Query 025922
Match_columns 246
No_of_seqs 158 out of 1681
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 11:04:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025922hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315 Predicted DHHC-type Zn 100.0 1.5E-52 3.2E-57 364.4 15.8 218 24-246 13-230 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 2E-43 4.3E-48 304.2 10.0 200 20-245 13-223 (414)
3 PF01529 zf-DHHC: DHHC palmito 100.0 7.4E-43 1.6E-47 284.7 11.2 169 76-246 2-171 (174)
4 KOG1311 DHHC-type Zn-finger pr 100.0 4.4E-41 9.5E-46 296.7 18.1 157 84-246 79-239 (299)
5 COG5273 Uncharacterized protei 100.0 1.6E-37 3.6E-42 273.3 14.2 168 65-245 60-229 (309)
6 KOG1313 DHHC-type Zn-finger pr 100.0 8.9E-36 1.9E-40 249.7 9.3 124 122-245 100-242 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 1.7E-30 3.7E-35 219.0 9.7 103 73-188 110-212 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 2.4E-26 5.3E-31 212.1 11.0 101 77-189 384-485 (600)
9 PF01529 zf-DHHC: DHHC palmito 95.0 0.68 1.5E-05 37.0 12.0 62 119-191 57-118 (174)
10 KOG1311 DHHC-type Zn-finger pr 93.1 0.58 1.3E-05 41.3 8.5 58 137-194 112-180 (299)
11 PF13240 zinc_ribbon_2: zinc-r 89.3 0.21 4.4E-06 26.7 1.1 21 126-146 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 89.3 0.22 4.7E-06 31.4 1.3 24 123-146 13-36 (48)
13 COG5273 Uncharacterized protei 85.8 15 0.00032 32.7 11.4 116 119-245 118-241 (309)
14 PF13248 zf-ribbon_3: zinc-rib 84.9 0.49 1.1E-05 25.9 1.0 22 125-146 3-24 (26)
15 PTZ00303 phosphatidylinositol 81.0 0.95 2.1E-05 44.7 1.9 23 124-146 460-489 (1374)
16 COG1552 RPL40A Ribosomal prote 78.4 0.45 9.7E-06 30.1 -0.8 26 122-147 12-37 (50)
17 PF12773 DZR: Double zinc ribb 76.2 2.6 5.7E-05 26.5 2.3 36 122-157 10-48 (50)
18 PF01020 Ribosomal_L40e: Ribos 74.6 2 4.4E-05 27.6 1.4 25 123-147 16-42 (52)
19 KOG0509 Ankyrin repeat and DHH 74.3 1.7 3.8E-05 41.7 1.6 55 121-176 322-376 (600)
20 PF10571 UPF0547: Uncharacteri 73.7 1.8 3.9E-05 23.7 0.9 22 125-146 1-22 (26)
21 PF01363 FYVE: FYVE zinc finge 71.4 1.7 3.6E-05 29.4 0.5 26 123-148 8-35 (69)
22 PF12773 DZR: Double zinc ribb 67.9 3.8 8.3E-05 25.7 1.6 25 121-145 26-50 (50)
23 smart00064 FYVE Protein presen 66.8 4.3 9.4E-05 27.2 1.9 25 124-148 10-36 (68)
24 PF00641 zf-RanBP: Zn-finger i 59.4 3.9 8.4E-05 22.9 0.4 21 126-146 6-26 (30)
25 KOG3183 Predicted Zn-finger pr 55.5 5.3 0.00011 34.0 0.8 13 147-159 37-49 (250)
26 PF06906 DUF1272: Protein of u 54.0 5.5 0.00012 26.1 0.5 36 125-163 6-49 (57)
27 KOG1842 FYVE finger-containing 52.2 4.3 9.3E-05 37.6 -0.2 26 122-147 178-205 (505)
28 cd00065 FYVE FYVE domain; Zinc 49.9 11 0.00024 24.1 1.5 22 126-147 4-27 (57)
29 PF09297 zf-NADH-PPase: NADH p 49.7 9.2 0.0002 21.7 1.0 23 124-146 3-29 (32)
30 KOG1315 Predicted DHHC-type Zn 48.8 2E+02 0.0043 25.7 10.6 29 137-165 108-136 (307)
31 PF07649 C1_3: C1-like domain; 45.1 8.4 0.00018 21.5 0.3 21 126-146 2-23 (30)
32 KOG1398 Uncharacterized conser 43.3 6.5 0.00014 35.9 -0.5 25 134-164 10-34 (460)
33 COG2093 DNA-directed RNA polym 42.9 14 0.0003 24.7 1.1 23 124-146 4-26 (64)
34 PF07282 OrfB_Zn_ribbon: Putat 42.2 16 0.00035 24.4 1.4 25 123-147 27-55 (69)
35 PF03107 C1_2: C1 domain; Int 41.2 17 0.00037 20.3 1.2 20 126-145 2-22 (30)
36 PF07010 Endomucin: Endomucin; 41.0 60 0.0013 27.6 4.8 23 69-91 202-224 (259)
37 PF08600 Rsm1: Rsm1-like; Int 40.7 15 0.00033 26.5 1.1 11 153-163 56-66 (91)
38 PLN00186 ribosomal protein S26 39.1 13 0.00028 27.8 0.5 19 137-155 19-37 (109)
39 PRK09335 30S ribosomal protein 38.4 13 0.00029 27.0 0.6 21 137-157 19-39 (95)
40 PRK03681 hypA hydrogenase nick 37.0 18 0.0004 27.2 1.1 26 121-146 67-95 (114)
41 PF02150 RNA_POL_M_15KD: RNA p 35.9 13 0.00027 21.8 0.1 8 125-132 2-9 (35)
42 PTZ00172 40S ribosomal protein 35.5 15 0.00033 27.3 0.5 19 137-155 19-37 (108)
43 smart00547 ZnF_RBZ Zinc finger 34.5 20 0.00044 19.0 0.8 21 126-146 4-24 (26)
44 PF01437 PSI: Plexin repeat; 34.5 9.1 0.0002 24.2 -0.7 18 142-159 6-23 (51)
45 smart00661 RPOL9 RNA polymeras 33.3 22 0.00047 22.2 0.9 7 126-132 2-8 (52)
46 PRK12286 rpmF 50S ribosomal pr 32.5 35 0.00076 22.4 1.8 23 122-146 25-48 (57)
47 KOG3611 Semaphorins [Signal tr 31.9 18 0.00038 36.2 0.4 37 138-174 491-535 (737)
48 KOG1819 FYVE finger-containing 30.9 15 0.00033 34.7 -0.2 24 123-146 900-925 (990)
49 PRK14559 putative protein seri 30.8 32 0.0007 33.9 2.0 39 124-164 15-53 (645)
50 PF12172 DUF35_N: Rubredoxin-l 29.7 21 0.00045 20.9 0.3 24 121-145 8-32 (37)
51 PHA02680 ORF090 IMV phosphoryl 29.1 2.2E+02 0.0048 20.4 7.6 31 212-245 50-80 (91)
52 COG4640 Predicted membrane pro 28.8 28 0.00061 32.0 1.1 25 124-148 1-25 (465)
53 PRK00432 30S ribosomal protein 28.7 35 0.00076 21.7 1.3 24 123-146 19-45 (50)
54 PF07754 DUF1610: Domain of un 28.6 40 0.00086 18.1 1.2 19 127-145 1-23 (24)
55 TIGR01031 rpmF_bact ribosomal 28.4 44 0.00095 21.7 1.7 23 122-146 24-47 (55)
56 smart00423 PSI domain found in 28.2 21 0.00045 21.9 0.2 16 143-158 6-21 (46)
57 PHA02942 putative transposase; 28.1 36 0.00079 31.2 1.7 24 123-146 324-350 (383)
58 PRK15033 tricarballylate utili 27.4 2.1E+02 0.0046 26.4 6.5 15 139-157 67-81 (389)
59 PF01283 Ribosomal_S26e: Ribos 27.0 22 0.00049 26.8 0.1 21 137-157 19-39 (113)
60 KOG1841 Smad anchor for recept 26.6 30 0.00066 35.9 1.0 24 123-146 556-581 (1287)
61 COG0603 Predicted PP-loop supe 26.1 22 0.00048 30.1 -0.0 19 133-151 187-205 (222)
62 PRK13130 H/ACA RNA-protein com 26.0 48 0.001 21.7 1.5 22 123-146 4-25 (56)
63 KOG1818 Membrane trafficking a 25.6 27 0.00058 34.1 0.4 23 124-146 165-189 (634)
64 KOG1729 FYVE finger containing 25.6 17 0.00037 32.0 -0.8 28 123-150 167-197 (288)
65 PRK14559 putative protein seri 24.5 41 0.0009 33.2 1.5 21 126-146 3-23 (645)
66 KOG1313 DHHC-type Zn-finger pr 23.1 1.8E+02 0.0038 25.7 4.9 55 119-184 111-165 (309)
67 PRK12380 hydrogenase nickel in 22.6 46 0.001 24.9 1.1 25 122-146 68-94 (113)
68 KOG1710 MYND Zn-finger and ank 21.9 36 0.00078 30.2 0.5 21 123-145 318-338 (396)
