Query 020836
Match_columns 320
No_of_seqs 149 out of 1590
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 05:32:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1314 DHHC-type Zn-finger pr 100.0 1.8E-43 3.8E-48 320.9 11.1 196 70-319 50-313 (414)
2 KOG1315 Predicted DHHC-type Zn 100.0 2.9E-41 6.4E-46 310.3 6.9 193 66-298 44-269 (307)
3 KOG1311 DHHC-type Zn-finger pr 100.0 1.1E-38 2.3E-43 297.9 14.5 135 156-296 104-276 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 7.6E-36 1.6E-40 257.2 7.2 96 161-256 44-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 2.6E-34 5.6E-39 253.9 7.6 146 166-313 103-305 (309)
6 COG5273 Uncharacterized protei 100.0 4.4E-33 9.5E-38 259.3 13.9 188 66-298 54-291 (309)
7 KOG0509 Ankyrin repeat and DHH 99.9 4.2E-27 9.2E-32 229.2 9.9 122 166-287 421-586 (600)
8 KOG1312 DHHC-type Zn-finger pr 99.9 1.5E-27 3.3E-32 212.0 4.9 47 166-212 149-195 (341)
9 KOG1311 DHHC-type Zn-finger pr 87.4 1.3 2.9E-05 41.3 5.9 35 178-212 112-147 (299)
10 PF13240 zinc_ribbon_2: zinc-r 86.0 0.41 9E-06 26.9 1.0 21 167-187 1-21 (23)
11 PF13248 zf-ribbon_3: zinc-rib 76.3 1.5 3.3E-05 25.2 1.1 22 166-187 3-24 (26)
12 PF01529 zf-DHHC: DHHC palmito 71.5 14 0.0003 31.1 6.5 38 175-212 44-81 (174)
13 PRK04136 rpl40e 50S ribosomal 69.5 2.8 6.1E-05 27.9 1.3 22 166-187 15-36 (48)
14 KOG0509 Ankyrin repeat and DHH 65.6 1.9 4E-05 43.8 -0.2 45 166-211 326-370 (600)
15 PTZ00303 phosphatidylinositol 58.8 5.2 0.00011 41.8 1.5 23 166-188 461-490 (1374)
16 PF12773 DZR: Double zinc ribb 56.4 10 0.00022 25.1 2.2 33 166-198 13-48 (50)
17 PF10571 UPF0547: Uncharacteri 54.9 7.3 0.00016 22.5 1.1 21 167-187 2-22 (26)
18 PF01363 FYVE: FYVE zinc finge 51.4 7.7 0.00017 27.5 1.0 24 166-189 10-35 (69)
19 PF12773 DZR: Double zinc ribb 49.2 12 0.00027 24.6 1.7 22 165-186 29-50 (50)
20 PRK02935 hypothetical protein; 48.4 70 0.0015 25.1 5.9 8 167-174 72-79 (110)
21 PF01020 Ribosomal_L40e: Ribos 43.8 16 0.00034 24.9 1.5 23 166-188 18-42 (52)
22 smart00064 FYVE Protein presen 43.0 18 0.00039 25.5 1.9 24 166-189 11-36 (68)
23 KOG1314 DHHC-type Zn-finger pr 41.0 63 0.0014 31.0 5.5 27 166-192 106-132 (414)
24 COG1552 RPL40A Ribosomal prote 40.0 6.1 0.00013 26.4 -0.9 23 166-188 15-37 (50)
25 COG4640 Predicted membrane pro 40.0 20 0.00043 34.7 2.1 26 166-191 2-27 (465)
26 KOG3183 Predicted Zn-finger pr 39.8 14 0.00029 33.3 0.9 11 190-200 39-49 (250)
27 PF11023 DUF2614: Protein of u 39.6 1.2E+02 0.0025 24.2 6.0 8 167-174 71-78 (114)
28 PF00641 zf-RanBP: Zn-finger i 38.2 15 0.00033 21.6 0.7 22 166-187 5-26 (30)
29 PF08600 Rsm1: Rsm1-like; Int 37.4 18 0.0004 27.5 1.2 12 194-205 56-67 (91)
30 KOG1842 FYVE finger-containing 36.7 9.4 0.0002 37.4 -0.6 24 166-189 181-206 (505)
31 COG3336 Predicted membrane pro 36.6 84 0.0018 29.3 5.5 53 45-97 133-186 (299)
32 PF06906 DUF1272: Protein of u 35.1 15 0.00033 25.3 0.4 36 167-205 7-50 (57)
33 KOG0860 Synaptobrevin/VAMP-lik 33.9 64 0.0014 25.8 3.8 29 209-237 85-113 (116)
34 cd00065 FYVE FYVE domain; Zinc 32.9 29 0.00063 23.4 1.5 24 166-189 3-28 (57)
35 PF13150 DUF3989: Protein of u 32.3 1.1E+02 0.0025 23.0 4.8 28 220-247 30-57 (85)
36 PF09297 zf-NADH-PPase: NADH p 31.8 31 0.00067 20.6 1.3 22 166-187 4-29 (32)
37 COG5249 RER1 Golgi protein inv 30.8 3.2E+02 0.0069 22.9 9.2 10 268-277 167-176 (180)
38 PF06143 Baculo_11_kDa: Baculo 27.6 1E+02 0.0022 23.2 3.8 31 223-253 39-69 (84)
39 COG5273 Uncharacterized protei 27.4 1.7E+02 0.0037 27.5 6.2 34 175-208 105-138 (309)
40 PRK14559 putative protein seri 26.5 43 0.00094 34.9 2.2 13 269-281 126-138 (645)
41 KOG1819 FYVE finger-containing 23.9 26 0.00057 34.9 0.0 22 166-187 902-925 (990)
42 PF03381 CDC50: LEM3 (ligand-e 22.6 1.4E+02 0.003 27.6 4.6 34 201-241 236-269 (278)
43 PF02150 RNA_POL_M_15KD: RNA p 22.4 38 0.00082 20.9 0.5 9 166-174 2-10 (35)
44 PF07010 Endomucin: Endomucin; 22.1 1.2E+02 0.0026 27.3 3.7 23 78-100 204-226 (259)
45 KOG1326 Membrane-associated pr 21.3 1E+02 0.0022 33.6 3.7 35 206-240 1060-1094(1105)
46 PF05297 Herpes_LMP1: Herpesvi 21.2 32 0.00069 32.0 0.0 10 60-69 128-137 (381)
47 KOG4004 Matricellular protein 20.9 46 0.00099 29.3 0.9 18 192-209 54-72 (259)
48 smart00661 RPOL9 RNA polymeras 20.6 58 0.0013 21.4 1.2 8 167-174 2-9 (52)
49 PF07649 C1_3: C1-like domain; 20.6 47 0.001 19.5 0.6 21 167-187 2-23 (30)
No 1
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.8e-43 Score=320.87 Aligned_cols=196 Identities=28% Similarity=0.545 Sum_probs=154.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCccCCccccchHHhHHhhhhccCCCCCCCCCCCCccccccCCCCCCCCCCCCCcch
Q 020836 70 YITFYLLLFVATLVQYFITSGSSPGYVLDAMRHANERNALFQKISTTSKQPASSKNGNMVITMEGSRPGRSFSGSNATSW 149 (320)
Q Consensus 70 ~~~i~~~l~~~~l~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (320)
.-+.|.+...+++++|+.+++++||++|.++.++..+++.+
T Consensus 50 n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~--------------------------------------- 90 (414)
