Query psy9305
Match_columns 465
No_of_seqs 455 out of 2605
Neff 8.2
Searched_HMMs 46136
Date Sat Aug 17 00:01:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315|consensus 100.0 1.9E-45 4.1E-50 354.4 15.3 217 79-304 43-278 (307)
2 KOG1314|consensus 100.0 2.6E-44 5.7E-49 339.7 11.8 257 73-347 39-323 (414)
3 KOG1311|consensus 100.0 6.8E-41 1.5E-45 330.9 20.0 252 34-291 9-278 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 9.5E-37 2.1E-41 278.1 12.7 161 97-260 2-174 (174)
5 KOG1313|consensus 100.0 1.8E-34 4E-39 265.2 13.7 186 90-291 76-292 (309)
6 COG5273 Uncharacterized protei 100.0 2.8E-33 6.1E-38 274.3 17.5 173 83-261 57-234 (309)
7 KOG1312|consensus 100.0 3.1E-28 6.7E-33 225.1 12.9 118 80-198 96-215 (341)
8 KOG1315|consensus 99.9 3.9E-27 8.4E-32 227.5 4.6 139 321-459 103-245 (307)
9 KOG0509|consensus 99.9 2.5E-25 5.5E-30 227.2 11.1 107 93-199 379-488 (600)
10 PF01529 zf-DHHC: DHHC palmito 99.9 8.2E-26 1.8E-30 206.0 4.8 125 321-445 42-172 (174)
11 KOG1311|consensus 99.9 2.2E-25 4.8E-30 220.3 5.7 119 327-445 113-240 (299)
12 COG5273 Uncharacterized protei 99.9 1.2E-24 2.6E-29 213.4 4.1 77 316-392 98-174 (309)
13 KOG1314|consensus 99.9 6.1E-24 1.3E-28 201.8 -0.7 55 328-382 92-146 (414)
14 KOG1313|consensus 99.9 1.8E-23 3.9E-28 192.8 1.3 61 329-389 104-164 (309)
15 KOG1312|consensus 99.9 2.1E-22 4.6E-27 186.6 3.6 73 318-390 137-211 (341)
16 KOG0509|consensus 99.8 3.1E-21 6.7E-26 197.4 6.2 195 98-394 293-487 (600)
17 PF13240 zinc_ribbon_2: zinc-r 77.6 1.5 3.3E-05 25.5 1.4 21 329-349 1-21 (23)
18 PF13248 zf-ribbon_3: zinc-rib 69.6 3 6.4E-05 25.0 1.3 22 328-349 3-24 (26)
19 PRK04136 rpl40e 50S ribosomal 68.0 3.3 7.2E-05 28.7 1.4 22 328-349 15-36 (48)
20 PRK04136 rpl40e 50S ribosomal 68.0 2.9 6.2E-05 29.0 1.1 24 130-153 13-36 (48)
21 PTZ00303 phosphatidylinositol 54.5 7.3 0.00016 42.6 1.8 22 132-153 461-489 (1374)
22 PF10571 UPF0547: Uncharacteri 52.6 9.5 0.00021 23.0 1.4 21 329-349 2-22 (26)
23 PF09889 DUF2116: Uncharacteri 49.4 13 0.00027 27.3 1.8 16 330-345 6-21 (59)
24 PF06906 DUF1272: Protein of u 46.2 12 0.00026 26.9 1.2 35 134-171 8-50 (57)
25 PTZ00303 phosphatidylinositol 45.2 12 0.00026 41.1 1.7 21 329-349 462-489 (1374)
26 PF01363 FYVE: FYVE zinc finge 43.0 11 0.00024 28.1 0.8 27 130-156 8-36 (69)
27 PF01020 Ribosomal_L40e: Ribos 41.2 8 0.00017 27.3 -0.2 23 328-350 18-42 (52)
28 PRK15103 paraquat-inducible me 41.1 4.1E+02 0.0089 27.7 12.2 31 131-161 221-251 (419)
29 PF01020 Ribosomal_L40e: Ribos 40.9 11 0.00025 26.5 0.5 25 130-154 16-42 (52)
30 PF12773 DZR: Double zinc ribb 38.2 24 0.00052 24.4 1.9 32 329-360 14-48 (50)
31 COG1552 RPL40A Ribosomal prote 36.7 7.9 0.00017 26.9 -0.8 22 329-350 16-37 (50)
32 COG1552 RPL40A Ribosomal prote 36.2 6 0.00013 27.5 -1.4 24 131-154 14-37 (50)
33 smart00064 FYVE Protein presen 36.1 25 0.00054 26.1 1.8 26 131-156 10-37 (68)
34 PF12773 DZR: Double zinc ribb 35.3 35 0.00075 23.6 2.3 22 327-348 29-50 (50)
35 KOG1842|consensus 29.1 15 0.00033 37.6 -0.5 29 128-156 177-207 (505)
36 TIGR00155 pqiA_fam integral me 28.8 5.1E+02 0.011 26.8 10.5 31 131-161 215-246 (403)
37 KOG3183|consensus 26.7 29 0.00062 32.8 0.8 14 153-166 36-49 (250)
38 PF00641 zf-RanBP: Zn-finger i 26.0 24 0.00051 21.7 0.1 21 133-153 6-26 (30)
39 PF03107 C1_2: C1 domain; Int 23.6 50 0.0011 20.3 1.2 20 329-348 2-22 (30)
40 COG2093 DNA-directed RNA polym 22.2 50 0.0011 24.4 1.2 21 329-349 6-26 (64)
41 PRK03681 hypA hydrogenase nick 21.0 51 0.0011 27.6 1.2 29 321-349 64-95 (114)
No 1
>KOG1315|consensus
Probab=100.00 E-value=1.9e-45 Score=354.38 Aligned_cols=217 Identities=33% Similarity=0.588 Sum_probs=169.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCchH----HHHhh----------cccCCcceeeCCCCCccCCCC
Q psy9305 79 MYRFFNMALFQTFAFLAFASHLRAMLTDPGAVPKGNATTE----IIQQM----------GFREGQVIFKCPKCCCIKPER 144 (465)
Q Consensus 79 ~~~~~~~~~~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~----~~~~~----------~~~~~~~~~~C~~C~~~kP~R 144 (465)
....+..++++.+.++.+++|++++++|||.+|..+.++. ..+.. .....+..++|.+|+.+||+|
T Consensus 43 ~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdR 122 (307)