69 KOG4399 C2HC-type Zn-finger pr 21.8 30 0.00064 30.0 -0.1 13 125-137 262-274 (325)
70 PRK15103 paraquat-inducible me 21.8 6.6E+02 0.014 23.4 12.7 33 123-155 220-252 (419)
71 CHL00031 psbT photosystem II p 21.5 1.8E+02 0.0039 16.8 3.3 15 77-91 17-31 (33)
72 PF00130 C1_1: Phorbol esters/ 20.9 55 0.0012 20.4 1.1 25 122-146 9-36 (53)
73 PRK11875 psbT photosystem II r 20.7 1.8E+02 0.0039 16.5 3.5 14 77-90 17-30 (31)
74 PHA02898 virion envelope prote 20.6 3.4E+02 0.0073 19.6 7.3 30 212-244 49-79 (92)
75 COG1579 Zn-ribbon protein, pos 20.3 86 0.0019 26.9 2.4 24 124-147 197-230 (239)
76 PF03842 Silic_transp: Silicon 20.1 7.3E+02 0.016 23.3 9.9 18 168-185 171-188 (512)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.5e-52 Score=364.37 Aligned_cols=218 Identities=41% Similarity=0.755 Sum_probs=174.8
Q ss_pred hhhHHHHHhhhhheeeeeeeeecccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchhhhcc
Q 025922 24 SIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGE 103 (246)
Q Consensus 24 ~~~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~dPG~vp~~~~~~~~~~~~~ 103 (246)
+++++++.++++|.||++++..+.+.+..+ ......+++++.++++.+|+|++++++|||.+|..+.++.++++..
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~----~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~ 88 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISLT----IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSL 88 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhhh----hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccc
Confidence 899999999999999999988887755332 3456777899999999999999999999999999988876655433
Q ss_pred CCCCCccccCCCCCCCCCCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHHHHHH
Q 025922 104 ADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSL 183 (246)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~ 183 (246)
+..............+..+..|+|++|+.+|||||||||.|+|||+||||||||+|||||.+|||+|++|++|+.+.+.+
T Consensus 89 ~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~ 168 (307)
T KOG1315|consen 89 ENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIY 168 (307)
T ss_pred cccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHH
Confidence 32111111111223356788999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCC
Q 025922 184 VTLSLLPHFISFFSEGEIPGTPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEVL 246 (246)
Q Consensus 184 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~~~~~l~~~~l~~~hl~li~~n~TT~E~l 246 (246)
.++.....+...+ ......++.....+.+.+++.+.+++.+.+|+++|++||++|+||+|..
T Consensus 169 ~lv~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~ 230 (307)
T KOG1315|consen 169 VLVTTLIGFTKYF-QGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAY 230 (307)
T ss_pred HHHHHHHHHHHHH-hccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhh
Confidence 8887777777766 2222233333444555566777888888889999999999999999963
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2e-43 Score=304.19 Aligned_cols=200 Identities=31% Similarity=0.569 Sum_probs=145.0
Q ss_pred cchhhhhHHHHHhhhhheeeeeeeeecccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchh
Q 025922 20 RGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDE 99 (246)
Q Consensus 20 ~~~~~~~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~dPG~vp~~~~~~~~~ 99 (246)
.++|++..+.+..+++...-......|.| .++..+....+.|.+...|.+++|+.+++++||++|++|+|...+
T Consensus 13 ~hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~ 86 (414)
T KOG1314|consen 13 LHWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK 86 (414)
T ss_pred eccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh
Confidence 44566655544444443332222234555 345556666777777888999999999999999999999985322
Q ss_pred hhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHH
Q 025922 100 ERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFL 179 (246)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i 179 (246)
++.-.+||.+|+.+||||||||+.|||||.||||||||+|||||..||.+|..||++..+
T Consensus 87 --------------------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~iv 146 (414)
T KOG1314|consen 87 --------------------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIV 146 (414)
T ss_pred --------------------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHH
Confidence 123469999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH----HHHHHh----cCCCCCC---CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccC
Q 025922 180 ETSLVTLSLLP----HFISFF----SEGEIPG---TPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEV 245 (246)
Q Consensus 180 ~~~~~~~~~~~----~~~~~~----~~~~~~~---~~~~~~~~~~~~vl~~~~~l~~~~l~~~hl~li~~n~TT~E~ 245 (246)
+|+-.++.+.. .+...+ ....++. .+.++..+++++.+++...+.++.|++.|+..|.+|+|.||+
T Consensus 147 G~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~ 223 (414)
T KOG1314|consen 147 GCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIES 223 (414)
T ss_pred hcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHH
Confidence 88764432221 122212 2222222 223344445555566666777888999999999999999996
No 3
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=7.4e-43 Score=284.66 Aligned_cols=169 Identities=32% Similarity=0.627 Sum_probs=121.7
Q ss_pred HHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccccccCcccccCCccc
Q 025922 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (246)
Q Consensus 76 ~~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhC 155 (246)
++|++++++|||++|+......+.+ .+ .............++..++.++|.+|+..||+|||||+.||+||+|+||||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC 79 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQ-EE-KEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHC 79 (174)
T ss_pred EEehhhheECCcccCCccccccccc-cc-cccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccc
Confidence 4688999999999997622111111 11 111111111122335678899999999999999999999999999999999
