Query 025960
Match_columns 245
No_of_seqs 181 out of 1594
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 11:31:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025960hhsearch_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 1.8E-48 3.8E-53 341.3 15.9 222 11-239 3-232 (307)
2 PF01529 zf-DHHC: DHHC palmito 100.0 2E-39 4.4E-44 265.6 11.0 161 76-238 2-172 (174)
3 KOG1311 DHHC-type Zn-finger pr 100.0 3.7E-38 8.1E-43 279.5 15.1 150 84-239 79-241 (299)
4 COG5273 Uncharacterized protei 100.0 3E-36 6.6E-41 267.0 14.8 166 63-238 58-231 (309)
5 KOG1314 DHHC-type Zn-finger pr 100.0 7.1E-37 1.5E-41 265.9 7.9 112 55-186 42-153 (414)
6 KOG1313 DHHC-type Zn-finger pr 100.0 2.4E-31 5.3E-36 224.9 10.3 75 123-197 101-175 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 1.9E-29 4.1E-34 214.5 10.0 105 74-191 111-215 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 2.7E-25 5.8E-30 206.7 8.3 102 77-190 384-486 (600)
9 PF01529 zf-DHHC: DHHC palmito 97.1 0.0031 6.7E-08 51.1 8.7 111 134-245 44-170 (174)
10 KOG1311 DHHC-type Zn-finger pr 96.4 0.017 3.7E-07 51.3 8.2 108 137-244 112-237 (299)
11 KOG1315 Predicted DHHC-type Zn 94.9 1.6 3.6E-05 39.0 14.9 108 137-244 108-228 (307)
12 COG5273 Uncharacterized protei 91.2 1.7 3.6E-05 39.0 9.1 32 121-152 120-151 (309)
13 PF13240 zinc_ribbon_2: zinc-r 91.1 0.12 2.5E-06 27.9 1.0 21 126-146 1-21 (23)
14 PF13248 zf-ribbon_3: zinc-rib 87.1 0.34 7.3E-06 26.8 1.0 22 125-146 3-24 (26)
15 PRK04136 rpl40e 50S ribosomal 86.6 0.41 8.8E-06 30.5 1.3 24 123-146 13-36 (48)
16 KOG0509 Ankyrin repeat and DHH 83.2 2.7 5.8E-05 40.7 5.8 52 122-174 323-374 (600)
17 PF12773 DZR: Double zinc ribb 82.5 1.2 2.5E-05 28.4 2.2 35 123-157 11-48 (50)
18 PTZ00303 phosphatidylinositol 81.3 0.94 2E-05 45.0 2.0 22 125-146 461-489 (1374)
19 KOG1314 DHHC-type Zn-finger pr 79.6 6.2 0.00013 35.9 6.4 119 50-190 42-160 (414)
20 PF10571 UPF0547: Uncharacteri 74.4 1.7 3.8E-05 24.0 1.0 22 125-146 1-22 (26)
21 COG1552 RPL40A Ribosomal prote 72.7 0.81 1.8E-05 29.2 -0.7 27 123-149 13-39 (50)
22 PF06906 DUF1272: Protein of u 71.1 2.1 4.6E-05 28.2 0.9 36 126-164 7-50 (57)
23 PF12773 DZR: Double zinc ribb 69.8 3.3 7.2E-05 26.2 1.7 25 121-145 26-50 (50)
24 PF01020 Ribosomal_L40e: Ribos 68.9 3.2 7E-05 26.9 1.4 25 123-147 16-42 (52)
25 PF01363 FYVE: FYVE zinc finge 62.4 3.4 7.3E-05 28.0 0.7 27 123-149 8-36 (69)
26 KOG1842 FYVE finger-containing 57.9 3.3 7.2E-05 38.6 -0.0 29 121-149 177-207 (505)
27 smart00064 FYVE Protein presen 56.7 8.3 0.00018 26.0 1.8 25 124-148 10-36 (68)
28 PF00641 zf-RanBP: Zn-finger i 55.2 5 0.00011 22.6 0.4 21 126-146 6-26 (30)
29 KOG1398 Uncharacterized conser 53.7 3.8 8.3E-05 37.6 -0.3 24 136-165 12-35 (460)
30 PF09297 zf-NADH-PPase: NADH p 46.9 10 0.00022 21.7 0.9 23 124-146 3-29 (32)
31 PF07010 Endomucin: Endomucin; 44.6 49 0.0011 28.3 4.9 27 64-90 197-223 (259)
32 PF07282 OrfB_Zn_ribbon: Putat 44.3 14 0.00031 24.9 1.4 25 123-147 27-55 (69)
33 PF00751 DM: DM DNA binding do 43.9 8.3 0.00018 24.6 0.2 15 145-159 12-28 (47)
34 KOG3183 Predicted Zn-finger pr 40.7 13 0.00027 32.0 0.8 12 148-159 38-49 (250)
35 PF08600 Rsm1: Rsm1-like; Int 40.6 15 0.00032 26.7 1.1 11 153-163 56-66 (91)
36 PF02150 RNA_POL_M_15KD: RNA p 40.5 9.5 0.00021 22.6 0.0 8 125-132 2-9 (35)
37 PRK14559 putative protein seri 39.7 19 0.00041 35.6 2.0 22 125-146 28-49 (645)
38 PF07649 C1_3: C1-like domain; 39.0 12 0.00026 21.1 0.3 21 126-146 2-23 (30)
39 smart00661 RPOL9 RNA polymeras 38.7 16 0.00035 23.0 0.9 7 126-132 2-8 (52)
40 PRK00432 30S ribosomal protein 35.6 22 0.00048 22.8 1.2 23 124-146 20-45 (50)
41 KOG1729 FYVE finger containing 33.6 12 0.00026 33.2 -0.4 28 123-150 167-197 (288)
42 KOG3457 Sec61 protein transloc 33.3 19 0.00042 25.8 0.7 35 193-227 46-82 (88)
43 cd00065 FYVE FYVE domain; Zinc 32.7 22 0.00048 22.8 0.9 24 125-148 3-28 (57)
44 CHL00031 psbT photosystem II p 32.7 1E+02 0.0022 18.1 3.4 15 77-91 17-31 (33)
45 PRK11875 psbT photosystem II r 32.3 1E+02 0.0023 17.7 3.6 14 77-90 17-30 (31)
46 KOG1819 FYVE finger-containing 32.0 15 0.00033 35.0 0.0 24 124-147 901-926 (990)
47 COG2093 DNA-directed RNA polym 31.8 27 0.00059 23.6 1.2 23 124-146 4-26 (64)
48 PRK03681 hypA hydrogenase nick 31.7 25 0.00054 26.6 1.1 24 123-146 69-95 (114)
49 PF00130 C1_1: Phorbol esters/ 31.5 43 0.00093 21.1 2.1 34 122-155 9-50 (53)
50 TIGR00155 pqiA_fam integral me 31.1 4.4E+02 0.0095 24.5 10.8 31 123-153 214-245 (403)
51 KOG4219 G protein-coupled rece 30.7 1.1E+02 0.0024 28.6 5.3 30 208-239 263-292 (423)
52 PRK14559 putative protein seri 30.5 28 0.0006 34.5 1.5 41 121-163 12-52 (645)
53 KOG1313 DHHC-type Zn-finger pr 30.2 1.2E+02 0.0026 26.9 5.1 110 119-239 111-245 (309)
