHhhCccchhhhcc
Q psy9546 152 LVVAVTFSSVWSVLGLAGFHTYLAASNQTTNEDIKG 187 (385)
Q Consensus 152 l~~i~~~~~~~~v~~L~~~hl~lI~~n~TT~E~ik~ 187 (385)
+++.+.+....++.....++.+.+.++.++-|....
T Consensus 209 ~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~ 244 (309)
T COG5273 209 TTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPL 244 (309)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHhccceecccccch
Confidence 222222223334445678899999999999998653
No 10
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=91.65 E-value=0.15 Score=45.49 Aligned_cols=34 Identities=24% Similarity=0.487 Sum_probs=20.9
Q ss_pred cccccccccccCcccCCCCccCcccCcccccccc
Q psy9546 59 SPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDH 92 (385)
Q Consensus 59 ~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDH 92 (385)
+..+.++|..|+.-...+-|||..-|+||.+.-|
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~ 91 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH 91 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH
Confidence 3445666666666666666666666666665544
No 11
>KOG1311|consensus
Probab=86.04 E-value=0.61 Score=45.84 Aligned_cols=41 Identities=24% Similarity=0.407 Sum_probs=35.4
Q ss_pred CccCcccCcccccccccCccccccccccc-----------chhhHHHhHHHH
Q psy9546 77 ASHCSICDNCVDHFDHHCPWVGNCVGKRN-----------YRFFYAFIVSLS 117 (385)
Q Consensus 77 S~HC~~C~rCV~rfDHHCpWv~NCIG~~N-----------~r~F~lFLl~l~ 117 (385)
.++|..|+..+...-|||+.-|+||-+.= +|-+-.|+.++.
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 79999999999999999999999998884 455668886655
No 12
>KOG1315|consensus
Probab=78.17 E-value=6.7 Score=39.24 Aligned_cols=52 Identities=21% Similarity=0.406 Sum_probs=39.9
Q ss_pred CCccCcccCcccccccccCcccccccccccc-----------hhhHHHhHHHHHHHHHHhhhc
Q psy9546 76 RASHCSICDNCVDHFDHHCPWVGNCVGKRNY-----------RFFYAFIVSLSFHIVFVFCCS 127 (385)
Q Consensus 76 RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N~-----------r~F~lFLl~l~l~~~~~~~~~ 127 (385)
+.+.|..|+.-....-|||.--+-||.+.=| +-+=.|++.+..+.++.+...
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~l 170 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVL 170 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHH
Confidence 7789999999999999999999999998744 344577777666555544333
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=73.19 E-value=2 Score=31.27 Aligned_cols=24 Identities=33% Similarity=0.754 Sum_probs=21.7
Q ss_pred ccccccccCcccCCCCccCcccCc
Q psy9546 62 HLKYCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 62 ~~k~C~tC~i~kP~RS~HC~~C~r 85 (385)
....|..|..+-|+|+.-|+.|+.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 467899999999999999998875
No 14
>KOG0509|consensus
Probab=66.01 E-value=2.1 Score=46.13 Aligned_cols=62 Identities=16% Similarity=0.001 Sum_probs=51.5
Q ss_pred ccCcccccccccccCcccCCCCccCcccCcccccccccCcccccccccccchh-hHHHhHHHHH
Q psy9546 56 LTSSPLHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRNYRF-FYAFIVSLSF 118 (385)
Q Consensus 56 ~~g~~~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N~r~-F~lFLl~l~l 118 (385)
..++..-.-.|.+|.+..+.+..++..+-.++..+++||+|+. ||+-.|-.. ++.|++++.+
T Consensus 318 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~ 380 (600)
T KOG0509|consen 318 ALGKLVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLA 380 (600)
T ss_pred hhhhhhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHH
Confidence 3455667788999999999999999999999999999999999 999999864 4445555443
No 15
>KOG4043|consensus
Probab=64.19 E-value=2 Score=39.12 Aligned_cols=20 Identities=10% Similarity=0.079 Sum_probs=9.1
Q ss_pred ccccccchhhcccccccccc
Q psy9546 301 KTVKHLSDKHRSANNNQGTC 320 (385)
Q Consensus 301 ~~~~~~~~~~~~~~~~~~~~ 320 (385)
|+.+|+|.|+.++||+.||.