Q ss_pred ccccceeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025922 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP-GTLATTFLAFVLNLAFALSVLGFLIMHIS 234 (246)
Q Consensus 156 pwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~vl~~~~~l~~~~l~~~hl~ 234 (246)
||+|||||.+|||+|++|+++..+.+++..+..+..+............. ......++.+++++++++++++++++|++
T Consensus 80 ~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 159 (174)
T PF01529_consen 80 PWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLY 159 (174)
T ss_pred hhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999988776665555543332111111 11111134445667788888899999999
Q ss_pred HHhcCcccccCC
Q 025922 235 LVSANTTTIEVL 246 (246)
Q Consensus 235 li~~n~TT~E~l 246 (246)
++++|+||+|.+
T Consensus 160 ~i~~n~Tt~E~~ 171 (174)
T PF01529_consen 160 LILRNITTYERI 171 (174)
T ss_pred HHHcCCcHHHHH
Confidence 999999999964
No 4
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.4e-41 Score=296.67 Aligned_cols=157 Identities=32% Similarity=0.639 Sum_probs=114.5
Q ss_pred cCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccccccCcccccCCcccccccceee
Q 025922 84 TDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVG 163 (246)
Q Consensus 84 ~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG 163 (246)
+|||.+|++..+..+. .++.+.. .....++...+.+||.+|+.+||||||||+.||+||+||||||||+|||||
T Consensus 79 sdpg~~p~~~~~~~~~--~~~~~~~----~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG 152 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIED--PERAPLY----KNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIG 152 (299)
T ss_pred CCCceecCcccCCCCC--ccccccC----CCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceEC
Confidence 5999999863111111 1111111 111233556789999999999999999999999999999999999999999
Q ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CC--CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025922 164 ALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGE--IP--GTPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSAN 239 (246)
Q Consensus 164 ~~N~r~F~~fl~~~~i~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~vl~~~~~l~~~~l~~~hl~li~~n 239 (246)
++|||+|+.|++++.+++++..+.....+.....+.. .. ..+......++..++++.+...+++|+.+|++++.+|
T Consensus 153 ~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~ 232 (299)
T KOG1311|consen 153 ERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSG 232 (299)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecC
Confidence 9999999999999999999988776655554332211 11 2222223333444667777778888999999999999
Q ss_pred cccccCC
Q 025922 240 TTTIEVL 246 (246)
Q Consensus 240 ~TT~E~l 246 (246)
+||+|.+
T Consensus 233 ~Tt~e~~ 239 (299)
T KOG1311|consen 233 STTYESI 239 (299)
T ss_pred cchhhhh
Confidence 9999974
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=1.6e-37 Score=273.28 Aligned_cols=168 Identities=36% Similarity=0.632 Sum_probs=120.6
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCcccccc
Q 025922 65 ILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVC 144 (246)
Q Consensus 65 ~~~~~l~~~~~~~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C 144 (246)
+.+.+...+....|++..++|||+.+++.....-++..+ ....++..+..++|.+|+.+||+|||||+.|
T Consensus 60 i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~C 129 (309)
T COG5273 60 ILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETIS----------RLLDDGKFGTENFCSTCNIYKPPRSHHCSIC 129 (309)
T ss_pred hhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhh----------hhhhcCccccceeccccccccCCCCccchhh
Confidence 344455667778899999999999986533322221111 1122355778999999999999999999999
Q ss_pred CcccccCCcccccccceeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCchhH-HHHHHH-HHHHHHHH
Q 025922 145 GRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTL-ATTFLA-FVLNLAFA 222 (246)
Q Consensus 145 ~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~vl~~~~~ 222 (246)
|+||+||||||||+|||||.+|||+|++||+++......++......+.... +....+... ..++.+ ..+...+.
T Consensus 130 n~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~li~~~~~~~~~~f 206 (309)
T COG5273 130 NRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIF---SIRHDTSLAICFLIFGCSLLGVVFF 206 (309)
T ss_pred cchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc---cccCChHHHHHHHHHhhhHHHHHHH
Confidence 9999999999999999999999999999999998877776665444333322 123333333 112221 23344455
Q ss_pred HHHHHHHHHHHHHHhcCcccccC
Q 025922 223 LSVLGFLIMHISLVSANTTTIEV 245 (246)
Q Consensus 223 l~~~~l~~~hl~li~~n~TT~E~ 245 (246)
+.+..++.+|.+++..|+||+|.
T Consensus 207 ~~~~~~~~~~~~~~~~~~t~~e~ 229 (309)
T COG5273 207 IITTLLLLFLIYLILNNLTTIEF 229 (309)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHH
Confidence 66677889999999999999985
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=8.9e-36 Score=249.67 Aligned_cols=124 Identities=37% Similarity=0.726 Sum_probs=95.5
Q ss_pred CCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---
Q 025922 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSE--- 198 (246)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~~~~~~~~~~--- 198 (246)
....+|.+|.-+||||+||||.||+||+||||||||+|||||.+|||||++|++|+.+++.|+.+......+.....
T Consensus 100 ~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~ 179 (309)
T KOG1313|consen 100 ENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE 179 (309)
T ss_pred ccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh
Confidence 34589999999999999999999999999999999999999999999999999999999999877655444432211
Q ss_pred -CCCCCC------chhHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccC
Q 025922 199 -GEIPGT------PGTLA---------TTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEV 245 (246)
Q Consensus 199 -~~~~~~------~~~~~---------~~~~~~vl~~~~~l~~~~l~~~hl~li~~n~TT~E~ 245 (246)
...+++ |..+. -+.-..+++..+.+.++.+..||.++|++|.|++|.