54 PLN00186 ribosomal protein S26 29.8 23 0.00049 26.7 0.6 15 137-151 19-33 (109)
55 PF01437 PSI: Plexin repeat; 29.5 14 0.00031 23.5 -0.5 17 142-158 6-22 (51)
56 PF14965 BRI3BP: Negative regu 29.2 3.2E+02 0.007 22.4 7.9 19 158-176 12-30 (177)
57 PHA02942 putative transposase; 28.9 34 0.00075 31.6 1.8 24 123-146 324-350 (383)
58 PF03107 C1_2: C1 domain; Int 28.6 37 0.0008 19.1 1.2 20 126-145 2-22 (30)
59 PRK09335 30S ribosomal protein 28.0 24 0.00052 25.9 0.5 20 137-156 19-38 (95)
60 PRK15103 paraquat-inducible me 27.8 5.1E+02 0.011 24.2 12.5 31 123-153 220-250 (419)
61 PRK12286 rpmF 50S ribosomal pr 27.6 47 0.001 21.9 1.8 24 121-146 24-48 (57)
62 smart00547 ZnF_RBZ Zinc finger 27.6 31 0.00068 18.4 0.8 21 126-146 4-24 (26)
63 PF07062 Clc-like: Clc-like; 27.3 3.8E+02 0.0083 22.6 8.7 10 144-153 64-73 (211)
64 KOG1841 Smad anchor for recept 27.1 61 0.0013 34.1 3.2 24 124-147 557-582 (1287)
65 PTZ00172 40S ribosomal protein 26.7 27 0.00057 26.3 0.5 16 137-152 19-34 (108)
66 PF09889 DUF2116: Uncharacteri 26.5 76 0.0016 21.2 2.6 23 124-146 3-26 (59)
67 COG4640 Predicted membrane pro 25.5 35 0.00075 31.7 1.1 26 125-150 2-27 (465)
68 PF12172 DUF35_N: Rubredoxin-l 25.2 27 0.00058 20.5 0.2 23 122-145 9-32 (37)
69 smart00423 PSI domain found in 24.9 30 0.00065 21.3 0.4 15 143-157 6-20 (46)
70 COG0603 Predicted PP-loop supe 24.0 29 0.00063 29.6 0.3 19 133-151 187-205 (222)
71 PRK13130 H/ACA RNA-protein com 23.9 53 0.0011 21.7 1.5 22 123-146 4-25 (56)
72 TIGR01031 rpmF_bact ribosomal 22.7 64 0.0014 21.1 1.7 23 122-146 24-47 (55)
73 PF07754 DUF1610: Domain of un 22.4 61 0.0013 17.6 1.3 11 127-137 1-11 (24)
74 KOG3611 Semaphorins [Signal tr 21.8 36 0.00078 34.3 0.5 37 138-174 491-535 (737)
75 COG5270 PUA domain (predicted 21.7 53 0.0012 27.3 1.4 24 121-146 11-34 (202)
76 KOG1818 Membrane trafficking a 21.1 37 0.00081 33.4 0.5 23 124-146 165-189 (634)
77 PF10066 DUF2304: Uncharacteri 20.6 3.7E+02 0.008 20.0 7.2 56 176-231 36-91 (115)
78 PF01283 Ribosomal_S26e: Ribos 20.6 38 0.00081 25.8 0.3 19 137-155 19-37 (113)
79 KOG4004 Matricellular protein 20.6 49 0.0011 27.9 0.9 15 152-166 55-70 (259)
80 PF13842 Tnp_zf-ribbon_2: DDE_ 20.5 71 0.0015 18.4 1.4 7 125-131 17-23 (32)
81 COG2816 NPY1 NTP pyrophosphohy 20.0 54 0.0012 29.0 1.2 24 123-146 110-137 (279)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.8e-48 Score=341.28 Aligned_cols=222 Identities=38% Similarity=0.686 Sum_probs=172.0
Q ss_pred ceeeeccccccchhHHHHhhhhheeeeeeeeeeeecccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCC
Q 025960 11 NVFKFCTALRGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVP 90 (245)
Q Consensus 11 ~~~~~c~~~r~~~~i~v~~i~~~i~~~~y~~~~~~~~p~l~~~~~~~~~~~~~~i~~~~l~~~~~~~y~~~~~~dPG~vp 90 (245)
+..+++..+| |++++++.+.++|.||++++..+.+.+... ..+++.+++++.++++.+|+|++++++|||.+|
T Consensus 3 ~~~~~~~~~r---~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~----~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp 75 (307)
T KOG1315|consen 3 GSRRFSKCLR---WIPVLIILLVIGWTYYVYVAVLCILSISLT----IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVP 75 (307)
T ss_pred Ccccchhhhc---chhheeeeeeEEEEEEEeehhhhHHHHhhh----hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCc
Confidence 3344444446 999999999999999999998887766433 456788999999999999999999999999999
Q ss_pred CCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccccccccCCCCccCcccCcccccCCcccccccceeccCchHHH
Q 025960 91 PNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYF 170 (245)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F 170 (245)
..+.++.++++..+.................+..|+|.+|+.+|||||||||.|+|||+||||||||+|||||.+|||+|
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF 155 (307)
T KOG1315|consen 76 DSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFF 155 (307)
T ss_pred cccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHH
Confidence 99888665443322211111111122234466889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhHH--------HHHHHHHHHHHHHHHHHHHHHHhHhhhhhcC
Q 025960 171 LLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTL--------ATTFLAFGMASLTYHSDLCNRLHQHFYVING 239 (245)
Q Consensus 171 ~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~l~fvl~~~~~h~~l~~~~~tt~~~~~~ 239 (245)
++|++|+.+++.+.++.....+..++.....+.+.... ++.+...+.+++.||+||+.+|.||+|.-+-
T Consensus 156 ~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~ 232 (307)
T KOG1315|consen 156 LLFLFYTNLYSIYVLVTTLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKS 232 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhcc
Confidence 99999999999999999999888888433222221222 2222233345799999999999999997653