T KOG1314|consen 50 NQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDEMF--------------------------------------- 90 (414)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHH---------------------------------------
Confidence 55777888999999999999999999999998654443322
Q ss_pred hhhhhccCCCCCcccceecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh-----------------
Q 020836 150 TKLVLDLYPPGTSIRSLTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW----------------- 212 (320)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~----------------- 212 (320)
.+||.+|+.+|++|||||+.|||||.+|||||||+|||||..||.+|.
T Consensus 91 ---------------lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~ 155 (414)
T KOG1314|consen 91 ---------------LQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIIL 155 (414)
T ss_pred ---------------HHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeee
Confidence 179999999999999999999999999999999999999999999987
Q ss_pred -----------hhh-------------hhHHHH----HHHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHh----ccccc
Q 020836 213 -----------WKD-------------VIMIVL----LIILAISLIFLLLLLLFHSYLILTNQTTYELVRR----RRIPY 260 (320)
Q Consensus 213 -----------~~~-------------~~~i~~----~~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~----~r~~~ 260 (320)
|.. ...++. +-+.+...+.+++||+.|+..|.+|+|.+|.+.- .|..+
T Consensus 156 ~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~ 235 (414)
T KOG1314|consen 156 VCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREY 235 (414)
T ss_pred hhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHh
Confidence 310 111122 2233444556779999999999999999999862 23333
Q ss_pred ccCC--CCccCCCCHhHHHhHhhccccc----CCc-------------cccccCCChhHhhhccCCceEeeccCcccc
Q 020836 261 LRGI--PERVYPFSDGVCRNLYKLCCVK----ASV-------------YNLERLPTAQEIEEKCRPYTCLDFLTCRCC 319 (320)
Q Consensus 261 ~~~~--~~~~npfd~G~~~N~~~~~~~~----~~~-------------~~~~~lp~~~~~~~~~~~~~~~~~~~~~~~ 319 (320)
.... .+...|||.|++.|+++++++. ..+ +...++-+..+.|.|.+.|.|.+.+||+||
T Consensus 236 ~~~d~~~~f~ypydlgWr~n~r~vf~~~~~~~gdg~~wPv~~gc~qytlt~eql~qk~~kr~rsr~~~~~~~~tG~~~ 313 (414)
T KOG1314|consen 236 YFNDDEGEFTYPYDLGWRINLREVFFQNKKEEGDGIEWPVVEGCVQYTLTIEQLTQKLDKRGRSRLFKCIEDVTGDCC 313 (414)
T ss_pred hccCCCCceeeeccccccccHHHHhhhccccCCCCccccccCcccccceeHHHHHHHHHhhcCeEEEEeccCCCCCcc
Confidence 3332 5567999999888999998775 222 223467788889999999999999999997
No 2
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.9e-41 Score=310.27 Aligned_cols=193 Identities=30% Similarity=0.478 Sum_probs=140.7
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhccCCCccCCccccchHHhHHhhhhccCCCCCCCCCCCCccccccCCCCCCCCCCCC
Q 020836 66 HEPWYITFYLLLFVATLVQYFITSGSSPGYVLDAMRHANERNALFQKISTTSKQPASSKNGNMVITMEGSRPGRSFSGSN 145 (320)
Q Consensus 66 ~~~~~~~i~~~l~~~~l~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (320)
...+..+++.+++++.+++|++++++|||.+|..+..+.+.++..++....+
T Consensus 44 ~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~---------------------------- 95 (307)
T KOG1315|consen 44 PSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNE---------------------------- 95 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccCccc----------------------------
Confidence 4455678888999999999999999999999988875443333221111000
Q ss_pred CcchhhhhhccCCCCCcccceecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh-------------
Q 020836 146 ATSWTKLVLDLYPPGTSIRSLTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW------------- 212 (320)
Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~------------- 212 (320)
.....+..+..+..++|.+|+.+||+|||||++|+|||+||||||||+|||||.+|||+|+
T Consensus 96 ------~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~ 169 (307)
T KOG1315|consen 96 ------RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYV 169 (307)
T ss_pred ------ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHH
Confidence 0111112233455699999999999999999999999999999999999999999999998
Q ss_pred -----------hhh---------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHhcccccccCCCCccCCCC
Q 020836 213 -----------WKD---------VIMIVLLIILAISLIFLLLLLLFHSYLILTNQTTYELVRRRRIPYLRGIPERVYPFS 272 (320)
Q Consensus 213 -----------~~~---------~~~i~~~~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~~r~~~~~~~~~~~npfd 272 (320)
+.. ....+++++.+.+.+.+++|+++|++||++|+||+|..+.. .........|.|+
T Consensus 170 lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~---~~~~~~~~~~~~~ 246 (307)
T KOG1315|consen 170 LVTTLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSP---VFRSGLHNKNGFN 246 (307)
T ss_pred HHHHHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccc---cccccccccCCcc
Confidence 100 11122334445556667789999999999999999999764 2222223457777
Q ss_pred HhHHHhHhhcccccCCccccccCCCh
Q 020836 273 DGVCRNLYKLCCVKASVYNLERLPTA 298 (320)
Q Consensus 273 ~G~~~N~~~~~~~~~~~~~~~~lp~~ 298 (320)
. ..|+.+ .+|++..+|+.|.++.