T Consensus 180 ~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~ 242 (309)
T KOG1313|consen 180 ITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQ 242 (309)
T ss_pred cccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHH
Confidence 111111 11110 111234555566777888999999999999999985
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=1.7e-30 Score=219.02 Aligned_cols=103 Identities=32% Similarity=0.676 Sum_probs=77.8
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccccccCcccccCC
Q 025922 73 MLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMD 152 (246)
Q Consensus 73 ~~~~~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 152 (246)
+=..++..++.+|||.+.++.. .+..++-|.+. ..-.....|+||++.||.||||||.|||||.|+|
T Consensus 110 vp~i~f~ltc~snpg~i~k~n~----s~~~~~ypYDy---------~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfD 176 (341)
T KOG1312|consen 110 VPLIFFTLTCGSNPGIITKANE----SLFLHVYPYDY---------VIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFD 176 (341)
T ss_pred HHHHHHhhhhcCCCCccchhhh----ccceeccCccc---------eeecCCCccccccCCCccccccchHHHHHHHHhc
Confidence 3344567789999999974210 11111122211 1123347899999999999999999999999999
Q ss_pred cccccccceeecCchHHHHHHHHHHHHHHHHHHHHH
Q 025922 153 HHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSL 188 (246)
Q Consensus 153 HhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~ 188 (246)
|||.|+|||||.+|.|||++||++...++.+....+
T Consensus 177 HHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrl 212 (341)
T KOG1312|consen 177 HHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRL 212 (341)
T ss_pred cceEeeecccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999977777765543
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.93 E-value=2.4e-26 Score=212.08 Aligned_cols=101 Identities=32% Similarity=0.578 Sum_probs=75.7
Q ss_pred HHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCc-eeccccCcccCCCCccccccCcccccCCccc
Q 025922 77 SYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRI-RYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (246)
Q Consensus 77 ~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhC 155 (246)
.+.+...+|||.+|.+.... .+...+- .+.++.+.. +||.+|.+.||.|||||+.|||||.||||||
T Consensus 384 ~f~~~~rsDPg~i~~~~~~~--~~tIs~l----------~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhC 451 (600)
T KOG0509|consen 384 TFGLFLRSDPGFIPTSTEVG--RETISQL----------IDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHC 451 (600)
T ss_pred HHHHHhccCCCCCCCchhhH--HHHHHHh----------hccccccccccceeeeeeecCCccchhhhhHHHHhccccCC
Confidence 44556669999998642211 1111111 111233344 7999999999999999999999999999999
Q ss_pred ccccceeecCchHHHHHHHHHHHHHHHHHHHHHH
Q 025922 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLL 189 (246)
Q Consensus 156 pwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~ 189 (246)
||++||||.+|||+|+.|++.+...+.+..+...
T Consensus 452 Pwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~ 485 (600)
T KOG0509|consen 452 PWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCL 485 (600)
T ss_pred CccccccCccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999988777766655443
No 9
>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=95.02 E-value=0.68 Score=37.03 Aligned_cols=62 Identities=32% Similarity=0.514 Sum_probs=47.2
Q ss_pred CCCCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 025922 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPH 191 (246)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~~~ 191 (246)
....+.+.|..|+.--..+-|||.--|.||-+--| +.+-.|+++..-..+...+.....+..
T Consensus 57 ~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~~~~~~ 118 (174)
T PF01529_consen 57 IKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSLYYLVR 118 (174)
T ss_pred cCCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677899999999999999999999999998777 456678777766666666654443333
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=93.07 E-value=0.58 Score=41.26 Aligned_cols=58 Identities=24% Similarity=0.393 Sum_probs=42.8
Q ss_pred CCccccccCcccccCCcccccccceeecCch-----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025922 137 RCHHCSVCGRCILKMDHHCVWVVNCVGALNY-----------KYFLLFLLYTFLETSLVTLSLLPHFIS 194 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~-----------r~F~~fl~~~~i~~~~~~~~~~~~~~~ 194 (246)
+.++|+.|+..+...-|||+.-|+||-+.-| |.+-.|+.++....+...+........
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~ 180 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYE 180 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999987655 778899977663333333333333333
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.32 E-value=0.21 Score=26.65 Aligned_cols=21 Identities=29% Similarity=0.842 Sum_probs=17.9
Q ss_pred eccccCcccCCCCccccccCc
Q 025922 126 YCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
+|..|...-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588898888888999998875
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=89.31 E-value=0.22 Score=31.42 Aligned_cols=24 Identities=33% Similarity=0.838 Sum_probs=22.0
Q ss_pred CceeccccCcccCCCCccccccCc
Q 025922 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
....|.+|...-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 468999999999999999999886
No 13
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=85.82 E-value=15 Score=32.74 Aligned_cols=116 Identities=20% Similarity=0.233 Sum_probs=68.0
Q ss_pred CCCCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025922 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSE 198 (246)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~~~~~~~~~~~~~~~ 198 (246)
.+.++.+.|+.|+.=-...-|||.==|+||-+--| +=.=.|++++....+..++............-.+
T Consensus 118 ~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (309)
T COG5273 118 YKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHD 186 (309)
T ss_pred ccCCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCC
Confidence 34677899999999999999999999999998776 5566788877655555544433222222111111
Q ss_pred CC------CCCCchhHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccC
Q 025922 199 GE------IPGTPGTLA--TTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEV 245 (246)
Q Consensus 199 ~~------~~~~~~~~~--~~~~~~vl~~~~~l~~~~l~~~hl~li~~n~TT~E~ 245 (246)
.. ....+.... .++....+......++......+.+.+.++.++-|.
T Consensus 187 ~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~ 241 (309)
T COG5273 187 TSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEF 241 (309)
T ss_pred hHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccc
Confidence 00 000111111 111111112223444556777888999999988764
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.93 E-value=0.49 Score=25.86 Aligned_cols=22 Identities=27% Similarity=0.854 Sum_probs=18.4
Q ss_pred eeccccCcccCCCCccccccCc
Q 025922 125 RYCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
++|..|...-++.++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6788898877888888888875
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=80.99 E-value=0.95 Score=44.70 Aligned_cols=23 Identities=35% Similarity=0.816 Sum_probs=18.8
Q ss_pred ceeccccCcccC-------CCCccccccCc
Q 025922 124 IRYCRKCNQLKP-------PRCHHCSVCGR 146 (246)
Q Consensus 124 ~~~C~~C~~~kP-------~Rs~HC~~C~~ 146 (246)
...|..|+..-. -|.||||.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 368999997663 39999999987
No 16
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=78.38 E-value=0.45 Score=30.11 Aligned_cols=26 Identities=35% Similarity=0.866 Sum_probs=22.4
Q ss_pred CCceeccccCcccCCCCccccccCcc
Q 025922 122 PRIRYCRKCNQLKPPRCHHCSVCGRC 147 (246)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~C 147 (246)
...+.|.+|...-|+|+..|+.|+.=
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccCC
Confidence 34689999999999999999988753
No 17
>PF12773 DZR: Double zinc ribbon
Probab=76.16 E-value=2.6 Score=26.48 Aligned_cols=36 Identities=19% Similarity=0.465 Sum_probs=23.6
Q ss_pred CCceeccccCcccC---CCCccccccCcccccCCccccc
Q 025922 122 PRIRYCRKCNQLKP---PRCHHCSVCGRCILKMDHHCVW 157 (246)
Q Consensus 122 ~~~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHhCpw 157 (246)
.+.++|..|...-+ .....|+.|+.=+...+.+|+.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 34577777776544 3356677777777777777764
No 18
>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=74.56 E-value=2 Score=27.58 Aligned_cols=25 Identities=40% Similarity=0.931 Sum_probs=17.1
Q ss_pred CceeccccCcccCCCCccccc--cCcc
Q 025922 123 RIRYCRKCNQLKPPRCHHCSV--CGRC 147 (246)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 147 (246)
+...|.+|...-|+|+..|+. ||.+
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 468999999999999999998 8764
No 19
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=74.29 E-value=1.7 Score=41.70 Aligned_cols=55 Identities=5% Similarity=-0.158 Sum_probs=47.3
Q ss_pred CCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHH
Q 025922 121 NPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLY 176 (246)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~ 176 (246)
......|.+|....+.+..++..+-.+...+++||+|+. +|+..|-..+-+..+.