No 2
>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=2e-39 Score=265.63 Aligned_cols=161 Identities=32% Similarity=0.607 Sum_probs=117.9
Q ss_pred HHHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccccccccCCCCccCcccCcccccCCccc
Q 025960 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (245)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhC 155 (245)
++|++++++|||++|+....+.+++ ++.............++..++.++|.+|+..||+|||||+.||+||+|+||||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC 79 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQ--EEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHC 79 (174)
T ss_pred EEehhhheECCcccCCccccccccc--cccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccc
Confidence 5789999999999997622111111 11111111111122344677889999999999999999999999999999999
Q ss_pred ccccceeccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCh-h---------HHHHHHHHHHHHHHHHHHH
Q 025960 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP-G---------TLATTFLAFGMASLTYHSD 225 (245)
Q Consensus 156 pwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---------~~~~~~l~fvl~~~~~h~~ 225 (245)
||+|||||++|||+|++|+++..+.+++.....+..+............. . ..++++..++..++.+|++
T Consensus 80 ~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 159 (174)
T PF01529_consen 80 PWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLY 159 (174)
T ss_pred hhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999888888777777665543222111 1 1122233445568899999
Q ss_pred HHHHHhHhhhhhc
Q 025960 226 LCNRLHQHFYVIN 238 (245)
Q Consensus 226 l~~~~~tt~~~~~ 238 (245)
++.+|.||+|.+|
T Consensus 160 ~i~~n~Tt~E~~~ 172 (174)
T PF01529_consen 160 LILRNITTYERIK 172 (174)
T ss_pred HHHcCCcHHHHHH
Confidence 9999999999987
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=3.7e-38 Score=279.49 Aligned_cols=150 Identities=33% Similarity=0.679 Sum_probs=111.4
Q ss_pred cCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccccccccCCCCccCcccCcccccCCcccccccceec
Q 025960 84 TDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVG 163 (245)
Q Consensus 84 ~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG 163 (245)
+|||.+|++..+..+.. ++.+ ...+...++...+.+||.+|+..|||||||||.||+||+||||||||+|||||
T Consensus 79 sdpg~~p~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG 152 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDP--ERAP----LYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIG 152 (299)
T ss_pred CCCceecCcccCCCCCc--cccc----cCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceEC
Confidence 59999998631111110 1111 11112234556678999999999999999999999999999999999999999
Q ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC----h----h-----HHHHHHHHHHHHHHHHHHHHHHHH
Q 025960 164 ALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGT----P----G-----TLATTFLAFGMASLTYHSDLCNRL 230 (245)
Q Consensus 164 ~~N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~----~-----~~~~~~l~fvl~~~~~h~~l~~~~ 230 (245)
++|||+|+.|++++.+.+++.++.....+.....+.....+ . . ...++++.++..++.+|.+++.++
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 99999999999999999999888888877765554322222 1 1 122333445556899999999999
Q ss_pred hHhhhhhcC
Q 025960 231 HQHFYVING 239 (245)
Q Consensus 231 ~tt~~~~~~ 239 (245)
+||+|-+++
T Consensus 233 ~Tt~e~~~~ 241 (299)
T KOG1311|consen 233 STTYESIKS 241 (299)
T ss_pred cchhhhhhc
Confidence 999999886
No 4
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=3e-36 Score=266.96 Aligned_cols=166 Identities=34% Similarity=0.567 Sum_probs=124.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccccccccCCCCccCc
Q 025960 63 VLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCS 142 (245)
Q Consensus 63 ~~i~~~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~ 142 (245)
..+.+.+...+...+|++..++|||+.+++-.....++..+ .....+..+..++|.+|+.+||+|||||+
T Consensus 58 ~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~C~~C~~~KP~RS~HC~ 127 (309)
T COG5273 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETIS----------RLLDDGKFGTENFCSTCNIYKPPRSHHCS 127 (309)
T ss_pred hhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhh----------hhhhcCccccceeccccccccCCCCccch
Confidence 44555666677888999999999999985432221111111 12233556788999999999999999999
Q ss_pred ccCcccccCCcccccccceeccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChh--------HHHHHHHH
Q 025960 143 VCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPG--------TLATTFLA 214 (245)
Q Consensus 143 ~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~l~ 214 (245)
.||+||+||||||||+|||||++|||+|++|+++....+..+++.....+....+.+..+.... .....++.