T KOG1315|consen 43 IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDR 122 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCc
Confidence 6677888899999999999999999999999998654331 11110 011234679999999999999
Q ss_pred CccCccccccccccCccCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCceeehhHH
Q psy9305 145 AHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSPPATVVFLVF 224 (465)
Q Consensus 145 s~HC~~C~~CV~~~DHHCpWi~nCIG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (465)
|||||+|+|||+||||||||+|||||.+|||+|++|++|+.+.+++.++.....+.....+.+ .........+++
T Consensus 123 aHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~-----~~~~~~~~~~~~ 197 (307)
T KOG1315|consen 123 AHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGA-----GPSSLLLFFIVF 197 (307)
T ss_pred cccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc-----cCchhHHHHHHH
Confidence 999999999999999999999999999999999999999999999988888777666552221 111223345555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHhhhhhhh-h-hcccc---cchhhhcccccceeecccccCCCCCCCccC
Q psy9305 225 LVFEALLFAIFTTVMLLSQLQAIWNDETGIEQLKKEEAK-W-ARKSR---WKSIQAVFGRFSLAWFSPFTQPPSRSKFES 299 (465)
Q Consensus 225 ~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~~~~~-~-~~~g~---~~N~~~vfG~~~~~W~~P~~~~~~~~~~dg 299 (465)
+++.+..+++.+..++++|+++|++|+||+|.++..... + .+++. ..|++|+||.++..|++|...+. +++
T Consensus 198 ~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~~~n~~~vfg~~~~~wl~P~~~s~----~~~ 273 (307)
T KOG1315|consen 198 LFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGFNLYVNFREVFGSNLLYWLLPIDSSW----GDG 273 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCcceeecHHHHhCCCceEEeccccCcc----ccC
Confidence 566677788888889999999999999999999886333 1 23333 36999999999999999998765 455
Q ss_pred cCCCC
Q psy9305 300 YLYPG 304 (465)
Q Consensus 300 ~~~p~ 304 (465)
...|.
T Consensus 274 ~~~~~ 278 (307)
T KOG1315|consen 274 VSFPL 278 (307)
T ss_pred ccccc
Confidence 54443
No 2
>KOG1314|consensus
Probab=100.00 E-value=2.6e-44 Score=339.71 Aligned_cols=257 Identities=26% Similarity=0.386 Sum_probs=187.9
Q ss_pred ecCCCchhHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCchHHHHhhcccCCcceeeCCCCCccCCCCCccCcccc
Q psy9305 73 IPNPHPMYRFFNMALFQTFAFLAFASHLRAMLTDPGAVPKGNATTEIIQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQ 152 (465)
Q Consensus 73 ~p~~~~~~~~~~~~~~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~ 152 (465)
++..++..+..+.+.|.+...+.+++|+.+++++||.+|+++.++... +....+||.+|+.+|+||||||+.||
T Consensus 39 w~p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~------D~~~lqfCk~CqgYKapRSHHCrkCn 112 (414)
T KOG1314|consen 39 WFPLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK------DEMFLQFCKKCQGYKAPRSHHCRKCN 112 (414)
T ss_pred hccccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh------hHHHHHHHhhccCcCCCccccchHHH
Confidence 444566788899999999999999999999999999999999876421 22356899999999999999999999
Q ss_pred ccccccCccCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCC-------CceeehhHHH
Q psy9305 153 RCIRKMDHHCPWVNNCVGENNQKYFVLFTFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSP-------PATVVFLVFL 225 (465)
Q Consensus 153 ~CV~~~DHHCpWi~nCIG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~ 225 (465)
|||.+|||||||+|||||..||.||+.||++..+++++..++....++.-+...|...-.... ....+.+++.
T Consensus 113 rCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfs 192 (414)
T KOG1314|consen 113 RCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFS 192 (414)
T ss_pred HHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHH
Confidence 999999999999999999999999999999999998887776655555444434421111111 1122233333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCchHHHhhhhhhh----------------hhcccccchhhhcccccceeeccccc
Q psy9305 226 VFEALLFAIFTTVMLLSQLQAIWNDETGIEQLKKEEAK----------------WARKSRWKSIQAVFGRFSLAWFSPFT 289 (465)
Q Consensus 226 ~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~~~~~----------------~~~~g~~~N~~~vfG~~~~~W~~P~~ 289 (465)
+.+++...+.+++||+.|+..|.+|+|.||.+..++.. ++|.|+..|+++||-.+.