T Consensus 322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~ 376 (600)
T KOG0509|consen 322 LVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFII 376 (600)
T ss_pred hhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHH
Confidence 344678999999999999999999999999999999999 9999998865444433
No 20
>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=73.71 E-value=1.8 Score=23.74 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=17.9
Q ss_pred eeccccCcccCCCCccccccCc
Q 025922 125 RYCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
+.|..|...-|.-++-|+.||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688888888888888888874
No 21
>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=71.44 E-value=1.7 Score=29.38 Aligned_cols=26 Identities=35% Similarity=0.765 Sum_probs=12.5
Q ss_pred CceeccccCc--ccCCCCccccccCccc
Q 025922 123 RIRYCRKCNQ--LKPPRCHHCSVCGRCI 148 (246)
Q Consensus 123 ~~~~C~~C~~--~kP~Rs~HC~~C~~CV 148 (246)
+...|..|+. ---.|-|||+.||+-|
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 3467777764 2247889999999854
No 22
>PF12773 DZR: Double zinc ribbon
Probab=67.86 E-value=3.8 Score=25.70 Aligned_cols=25 Identities=28% Similarity=0.894 Sum_probs=22.0
Q ss_pred CCCceeccccCcccCCCCccccccC
Q 025922 121 NPRIRYCRKCNQLKPPRCHHCSVCG 145 (246)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~ 145 (246)
.....+|..|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 4457899999999999999999986
No 23
>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 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=59.40 E-value=3.9 Score=22.90 Aligned_cols=21 Identities=29% Similarity=0.882 Sum_probs=14.2
Q ss_pred eccccCcccCCCCccccccCc
Q 025922 126 YCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
.|..|...-++++.+|..|+.
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 577888877888888887764
No 25
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=55.51 E-value=5.3 Score=34.01 Aligned_cols=13 Identities=23% Similarity=0.189 Sum_probs=9.8
Q ss_pred ccccCCccccccc
Q 025922 147 CILKMDHHCVWVV 159 (246)
Q Consensus 147 CV~~~DHhCpwi~ 159 (246)
=..+.+|||||..
T Consensus 37 Hrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 37 HRSYESHHCPKGL 49 (250)
T ss_pred cchHhhcCCCccc
Confidence 3567889999874
No 26
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=54.03 E-value=5.5 Score=26.07 Aligned_cols=36 Identities=33% Similarity=0.883 Sum_probs=25.9
Q ss_pred eeccccCcccCCCC-------ccccccCcccccC-Ccccccccceee
Q 025922 125 RYCRKCNQLKPPRC-------HHCSVCGRCILKM-DHHCVWVVNCVG 163 (246)
Q Consensus 125 ~~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHhCpwi~nCIG 163 (246)
.-|..|+.--|+-| +-|-.|..|+..+ ++.|| ||=|
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgG 49 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGG 49 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCC
Confidence 34666666555543 6688899999998 99998 5554
No 27
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=52.23 E-value=4.3 Score=37.62 Aligned_cols=26 Identities=35% Similarity=0.982 Sum_probs=20.6
Q ss_pred CCceeccccCc--ccCCCCccccccCcc
Q 025922 122 PRIRYCRKCNQ--LKPPRCHHCSVCGRC 147 (246)
Q Consensus 122 ~~~~~C~~C~~--~kP~Rs~HC~~C~~C 147 (246)
....+|..|.. ---.|-|||+.||+-
T Consensus 178 s~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred CcccccccccchhhhHHHhhhhhhcchH
Confidence 45789999985 335689999999984
No 28
>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=49.92 E-value=11 Score=24.09 Aligned_cols=22 Identities=41% Similarity=0.928 Sum_probs=14.2
Q ss_pred eccccCc--ccCCCCccccccCcc
Q 025922 126 YCRKCNQ--LKPPRCHHCSVCGRC 147 (246)
Q Consensus 126 ~C~~C~~--~kP~Rs~HC~~C~~C 147 (246)
-|..|+. -.-.|.|||+.||+-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 4555543 235678889888875
No 29
>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=49.66 E-value=9.2 Score=21.72 Aligned_cols=23 Identities=30% Similarity=0.882 Sum_probs=10.7
Q ss_pred ceeccccCc-cc---CCCCccccccCc
Q 025922 124 IRYCRKCNQ-LK---PPRCHHCSVCGR 146 (246)
Q Consensus 124 ~~~C~~C~~-~k---P~Rs~HC~~C~~ 146 (246)
.+||..|.. .+ -.++..|+.|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 478888874 22 335556666553
No 30
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=48.79 E-value=2e+02 Score=25.70 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=15.7
Q ss_pred CCccccccCcccccCCcccccccceeecC
Q 025922 137 RCHHCSVCGRCILKMDHHCVWVVNCVGAL 165 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~ 165 (246)
+.+-|..|+.-....-|||.--+.||.+.
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKm 136 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKM 136 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhcc
Confidence 34455555555555555555555555544
No 31
>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=45.11 E-value=8.4 Score=21.49 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=8.1
Q ss_pred eccccCcccCC-CCccccccCc
Q 025922 126 YCRKCNQLKPP-RCHHCSVCGR 146 (246)
Q Consensus 126 ~C~~C~~~kP~-Rs~HC~~C~~ 146 (246)
.|..|+..... ...+|+.|+-
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 47777765555 6777877764
No 32
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.34 E-value=6.5 Score=35.94 Aligned_cols=25 Identities=40% Similarity=0.858 Sum_probs=18.8
Q ss_pred cCCCCccccccCcccccCCcccccccceeec
Q 025922 134 KPPRCHHCSVCGRCILKMDHHCVWVVNCVGA 164 (246)
Q Consensus 134 kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~ 164 (246)
+-.|..||..|+. .|| +|+.||||.
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga 34 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGA 34 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHH
Confidence 4456667777765 577 899999996
No 33
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=42.87 E-value=14 Score=24.74 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=20.6
Q ss_pred ceeccccCcccCCCCccccccCc
Q 025922 124 IRYCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
.+-|..|+..-|+.+.-|+.||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999987
No 34
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=42.18 E-value=16 Score=24.44 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=18.4
Q ss_pred CceeccccCccc----CCCCccccccCcc
Q 025922 123 RIRYCRKCNQLK----PPRCHHCSVCGRC 147 (246)
Q Consensus 123 ~~~~C~~C~~~k----P~Rs~HC~~C~~C 147 (246)
..+.|+.|.... ..|.++|+.||.-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 568899998644 4467788888764
No 35
>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=41.21 E-value=17 Score=20.30 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=12.9
Q ss_pred eccccCcccCCC-CccccccC
Q 025922 126 YCRKCNQLKPPR-CHHCSVCG 145 (246)
Q Consensus 126 ~C~~C~~~kP~R-s~HC~~C~ 145 (246)
+|..|+..-... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 466776655555 77777666
No 36
>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=41.01 E-value=60 Score=27.60 Aligned_cols=23 Identities=22% Similarity=0.122 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCC
Q 025922 69 CLLVMLLWSYFSVVLTDAGSVPP 91 (246)
Q Consensus 69 ~l~~~~~~~~~~~~~~dPG~vp~ 91 (246)
++.+.++-.|..|.-.|||....