T Consensus 171 ~e~~hKK~KkhedDKeRKK~ 190 (214)
T KOG4043|consen 171 EEGFHKKHKKHEDDKERKKE 190 (214)
T ss_pred hhcchhhhhhhhhhHHHHHH
Confidence 44455554444444444333
No 16
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.68 E-value=5.3 Score=24.52 Aligned_cols=21 Identities=29% Similarity=0.657 Sum_probs=16.9
Q ss_pred cccccCcccCCCCccCcccCc
Q psy9546 65 YCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 65 ~C~tC~i~kP~RS~HC~~C~r 85 (385)
||..|...-++.++.|..|+.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588888888888888888874
No 17
>KOG1314|consensus
Probab=56.71 E-value=1 Score=45.50 Aligned_cols=44 Identities=23% Similarity=0.431 Sum_probs=26.5
Q ss_pred cccccccccCcccCCCCccCcccCcccccccccCcccccccccccchhhHHHhHH
Q psy9546 61 LHLKYCFTCKIFRPPRASHCSICDNCVDHFDHHCPWVGNCVGKRNYRFFYAFIVS 115 (385)
Q Consensus 61 ~~~k~C~tC~i~kP~RS~HC~~C~rCV~rfDHHCpWv~NCIG~~N~r~F~lFLl~ 115 (385)
-+.+.|++|+.=.-.=-|||..-|+||--..| .-.-+|++|.+.
T Consensus 103 pRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh-----------~~F~~FLlf~iv 146 (414)
T KOG1314|consen 103 PRSHHCRKCNRCVMKMDHHCPWINNCVGWANH-----------AYFLRFLLFSIV 146 (414)
T ss_pred CccccchHHHHHHHhhccCCcchhhccccccc-----------HHHHHHHHHHHH
Confidence 45667777764444445778888888754433 223566666655
No 18
>PF10278 Med19: Mediator of RNA pol II transcription subunit 19 ; InterPro: IPR019403 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=56.36 E-value=3.6 Score=37.98 Aligned_cols=16 Identities=19% Similarity=0.297 Sum_probs=9.5
Q ss_pred HHHHHHhhCccchhhh
Q psy9546 170 FHTYLAASNQTTNEDI 185 (385)
Q Consensus 170 ~hl~lI~~n~TT~E~i 185 (385)
-|.|.-+.|..--|.+
T Consensus 28 ~~~y~kf~~kklke~l 43 (178)
T PF10278_consen 28 EHSYNKFCGKKLKESL 43 (178)
T ss_pred HHHHHHHhCCcchhhH
Confidence 4666666665555554
No 19
>KOG4043|consensus
Probab=54.36 E-value=3 Score=37.97 Aligned_cols=25 Identities=28% Similarity=0.246 Sum_probs=20.8
Q ss_pred ccccccchhhcccccccccchhhhc
Q psy9546 301 KTVKHLSDKHRSANNNQGTCKLKMN 325 (385)
Q Consensus 301 ~~~~~~~~~~~~~~~~~~~~~~~~~ 325 (385)
+.+||.+||+|||.|+.+++++|..
T Consensus 177 K~KkhedDKeRKK~KeEk~~~eKnk 201 (214)
T KOG4043|consen 177 KHKKHEDDKERKKEKEEKGDAEKNK 201 (214)
T ss_pred hhhhhhhhHHHHHHHHHhhhhhhcc
Confidence 6788999999999999888876643
No 20
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=54.17 E-value=7.7 Score=43.27 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=21.8
Q ss_pred cCcccc--cccccccCcccC-------CCCccCcccCc
Q psy9546 57 TSSPLH--LKYCFTCKIFRP-------PRASHCSICDN 85 (385)
Q Consensus 57 ~g~~~~--~k~C~tC~i~kP-------~RS~HC~~C~r 85 (385)
.|+.+. .+-|..|...-. .|-||||.|++
T Consensus 452 vWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 452 SWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCCCCcccCCcccCcCCcccccccccccccccccCCcc
Confidence 355444 368999998774 39999999977
No 21
>PF12773 DZR: Double zinc ribbon
Probab=52.23 E-value=12 Score=26.61 Aligned_cols=36 Identities=22% Similarity=0.417 Sum_probs=27.5
Q ss_pred cccccccccCcccC--C-CCccCcccCcccccccccCcc
Q psy9546 61 LHLKYCFTCKIFRP--P-RASHCSICDNCVDHFDHHCPW 96 (385)
Q Consensus 61 ~~~k~C~tC~i~kP--~-RS~HC~~C~rCV~rfDHHCpW 96 (385)
...+||..|...-+ . ....|..|+.=+...+.+|++
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 45788888888777 3 356788888888888888875
No 22
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.67 E-value=8.5 Score=24.07 Aligned_cols=22 Identities=27% Similarity=0.676 Sum_probs=17.3
Q ss_pred ccccccCcccCCCCccCcccCc
Q psy9546 64 KYCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 64 k~C~tC~i~kP~RS~HC~~C~r 85 (385)
++|..|...-++-++.|..|+.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 5788888877888888888764
No 23
>KOG1842|consensus
Probab=50.73 E-value=3.2 Score=43.22 Aligned_cols=46 Identities=13% Similarity=0.244 Sum_probs=29.8