T Consensus 193 lgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~-------- 264 (414)
T KOG1314|consen 193 LGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNK-------- 264 (414)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhcc--------
Confidence 33344455667789999999999999999998843321 467797779999997441
Q ss_pred CCCCCCCccCcCCCCCCCCCC---cchhhhhhccccccceeecCCC--CCCCCCCCCCCCccc
Q psy9305 290 QPPSRSKFESYLYPGAVPKGN---ATTEIIQQMGFREGQVIFKCPK--CCCIKPERAHHCSVC 347 (465)
Q Consensus 290 ~~~~~~~~dg~~~p~~~p~g~---~~~eilq~~~~~~~~~~~~c~~--c~~~~p~r~~hc~~c 347 (465)
...+|+..||+.+.-.+ ..+++.|+.+++-......|.. -+..-|.++.-|+++
T Consensus 265 ----~~~gdg~~wPv~~gc~qytlt~eql~qk~~kr~rsr~~~~~~~~tG~~~p~~k~G~~v~ 323 (414)
T KOG1314|consen 265 ----KEEGDGIEWPVVEGCVQYTLTIEQLTQKLDKRGRSRLFKCIEDVTGDCCPIFKQGIKVY 323 (414)
T ss_pred ----ccCCCCccccccCcccccceeHHHHHHHHHhhcCeEEEEeccCCCCCcccccccceeee
Confidence 24589999999765433 2355556666665555555643 234456666666665
No 3
>KOG1311|consensus
Probab=100.00 E-value=6.8e-41 Score=330.88 Aligned_cols=252 Identities=30% Similarity=0.511 Sum_probs=171.9
Q ss_pred cccCCceeEEEecccceehhhhhHHHHHhhe-eeEEEEEEecC-CCchhHHHHHHHHHHHHHHHHHHHHHhhc---cCCC
Q psy9305 34 NKCCGGMVWCIKDICGVICAILTWLLILYAE-FVVMAVMLIPN-PHPMYRFFNMALFQTFAFLAFASHLRAML---TDPG 108 (465)
Q Consensus 34 ~~~c~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~p~-~~~~~~~~~~~~~~~l~~~~~~s~~~~~~---~dPG 108 (465)
...+.++ ..++.+.+..+.+++++++.. ++++...+.+. ........+.+++ ....+.+...+.+ +|||
T Consensus 9 ~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~if---~~~~~~~~~~~~~~~~sdpg 82 (299)
T KOG1311|consen 9 IPRRGGR---ILDPPVALPVLVTYVLLVGSETFFVFLPPLLPRGGVSPAVLVLGAIF---FLLNILNLMLACFRMLSDPG 82 (299)
T ss_pred ccCCCce---eeccccchhHHHHHHHHhhheEEEEEEeeecCCcccchHHHHHHHHH---HHHHHHHHHHHHhcccCCCc
Confidence 3344444 344556777788888888877 44444434443 2212222233333 3333333344444 4999
Q ss_pred CCCCCC-CchHHHHhhcc-------cCCcceeeCCCCCccCCCCCccCccccccccccCccCcccccccccchhHHHHHH
Q psy9305 109 AVPKGN-ATTEIIQQMGF-------REGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLF 180 (465)
Q Consensus 109 ~vp~~~-~~~~~~~~~~~-------~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpWi~nCIG~~N~r~F~lf 180 (465)
.+|++. .+.+..++... ....+.++|.+|+..||||||||+.||+||.||||||||+|||||++|||+|+.|
T Consensus 83 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f 162 (299)
T KOG1311|consen 83 IVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLF 162 (299)
T ss_pred eecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHH
Confidence 999962 22111111111 1123578999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCceeehhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHhhh-
Q psy9305 181 TFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSPPATVVFLVFLVFEALLFAIFTTVMLLSQLQAIWNDETGIEQLKK- 259 (465)
Q Consensus 181 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~- 259 (465)
++++.+++++.++.....+.......................+++.+.++++..+++.|+.+|++++.+|+||+|.+++
T Consensus 163 ~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~ 242 (299)
T KOG1311|consen 163 LFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSL 242 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhcc
Confidence 9999999999988887776553322211111111122233444444566677777888999999999999999999885
Q ss_pred --hhh-hhhcccccchhhhccc-ccceeecccccCC
Q psy9305 260 --EEA-KWARKSRWKSIQAVFG-RFSLAWFSPFTQP 291 (465)
Q Consensus 260 --~~~-~~~~~g~~~N~~~vfG-~~~~~W~~P~~~~ 291 (465)
+.. +++++|.++|++++|| +....|+.|....
T Consensus 243 ~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~ 278 (299)
T KOG1311|consen 243 DFVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARS 278 (299)
T ss_pred ccccccCCCchhHHHHHHHHhCCCCCcccccccccC
Confidence 222 5678889999999999 8999999999865
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=9.5e-37 Score=278.12 Aligned_cols=161 Identities=32% Similarity=0.626 Sum_probs=121.9
Q ss_pred HHHHHhhccCCCCCCCCCCch---------H---HHHhhcccCCcceeeCCCCCccCCCCCccCccccccccccCccCcc
Q psy9305 97 ASHLRAMLTDPGAVPKGNATT---------E---IIQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPW 164 (465)
Q Consensus 97 ~s~~~~~~~dPG~vp~~~~~~---------~---~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpW 164 (465)
++|++++++|||++|+...++ + ..+..+....+..++|.+|+..||+|||||+.||+||+||||||||
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 578999999999999881110 0 1111222344677899999999999999999999999999999999
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCceeehhHHHHHHHHHHHHHHHHHHHHHH
Q psy9305 165 VNNCVGENNQKYFVLFTFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSPPATVVFLVFLVFEALLFAIFTTVMLLSQL 244 (465)
Q Consensus 165 i~nCIG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l 244 (465)
+|||||++|||+|++|+++..+.+++.+...+..+............ ........+++++.+++++++++.+++.|+
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 158 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSF---WIFSNFSSIFLLIISIFFFIFVGFLLIFQL 158 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc---ccchhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998888777766654433221100 000111114444556677788889999999
Q ss_pred HHHhcCCchHHHhhhh
Q psy9305 245 QAIWNDETGIEQLKKE 260 (465)
Q Consensus 245 ~~i~~n~Tt~E~~~~~ 260 (465)
+++++|+||+|.++++
T Consensus 159 ~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 159 YLILRNITTYERIKRK 174 (174)
T ss_pred HHHHcCCcHHHHHHcC
Confidence 9999999999998763
No 5
>KOG1313|consensus
Probab=100.00 E-value=1.8e-34 Score=265.15 Aligned_cols=186 Identities=28% Similarity=0.485 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCCCCchHHHHhhcccCCcceeeCCCCCccCCCCCccCccccccccccCccCccccccc
Q psy9305 90 TFAFLAFASHLRAMLTDPGAVPKGNATTEIIQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCV 169 (465)
Q Consensus 90 ~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpWi~nCI 169 (465)
.+...++..|+++..+.|=..|.. ....+|.+|..+||||+||||.|||||+||||||||+||||
T Consensus 76 ~~l~nvi~hy~ka~t~pPvgn~~~---------------~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCV 140 (309)
T KOG1313|consen 76 YLLSNVIFHYYKARTKPPVGNPGL---------------ENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCV 140 (309)
T ss_pred HHHHHHHHhheeecccCCcCCCCC---------------ccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhccc
Confidence 334455566788887776211111 12458999999999999999999999999999999999999
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc----cC---CCCCcee---------ehhHHHHHHHHHHH
Q psy9305 170 GENNQKYFVLFTFYIATISIHSLFLAVNQFLMCVRNEWREC----SS---YSPPATV---------VFLVFLVFEALLFA 233 (465)
Q Consensus 170 G~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~---~~~~~~~---------~~~~~~~~~~~~~~ 233 (465)
|..|||||++|++|+++++.+..++..+.+...... +++. ++ ..|+... .-+..+.+++..+.