T Consensus 202 l~vf~LvgLyr~C~k~dPg~p~~ 224 (259)
T PF07010_consen 202 LSVFTLVGLYRMCWKTDPGTPEN 224 (259)
T ss_pred HHHHHHHHHHHHhhcCCCCCccc
Confidence 33344445566788899996543
No 37
>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=40.74 E-value=15 Score=26.46 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.4
Q ss_pred cccccccceee
Q 025922 153 HHCVWVVNCVG 163 (246)
Q Consensus 153 HhCpwi~nCIG 163 (246)
.||||++.-..
T Consensus 56 ~~CPwv~~~~q 66 (91)
T PF08600_consen 56 EYCPWVNPSTQ 66 (91)
T ss_pred ccCCccCCccc
Confidence 58999987643
No 38
>PLN00186 ribosomal protein S26; Provisional
Probab=39.07 E-value=13 Score=27.77 Aligned_cols=19 Identities=32% Similarity=0.674 Sum_probs=13.8
Q ss_pred CCccccccCcccccCCccc
Q 025922 137 RCHHCSVCGRCILKMDHHC 155 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhC 155 (246)
+.-||..|++||++=---+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIK 37 (109)
T ss_pred cceeeCCCcccccccceEE
Confidence 3458999999999744333
No 39
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=38.42 E-value=13 Score=26.99 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=15.6
Q ss_pred CCccccccCcccccCCccccc
Q 025922 137 RCHHCSVCGRCILKMDHHCVW 157 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpw 157 (246)
+.-+|..|++||++----+.+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEE
Confidence 455899999999986555543
No 40
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=36.97 E-value=18 Score=27.16 Aligned_cols=26 Identities=19% Similarity=0.519 Sum_probs=19.0
Q ss_pred CCCceeccccCcccCCCCcc---ccccCc
Q 025922 121 NPRIRYCRKCNQLKPPRCHH---CSVCGR 146 (246)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~H---C~~C~~ 146 (246)
.+..-+|..|+..-|...++ |+.||.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 34568999999877765444 888885
No 41
>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=35.95 E-value=13 Score=21.83 Aligned_cols=8 Identities=38% Similarity=1.423 Sum_probs=4.4
Q ss_pred eeccccCc
Q 025922 125 RYCRKCNQ 132 (246)
Q Consensus 125 ~~C~~C~~ 132 (246)
+||.+|+.
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 56677753
No 42
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=35.47 E-value=15 Score=27.31 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=13.9
Q ss_pred CCccccccCcccccCCccc
Q 025922 137 RCHHCSVCGRCILKMDHHC 155 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhC 155 (246)
+.-||..|++||++=---+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIK 37 (108)
T ss_pred ccEEeCCccccccccceEE
Confidence 3458999999999744433
No 43
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=34.54 E-value=20 Score=18.96 Aligned_cols=21 Identities=29% Similarity=0.675 Sum_probs=15.0
Q ss_pred eccccCcccCCCCccccccCc
Q 025922 126 YCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477777777777777777764
No 44
>PF01437 PSI: Plexin repeat; InterPro: IPR002165 This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin (P70206 from SWISSPROT) []. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein (Q19981 from SWISSPROT) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.; GO: 0016020 membrane; PDB: 3NVQ_B 3NVN_B 3OL2_B 3OKT_A 3AL8_A 3OKW_A 3OKY_B 3AFC_B 1OLZ_B 1SHY_B ....
Probab=34.52 E-value=9.1 Score=24.20 Aligned_cols=18 Identities=28% Similarity=0.844 Sum_probs=13.3
Q ss_pred cccCcccccCCccccccc
Q 025922 142 SVCGRCILKMDHHCVWVV 159 (246)
Q Consensus 142 ~~C~~CV~~~DHhCpwi~ 159 (246)
..|+.|+...|-+|.|-.
T Consensus 6 ~sC~~Cl~~~dp~CgWc~ 23 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWCS 23 (51)
T ss_dssp SSHHHHHHSTCTTEEEET
T ss_pred CcHHHHHcCCCcCccccC
Confidence 567778887777887753
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.31 E-value=22 Score=22.24 Aligned_cols=7 Identities=43% Similarity=1.497 Sum_probs=3.6
Q ss_pred eccccCc
Q 025922 126 YCRKCNQ 132 (246)
Q Consensus 126 ~C~~C~~ 132 (246)
||..|+.
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 4555543
No 46
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=32.46 E-value=35 Score=22.37 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=16.0
Q ss_pred CCceeccccCcccCCCCcc-ccccCc
Q 025922 122 PRIRYCRKCNQLKPPRCHH-CSVCGR 146 (246)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H-C~~C~~ 146 (246)
+....|..|+..+ ++|| |..||.
T Consensus 25 ~~l~~C~~CG~~~--~~H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPK--LPHRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCcc--CCeEECCCCCc
Confidence 4457799998655 4476 777774
No 47
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=31.92 E-value=18 Score=36.25 Aligned_cols=37 Identities=27% Similarity=0.614 Sum_probs=28.5
Q ss_pred Ccccc---ccCcccccCCccccccc---cee--ecCchHHHHHHH
Q 025922 138 CHHCS---VCGRCILKMDHHCVWVV---NCV--GALNYKYFLLFL 174 (246)
Q Consensus 138 s~HC~---~C~~CV~~~DHhCpwi~---nCI--G~~N~r~F~~fl 174 (246)
-|+|+ .|..|++..|.||.|-+ .|+ +..|.|.+..=+
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~ 535 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDV 535 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhh
Confidence 46788 89998889999999998 687 445666666544
No 48
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=30.87 E-value=15 Score=34.75 Aligned_cols=24 Identities=33% Similarity=0.675 Sum_probs=17.1
Q ss_pred CceeccccCccc--CCCCccccccCc
Q 025922 123 RIRYCRKCNQLK--PPRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~~~k--P~Rs~HC~~C~~ 146 (246)
....|..|+..- -.|-|||+.||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 345688887532 347899999987
No 49
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.80 E-value=32 Score=33.88 Aligned_cols=39 Identities=26% Similarity=0.558 Sum_probs=19.3
Q ss_pred ceeccccCcccCCCCccccccCcccccCCcccccccceeec
Q 025922 124 IRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGA 164 (246)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~ 164 (246)
.+||..|+..-+ .+.|..||.=+..=..+||=-|.-.|.
T Consensus 15 akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCC--CCcCCCCCCCCCcccccccccCCcccc
Confidence 455666654222 234555555555555555544444443
No 50
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=29.67 E-value=21 Score=20.86 Aligned_cols=24 Identities=38% Similarity=0.960 Sum_probs=13.3
Q ss_pred CCCceeccccCccc-CCCCccccccC
Q 025922 121 NPRIRYCRKCNQLK-PPRCHHCSVCG 145 (246)
Q Consensus 121 ~~~~~~C~~C~~~k-P~Rs~HC~~C~ 145 (246)
....+.|..|..+. ||| ..|+.|+
T Consensus 8 ~l~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp -EEEEE-TTT--EEES---SEETTTT
T ss_pred EEEEEEcCCCCCEecCCC-cCCCCcC
Confidence 34468899999875 777 7787775
No 51
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=29.13 E-value=2.2e+02 Score=20.44 Aligned_cols=31 Identities=13% Similarity=0.337 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccC
Q 025922 212 FLAFVLNLAFALSVLGFLIMHISLVSANTTTIEV 245 (246)
Q Consensus 212 ~~~~vl~~~~~l~~~~l~~~hl~li~~n~TT~E~ 245 (246)
++.|++.+ +.+.+++++..|--+++.++.|.