T Consensus 128 ~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~ 207 (309)
T COG5273 128 ICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFI 207 (309)
T ss_pred hhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHhhhHHHHHHHH
Confidence 9999999999999999999999999999999999988888877777776666554433333220 12223345
Q ss_pred HHHHHHHHHHHHHHHHhHhhhhhc
Q 025960 215 FGMASLTYHSDLCNRLHQHFYVIN 238 (245)
Q Consensus 215 fvl~~~~~h~~l~~~~~tt~~~~~ 238 (245)
++.+++.+|.++++-+.||+|+..
T Consensus 208 ~~~~~~~~~~~~~~~~~t~~e~~~ 231 (309)
T COG5273 208 ITTLLLLFLIYLILNNLTTIEFIQ 231 (309)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHH
Confidence 566789999999999999998764
No 5
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=7.1e-37 Score=265.86 Aligned_cols=112 Identities=41% Similarity=0.873 Sum_probs=96.2
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceecccccccc
Q 025960 55 LDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLK 134 (245)
Q Consensus 55 ~~~~~~~~~~i~~~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~k 134 (245)
..+..++..-+.|.+...|++++|+.+++++||++|++|.|+... +..-.+||.+|+.+|
T Consensus 42 ~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~--------------------D~~~lqfCk~CqgYK 101 (414)
T KOG1314|consen 42 LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK--------------------DEMFLQFCKKCQGYK 101 (414)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh--------------------hHHHHHHHhhccCcC
Confidence 344456667777888899999999999999999999999884321 123468999999999
Q ss_pred CCCCccCcccCcccccCCcccccccceeccCchHHHHHHHHHHHHHHHHHHH
Q 025960 135 PPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTL 186 (245)
Q Consensus 135 P~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~ 186 (245)
+|||||||.|||||++|||||||+|||||..||.+|..||++..++|+...+
T Consensus 102 apRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~ti 153 (414)
T KOG1314|consen 102 APRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTI 153 (414)
T ss_pred CCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhccccee
Confidence 9999999999999999999999999999999999999999999997655433
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=2.4e-31 Score=224.85 Aligned_cols=75 Identities=49% Similarity=1.066 Sum_probs=68.7
Q ss_pred CceeccccccccCCCCccCcccCcccccCCcccccccceeccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFS 197 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~ 197 (245)
...+|.+|+.+||||+||||.||+||+||||||||+|||||.+|||||++|++|+.+++.++.++..+.+++...
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le 175 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLE 175 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 458999999999999999999999999999999999999999999999999999999999988887666665443
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.96 E-value=1.9e-29 Score=214.51 Aligned_cols=105 Identities=31% Similarity=0.623 Sum_probs=79.7
Q ss_pred HHHHHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccccccccCCCCccCcccCcccccCCc
Q 025960 74 LLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDH 153 (245)
Q Consensus 74 ~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DH 153 (245)
=..++..++.+|||.+.++-... ..++.|- ++....+...|++|+..||.||||||.|||||.||||
T Consensus 111 p~i~f~ltc~snpg~i~k~n~s~----~~~~ypY---------Dy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDH 177 (341)
T KOG1312|consen 111 PLIFFTLTCGSNPGIITKANESL----FLHVYPY---------DYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDH 177 (341)
T ss_pred HHHHHhhhhcCCCCccchhhhcc----ceeccCc---------cceeecCCCccccccCCCccccccchHHHHHHHHhcc
Confidence 34466788999999997531111 1111111 1112334578999999999999999999999999999
Q ss_pred ccccccceeccCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 025960 154 HCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPH 191 (245)
Q Consensus 154 hCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~~ 191 (245)
||.|+|||||.+|+|||++|+++...++.+..+.+...
T Consensus 178 HCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi 215 (341)
T KOG1312|consen 178 HCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFI 215 (341)
T ss_pred ceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHhe
Confidence 99999999999999999999999977777776665544
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.92 E-value=2.7e-25 Score=206.68 Aligned_cols=102 Identities=31% Similarity=0.582 Sum_probs=76.0
Q ss_pred HHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCc-eeccccccccCCCCccCcccCcccccCCccc
Q 025960 77 SYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRI-RYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (245)
Q Consensus 77 ~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhC 155 (245)
++.+...+|||++|...... ++. ..+..+.++.+.. +||.+|...||.|||||+.|||||.||||||
T Consensus 384 ~f~~~~rsDPg~i~~~~~~~------~~t------Is~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhC 451 (600)
T KOG0509|consen 384 TFGLFLRSDPGFIPTSTEVG------RET------ISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHC 451 (600)
T ss_pred HHHHHhccCCCCCCCchhhH------HHH------HHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCC
Confidence 44455559999998542221 000 0011122334445 6999999999999999999999999999999
Q ss_pred ccccceeccCchHHHHHHHHHHHHHHHHHHHHHHH
Q 025960 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLP 190 (245)
Q Consensus 156 pwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~ 190 (245)
||++||||.+|||+|+.|++.....+.+.+....+
T Consensus 452 Pwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~ 486 (600)
T KOG0509|consen 452 PWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLY 486 (600)
T ss_pred CccccccCccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999877766665555433
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=97.13 E-value=0.0031 Score=51.11 Aligned_cols=111 Identities=11% Similarity=0.132 Sum_probs=76.2
Q ss_pred cCCCCccCcccCcccccCCcccccccceeccCch-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 025960 134 KPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNY-----------KYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIP 202 (245)
Q Consensus 134 kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~-----------k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (245)
...+.+.|+.|+.=....-|||+.-+.||-+.-| +..-.|+.++....+..+......+........ .