T Consensus 141 G~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~-~~~~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~l 219 (309)
T KOG1313|consen 141 GAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEP-IEEITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVL 219 (309)
T ss_pred ccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcch-HhhcccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHH
Confidence 999999999999999999999888877665543321 1110 11 0111111 11222333445556
Q ss_pred HHHHHHHHHHHHHHhcCCchHHHhhhhhh----------hhhcccccchhhhccc--ccceee---cccccCC
Q psy9305 234 IFTTVMLLSQLQAIWNDETGIEQLKKEEA----------KWARKSRWKSIQAVFG--RFSLAW---FSPFTQP 291 (465)
Q Consensus 234 ~~~~~l~~~~l~~i~~n~Tt~E~~~~~~~----------~~~~~g~~~N~~~vfG--~~~~~W---~~P~~~~ 291 (465)
++++.+..+|.++|.+|+|++|.....+. ++++.|..+|++..+| +.+-.| ++|....
T Consensus 220 v~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~ 292 (309)
T KOG1313|consen 220 VAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNPTNFGGKANWRNFLGLFRGRHFWKTVLLPTIRK 292 (309)
T ss_pred HHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCCcccchHHHHHHhhccccCCceeEEEecccccc
Confidence 66778888999999999999998765432 2356788899999998 555455 4555443
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=2.8e-33 Score=274.27 Aligned_cols=173 Identities=31% Similarity=0.550 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCchH----HHHhhcccCCcceeeCCCCCccCCCCCccCcccccccccc
Q psy9305 83 FNMALFQTFAFLAFASHLRAMLTDPGAVPKGNATTE----IIQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKM 158 (465)
Q Consensus 83 ~~~~~~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~----~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~ 158 (465)
...+.+.++..+...++++.+++|||+.+++..... ..+..+....+..++|.+|+.+||+|||||+.||+||+||
T Consensus 57 ~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~ 136 (309)
T COG5273 57 LFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKF 136 (309)
T ss_pred hhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhcc
Confidence 334455666678888999999999999986533222 2233344455678899999999999999999999999999
Q ss_pred CccCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCceeehhHHH-HHHHHHHHHHHH
Q psy9305 159 DHHCPWVNNCVGENNQKYFVLFTFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSPPATVVFLVFL-VFEALLFAIFTT 237 (465)
Q Consensus 159 DHHCpWi~nCIG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 237 (465)
||||||+|||||++|||+|++||+++...+++.+......+....... .. +....-+++.. ...+..+++.+.
T Consensus 137 DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~-~~-----~~~~~~~li~~~~~~~~~~f~~~~ 210 (309)
T COG5273 137 DHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIR-HD-----TSLAICFLIFGCSLLGVVFFIITT 210 (309)
T ss_pred CccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc-CC-----hHHHHHHHHHhhhHHHHHHHHHHH
Confidence 999999999999999999999999998887777776655544322111 00 00111111221 233444566677
Q ss_pred HHHHHHHHHHhcCCchHHHhhhhh
Q psy9305 238 VMLLSQLQAIWNDETGIEQLKKEE 261 (465)
Q Consensus 238 ~l~~~~l~~i~~n~Tt~E~~~~~~ 261 (465)
.++..+.+++..|+|++|..+..+
T Consensus 211 ~~~~~~~~~~~~~~t~~e~~~~~~ 234 (309)
T COG5273 211 LLLLFLIYLILNNLTTIEFIQISR 234 (309)
T ss_pred HHHHHHHHHHHhhHHHHHHHHhcc
Confidence 788899999999999999877654
No 7
>KOG1312|consensus
Probab=99.95 E-value=3.1e-28 Score=225.14 Aligned_cols=118 Identities=26% Similarity=0.579 Sum_probs=89.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCchHHHHhhcccC--CcceeeCCCCCccCCCCCccCccccccccc
Q psy9305 80 YRFFNMALFQTFAFLAFASHLRAMLTDPGAVPKGNATTEIIQQMGFRE--GQVIFKCPKCCCIKPERAHHCSVCQRCIRK 157 (465)
Q Consensus 80 ~~~~~~~~~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~~~~~~~~--~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~ 157 (465)
.+....+.-..+.++-.+++..+..+|||.+.+.+..+.. +..+.+. -.+...|++|+..||.||||||.||+||.|
T Consensus 96 lsl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~-~~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~r 174 (341)
T KOG1312|consen 96 LSLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFL-HVYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHR 174 (341)
T ss_pred hhHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccce-eccCccceeecCCCccccccCCCccccccchHHHHHHHH
Confidence 3444444444555566678889999999999776543221 1111111 012356999999999999999999999999
Q ss_pred cCccCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9305 158 MDHHCPWVNNCVGENNQKYFVLFTFYIATISIHSLFLAVNQ 198 (465)
Q Consensus 158 ~DHHCpWi~nCIG~~N~r~F~lfl~~~~~~~~~~~~~~~~~ 198 (465)
|||||.|+|||||++|.|||++||++...++.+++....+.
T Consensus 175 fDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi 215 (341)
T KOG1312|consen 175 FDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFI 215 (341)
T ss_pred hccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHhe
Confidence 99999999999999999999999999988888777766544
No 8
>KOG1315|consensus
Probab=99.93 E-value=3.9e-27 Score=227.51 Aligned_cols=139 Identities=31% Similarity=0.445 Sum_probs=101.0
Q ss_pred ccccceeecCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhccCCCC----C
Q psy9305 321 FREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCDQAPDK----D 396 (465)
Q Consensus 321 ~~~~~~~~~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~~~~~~----~ 396 (465)
.+..+..++|.+|+.+||+|||||+.|++||+||||||||+|||||.+|||+|++|++|..+...+.++...... .