Q ss_pred CCCCCCcccccccccCccc-ccccccccCcccCC--CCccCcccCcccc
Q psy9546 43 LSPGEKPLHNFQTLTSSPL-HLKYCFTCKIFRPP--RASHCSICDNCVD 88 (385)
Q Consensus 43 ~~~~~~p~~kel~~~g~~~-~~k~C~tC~i~kP~--RS~HC~~C~rCV~ 88 (385)
.++.++..++.-.+.|..+ ...+|+.|...=.. |-||||.||+-+-
T Consensus 159 ~d~~k~k~~EqsvVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 159 KDSVKRKRLEQSVVPWLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred cchHHHHHHHhccccccCCCcccccccccchhhhHHHhhhhhhcchHHH
Confidence 3333333444444555544 57899999865443 7899999998554
No 24
>KOG3045|consensus
Probab=50.11 E-value=11 Score=37.14 Aligned_cols=58 Identities=21% Similarity=0.149 Sum_probs=28.5
Q ss_pred CCCCccccccchhhcccccccccchhhhcCCCCCCCCCCCcchhccc-cccccccccccCCC
Q psy9546 297 LPENKTVKHLSDKHRSANNNQGTCKLKMNNLDSVDTVPSYPQIVVNK-NTHENSQAQFSNSP 357 (385)
Q Consensus 297 ~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 357 (385)
...+++++.+++|||++-+..-+++|--..+ |.|++-|-.++-+ -+++|+..+-.|.+
T Consensus 27 ~~~sk~~~~kKkkKRkk~~rkl~~~k~A~~~---e~v~~~p~g~~ak~~~~~n~~kk~r~~~ 85 (325)
T KOG3045|consen 27 PTSSKTKEEKKKKKRKKGERKLKAKKAAELK---ENVEEPPLGSEAKSSPKENSKKKRRNET 85 (325)
T ss_pred ccccccchhhhhhhhhhHHHhhhhhhhhhhh---cCccCCCCcccCCCCCcccchhhccCcc
Confidence 3344555555556555442222222222222 5555555555544 46777776655543
No 25
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=48.16 E-value=4.7 Score=29.48 Aligned_cols=24 Identities=38% Similarity=0.822 Sum_probs=21.1
Q ss_pred ccccccccCcccCCCCccCcccCc
Q psy9546 62 HLKYCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 62 ~~k~C~tC~i~kP~RS~HC~~C~r 85 (385)
..+.|..|..+-|+|+.-|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 457899999999999999998864
No 26
>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=44.76 E-value=13 Score=27.57 Aligned_cols=25 Identities=32% Similarity=0.732 Sum_probs=16.8
Q ss_pred ccccccccCcccCCCCccCcc--cCcc
Q psy9546 62 HLKYCFTCKIFRPPRASHCSI--CDNC 86 (385)
Q Consensus 62 ~~k~C~tC~i~kP~RS~HC~~--C~rC 86 (385)
....|..|..+-|+|+..|+. ||.+
T Consensus 16 ~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 16 DKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp S-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cceecccccCcCCCCccceecccCCCC
Confidence 457899999999999999998 7754
No 27
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=35.67 E-value=16 Score=33.02 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=0.0
Q ss_pred hhhcccccccCCCCCCCCCCch
Q psy9546 183 EDIKGSFTSRRGRASFNPYSYG 204 (385)
Q Consensus 183 E~ik~~~~~k~~~~~~nPyd~G 204 (385)
|.+...+..+..+...|||...
T Consensus 4 EEl~rrReaR~~Eq~NNP~YLK 25 (154)
T PF06375_consen 4 EELERRREARKAEQENNPHYLK 25 (154)
T ss_dssp ----------------------
T ss_pred HHHHHHHHHHHHHHHcCCceec
Confidence 4444443344455577898876
No 28
>PF12773 DZR: Double zinc ribbon
Probab=29.66 E-value=37 Score=23.96 Aligned_cols=25 Identities=32% Similarity=0.676 Sum_probs=21.7
Q ss_pred ccccccccccCcccCCCCccCcccC
Q psy9546 60 PLHLKYCFTCKIFRPPRASHCSICD 84 (385)
Q Consensus 60 ~~~~k~C~tC~i~kP~RS~HC~~C~ 84 (385)
.....+|..|....++.+.+|..|+
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3457899999999999999999886
No 29
>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=28.78 E-value=32 Score=21.73 Aligned_cols=22 Identities=32% Similarity=0.634 Sum_probs=16.9
Q ss_pred ccccccCcccCCCCccCcccCc
Q psy9546 64 KYCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 64 k~C~tC~i~kP~RS~HC~~C~r 85 (385)
+.|..|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4588888888888888887763
No 30
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=28.67 E-value=25 Score=22.45 Aligned_cols=21 Identities=29% Similarity=0.833 Sum_probs=15.6
Q ss_pred cccccCcccCCCCccCcccCc
Q psy9546 65 YCFTCKIFRPPRASHCSICDN 85 (385)
Q Consensus 65 ~C~tC~i~kP~RS~HC~~C~r 85 (385)
.|..|...-++++.+|..|+.