T Consensus 247 ~--~~n~~~-vfg~~~~~wl~P~~~s 269 (307)
T KOG1315|consen 247 L--YVNFRE-VFGSNLLYWLLPIDSS 269 (307)
T ss_pred e--eecHHH-HhCCCceEEeccccCc
Confidence 7 789999 6688888888887755
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.1e-38 Score=297.94 Aligned_cols=135 Identities=33% Similarity=0.612 Sum_probs=107.8
Q ss_pred cCCCCCcccceecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhhh----------------------
Q 020836 156 LYPPGTSIRSLTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFWW---------------------- 213 (320)
Q Consensus 156 ~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~~---------------------- 213 (320)
..++|...+.+||.+|+..||+|||||++||+||+||||||||+|||||++|||+|++
T Consensus 104 ~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~ 183 (299)
T KOG1311|consen 104 VDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQ 183 (299)
T ss_pred cccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3356667778999999999999999999999999999999999999999999999981
Q ss_pred ---------h-------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHhcccccccCCCCccCCCCHhHHH
Q 020836 214 ---------K-------DVIMIVLLIILAISLIFLLLLLLFHSYLILTNQTTYELVRRRRIPYLRGIPERVYPFSDGVCR 277 (320)
Q Consensus 214 ---------~-------~~~~i~~~~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~~r~~~~~~~~~~~npfd~G~~~ 277 (320)
. ....+++.+++++.+++++.|+.+|+++|.+|+||+|.++.. . .....+|||.|.++
T Consensus 184 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~---~---~~~~~~~~~~g~~~ 257 (299)
T KOG1311|consen 184 RADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSL---D---FVSRSNPYDLGLLK 257 (299)
T ss_pred hcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhcc---c---cccccCCCchhHHH
Confidence 0 011223334456666777889999999999999999998761 1 11225899999999
Q ss_pred hHhhcccccCCccccccCC
Q 020836 278 NLYKLCCVKASVYNLERLP 296 (320)
Q Consensus 278 N~~~~~~~~~~~~~~~~lp 296 (320)
|+.++++++.+..|+.+.-
T Consensus 258 n~~~~~~~~~~~~~~~p~~ 276 (299)
T KOG1311|consen 258 NLQEVFGGPLPLSWLSPFA 276 (299)
T ss_pred HHHHHhCCCCCcccccccc
Confidence 9999888877776665443
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=7.6e-36 Score=257.17 Aligned_cols=96 Identities=48% Similarity=0.927 Sum_probs=81.2
Q ss_pred CcccceecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh----------------------------
Q 020836 161 TSIRSLTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW---------------------------- 212 (320)
Q Consensus 161 ~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~---------------------------- 212 (320)
...+.++|.+|+..||+|||||+.||+||++|||||||+|||||++|||+|+
T Consensus 44 ~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~ 123 (174)
T PF01529_consen 44 ENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSI 123 (174)
T ss_pred cCCCCEECcccCCcCCCcceeccccccccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3455599999999999999999999999999999999999999999999997
Q ss_pred ----hhh--hh-HHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHhc
Q 020836 213 ----WKD--VI-MIVLLIILAISLIFLLLLLLFHSYLILTNQTTYELVRRR 256 (320)
Q Consensus 213 ----~~~--~~-~i~~~~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~~ 256 (320)
+.. .. .+++++++++.+++++.|+++|+++|++|+||+|.++++
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 124 SFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred cccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 000 00 144555667777888999999999999999999999753
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2.6e-34 Score=253.85 Aligned_cols=146 Identities=29% Similarity=0.504 Sum_probs=115.5
Q ss_pred eecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh--------------------hh-----------
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW--------------------WK----------- 214 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~--------------------~~----------- 214 (320)
.+|.+|..+||+|+|||++|||||++|||||||+|||||..|||||+ |.