T Consensus 103 ~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~ 182 (307)
T KOG1315|consen 103 RTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQ 182 (307)
T ss_pred ecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455667789999999999999999999999999999999999999999999999999988766544443322111 1
Q ss_pred CCCCccccCccchhhhhhhhhhhhhhhhhhhhhccccceeeccCcchhhcccccccccccCCc
Q psy9305 397 DTEDDVTTTPASEFEAFYPREAYGIPNSVVRAPHGHGSFYKYRNPALVDTKNAAAYGFRFDGK 459 (465)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~f~l~~~~~~~~h~~~~~y~~~~~~~i~~~~~~~~~~~~~~~ 459 (465)
+...............+++..+|++..++++..|.+.+..|.||+|..+.+.-+....+.++.
T Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~ 245 (307)
T KOG1315|consen 183 GGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGF 245 (307)
T ss_pred ccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCc
Confidence 111111112244555677778888888888889988888888888777755333333444443
No 9
>KOG0509|consensus
Probab=99.92 E-value=2.5e-25 Score=227.19 Aligned_cols=107 Identities=35% Similarity=0.744 Sum_probs=83.5
Q ss_pred HHHHHHHHHhhccCCCCCCCCCCch--HHHHhhcccCCcce-eeCCCCCccCCCCCccCccccccccccCccCccccccc
Q psy9305 93 FLAFASHLRAMLTDPGAVPKGNATT--EIIQQMGFREGQVI-FKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCV 169 (465)
Q Consensus 93 ~~~~~s~~~~~~~dPG~vp~~~~~~--~~~~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpWi~nCI 169 (465)
+..++++.+..-+|||.+|...+.. ...+-.+...-+.. ++|.+|...||.|||||+.|||||.||||||||++|||
T Consensus 379 l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncV 458 (600)
T KOG0509|consen 379 LAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCV 458 (600)
T ss_pred HHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCcccccc
Confidence 3344556666679999999875543 22233333333334 69999999999999999999999999999999999999
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9305 170 GENNQKYFVLFTFYIATISIHSLFLAVNQF 199 (465)
Q Consensus 170 G~~N~r~F~lfl~~~~~~~~~~~~~~~~~~ 199 (465)
|.+|||+|+.|++.+...+.+.+.....++
T Consensus 459 G~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~ 488 (600)
T KOG0509|consen 459 GLKNHRLFVFFLLTLLTVIVFYLYLCLYYI 488 (600)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999988777777666665544
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=99.92 E-value=8.2e-26 Score=205.99 Aligned_cols=125 Identities=26% Similarity=0.418 Sum_probs=87.5
Q ss_pred ccccceeecCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhccCCCCCCCCC
Q psy9305 321 FREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCDQAPDKDDTED 400 (465)
Q Consensus 321 ~~~~~~~~~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~ 400 (465)
.++....++|.+|+..||+||+||+.||+||.++||||+|+|||||++|||+|++|+++..+.+++.++...........
T Consensus 42 ~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~ 121 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIP 121 (174)
T ss_pred cccCCCCEECcccCCcCCCcceeccccccccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34555677899999999999999999999999999999999999999999999999998877666655432222111111
Q ss_pred ccccC---ccch---hhhhhhhhhhhhhhhhhhhhccccceeeccCcchhh
Q psy9305 401 DVTTT---PASE---FEAFYPREAYGIPNSVVRAPHGHGSFYKYRNPALVD 445 (465)
Q Consensus 401 ~~~~~---~~~~---~~~~~~~~~f~l~~~~~~~~h~~~~~y~~~~~~~i~ 445 (465)
..... .... ++.++...+++++.+.+...|.+.+.-|.||.|.++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~ 172 (174)
T PF01529_consen 122 SISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYERIK 172 (174)
T ss_pred cccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHH
Confidence 11111 1111 233333344467777777778888877777666655
No 11
>KOG1311|consensus
Probab=99.91 E-value=2.2e-25 Score=220.31 Aligned_cols=119 Identities=30% Similarity=0.442 Sum_probs=82.5
Q ss_pred eecCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhccCCCCCC----CCCcc
Q psy9305 327 IFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCDQAPDKDD----TEDDV 402 (465)
Q Consensus 327 ~~~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ 402 (465)
..||.+|+..||+||+||+.||+||++|||||+|+|||||++|||+|+.|+++.++..++.+......... .....
T Consensus 113 ~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~ 192 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNL 192 (299)
T ss_pred eEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 56899999999999999999999999999999999999999999999999997766655555443322110 11110
Q ss_pred c--cCc--cchhhhhhhhhhh-hhhhhhhhhhccccceeeccCcchhh
Q psy9305 403 T--TTP--ASEFEAFYPREAY-GIPNSVVRAPHGHGSFYKYRNPALVD 445 (465)
Q Consensus 403 ~--~~~--~~~~~~~~~~~~f-~l~~~~~~~~h~~~~~y~~~~~~~i~ 445 (465)
+ ... ....+...+..++ ....+.+..-|.+.+..+.|+.+.+.