T Consensus 50 ii~FIlG~---vl~lGilifs~y~~C~~~~~~~r 80 (91)
T PHA02680 50 VTCFIVGA---VLLLGLFVFSMYRKCSGSMPYER 80 (91)
T ss_pred HHHHHHHH---HHHHHHHHHHHhcccCCCceeec
Confidence 44444433 33445666777766666665553
No 52
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.82 E-value=28 Score=31.99 Aligned_cols=25 Identities=28% Similarity=0.822 Sum_probs=21.0
Q ss_pred ceeccccCcccCCCCccccccCccc
Q 025922 124 IRYCRKCNQLKPPRCHHCSVCGRCI 148 (246)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~~CV 148 (246)
.++|..|+..+-+-+..|..||.=+
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~ 25 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKF 25 (465)
T ss_pred CCcccccccccccccccccccCCcC
Confidence 3789999999999998888888743
No 53
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.70 E-value=35 Score=21.69 Aligned_cols=24 Identities=25% Similarity=0.826 Sum_probs=14.5
Q ss_pred CceeccccCc-cc--CCCCccccccCc
Q 025922 123 RIRYCRKCNQ-LK--PPRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~~-~k--P~Rs~HC~~C~~ 146 (246)
..++|..|.. .- -....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3578999976 22 223556777763
No 54
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=28.58 E-value=40 Score=18.10 Aligned_cols=19 Identities=37% Similarity=0.992 Sum_probs=10.1
Q ss_pred ccccCcccCCCC----ccccccC
Q 025922 127 CRKCNQLKPPRC----HHCSVCG 145 (246)
Q Consensus 127 C~~C~~~kP~Rs----~HC~~C~ 145 (246)
|..|+..-.+|- ..|..||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 555655444442 4466665
No 55
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.43 E-value=44 Score=21.72 Aligned_cols=23 Identities=30% Similarity=0.814 Sum_probs=15.9
Q ss_pred CCceeccccCcccCCCCcc-ccccCc
Q 025922 122 PRIRYCRKCNQLKPPRCHH-CSVCGR 146 (246)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H-C~~C~~ 146 (246)
.....|..|.. +-++|| |..||.
T Consensus 24 p~l~~C~~cG~--~~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGE--FKLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCC--cccCeeECCccCe
Confidence 34566888885 456777 777774
No 56
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=28.22 E-value=21 Score=21.88 Aligned_cols=16 Identities=38% Similarity=1.138 Sum_probs=8.6
Q ss_pred ccCcccccCCcccccc
Q 025922 143 VCGRCILKMDHHCVWV 158 (246)
Q Consensus 143 ~C~~CV~~~DHhCpwi 158 (246)
.|..|+...|-||.|=
T Consensus 6 sC~~C~~~~~~~C~Wc 21 (46)
T smart00423 6 SCSECLLARDPYCAWC 21 (46)
T ss_pred cHHHHHcCCCCCCCcc
Confidence 4555555555555554
No 57
>PHA02942 putative transposase; Provisional
Probab=28.05 E-value=36 Score=31.24 Aligned_cols=24 Identities=33% Similarity=0.721 Sum_probs=18.0
Q ss_pred CceeccccCcccC---CCCccccccCc
Q 025922 123 RIRYCRKCNQLKP---PRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~~~kP---~Rs~HC~~C~~ 146 (246)
..+.|+.|+...+ .|.+.|..||.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCC
Confidence 5688999986544 37778888776
No 58
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=27.40 E-value=2.1e+02 Score=26.42 Aligned_cols=15 Identities=40% Similarity=1.170 Sum_probs=12.8
Q ss_pred ccccccCcccccCCccccc
Q 025922 139 HHCSVCGRCILKMDHHCVW 157 (246)
Q Consensus 139 ~HC~~C~~CV~~~DHhCpw 157 (246)
..|..||.| +|+||.
T Consensus 67 ~~C~~Cg~C----~~~CP~ 81 (389)
T PRK15033 67 NLCHNCGAC----LHACQY 81 (389)
T ss_pred HhCcCcccc----cccCcC
Confidence 389999999 569998
No 59
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=26.97 E-value=22 Score=26.76 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=12.7
Q ss_pred CCccccccCcccccCCccccc
Q 025922 137 RCHHCSVCGRCILKMDHHCVW 157 (246)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpw 157 (246)
+.-||..|++||++----..+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKRF 39 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEEE
T ss_pred cCEeeCcccccCcCCceEEEE
Confidence 345899999999985544433
No 60
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=26.62 E-value=30 Score=35.94 Aligned_cols=24 Identities=33% Similarity=0.765 Sum_probs=18.1
Q ss_pred CceeccccC--cccCCCCccccccCc
Q 025922 123 RIRYCRKCN--QLKPPRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~--~~kP~Rs~HC~~C~~ 146 (246)
+..-|..|. ..--.|-||||.||+
T Consensus 556 e~pncm~clqkft~ikrrhhcRacgk 581 (1287)
T KOG1841|consen 556 EAPNCMDCLQKFTPIKRRHHCRACGK 581 (1287)
T ss_pred cCchHHHHHhhcccccccccchhccc
Confidence 345677776 455678999999998
No 61
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=26.10 E-value=22 Score=30.11 Aligned_cols=19 Identities=26% Similarity=0.740 Sum_probs=15.1
Q ss_pred ccCCCCccccccCcccccC
Q 025922 133 LKPPRCHHCSVCGRCILKM 151 (246)
Q Consensus 133 ~kP~Rs~HC~~C~~CV~~~ 151 (246)
+++.+..||..|+.|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 3666666999999999874
No 62
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.02 E-value=48 Score=21.73 Aligned_cols=22 Identities=41% Similarity=0.895 Sum_probs=15.8
Q ss_pred CceeccccCcccCCCCccccccCc
Q 025922 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
..+.|..|..+-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4578888887766 667777775
No 63
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.59 E-value=27 Score=34.13 Aligned_cols=23 Identities=35% Similarity=0.775 Sum_probs=17.0
Q ss_pred ceeccccCc--ccCCCCccccccCc
Q 025922 124 IRYCRKCNQ--LKPPRCHHCSVCGR 146 (246)
Q Consensus 124 ~~~C~~C~~--~kP~Rs~HC~~C~~ 146 (246)
..-|.+|.. ----|.|||+.||+
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccceeeeeeeeccccccccccch
Confidence 356888864 12349999999998
No 64
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=25.56 E-value=17 Score=32.04 Aligned_cols=28 Identities=29% Similarity=0.591 Sum_probs=20.7
Q ss_pred CceeccccCc-cc--CCCCccccccCccccc
Q 025922 123 RIRYCRKCNQ-LK--PPRCHHCSVCGRCILK 150 (246)
Q Consensus 123 ~~~~C~~C~~-~k--P~Rs~HC~~C~~CV~~ 150 (246)
+..-|..|.. .. -.|-|||+.||+=|-.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 5667888775 22 5689999999997665
No 65
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.54 E-value=41 Score=33.16 Aligned_cols=21 Identities=29% Similarity=0.835 Sum_probs=12.2
Q ss_pred eccccCcccCCCCccccccCc
Q 025922 126 YCRKCNQLKPPRCHHCSVCGR 146 (246)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (246)
.|..|+..-|+.++.|..||.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~ 23 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGT 23 (645)
T ss_pred cCCCCCCcCCCCCccccccCC
Confidence 455565555666655555554
No 66
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=23.11 E-value=1.8e+02 Score=25.66 Aligned_cols=55 Identities=25% Similarity=0.533 Sum_probs=43.0
Q ss_pred CCCCCceeccccCcccCCCCccccccCcccccCCcccccccceeecCchHHHHHHHHHHHHHHHHH
Q 025922 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLV 184 (246)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~r~F~~fl~~~~i~~~~~ 184 (246)
++.++..-|+.|+.=--.=-|||.-=|+||--..| +=.=.|+.++.-.+..+.+.