T Consensus 103 SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ta 182 (309)
T KOG1313|consen 103 SFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEITA 182 (309)
T ss_pred cHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhccc
Confidence 78999999999999999999999999999999999999999999998 10
Q ss_pred ----------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHhc--ccccccCCCCccCC
Q 020836 215 ----------------------DVIMIVLLIILAISLIFLLLLLLFHSYLILTNQTTYELVRRR--RIPYLRGIPERVYP 270 (320)
Q Consensus 215 ----------------------~~~~i~~~~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~~--r~~~~~~~~~~~np 270 (320)
......++++++.+++.++.+..+|.++|.+|+|++|..... |.+++.. .+.||
T Consensus 183 y~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~--~R~~~ 260 (309)
T KOG1313|consen 183 YASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAH--LRSNP 260 (309)
T ss_pred ccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHh--ccCCC
Confidence 001122456667777888999999999999999999987543 2233332 33799
Q ss_pred CCHhHHHhHhhccc-ccCCccccc-cCCChhHhhhccCCceEeec
Q 020836 271 FSDGVCRNLYKLCC-VKASVYNLE-RLPTAQEIEEKCRPYTCLDF 313 (320)
Q Consensus 271 fd~G~~~N~~~~~~-~~~~~~~~~-~lp~~~~~~~~~~~~~~~~~ 313 (320)
++.|.++||+.|+. .+++..|.. -+|+....+......|-.|+
T Consensus 261 ~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p~~~~~~~~~~da 305 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLFRGRHFWKTVLLPTIRKPVKYGDSKEKSDA 305 (309)
T ss_pred cccchHHHHHHhhccccCCceeEEEeccccccccccCCcccccch
Confidence 99999999999873 344546655 88888888877777774443
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=4.4e-33 Score=259.30 Aligned_cols=188 Identities=32% Similarity=0.582 Sum_probs=132.5
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhccCCCccCCccccchHHhHHhhhhccCCCCCCCCCCCCccccccCCCCCCCCCCCC
Q 020836 66 HEPWYITFYLLLFVATLVQYFITSGSSPGYVLDAMRHANERNALFQKISTTSKQPASSKNGNMVITMEGSRPGRSFSGSN 145 (320)
Q Consensus 66 ~~~~~~~i~~~l~~~~l~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (320)
......+.+.++..++.++|+..+.+|||+++++......+
T Consensus 54 ~~~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~--------------------------------------- 94 (309)
T COG5273 54 LVVLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYR--------------------------------------- 94 (309)
T ss_pred chhhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchh---------------------------------------
Confidence 34446677788888999999999999999998765422211
Q ss_pred CcchhhhhhccCCCCCcccceecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhhh----h-------
Q 020836 146 ATSWTKLVLDLYPPGTSIRSLTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFWW----K------- 214 (320)
Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~~----~------- 214 (320)
+.+...+..+..++.++|.+|+.+||+|||||+.||+||+||||||||+|||||.+|||+|+. .
T Consensus 95 -----~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~ 169 (309)
T COG5273 95 -----ETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVV 169 (309)
T ss_pred -----hhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHH
Confidence 111223334555667999999999999999999999999999999999999999999999980 0
Q ss_pred -------------------hhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHhCchhHHHHHhcccccc-------cC--
Q 020836 215 -------------------DVIMIVLL---IILAISLIFLLLLLLFHSYLILTNQTTYELVRRRRIPYL-------RG-- 263 (320)
Q Consensus 215 -------------------~~~~i~~~---~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~~~~r~~~~-------~~-- 263 (320)
.....++. .+....++++..++.+|.+++..|.||.|..+..|.... ++
T Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~ 249 (309)
T COG5273 170 LLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESN 249 (309)
T ss_pred HHHHHHHHHhhccccCChHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCC
Confidence 00011111 223334556778899999999999999999865543211 11
Q ss_pred --------CCCccCCCCHhHHHhHhhcccccCCccccccCCCh
Q 020836 264 --------IPERVYPFSDGVCRNLYKLCCVKASVYNLERLPTA 298 (320)
Q Consensus 264 --------~~~~~npfd~G~~~N~~~~~~~~~~~~~~~~lp~~ 298 (320)
..+..+|++.|.-+|+.. ..+.+..+|..+.+..
T Consensus 250 ~~~~~~~d~~~~~~~~~~~~~~~~~~-i~~~~~~~~~~~~~~~ 291 (309)
T COG5273 250 LPFTNIFDSSEGALPLDLGIGQNLST-IKGSNALYWLTPLHTN 291 (309)
T ss_pred cCceeccCCCccccccccCcccccee-ecCCCceeeccccccC
Confidence 122346778888888876 4466666766664433
No 7
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.94 E-value=4.2e-27 Score=229.24 Aligned_cols=122 Identities=35% Similarity=0.600 Sum_probs=86.7
Q ss_pred eecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhhhh---hhhHHHHHHHHHH---------HHHHHH
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFWWK---DVIMIVLLIILAI---------SLIFLL 233 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~~~---~~~~i~~~~~~~~---------~~~~~~ 233 (320)
+||.+|.+.||.||+||+.|||||.+|||||||++||||.+|||+|+.. ....+..++.... ..+.+.
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~~~~~~ 500 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENASTIYVG 500 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHH
Confidence 6999999999999999999999999999999999999999999999710 0000000000000 000011
Q ss_pred H-------------------------------HHHHHHHHHHhCchhHHHHHhcccccccCC-CCccCCCCHhHHHhHhh
Q 020836 234 L-------------------------------LLLFHSYLILTNQTTYELVRRRRIPYLRGI-PERVYPFSDGVCRNLYK 281 (320)
Q Consensus 234 ~-------------------------------L~~~h~~lI~~n~TT~E~~~~~r~~~~~~~-~~~~npfd~G~~~N~~~ 281 (320)
+ .-..|...++.+.||+|.++..|.++++.. ....+|++.|+.+|+.+
T Consensus 501 ~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g~~~Nl~d 580 (600)
T KOG0509|consen 501 FLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPGPIRNLVD 580 (600)
T ss_pred HHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCchhhhcchh
Confidence 1 112233347889999999999888877643 23578999999999999
Q ss_pred cccccC
Q 020836 282 LCCVKA 287 (320)
Q Consensus 282 ~~~~~~ 287 (320)
|+-.+.