T Consensus 44 ~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~-~ 122 (174)
T PF01529_consen 44 ENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIP-S 122 (174)
T ss_pred cCCCCEECcccCCcCCCcceeccccccccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-c
Confidence 6677899999998888889999999999977654 456678877777777766666666655555433 2
Q ss_pred CChhHHH-HH----HHHHHHHHHHHHHHHHHHHhHhhhhhcCceeecC
Q 025960 203 GTPGTLA-TT----FLAFGMASLTYHSDLCNRLHQHFYVINGVSLLQF 245 (245)
Q Consensus 203 ~~~~~~~-~~----~l~fvl~~~~~h~~l~~~~~tt~~~~~~~~~~~~ 245 (245)
....... .. ++.++.+.+..-.-..+...+++.+.+|.|+.|.
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~ 170 (174)
T PF01529_consen 123 ISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYER 170 (174)
T ss_pred ccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHH
Confidence 3333333 22 2333333444444456677799999999999884
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=96.37 E-value=0.017 Score=51.28 Aligned_cols=108 Identities=19% Similarity=0.223 Sum_probs=70.5
Q ss_pred CCccCcccCcccccCCcccccccceeccC-----------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCh
Q 025960 137 RCHHCSVCGRCILKMDHHCVWVVNCVGAL-----------NYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP 205 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~-----------N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (245)
+.++|..|+..+.+.-|||+.=|+||-+. ..|.+-.|+.++....+..+..+...++......+.....
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~ 191 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVN 191 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 47999999999999999999999999776 4578899997777554444444544555544432222111
Q ss_pred hH--H--HHH---HHHHHHHHHHHHHHHHHHHhHhhhhhcCceeec
Q 025960 206 GT--L--ATT---FLAFGMASLTYHSDLCNRLHQHFYVINGVSLLQ 244 (245)
Q Consensus 206 ~~--~--~~~---~l~fvl~~~~~h~~l~~~~~tt~~~~~~~~~~~ 244 (245)
.. . ... ++..+++.++.-....+...+.+-+.+|.|+.|
T Consensus 192 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e 237 (299)
T KOG1311|consen 192 LTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYE 237 (299)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhh
Confidence 22 1 111 122233444444445677778888888988866
No 11
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=94.90 E-value=1.6 Score=38.97 Aligned_cols=108 Identities=19% Similarity=0.300 Sum_probs=76.2
Q ss_pred CCccCcccCcccccCCcccccccceeccC-----------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCh
Q 025960 137 RCHHCSVCGRCILKMDHHCVWVVNCVGAL-----------NYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP 205 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~-----------N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (245)
+.+.|..|+.-....-|||.--+.||.+. +++.+=-|+++..-+.++....+...+......-.....+
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~~ 187 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAGP 187 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccC
Confidence 77899999999999999999999999876 4567778888877777666666766666666543111222
Q ss_pred hHHHHHHHHH--HHHHHHHHHHHHHHHhHhhhhhcCceeec
Q 025960 206 GTLATTFLAF--GMASLTYHSDLCNRLHQHFYVINGVSLLQ 244 (245)
Q Consensus 206 ~~~~~~~l~f--vl~~~~~h~~l~~~~~tt~~~~~~~~~~~ 244 (245)
......+..+ +++..+.-..+.+...++..+++|.|+.|
T Consensus 188 ~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE 228 (307)
T KOG1315|consen 188 SSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIE 228 (307)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHh
Confidence 3445555543 22322223334478889999999999987
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=91.16 E-value=1.7 Score=38.99 Aligned_cols=32 Identities=28% Similarity=0.519 Sum_probs=16.9
Q ss_pred CcCceeccccccccCCCCccCcccCcccccCC
Q 025960 121 NPRIRYCRKCNQLKPPRCHHCSVCGRCILKMD 152 (245)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 152 (245)
+++.+.|+.|+.=-...-|||.--|+||-+--
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N 151 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRN 151 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcch
Confidence 44445555555555555555555555555433
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.13 E-value=0.12 Score=27.91 Aligned_cols=21 Identities=29% Similarity=0.842 Sum_probs=18.1
Q ss_pred eccccccccCCCCccCcccCc
Q 025960 126 YCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
+|+.|+..-++.++.|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588899888999999998875
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.05 E-value=0.34 Score=26.78 Aligned_cols=22 Identities=27% Similarity=0.854 Sum_probs=18.6
Q ss_pred eeccccccccCCCCccCcccCc
Q 025960 125 RYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
++|+.|+..-++.++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6789999887888899988875
No 15
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=86.58 E-value=0.41 Score=30.52 Aligned_cols=24 Identities=33% Similarity=0.838 Sum_probs=21.7
Q ss_pred CceeccccccccCCCCccCcccCc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
..+.|..|+..-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 457899999999999999999886
No 16
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=83.20 E-value=2.7 Score=40.69 Aligned_cols=52 Identities=6% Similarity=-0.161 Sum_probs=45.3
Q ss_pred cCceeccccccccCCCCccCcccCcccccCCcccccccceeccCchHHHHHHH
Q 025960 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFL 174 (245)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl 174 (245)
.....|.+|....+.+..++..+-.+...+++||+|+. +|+.+|...+....