T Consensus 193 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~ 240 (299)
T KOG1311|consen 193 TPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIK 240 (299)
T ss_pred cccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhh
Confidence 0 111 1111111122223 55566688888888888888875554
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.90 E-value=1.2e-24 Score=213.45 Aligned_cols=77 Identities=39% Similarity=0.808 Sum_probs=66.3
Q ss_pred hhhccccccceeecCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhccC
Q psy9305 316 IQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCDQA 392 (465)
Q Consensus 316 lq~~~~~~~~~~~~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~~~ 392 (465)
.+..+.++.+.+++|.+|+.+||+|||||+.||+||++|||||+|+|||||.+|||+|++|+++.......+++..+
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~ 174 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTA 174 (309)
T ss_pred hhhhhcCccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455667777889999999999999999999999999999999999999999999999999998665555554444
No 13
>KOG1314|consensus
Probab=99.87 E-value=6.1e-24 Score=201.82 Aligned_cols=55 Identities=51% Similarity=1.160 Sum_probs=53.1
Q ss_pred ecCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHH
Q psy9305 328 FKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLML 382 (465)
Q Consensus 328 ~~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~ 382 (465)
.+|.+|+.+|+||||||+.|+|||++|||||||+|||||..||.+|+.||++..+
T Consensus 92 qfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~iv 146 (414)
T KOG1314|consen 92 QFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIV 146 (414)
T ss_pred HHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHH
Confidence 4699999999999999999999999999999999999999999999999999876
No 14
>KOG1313|consensus
Probab=99.87 E-value=1.8e-23 Score=192.79 Aligned_cols=61 Identities=52% Similarity=1.136 Sum_probs=56.4
Q ss_pred cCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhh
Q psy9305 329 KCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALC 389 (465)
Q Consensus 329 ~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~ 389 (465)
.|.+|..+||+|+|||+.||+||++|||||||+|||||..|||+|++|++++.+..++..+
T Consensus 104 fC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i 164 (309)
T KOG1313|consen 104 FCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAI 164 (309)
T ss_pred HHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHH
Confidence 5999999999999999999999999999999999999999999999999998776655443
No 15
>KOG1312|consensus
Probab=99.85 E-value=2.1e-22 Score=186.59 Aligned_cols=73 Identities=40% Similarity=0.881 Sum_probs=62.1
Q ss_pred hccccccceee--cCCCCCCCCCCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhc
Q psy9305 318 QMGFREGQVIF--KCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCD 390 (465)
Q Consensus 318 ~~~~~~~~~~~--~c~~c~~~~p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~ 390 (465)
...+|+.-++. .|++|+..||.||+||+.||+||.++||||.|+|||||++|.|||++|+++...++.++.+.
T Consensus 137 ~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivr 211 (341)
T KOG1312|consen 137 VYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVR 211 (341)
T ss_pred ccCccceeecCCCccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555433 59999999999999999999999999999999999999999999999999887666555543
No 16
>KOG0509|consensus
Probab=99.83 E-value=3.1e-21 Score=197.40 Aligned_cols=195 Identities=21% Similarity=0.269 Sum_probs=127.0
Q ss_pred HHHHhhccCCCCCCCCCCchHHHHhhcccCCcceeeCCCCCccCCCCCccCccccccccccCccCcccccccccchhHHH
Q psy9305 98 SHLRAMLTDPGAVPKGNATTEIIQQMGFREGQVIFKCPKCCCIKPERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYF 177 (465)
Q Consensus 98 s~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpWi~nCIG~~N~r~F 177 (465)
-.+..+.-+||++-.... .-......+........|.+|....+.+..++..+-.++..+++||+|+. +|+.+|...|
T Consensus 293 ~~~~~~~~~~g~i~~~~~-~w~i~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~ 370 (600)
T KOG0509|consen 293 LFYFISSWLPGVIFLINS-LWLIKGLALGKLVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDF 370 (600)
T ss_pred HHHHHHhhccchhhhhhh-HHHHhhhhhhhhhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhh
Confidence 345566778888765543 22222222233344567999999999999999999999999999999999 9999885433
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCceeehhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHh
Q psy9305 178 VLFTFYIATISIHSLFLAVNQFLMCVRNEWRECSSYSPPATVVFLVFLVFEALLFAIFTTVMLLSQLQAIWNDETGIEQL 257 (465)
Q Consensus 178 ~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~ 257 (465)
-...+...+. .++.... ..+
T Consensus 371 ~~~~i~~~l~----------------------------------------------~~~~f~~------~~r-------- 390 (600)
T KOG0509|consen 371 HYCFIISVLA----------------------------------------------YFITFGL------FLR-------- 390 (600)
T ss_pred HHHHHHHHHH----------------------------------------------HHHHHHH------Hhc--------
Confidence 2222110000 0000000 000
Q ss_pred hhhhhhhhcccccchhhhcccccceeecccccCCCCCCCccCcCCCCCCCCCCcchhhhhhccccccceeecCCCCCCCC
Q psy9305 258 KKEEAKWARKSRWKSIQAVFGRFSLAWFSPFTQPPSRSKFESYLYPGAVPKGNATTEIIQQMGFREGQVIFKCPKCCCIK 337 (465)
Q Consensus 258 ~~~~~~~~~~g~~~N~~~vfG~~~~~W~~P~~~~~~~~~~dg~~~p~~~p~g~~~~eilq~~~~~~~~~~~~c~~c~~~~ 337 (465)
.|.| ..+. .+ +...+.+.++.+...++... ++|.+|...|
T Consensus 391 -------sDPg--------------------~i~~----~~-------~~~~~tIs~l~d~gkf~~en--~FC~~clirK 430 (600)
T KOG0509|consen 391 -------SDPG--------------------FIPT----ST-------EVGRETISQLIDFGKFDLEN--RFCLTCLIRK 430 (600)
T ss_pred -------cCCC--------------------CCCC----ch-------hhHHHHHHHhhccccccccc--cceeeeeeec
Confidence 0111 0110 00 00122334444444444433 5899999999
Q ss_pred CCCCCCCccccccccCcccccccccccccCCchHHHHHHHHHHHHHhhhhhhccCCC
Q psy9305 338 PERAHHCSVCQRCIRKMDHHCPWVNNCVGENNQKYFVLFTILLMLLLGPALCDQAPD 394 (465)
Q Consensus 338 p~r~~hc~~c~~cv~~~dhhc~~~~~cig~~n~~~f~~~~~~~~~~~~~~~~~~~~~ 394 (465)
|.||+||++|+|||.+|||||||++||||.+|+++|+.|++.+.......+.....+
T Consensus 431 p~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y 487 (600)
T KOG0509|consen 431 PLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYY 487 (600)
T ss_pred CCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999988876665555444433
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.58 E-value=1.5 Score=25.53 Aligned_cols=21 Identities=29% Similarity=0.759 Sum_probs=18.2
Q ss_pred cCCCCCCCCCCCCCCCccccc
Q psy9305 329 KCPKCCCIKPERAHHCSVCQR 349 (465)
Q Consensus 329 ~c~~c~~~~p~r~~hc~~c~~ 349 (465)
+|..|+..-++.+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 589999988999999999885
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=69.58 E-value=3 Score=25.02 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=18.0
Q ss_pred ecCCCCCCCCCCCCCCCccccc
Q psy9305 328 FKCPKCCCIKPERAHHCSVCQR 349 (465)
Q Consensus 328 ~~c~~c~~~~p~r~~hc~~c~~ 349 (465)
.+|..|+..-++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 4699999877888888888875
No 19
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=68.00 E-value=3.3 Score=28.69 Aligned_cols=22 Identities=32% Similarity=0.667 Sum_probs=20.1
Q ss_pred ecCCCCCCCCCCCCCCCccccc
Q psy9305 328 FKCPKCCCIKPERAHHCSVCQR 349 (465)
Q Consensus 328 ~~c~~c~~~~p~r~~hc~~c~~ 349 (465)
..|..|...-|+|+..|+.||.