T Consensus 581 f~~~~~ 586 (600)
T KOG0509|consen 581 FFLCSD 586 (600)
T ss_pred eeeccc
Confidence 875543
No 8
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.94 E-value=1.5e-27 Score=211.98 Aligned_cols=47 Identities=47% Similarity=1.217 Sum_probs=46.2
Q ss_pred eecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW 212 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~ 212 (320)
..|+||+..||.||+|||.|||||.||||||.|+|||||++|+|||+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~ 195 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFL 195 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHhccceEeeecccccchHHHHH
Confidence 67999999999999999999999999999999999999999999998
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=87.40 E-value=1.3 Score=41.28 Aligned_cols=35 Identities=26% Similarity=0.528 Sum_probs=29.9
Q ss_pred CCccCcCCCcccCCCcccCcCCCcccccccc-hhhh
Q 020836 178 RAKHCHDCDRCVLQFDHHCVWLGTCVGLVNH-CRFW 212 (320)
Q Consensus 178 Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~-r~F~ 212 (320)
+.++|..|+..+...-|||..=|+||-+.=| -.++
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~Wv 147 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWL 147 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCc
Confidence 5899999999999999999999999976555 4444
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.99 E-value=0.41 Score=26.90 Aligned_cols=21 Identities=33% Similarity=0.798 Sum_probs=18.5
Q ss_pred ecccCCcccCCCCccCcCCCc
Q 020836 167 TCSYCNVEQPPRAKHCHDCDR 187 (320)
Q Consensus 167 ~C~~C~~~kP~Rs~HC~~C~r 187 (320)
||+.|...-++.+.+|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688999999999999999885
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.29 E-value=1.5 Score=25.22 Aligned_cols=22 Identities=36% Similarity=0.916 Sum_probs=19.0
Q ss_pred eecccCCcccCCCCccCcCCCc
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDR 187 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~r 187 (320)
++|..|...-++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6799999988889999998875
No 12
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=71.53 E-value=14 Score=31.05 Aligned_cols=38 Identities=26% Similarity=0.469 Sum_probs=32.0
Q ss_pred cCCCCccCcCCCcccCCCcccCcCCCcccccccchhhh
Q 020836 175 QPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRFW 212 (320)
Q Consensus 175 kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F~ 212 (320)
.....+.|..|+.=....-|||..-+.||-+.-|-=.+
T Consensus 44 ~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 44 ENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred cCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 67788999999988888899999999999877774333
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=69.50 E-value=2.8 Score=27.95 Aligned_cols=22 Identities=36% Similarity=0.831 Sum_probs=20.6
Q ss_pred eecccCCcccCCCCccCcCCCc
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDR 187 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~r 187 (320)
+.|.+|...-|+|+..|+.||.
T Consensus 15 ~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cchhcccCCCCccccccccCCC
Confidence 7899999999999999998886
No 14
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=65.58 E-value=1.9 Score=43.78 Aligned_cols=45 Identities=9% Similarity=-0.041 Sum_probs=42.2
Q ss_pred eecccCCcccCCCCccCcCCCcccCCCcccCcCCCcccccccchhh
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNHCRF 211 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~r~F 211 (320)
..|.+|....+.+..++..+-.++..+++||+|+. +|+.+|...|
T Consensus 326 ~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~ 370 (600)
T KOG0509|consen 326 CLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDF 370 (600)
T ss_pred eeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhh
Confidence 67999999999999999999999999999999999 9999998655
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=58.84 E-value=5.2 Score=41.83 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=18.8
Q ss_pred eecccCCcccC-------CCCccCcCCCcc
Q 020836 166 LTCSYCNVEQP-------PRAKHCHDCDRC 188 (320)
Q Consensus 166 ~~C~~C~~~kP-------~Rs~HC~~C~rC 188 (320)
.-|..|+..-. .|-|||+.||+.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrV 490 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIR 490 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccc
Confidence 56999988764 399999999883
No 16
>PF12773 DZR: Double zinc ribbon
Probab=56.41 E-value=10 Score=25.10 Aligned_cols=33 Identities=21% Similarity=0.426 Sum_probs=24.9
Q ss_pred eecccCCcccC---CCCccCcCCCcccCCCcccCcC
Q 020836 166 LTCSYCNVEQP---PRAKHCHDCDRCVLQFDHHCVW 198 (320)
Q Consensus 166 ~~C~~C~~~kP---~Rs~HC~~C~rCV~r~DHHCpW 198 (320)
+||..|...-+ .....|..|+.=+...+.+|+.
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 78888888655 4467788888888777777764
No 17
>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=54.87 E-value=7.3 Score=22.53 Aligned_cols=21 Identities=43% Similarity=0.933 Sum_probs=17.4
Q ss_pred ecccCCcccCCCCccCcCCCc
Q 020836 167 TCSYCNVEQPPRAKHCHDCDR 187 (320)
Q Consensus 167 ~C~~C~~~kP~Rs~HC~~C~r 187 (320)
.|+.|...-|.-++-|..||.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 488898888888888888774
No 18
>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=51.38 E-value=7.7 Score=27.54 Aligned_cols=24 Identities=33% Similarity=0.800 Sum_probs=13.1
Q ss_pred eecccCCcc--cCCCCccCcCCCccc
Q 020836 166 LTCSYCNVE--QPPRAKHCHDCDRCV 189 (320)
Q Consensus 166 ~~C~~C~~~--kP~Rs~HC~~C~rCV 189 (320)
..|..|+.. --.|-|||+.||+.|
T Consensus 10 ~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CcCcCcCCcCCCceeeEccCCCCCEE
Confidence 678888774 357999999999865
No 19
>PF12773 DZR: Double zinc ribbon
Probab=49.16 E-value=12 Score=24.64 Aligned_cols=22 Identities=41% Similarity=1.050 Sum_probs=20.1
Q ss_pred ceecccCCcccCCCCccCcCCC
Q 020836 165 SLTCSYCNVEQPPRAKHCHDCD 186 (320)
Q Consensus 165 ~~~C~~C~~~kP~Rs~HC~~C~ 186 (320)
..+|..|....+..+.+|..||
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCCCcCCcCccCccc
Confidence 3789999999999999999986
No 20
>PRK02935 hypothetical protein; Provisional
Probab=48.37 E-value=70 Score=25.13 Aligned_cols=8 Identities=25% Similarity=0.816 Sum_probs=4.0
Q ss_pred ecccCCcc
Q 020836 167 TCSYCNVE 174 (320)
Q Consensus 167 ~C~~C~~~ 174 (320)
.|+.|+..