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~ 374 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCF 374 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHH
Confidence 34577899999999999999999999999999999999 99999987654433
No 17
>PF12773 DZR: Double zinc ribbon
Probab=82.47 E-value=1.2 Score=28.35 Aligned_cols=35 Identities=20% Similarity=0.485 Sum_probs=22.9
Q ss_pred CceeccccccccC---CCCccCcccCcccccCCccccc
Q 025960 123 RIRYCRKCNQLKP---PRCHHCSVCGRCILKMDHHCVW 157 (245)
Q Consensus 123 ~~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHhCpw 157 (245)
..++|..|+..-+ .....|+.|++=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 3577777776655 2356677777776666666663
No 18
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=81.30 E-value=0.94 Score=45.03 Aligned_cols=22 Identities=36% Similarity=0.880 Sum_probs=18.2
Q ss_pred eeccccccccC-------CCCccCcccCc
Q 025960 125 RYCRKCNQLKP-------PRCHHCSVCGR 146 (245)
Q Consensus 125 ~~C~~C~~~kP-------~Rs~HC~~C~~ 146 (245)
+.|..|+..-. .|-||||.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 67999987664 39999999977
No 19
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=79.58 E-value=6.2 Score=35.85 Aligned_cols=119 Identities=18% Similarity=0.162 Sum_probs=74.5
Q ss_pred cccCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCcCceeccc
Q 025960 50 LYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRK 129 (245)
Q Consensus 50 l~~~~~~~~~~~~~~i~~~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~ 129 (245)
+.+-........+.+-.+.+++..+...+.---+..||.-|++...+.-..--.+- ..-+.++..-|.+
T Consensus 42 ~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~lqfCk~C-----------qgYKapRSHHCrk 110 (414)
T KOG1314|consen 42 LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDEMFLQFCKKC-----------QGYKAPRSHHCRK 110 (414)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHhhc-----------cCcCCCccccchH
Confidence 33333344444455556667777777788888999999999765442211111100 0012334567888
Q ss_pred cccccCCCCccCcccCcccccCCcccccccceeccCchHHHHHHHHHHHHHHHHHHHHHHH
Q 025960 130 CNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLP 190 (245)
Q Consensus 130 C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~ 190 (245)
|+.---.=-|||.--|.||--..| .-.-+|++|.....+-.+.++.+..+
T Consensus 111 CnrCvmkMDHHCPWinnCVG~aNh-----------~~F~~FLlf~ivG~ih~tiI~~~~~~ 160 (414)
T KOG1314|consen 111 CNRCVMKMDHHCPWINNCVGWANH-----------AYFLRFLLFSIVGCIHGTIILVCAQY 160 (414)
T ss_pred HHHHHHhhccCCcchhhccccccc-----------HHHHHHHHHHHHhcccceeeehhHHH
Confidence 775455557999999999875555 56789999999877766555555444
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=74.44 E-value=1.7 Score=24.04 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=18.0
Q ss_pred eeccccccccCCCCccCcccCc
Q 025960 125 RYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
+.|+.|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688898888888888888874
No 21
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=72.74 E-value=0.81 Score=29.25 Aligned_cols=27 Identities=37% Similarity=0.896 Sum_probs=22.6
Q ss_pred CceeccccccccCCCCccCcccCcccc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSVCGRCIL 149 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~ 149 (245)
..+.|..|+..-|+|+.-|+.|+.=-+
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~k~L 39 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGYKNL 39 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccCCCc
Confidence 457899999999999999999876433
No 22
>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=71.15 E-value=2.1 Score=28.25 Aligned_cols=36 Identities=33% Similarity=0.891 Sum_probs=26.5
Q ss_pred eccccccccCCCC-------ccCcccCcccccC-Ccccccccceecc
Q 025960 126 YCRKCNQLKPPRC-------HHCSVCGRCILKM-DHHCVWVVNCVGA 164 (245)
Q Consensus 126 ~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHhCpwi~nCIG~ 164 (245)
-|..|+.--|+-+ +-|..|..|+..+ ++.|| ||=|.
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 4666666655553 5688999999998 99999 66553
No 23
>PF12773 DZR: Double zinc ribbon
Probab=69.83 E-value=3.3 Score=26.17 Aligned_cols=25 Identities=28% Similarity=0.894 Sum_probs=21.6
Q ss_pred CcCceeccccccccCCCCccCcccC
Q 025960 121 NPRIRYCRKCNQLKPPRCHHCSVCG 145 (245)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~ 145 (245)
.....+|..|+...++.++.|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456899999999999999999986
No 24
>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=68.92 E-value=3.2 Score=26.91 Aligned_cols=25 Identities=40% Similarity=0.931 Sum_probs=16.9
Q ss_pred CceeccccccccCCCCccCcc--cCcc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSV--CGRC 147 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 147 (245)
....|..|...-|+|+..|+. ||.+
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 347899999999999999998 8764
No 25
>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=62.43 E-value=3.4 Score=28.01 Aligned_cols=27 Identities=33% Similarity=0.719 Sum_probs=12.7
Q ss_pred Cceeccccccc--cCCCCccCcccCcccc
Q 025960 123 RIRYCRKCNQL--KPPRCHHCSVCGRCIL 149 (245)
Q Consensus 123 ~~~~C~~C~~~--kP~Rs~HC~~C~~CV~ 149 (245)
+...|..|+.. --.|-|||+.||+.+=
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 34677777632 2368899999998653
No 26
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=57.94 E-value=3.3 Score=38.61 Aligned_cols=29 Identities=31% Similarity=0.930 Sum_probs=21.5
Q ss_pred CcCceecccccccc--CCCCccCcccCcccc
Q 025960 121 NPRIRYCRKCNQLK--PPRCHHCSVCGRCIL 149 (245)
Q Consensus 121 ~~~~~~C~~C~~~k--P~Rs~HC~~C~~CV~ 149 (245)
.....+|+.|...= ..|-||||.||+-+-
T Consensus 177 Ds~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 177 DSSVQFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred CCcccccccccchhhhHHHhhhhhhcchHHH
Confidence 34578999997533 358899999998543
No 27
>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=55.18 E-value=5 Score=22.61 Aligned_cols=21 Identities=29% Similarity=0.882 Sum_probs=14.3
Q ss_pred eccccccccCCCCccCcccCc
Q 025960 126 YCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
.|..|...-++++.+|..|+.
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 478888888888888887764
No 29
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.70 E-value=3.8 Score=37.63 Aligned_cols=24 Identities=46% Similarity=0.980 Sum_probs=16.5
Q ss_pred CCCccCcccCcccccCCcccccccceeccC
Q 025960 136 PRCHHCSVCGRCILKMDHHCVWVVNCVGAL 165 (245)
Q Consensus 136 ~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~ 165 (245)
.|..||..|+. +|| +|+.||||.-
T Consensus 12 ~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 12 ARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred cCchHhhhhhh----ccC--CcccchhHHH
Confidence 34455665554 677 8999999853
No 30
>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=46.93 E-value=10 Score=21.70 Aligned_cols=23 Identities=26% Similarity=0.813 Sum_probs=10.9
Q ss_pred ceeccccccc----cCCCCccCcccCc
Q 025960 124 IRYCRKCNQL----KPPRCHHCSVCGR 146 (245)
Q Consensus 124 ~~~C~~C~~~----kP~Rs~HC~~C~~ 146 (245)
.+||..|... .-.++..|..|+.