T Consensus 15 ~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cchhcccCCCCccccccccCCC
Confidence 3599999999999999999986
No 20
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=67.98 E-value=2.9 Score=29.00 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=21.3
Q ss_pred ceeeCCCCCccCCCCCccCccccc
Q psy9305 130 VIFKCPKCCCIKPERAHHCSVCQR 153 (465)
Q Consensus 130 ~~~~C~~C~~~kP~Rs~HC~~C~~ 153 (465)
....|..|...-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 346799999999999999998876
No 21
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=54.52 E-value=7.3 Score=42.63 Aligned_cols=22 Identities=41% Similarity=0.800 Sum_probs=17.7
Q ss_pred eeCCCCCccCC-------CCCccCccccc
Q psy9305 132 FKCPKCCCIKP-------ERAHHCSVCQR 153 (465)
Q Consensus 132 ~~C~~C~~~kP-------~Rs~HC~~C~~ 153 (465)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999986553 39999999987
No 22
>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=52.64 E-value=9.5 Score=22.96 Aligned_cols=21 Identities=38% Similarity=0.928 Sum_probs=18.3
Q ss_pred cCCCCCCCCCCCCCCCccccc
Q psy9305 329 KCPKCCCIKPERAHHCSVCQR 349 (465)
Q Consensus 329 ~c~~c~~~~p~r~~hc~~c~~ 349 (465)
.|..|....|.-++-|..||.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 489999999999999998875
No 23
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=49.44 E-value=13 Score=27.30 Aligned_cols=16 Identities=38% Similarity=0.825 Sum_probs=7.7
Q ss_pred CCCCCCCCCCCCCCCc
Q psy9305 330 CPKCCCIKPERAHHCS 345 (465)
Q Consensus 330 c~~c~~~~p~r~~hc~ 345 (465)
|..|+..-|+.-..|+
T Consensus 6 C~~CG~~Ip~~~~fCS 21 (59)
T PF09889_consen 6 CPVCGKPIPPDESFCS 21 (59)
T ss_pred CCcCCCcCCcchhhhC
Confidence 5555544444444443
No 24
>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=46.23 E-value=12 Score=26.94 Aligned_cols=35 Identities=37% Similarity=0.911 Sum_probs=27.8
Q ss_pred CCCCCccCCCCC-------ccCcccccccccc-CccCccccccccc
Q psy9305 134 CPKCCCIKPERA-------HHCSVCQRCIRKM-DHHCPWVNNCVGE 171 (465)
Q Consensus 134 C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHHCpWi~nCIG~ 171 (465)
|..|...-|+-| +-|-.|..|+..+ +++|| ||=|.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 777776666654 6688999999998 99999 77664
No 25
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=45.20 E-value=12 Score=41.07 Aligned_cols=21 Identities=43% Similarity=0.909 Sum_probs=17.3
Q ss_pred cCCCCCCCCC-------CCCCCCccccc
Q psy9305 329 KCPKCCCIKP-------ERAHHCSVCQR 349 (465)
Q Consensus 329 ~c~~c~~~~p-------~r~~hc~~c~~ 349 (465)
-|..|+..-. .|-|||+.||+
T Consensus 462 tC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred cccCcCCcccccccccccccccccCCcc
Confidence 4999987764 38999999987
No 26
>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=43.01 E-value=11 Score=28.11 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=12.7
Q ss_pred ceeeCCCCCc-cC-CCCCccCcccccccc
Q psy9305 130 VIFKCPKCCC-IK-PERAHHCSVCQRCIR 156 (465)
Q Consensus 130 ~~~~C~~C~~-~k-P~Rs~HC~~C~~CV~ 156 (465)
....|..|.. +. -.|-|||+.||+.|=
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 3456888852 22 368899999998654
No 27
>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=41.20 E-value=8 Score=27.32 Aligned_cols=23 Identities=35% Similarity=0.814 Sum_probs=16.0
Q ss_pred ecCCCCCCCCCCCCCCCcc--cccc
Q psy9305 328 FKCPKCCCIKPERAHHCSV--CQRC 350 (465)
Q Consensus 328 ~~c~~c~~~~p~r~~hc~~--c~~c 350 (465)
..|..|...-|+|+..|+. ||.+
T Consensus 18 ~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 18 MICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred eecccccCcCCCCccceecccCCCC
Confidence 4699999999999999998 8765
No 28
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=41.14 E-value=4.1e+02 Score=27.67 Aligned_cols=31 Identities=19% Similarity=0.405 Sum_probs=22.7
Q ss_pred eeeCCCCCccCCCCCccCccccccccccCcc
Q psy9305 131 IFKCPKCCCIKPERAHHCSVCQRCIRKMDHH 161 (465)
Q Consensus 131 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHH 161 (465)
...|..|+..-|....||..|+.-..+..++
T Consensus 221 l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~ 251 (419)
T PRK15103 221 LRSCSCCTAILPADQPVCPRCHTKGYVRRRN 251 (419)
T ss_pred CCcCCCCCCCCCCCCCCCCCCCCcCcCCCCC
Confidence 4569999988777777888888766554444
No 29
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=40.95 E-value=11 Score=26.54 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=16.7
Q ss_pred ceeeCCCCCccCCCCCccCcc--cccc
Q psy9305 130 VIFKCPKCCCIKPERAHHCSV--CQRC 154 (465)
Q Consensus 130 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 154 (465)
....|..|...-|+|+-.|+. ||.+
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 456899999999999999998 7754
No 30
>PF12773 DZR: Double zinc ribbon
Probab=38.19 E-value=24 Score=24.40 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=18.7
Q ss_pred cCCCCCCCCC--C-CCCCCccccccccCccccccc
Q psy9305 329 KCPKCCCIKP--E-RAHHCSVCQRCIRKMDHHCPW 360 (465)
Q Consensus 329 ~c~~c~~~~p--~-r~~hc~~c~~cv~~~dhhc~~ 360 (465)
+|..|+..-+ . ....|..||.=+...+.+|+.