T Consensus 72 ~CP~C~K~ 79 (110)
T PRK02935 72 ICPSCEKP 79 (110)
T ss_pred ECCCCCch
Confidence 45555543
No 21
>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=43.77 E-value=16 Score=24.85 Aligned_cols=23 Identities=35% Similarity=0.998 Sum_probs=16.5
Q ss_pred eecccCCcccCCCCccCcC--CCcc
Q 020836 166 LTCSYCNVEQPPRAKHCHD--CDRC 188 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~--C~rC 188 (320)
..|.+|...-|+||..|+. ||.+
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 7899999999999999998 8764
No 22
>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 KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=41.04 E-value=63 Score=30.96 Aligned_cols=27 Identities=26% Similarity=0.365 Sum_probs=23.2
Q ss_pred eecccCCcccCCCCccCcCCCcccCCC
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQF 192 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r~ 192 (320)
.-|.+|+.-...--|||..-+.||---
T Consensus 106 HHCrkCnrCvmkMDHHCPWinnCVG~a 132 (414)
T KOG1314|consen 106 HHCRKCNRCVMKMDHHCPWINNCVGWA 132 (414)
T ss_pred ccchHHHHHHHhhccCCcchhhccccc
Confidence 569999988888889999999999543
No 24
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=40.03 E-value=6.1 Score=26.44 Aligned_cols=23 Identities=35% Similarity=0.879 Sum_probs=20.5
Q ss_pred eecccCCcccCCCCccCcCCCcc
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRC 188 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rC 188 (320)
+.|.+|...-|+++.-|+.|+.=
T Consensus 15 kIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 15 KICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHHhcCCCCcchhHHhhccCC
Confidence 78999999999999999988653
No 25
>COG4640 Predicted membrane protein [Function unknown]
Probab=40.01 E-value=20 Score=34.71 Aligned_cols=26 Identities=15% Similarity=0.498 Sum_probs=21.8
Q ss_pred eecccCCcccCCCCccCcCCCcccCC
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDRCVLQ 191 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~rCV~r 191 (320)
++|..|...+-..+..|..||.=+-.
T Consensus 2 ~fC~kcG~qk~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 2 KFCPKCGSQKAEDDVQCTQCGHKFTS 27 (465)
T ss_pred CcccccccccccccccccccCCcCCc
Confidence 68999999999999999998875543
No 26
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=39.83 E-value=14 Score=33.33 Aligned_cols=11 Identities=27% Similarity=0.069 Sum_probs=8.7
Q ss_pred CCCcccCcCCC
Q 020836 190 LQFDHHCVWLG 200 (320)
Q Consensus 190 ~r~DHHCpWv~ 200 (320)
...+|||||..
T Consensus 39 sye~H~Cp~~~ 49 (250)
T KOG3183|consen 39 SYESHHCPKGL 49 (250)
T ss_pred hHhhcCCCccc
Confidence 56789999864
No 27
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=39.62 E-value=1.2e+02 Score=24.21 Aligned_cols=8 Identities=25% Similarity=0.929 Sum_probs=4.6
Q ss_pred ecccCCcc
Q 020836 167 TCSYCNVE 174 (320)
Q Consensus 167 ~C~~C~~~ 174 (320)
-|+.|+..
T Consensus 71 ~CP~C~K~ 78 (114)
T PF11023_consen 71 ECPNCGKQ 78 (114)
T ss_pred ECCCCCCh
Confidence 36666554
No 28
>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=38.17 E-value=15 Score=21.60 Aligned_cols=22 Identities=23% Similarity=0.730 Sum_probs=16.9
Q ss_pred eecccCCcccCCCCccCcCCCc
Q 020836 166 LTCSYCNVEQPPRAKHCHDCDR 187 (320)
Q Consensus 166 ~~C~~C~~~kP~Rs~HC~~C~r 187 (320)
..|..|...-+.++.+|..|+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--
T ss_pred ccCCCCcCCchHHhhhhhCcCC
Confidence 6799999999999999998874
No 29
>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=37.37 E-value=18 Score=27.53 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=9.5
Q ss_pred ccCcCCCccccc
Q 020836 194 HHCVWLGTCVGL 205 (320)
Q Consensus 194 HHCpWv~nCIG~ 205 (320)
.||||++.-...
T Consensus 56 ~~CPwv~~~~q~ 67 (91)
T PF08600_consen 56 EYCPWVNPSTQS 67 (91)
T ss_pred ccCCccCCcccc
Confidence 689999987643
No 30
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=36.68 E-value=9.4 Score=37.40 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=20.0
Q ss_pred eecccCCcc--cCCCCccCcCCCccc
Q 020836 166 LTCSYCNVE--QPPRAKHCHDCDRCV 189 (320)
Q Consensus 166 ~~C~~C~~~--kP~Rs~HC~~C~rCV 189 (320)
.+|+.|... --.|-|||+.||+-+
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHH
Confidence 799999875 466899999999854
No 31
>COG3336 Predicted membrane protein [Function unknown]
Probab=36.62 E-value=84 Score=29.33 Aligned_cols=53 Identities=19% Similarity=0.211 Sum_probs=29.9
Q ss_pred HHHHHhhhhhhcchhhhhccCCchHHHHHHHHHHHHHHHHHH-HHhccCCCccC
Q 020836 45 LHLVFVGVIFLFDSELIEKTKHEPWYITFYLLLFVATLVQYF-ITSGSSPGYVL 97 (320)
Q Consensus 45 l~l~~~~~~~~~~~~l~~~~~~~~~~~~i~~~l~~~~l~~y~-~~~~~dPG~vp 97 (320)
+++...+.++.+.+.++......++...+..++++.+-+.|+ ..+-.|||-=+
T Consensus 133 ~ilfig~~~~~hvpplfda~v~~p~~H~lm~~~~f~~aylfww~mI~~dpg~r~ 186 (299)
T COG3336 133 LILFIGAFWAWHVPPLFDAAVTSPTLHLLMNLLFFLSAYLFWWAMIGPDPGPRR 186 (299)
T ss_pred HHHHHHHHHHhccchhhhhhhhcccHHHHHHHHHHHHHHHHHHHHHccCCCCcc
Confidence 333333445556666676666777766666555554444444 44445998643
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=35.09 E-value=15 Score=25.34 Aligned_cols=36 Identities=28% Similarity=0.804 Sum_probs=27.5
Q ss_pred ecccCCcccCCCC-------ccCcCCCcccCCC-cccCcCCCccccc
Q 020836 167 TCSYCNVEQPPRA-------KHCHDCDRCVLQF-DHHCVWLGTCVGL 205 (320)
Q Consensus 167 ~C~~C~~~kP~Rs-------~HC~~C~rCV~r~-DHHCpWv~nCIG~ 205 (320)
-|..|+.--|+-+ +-|.-|..|+..+ +++|| ||=|.