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 4788888642 2235666666654
No 31
>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=44.56 E-value=49 Score=28.33 Aligned_cols=27 Identities=26% Similarity=0.245 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCCC
Q 025960 64 LILFHCLLVMLLWSYFSVVLTDAGSVP 90 (245)
Q Consensus 64 ~i~~~~l~~~~~~~y~~~~~~dPG~vp 90 (245)
+++..++.+..+..|..|.-+|||.+.
T Consensus 197 liVitl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 197 LIVITLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 344445555556678888889999654
No 32
>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=44.31 E-value=14 Score=24.88 Aligned_cols=25 Identities=24% Similarity=0.618 Sum_probs=18.2
Q ss_pred CceeccccccccC----CCCccCcccCcc
Q 025960 123 RIRYCRKCNQLKP----PRCHHCSVCGRC 147 (245)
Q Consensus 123 ~~~~C~~C~~~kP----~Rs~HC~~C~~C 147 (245)
..+.|+.|+.... .|.++|..||.-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 5678999976544 467788888764
No 33
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=43.91 E-value=8.3 Score=24.57 Aligned_cols=15 Identities=20% Similarity=0.293 Sum_probs=6.4
Q ss_pred CcccccCCc--cccccc
Q 025960 145 GRCILKMDH--HCVWVV 159 (245)
Q Consensus 145 ~~CV~~~DH--hCpwi~ 159 (245)
|.-+..-+| +|||-+
T Consensus 12 G~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 12 GVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp T---TTTT-GGG-TTTT
T ss_pred CcccchhhhccccCcCC
Confidence 555666677 688753
No 34
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=40.69 E-value=13 Score=32.01 Aligned_cols=12 Identities=25% Similarity=0.241 Sum_probs=9.2
Q ss_pred cccCCccccccc
Q 025960 148 ILKMDHHCVWVV 159 (245)
Q Consensus 148 V~~~DHhCpwi~ 159 (245)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 456789999875
No 35
>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=40.61 E-value=15 Score=26.70 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.8
Q ss_pred cccccccceec
Q 025960 153 HHCVWVVNCVG 163 (245)
Q Consensus 153 HhCpwi~nCIG 163 (245)
.||||++.-..
T Consensus 56 ~~CPwv~~~~q 66 (91)
T PF08600_consen 56 EYCPWVNPSTQ 66 (91)
T ss_pred ccCCccCCccc
Confidence 68999998653
No 36
>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=40.53 E-value=9.5 Score=22.57 Aligned_cols=8 Identities=38% Similarity=1.423 Sum_probs=4.9
Q ss_pred eecccccc
Q 025960 125 RYCRKCNQ 132 (245)
Q Consensus 125 ~~C~~C~~ 132 (245)
+||++|+.
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 57777764
No 37
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=39.73 E-value=19 Score=35.64 Aligned_cols=22 Identities=32% Similarity=0.818 Sum_probs=11.5
Q ss_pred eeccccccccCCCCccCcccCc
Q 025960 125 RYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
+.|..|+..-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 3455555555555555555554
No 38
>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=38.96 E-value=12 Score=21.07 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=7.9
Q ss_pred eccccccccCC-CCccCcccCc
Q 025960 126 YCRKCNQLKPP-RCHHCSVCGR 146 (245)
Q Consensus 126 ~C~~C~~~kP~-Rs~HC~~C~~ 146 (245)
.|..|+..... ...+|+.|+-
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 46677666655 6677777764
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=38.72 E-value=16 Score=23.03 Aligned_cols=7 Identities=43% Similarity=1.497 Sum_probs=3.5
Q ss_pred ecccccc
Q 025960 126 YCRKCNQ 132 (245)
Q Consensus 126 ~C~~C~~ 132 (245)
||+.|+.