T Consensus 111 pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~ 165 (309)
T KOG1313|consen 111 PKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIM 165 (309)
T ss_pred CCCCCcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHH
Confidence 56677889999987656667999999999998888 55677888886665555554
No 67
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=22.56 E-value=46 Score=24.92 Aligned_cols=25 Identities=28% Similarity=0.729 Sum_probs=16.8
Q ss_pred CCceeccccCcccCCCCcc--ccccCc
Q 025922 122 PRIRYCRKCNQLKPPRCHH--CSVCGR 146 (246)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H--C~~C~~ 146 (246)
+..-+|..|+..-+....+ |+.||.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCC
Confidence 4568999998755553333 888874
No 68
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=21.91 E-value=36 Score=30.20 Aligned_cols=21 Identities=24% Similarity=0.790 Sum_probs=16.0
Q ss_pred CceeccccCcccCCCCccccccC
Q 025922 123 RIRYCRKCNQLKPPRCHHCSVCG 145 (246)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~ 145 (246)
.-+||++|...+|. +.|+.|+
T Consensus 318 d~~fCstCG~~ga~--KrCs~CK 338 (396)
T KOG1710|consen 318 DCQFCSTCGHPGAK--KRCSQCK 338 (396)
T ss_pred ecccccccCCCCcc--chhhhhH
Confidence 36899999988774 4577766
No 69
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=21.85 E-value=30 Score=30.03 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=5.6
Q ss_pred eeccccCcccCCC
Q 025922 125 RYCRKCNQLKPPR 137 (246)
Q Consensus 125 ~~C~~C~~~kP~R 137 (246)
+.|..|+.+--.|
T Consensus 262 ~~C~iC~~~~~~R 274 (325)
T KOG4399|consen 262 HGCFICGELDHKR 274 (325)
T ss_pred cceeecccccccc
Confidence 3444444444444
No 70
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=21.76 E-value=6.6e+02 Score=23.39 Aligned_cols=33 Identities=18% Similarity=0.389 Sum_probs=24.9
Q ss_pred CceeccccCcccCCCCccccccCcccccCCccc
Q 025922 123 RIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (246)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhC 155 (246)
...-|..|+..-|....||+.||.-..+.+++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 456799999887777778988888776655544
No 71
>CHL00031 psbT photosystem II protein T
Probab=21.50 E-value=1.8e+02 Score=16.82 Aligned_cols=15 Identities=20% Similarity=0.645 Sum_probs=11.6
Q ss_pred HHHHHhhcCCCCCCC
Q 025922 77 SYFSVVLTDAGSVPP 91 (246)
Q Consensus 77 ~~~~~~~~dPG~vp~ 91 (246)
.++...++||-.+++
T Consensus 17 lFFAI~FRePPri~k 31 (33)
T CHL00031 17 IFFAIFFREPPKVPT 31 (33)
T ss_pred HHHhheecCCCCCCC
Confidence 456788899988874
No 72
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=20.86 E-value=55 Score=20.40 Aligned_cols=25 Identities=28% Similarity=0.715 Sum_probs=17.3
Q ss_pred CCceeccccCccc---CCCCccccccCc
Q 025922 122 PRIRYCRKCNQLK---PPRCHHCSVCGR 146 (246)
Q Consensus 122 ~~~~~C~~C~~~k---P~Rs~HC~~C~~ 146 (246)
..+.+|..|+..- -..+.+|+.|+.
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGL 36 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCC
Confidence 4568999998655 556788998874
No 73
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=20.71 E-value=1.8e+02 Score=16.55 Aligned_cols=14 Identities=14% Similarity=0.524 Sum_probs=10.6
Q ss_pred HHHHHhhcCCCCCC
Q 025922 77 SYFSVVLTDAGSVP 90 (246)
Q Consensus 77 ~~~~~~~~dPG~vp 90 (246)
.++...++||-.++
T Consensus 17 iFFAIfFRepPri~ 30 (31)
T PRK11875 17 LFFAIAFRDPPKID 30 (31)
T ss_pred HHHhhhccCCCCCC
Confidence 45677889998775
No 74
>PHA02898 virion envelope protein; Provisional
Probab=20.56 E-value=3.4e+02 Score=19.56 Aligned_cols=30 Identities=23% Similarity=0.444 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HhcCccccc
Q 025922 212 FLAFVLNLAFALSVLGFLIMHISL-VSANTTTIE 244 (246)
Q Consensus 212 ~~~~vl~~~~~l~~~~l~~~hl~l-i~~n~TT~E 244 (246)
++.|++.+ +.+++++++..|- -+++.++.|
T Consensus 49 ii~FIlgi---vl~lG~~ifs~y~r~C~~~~~~e 79 (92)
T PHA02898 49 IISFILAI---ILILGIIFFKGYNMFCGGNTTDE 79 (92)
T ss_pred HHHHHHHH---HHHHHHHHHHHHhhhcCCCcccc
Confidence 44444433 3344566666776 556666655
No 75
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.33 E-value=86 Score=26.93 Aligned_cols=24 Identities=33% Similarity=0.682 Sum_probs=17.9
Q ss_pred ceeccccC----------cccCCCCccccccCcc
Q 025922 124 IRYCRKCN----------QLKPPRCHHCSVCGRC 147 (246)
Q Consensus 124 ~~~C~~C~----------~~kP~Rs~HC~~C~~C 147 (246)
.+-|..|+ +.+++.--+|+.|||-
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 46788886 3456677899999984
No 76
>PF03842 Silic_transp: Silicon transporter; InterPro: IPR004693 Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms, which make their "glass houses" out of silicon.
Probab=20.09 E-value=7.3e+02 Score=23.31 Aligned_cols=18 Identities=33% Similarity=0.665 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 025922 168 KYFLLFLLYTFLETSLVT 185 (246)
Q Consensus 168 r~F~~fl~~~~i~~~~~~ 185 (246)
.||.+|.+|+.+..=+.-
T Consensus 171 nyFalFTlyvam~IEfsG 188 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFSG 188 (512)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 589999999887765543
Done!