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 3777877666654 6688999999997 99999 66554
No 33
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.93 E-value=64 Score=25.81 Aligned_cols=29 Identities=24% Similarity=0.770 Sum_probs=16.3
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 020836 209 CRFWWKDVIMIVLLIILAISLIFLLLLLL 237 (320)
Q Consensus 209 r~F~~~~~~~i~~~~~~~~~~~~~~~L~~ 237 (320)
|.|+|++.-+.+++.+.++++++++.+++
T Consensus 85 rk~wWkn~Km~~il~~v~~i~l~iiii~~ 113 (116)
T KOG0860|consen 85 RKMWWKNCKMRIILGLVIIILLVVIIIYI 113 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778887666555554444444444433
No 34
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=32.90 E-value=29 Score=23.35 Aligned_cols=24 Identities=29% Similarity=0.738 Sum_probs=16.7
Q ss_pred eecccCCcc--cCCCCccCcCCCccc
Q 020836 166 LTCSYCNVE--QPPRAKHCHDCDRCV 189 (320)
Q Consensus 166 ~~C~~C~~~--kP~Rs~HC~~C~rCV 189 (320)
.-|..|+.. .-.|.|||+.||+-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 346777652 456889999998854
No 35
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=32.34 E-value=1.1e+02 Score=22.96 Aligned_cols=28 Identities=21% Similarity=0.294 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCc
Q 020836 220 VLLIILAISLIFLLLLLLFHSYLILTNQ 247 (320)
Q Consensus 220 ~~~~~~~~~~~~~~~L~~~h~~lI~~n~ 247 (320)
+++++++++++..+.+++-.+|-+-++.
T Consensus 30 vvl~ml~~fa~l~ly~~~~ai~~~Gk~~ 57 (85)
T PF13150_consen 30 VVLVMLVLFAALCLYMTVSAIYDIGKED 57 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 3344444444445556666777777655
No 36
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=31.81 E-value=31 Score=20.64 Aligned_cols=22 Identities=23% Similarity=0.622 Sum_probs=11.1
Q ss_pred eecccCCcc----cCCCCccCcCCCc
Q 020836 166 LTCSYCNVE----QPPRAKHCHDCDR 187 (320)
Q Consensus 166 ~~C~~C~~~----kP~Rs~HC~~C~r 187 (320)
+||..|... .-..+..|..|+.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 789999775 2335666666654
No 37
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=30.81 E-value=3.2e+02 Score=22.85 Aligned_cols=10 Identities=30% Similarity=0.454 Sum_probs=8.1
Q ss_pred cCCCCHhHHH
Q 020836 268 VYPFSDGVCR 277 (320)
Q Consensus 268 ~npfd~G~~~ 277 (320)
.||||.|..+
T Consensus 167 Y~PfdigKkk 176 (180)
T COG5249 167 YNPFDIGKKK 176 (180)
T ss_pred CCchhhhhhh
Confidence 6899999764
No 38
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=27.56 E-value=1e+02 Score=23.20 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCchhHHHH
Q 020836 223 IILAISLIFLLLLLLFHSYLILTNQTTYELV 253 (320)
Q Consensus 223 ~~~~~~~~~~~~L~~~h~~lI~~n~TT~E~~ 253 (320)
+++.+..+.+..+|+.-++.|.+|.-..|..
T Consensus 39 Vic~~lVfVii~lFi~ll~~i~~~~e~~~~~ 69 (84)
T PF06143_consen 39 VICCFLVFVIIVLFILLLYNINKNAEQDRAE 69 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 4444434444455555556666666444433
No 39
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=27.40 E-value=1.7e+02 Score=27.52 Aligned_cols=34 Identities=24% Similarity=0.470 Sum_probs=29.3
Q ss_pred cCCCCccCcCCCcccCCCcccCcCCCcccccccc
Q 020836 175 QPPRAKHCHDCDRCVLQFDHHCVWLGTCVGLVNH 208 (320)
Q Consensus 175 kP~Rs~HC~~C~rCV~r~DHHCpWv~nCIG~~N~ 208 (320)
+-.+.+.|++|+.-...--|||.--|.||-+-=|
T Consensus 105 ~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DH 138 (309)
T COG5273 105 KFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDH 138 (309)
T ss_pred ccccceeccccccccCCCCccchhhcchhhccCc
Confidence 4457889999999999999999999999977666
No 40
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.45 E-value=43 Score=34.88 Aligned_cols=13 Identities=15% Similarity=0.253 Sum_probs=8.8
Q ss_pred CCCCHhHHHhHhh
Q 020836 269 YPFSDGVCRNLYK 281 (320)
Q Consensus 269 npfd~G~~~N~~~ 281 (320)
.|+-.+.++++.+
T Consensus 126 ~p~~~s~~~~~~~ 138 (645)
T PRK14559 126 QPLQPSPLEALLE 138 (645)
T ss_pred CCCccCHHHHHHH
Confidence 5777777777644
No 41
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=23.89 E-value=26 Score=34.90 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=15.6
Q ss_pred eecccCCcc--cCCCCccCcCCCc
Q 020836 166 LTCSYCNVE--QPPRAKHCHDCDR 187 (320)
Q Consensus 166 ~~C~~C~~~--kP~Rs~HC~~C~r 187 (320)
..|..|+.. --.|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 357777664 2348899999886
No 42
>PF03381 CDC50: LEM3 (ligand-effect modulator 3) family / CDC50 family; InterPro: IPR005045 Members of this family have no known function. They have predicted transmembrane helices.; GO: 0016020 membrane
Probab=22.60 E-value=1.4e+02 Score=27.59 Aligned_cols=34 Identities=24% Similarity=0.482 Sum_probs=20.5
Q ss_pred cccccccchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 020836 201 TCVGLVNHCRFWWKDVIMIVLLIILAISLIFLLLLLLFHSY 241 (320)
Q Consensus 201 nCIG~~N~r~F~~~~~~~i~~~~~~~~~~~~~~~L~~~h~~ 241 (320)
+.+|-+|+ .+.++.+++.++.+++.++|++.|+.