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 5666666554 2 245566666666666666653
No 31
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=36.74 E-value=7.9 Score=26.94 Aligned_cols=22 Identities=32% Similarity=0.774 Sum_probs=19.6
Q ss_pred cCCCCCCCCCCCCCCCcccccc
Q psy9305 329 KCPKCCCIKPERAHHCSVCQRC 350 (465)
Q Consensus 329 ~c~~c~~~~p~r~~hc~~c~~c 350 (465)
.|..|...-|+|+..|+.|+.=
T Consensus 16 IC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 16 ICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHhcCCCCcchhHHhhccCC
Confidence 4999999999999999998753
No 32
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=36.21 E-value=6 Score=27.52 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=20.7
Q ss_pred eeeCCCCCccCCCCCccCcccccc
Q psy9305 131 IFKCPKCCCIKPERAHHCSVCQRC 154 (465)
Q Consensus 131 ~~~C~~C~~~kP~Rs~HC~~C~~C 154 (465)
.+.|..|...-|+|+--|+.|+.=
T Consensus 14 kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 14 KKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHHHhcCCCCcchhHHhhccCC
Confidence 457999999999999999988753
No 33
>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 PF12773 DZR: Double zinc ribbon
Probab=35.35 E-value=35 Score=23.58 Aligned_cols=22 Identities=32% Similarity=0.772 Sum_probs=18.1
Q ss_pred eecCCCCCCCCCCCCCCCcccc
Q psy9305 327 IFKCPKCCCIKPERAHHCSVCQ 348 (465)
Q Consensus 327 ~~~c~~c~~~~p~r~~hc~~c~ 348 (465)
..+|..|....++.+..|..||
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCCCcCCcCccCccc
Confidence 4569999988888888888886
No 35
>KOG1842|consensus
Probab=29.09 E-value=15 Score=37.64 Aligned_cols=29 Identities=31% Similarity=0.771 Sum_probs=21.0
Q ss_pred CcceeeCCCCCccC--CCCCccCcccccccc
Q psy9305 128 GQVIFKCPKCCCIK--PERAHHCSVCQRCIR 156 (465)
Q Consensus 128 ~~~~~~C~~C~~~k--P~Rs~HC~~C~~CV~ 156 (465)
+....+|+.|...= --|-|||+.||+-+-
T Consensus 177 Ds~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 177 DSSVQFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred CCcccccccccchhhhHHHhhhhhhcchHHH
Confidence 45668999996332 457899999998543
No 36
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=28.83 E-value=5.1e+02 Score=26.80 Aligned_cols=31 Identities=19% Similarity=0.498 Sum_probs=20.8
Q ss_pred eeeCCCCCc-cCCCCCccCccccccccccCcc
Q psy9305 131 IFKCPKCCC-IKPERAHHCSVCQRCIRKMDHH 161 (465)
Q Consensus 131 ~~~C~~C~~-~kP~Rs~HC~~C~~CV~~~DHH 161 (465)
..-|..|+. .+|....+|..|+.-..+..++
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~ 246 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRN 246 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCC
Confidence 345999986 5555567788887766554444
No 37
>KOG3183|consensus
Probab=26.70 E-value=29 Score=32.76 Aligned_cols=14 Identities=29% Similarity=0.340 Sum_probs=10.9
Q ss_pred ccccccCccCcccc
Q psy9305 153 RCIRKMDHHCPWVN 166 (465)
Q Consensus 153 ~CV~~~DHHCpWi~ 166 (465)
.=..+.+|||||..
T Consensus 36 eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 36 EHRSYESHHCPKGL 49 (250)
T ss_pred ccchHhhcCCCccc
Confidence 34678899999975
No 38
>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=26.04 E-value=24 Score=21.70 Aligned_cols=21 Identities=33% Similarity=1.009 Sum_probs=15.1
Q ss_pred eCCCCCccCCCCCccCccccc
Q psy9305 133 KCPKCCCIKPERAHHCSVCQR 153 (465)
Q Consensus 133 ~C~~C~~~kP~Rs~HC~~C~~ 153 (465)
.|..|...-++++.+|..|+.
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 488888888888888888864
No 39
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=23.57 E-value=50 Score=20.35 Aligned_cols=20 Identities=30% Similarity=0.438 Sum_probs=13.6
Q ss_pred cCCCCCCCCCCC-CCCCcccc
Q psy9305 329 KCPKCCCIKPER-AHHCSVCQ 348 (465)
Q Consensus 329 ~c~~c~~~~p~r-~~hc~~c~ 348 (465)
+|..|...-... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477776665555 67777766
No 40
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.20 E-value=50 Score=24.39 Aligned_cols=21 Identities=33% Similarity=0.888 Sum_probs=18.9
Q ss_pred cCCCCCCCCCCCCCCCccccc
Q psy9305 329 KCPKCCCIKPERAHHCSVCQR 349 (465)
Q Consensus 329 ~c~~c~~~~p~r~~hc~~c~~ 349 (465)
-|..|+...|+.+.-|..||.
T Consensus 6 AC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 6 ACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred HHhhccccCCCCCccCCCCCC
Confidence 499999999999999999986
No 41
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.04 E-value=51 Score=27.56 Aligned_cols=29 Identities=17% Similarity=0.401 Sum_probs=19.9
Q ss_pred ccccceeecCCCCCCCCCCCCCC---Cccccc
Q psy9305 321 FREGQVIFKCPKCCCIKPERAHH---CSVCQR 349 (465)
Q Consensus 321 ~~~~~~~~~c~~c~~~~p~r~~h---c~~c~~ 349 (465)
.++.....+|..|+..-|....+ |..||.
T Consensus 64 i~~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 64 LEEQEAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEeeCcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 34445566799999887765444 888874
Done!