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--
T ss_pred cCCCCcCCchHHhhhhhCcCC
Confidence 488899888999999988864
No 31
>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=28.30 E-value=34 Score=27.96 Aligned_cols=16 Identities=25% Similarity=0.756 Sum_probs=11.3
Q ss_pred ccccccCccccccccc
Q psy9546 88 DHFDHHCPWVGNCVGK 103 (385)
Q Consensus 88 ~rfDHHCpWv~NCIG~ 103 (385)
..+-.||||++.-...
T Consensus 52 ~eHr~~CPwv~~~~q~ 67 (91)
T PF08600_consen 52 EEHREYCPWVNPSTQS 67 (91)
T ss_pred ccccccCCccCCcccc
Confidence 4455799999976543
No 32
>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=26.61 E-value=35 Score=25.77 Aligned_cols=36 Identities=33% Similarity=0.955 Sum_probs=26.5
Q ss_pred cccccCcccCCCC-------ccCcccCcccccc-cccCccccccccc
Q psy9546 65 YCFTCKIFRPPRA-------SHCSICDNCVDHF-DHHCPWVGNCVGK 103 (385)
Q Consensus 65 ~C~tC~i~kP~RS-------~HC~~C~rCV~rf-DHHCpWv~NCIG~ 103 (385)
-|..|..--|+-| +-|..|..|+... ++.|| ||=|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 3556665555543 5689999999988 99998 77664
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=25.61 E-value=22 Score=26.84 Aligned_cols=27 Identities=26% Similarity=0.470 Sum_probs=12.8
Q ss_pred ccccccccCccc--CCCCccCcccCcccc
Q psy9546 62 HLKYCFTCKIFR--PPRASHCSICDNCVD 88 (385)
Q Consensus 62 ~~k~C~tC~i~k--P~RS~HC~~C~rCV~ 88 (385)
+...|..|...= -.|-|||+.||+.|=
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 456788887533 357899999998654
No 34
>KOG3183|consensus
Probab=25.46 E-value=32 Score=33.26 Aligned_cols=12 Identities=33% Similarity=0.357 Sum_probs=10.0
Q ss_pred cccccccCcccc
Q psy9546 87 VDHFDHHCPWVG 98 (385)
Q Consensus 87 V~rfDHHCpWv~ 98 (385)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 467899999985
No 35
>KOG3598|consensus
Probab=24.00 E-value=62 Score=38.87 Aligned_cols=22 Identities=9% Similarity=-0.148 Sum_probs=14.2
Q ss_pred cccchhhhcCCCCCCCCCCCcc
Q psy9546 317 QGTCKLKMNNLDSVDTVPSYPQ 338 (385)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~ 338 (385)
.||+++++.|-.+++++.|+|+
T Consensus 1818 ~KK~~~~g~K~ks~~~~~e~~~ 1839 (2220)
T KOG3598|consen 1818 NKKDTKEGEKGKSKDKEKEGEK 1839 (2220)
T ss_pred hhccccccccCCCccccccccc
Confidence 4556666666666777777665
No 36
>PF10268 Tmemb_161AB: Predicted transmembrane protein 161AB; InterPro: IPR019395 This entry represents a family of conserved eukaryotic proteins. Members are putative transmembrane proteins but otherwise the function is not known.
Probab=20.71 E-value=43 Score=35.70 Aligned_cols=16 Identities=19% Similarity=0.563 Sum_probs=12.3
Q ss_pred cCCCCccccccchhhc
Q psy9546 296 VLPENKTVKHLSDKHR 311 (385)
Q Consensus 296 ~~~t~~~~~~~~~~~~ 311 (385)
-.|||||.|.+.-|.+
T Consensus 40 l~Psd~eL~~lagk~~ 55 (486)
T PF10268_consen 40 LHPSDEELRALAGKQK 55 (486)
T ss_pred CCCCHHHHHHHcCCCC
Confidence 3688999998887544
Done!