T Consensus 236 s~~Ggkn~-------~Lgi~ylvvg~i~~v~~i~~~~~~~~ 269 (278)
T PF03381_consen 236 SWFGGKNY-------FLGIAYLVVGGICLVLAIIFLIIHYF 269 (278)
T ss_pred cccCcccc-------HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45666666 34455556666666666666666654
No 43
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.37 E-value=38 Score=20.93 Aligned_cols=9 Identities=22% Similarity=0.434 Sum_probs=6.0
Q ss_pred eecccCCcc
Q 020836 166 LTCSYCNVE 174 (320)
Q Consensus 166 ~~C~~C~~~ 174 (320)
+||++|+..
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 578888765
No 44
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=22.06 E-value=1.2e+02 Score=27.29 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHhccCCCccCCcc
Q 020836 78 FVATLVQYFITSGSSPGYVLDAM 100 (320)
Q Consensus 78 ~~~~l~~y~~~~~~dPG~vp~~~ 100 (320)
.+..+..|.++.-+|||.+....
T Consensus 204 vf~LvgLyr~C~k~dPg~p~~g~ 226 (259)
T PF07010_consen 204 VFTLVGLYRMCWKTDPGTPENGP 226 (259)
T ss_pred HHHHHHHHHHhhcCCCCCcccCC
Confidence 33344456667779999765443
No 45
>KOG1326 consensus Membrane-associated protein FER-1 and related ferlins, contain multiple C2 domains [Cell wall/membrane/envelope biogenesis]
Probab=21.28 E-value=1e+02 Score=33.58 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=24.1
Q ss_pred ccchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 020836 206 VNHCRFWWKDVIMIVLLIILAISLIFLLLLLLFHS 240 (320)
Q Consensus 206 ~N~r~F~~~~~~~i~~~~~~~~~~~~~~~L~~~h~ 240 (320)
++.++++|...-+.+++.+.+++++.+..++++|+
T Consensus 1060 K~~~~i~W~~yr~~il~~l~ililll~l~~fly~~ 1094 (1105)
T KOG1326|consen 1060 KSFKFILWHRYRWYILLLLLILILLLLLALFLYSL 1094 (1105)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 56778888776666666666666666667777776
No 46
>PF05297 Herpes_LMP1: Herpesvirus latent membrane protein 1 (LMP1); InterPro: IPR007961 This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4). LMP1 of HHV-4 is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N terminus and a long cytoplasmic carboxy tail of 200 amino acids. HHV-4 virus latent membrane protein 1 (LMP1) is essential for HHV-4 mediated transformation and has been associated with several cases of malignancies. HHV-4-like viruses in Macaca fascicularis (Cynomolgus monkeys) have been associated with high lymphoma rates in immunosuppressed monkeys [].; GO: 0019087 transformation of host cell by virus, 0016021 integral to membrane; PDB: 1CZY_E 1ZMS_B.
Probab=21.21 E-value=32 Score=32.01 Aligned_cols=10 Identities=20% Similarity=0.528 Sum_probs=0.0
Q ss_pred hhhccCCchH
Q 020836 60 LIEKTKHEPW 69 (320)
Q Consensus 60 l~~~~~~~~~ 69 (320)
+.+....+.|
T Consensus 128 lLr~~GAs~W 137 (381)
T PF05297_consen 128 LLRELGASFW 137 (381)
T ss_dssp ----------
T ss_pred HHHHhhhHHH
Confidence 3444444444
No 47
>KOG4004 consensus Matricellular protein Osteonectin/SPARC/BM-40 [Extracellular structures]
Probab=20.93 E-value=46 Score=29.35 Aligned_cols=18 Identities=28% Similarity=0.403 Sum_probs=13.0
Q ss_pred CcccCcCCCccc-ccccch
Q 020836 192 FDHHCVWLGTCV-GLVNHC 209 (320)
Q Consensus 192 ~DHHCpWv~nCI-G~~N~r 209 (320)
-||||.|--||+ |.+|..
T Consensus 54 ~dh~Cg~gk~C~vd~~~~P 72 (259)
T KOG4004|consen 54 ADHKCGPGKNCLVDLQTQP 72 (259)
T ss_pred ccccCCCCceeeecCCCCc
Confidence 389999988884 666643
No 48
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.64 E-value=58 Score=21.41 Aligned_cols=8 Identities=25% Similarity=0.638 Sum_probs=4.7
Q ss_pred ecccCCcc
Q 020836 167 TCSYCNVE 174 (320)
Q Consensus 167 ~C~~C~~~ 174 (320)
||+.|+..
T Consensus 2 FCp~Cg~~ 9 (52)
T smart00661 2 FCPKCGNM 9 (52)
T ss_pred CCCCCCCc
Confidence 56666554
No 49
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.56 E-value=47 Score=19.46 Aligned_cols=21 Identities=24% Similarity=0.583 Sum_probs=7.9
Q ss_pred ecccCCcccCC-CCccCcCCCc
Q 020836 167 TCSYCNVEQPP-RAKHCHDCDR 187 (320)
Q Consensus 167 ~C~~C~~~kP~-Rs~HC~~C~r 187 (320)
.|..|+..... ...+|..|+-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 36667666555 6777877763
Done!