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 4555543
No 40
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.60 E-value=22 Score=22.82 Aligned_cols=23 Identities=26% Similarity=0.843 Sum_probs=14.5
Q ss_pred ceecccccc-ccC--CCCccCcccCc
Q 025960 124 IRYCRKCNQ-LKP--PRCHHCSVCGR 146 (245)
Q Consensus 124 ~~~C~~C~~-~kP--~Rs~HC~~C~~ 146 (245)
.++|+.|+. .-. ....+|..|+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCC
Confidence 468999976 222 23556777764
No 41
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=33.56 E-value=12 Score=33.22 Aligned_cols=28 Identities=29% Similarity=0.591 Sum_probs=19.4
Q ss_pred Cceecccccc-cc--CCCCccCcccCccccc
Q 025960 123 RIRYCRKCNQ-LK--PPRCHHCSVCGRCILK 150 (245)
Q Consensus 123 ~~~~C~~C~~-~k--P~Rs~HC~~C~~CV~~ 150 (245)
+..-|..|.. .. -.|-|||+.||+-|-.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 4466777765 22 2578999999887765
No 42
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=33.26 E-value=19 Score=25.81 Aligned_cols=35 Identities=11% Similarity=0.169 Sum_probs=24.9
Q ss_pred HHHhcCC--CCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 025960 193 ISFFSEG--EIPGTPGTLATTFLAFGMASLTYHSDLC 227 (245)
Q Consensus 193 ~~~~~~~--~~~~~~~~~~~~~l~fvl~~~~~h~~l~ 227 (245)
++++.++ .+..+|..+.++.++|+...+.+|+|-=
T Consensus 46 lkfYTDda~GlKV~PvvVLvmSvgFIasV~~LHi~gK 82 (88)
T KOG3457|consen 46 LKFYTDDAPGLKVDPVVVLVMSVGFIASVFALHIWGK 82 (88)
T ss_pred eEEeecCCCCceeCCeeehhhhHHHHHHHHHHHHHHH
Confidence 4556542 2344566788888999999999999743
No 43
>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=32.69 E-value=22 Score=22.78 Aligned_cols=24 Identities=38% Similarity=0.862 Sum_probs=15.5
Q ss_pred eecccccc--ccCCCCccCcccCccc
Q 025960 125 RYCRKCNQ--LKPPRCHHCSVCGRCI 148 (245)
Q Consensus 125 ~~C~~C~~--~kP~Rs~HC~~C~~CV 148 (245)
+-|..|+. -.-.|.|||+.||+-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 34556643 2245889999998753
No 44
>CHL00031 psbT photosystem II protein T
Probab=32.67 E-value=1e+02 Score=18.06 Aligned_cols=15 Identities=20% Similarity=0.645 Sum_probs=11.5
Q ss_pred HHHHhhhcCCCCCCC
Q 025960 77 SYFSVVLTDAGSVPP 91 (245)
Q Consensus 77 ~y~~~~~~dPG~vp~ 91 (245)
.++...+.||-.+++
T Consensus 17 lFFAI~FRePPri~k 31 (33)
T CHL00031 17 IFFAIFFREPPKVPT 31 (33)
T ss_pred HHHhheecCCCCCCC
Confidence 567778899988874
No 45
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=32.27 E-value=1e+02 Score=17.70 Aligned_cols=14 Identities=14% Similarity=0.524 Sum_probs=10.5
Q ss_pred HHHHhhhcCCCCCC
Q 025960 77 SYFSVVLTDAGSVP 90 (245)
Q Consensus 77 ~y~~~~~~dPG~vp 90 (245)
.++...+.||-.++
T Consensus 17 iFFAIfFRepPri~ 30 (31)
T PRK11875 17 LFFAIAFRDPPKID 30 (31)
T ss_pred HHHhhhccCCCCCC
Confidence 55677888988775
No 46
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=31.95 E-value=15 Score=34.96 Aligned_cols=24 Identities=33% Similarity=0.704 Sum_probs=16.3
Q ss_pred ceeccccccccC--CCCccCcccCcc
Q 025960 124 IRYCRKCNQLKP--PRCHHCSVCGRC 147 (245)
Q Consensus 124 ~~~C~~C~~~kP--~Rs~HC~~C~~C 147 (245)
...|..|..+-. .|-|||+.||.-
T Consensus 901 a~~cmacq~pf~afrrrhhcrncggi 926 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGGI 926 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCce
Confidence 355777765432 478999999863
No 47
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=31.76 E-value=27 Score=23.61 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=20.1
Q ss_pred ceeccccccccCCCCccCcccCc
Q 025960 124 IRYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
.+-|..|+..-|+-+.-|+.||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999986
No 48
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.73 E-value=25 Score=26.60 Aligned_cols=24 Identities=21% Similarity=0.559 Sum_probs=17.4
Q ss_pred CceeccccccccCCCCcc---CcccCc
Q 025960 123 RIRYCRKCNQLKPPRCHH---CSVCGR 146 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~H---C~~C~~ 146 (245)
..-+|..|+..-|...++ |+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 357899998877765444 888874
No 49
>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=31.46 E-value=43 Score=21.07 Aligned_cols=34 Identities=29% Similarity=0.833 Sum_probs=22.1
Q ss_pred cCceecccccccc---CCCCccCcccC-----cccccCCccc
Q 025960 122 PRIRYCRKCNQLK---PPRCHHCSVCG-----RCILKMDHHC 155 (245)
Q Consensus 122 ~~~~~C~~C~~~k---P~Rs~HC~~C~-----~CV~~~DHhC 155 (245)
....+|..|+..- .....+|+.|+ +|..+.+.-|
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 4567899998766 45677899985 4555555444
No 50
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=31.15 E-value=4.4e+02 Score=24.53 Aligned_cols=31 Identities=19% Similarity=0.582 Sum_probs=20.8
Q ss_pred Cceecccccc-ccCCCCccCcccCcccccCCc
Q 025960 123 RIRYCRKCNQ-LKPPRCHHCSVCGRCILKMDH 153 (245)
Q Consensus 123 ~~~~C~~C~~-~kP~Rs~HC~~C~~CV~~~DH 153 (245)
...-|+.|+. .+|....+|..||.-..+.++
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~ 245 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVRRR 245 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCCCC
Confidence 3456999997 455556678888776655444
No 51
>KOG4219 consensus G protein-coupled receptor [Signal transduction mechanisms]
Probab=30.70 E-value=1.1e+02 Score=28.55 Aligned_cols=30 Identities=23% Similarity=0.219 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhhhhhcC
Q 025960 208 LATTFLAFGMASLTYHSDLCNRLHQHFYVING 239 (245)
Q Consensus 208 ~~~~~l~fvl~~~~~h~~l~~~~~tt~~~~~~ 239 (245)
+.+++..|.++.+-||.|.++-- |+|-+++
T Consensus 263 liiVV~~FaicWlPyh~y~il~~--~~~~i~~ 292 (423)
T KOG4219|consen 263 LIIVVVIFAICWLPYHIYFILNA--TNPEINR 292 (423)
T ss_pred HHHHHHHHHHhccChhHHHHHHH--hHHHHHH
Confidence 45566778889999999988764 4554443
No 52
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.48 E-value=28 Score=34.54 Aligned_cols=41 Identities=24% Similarity=0.514 Sum_probs=29.2
Q ss_pred CcCceeccccccccCCCCccCcccCcccccCCcccccccceec
Q 025960 121 NPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVG 163 (245)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG 163 (245)
....+||..|+..-+ .+.|..||.=+..-..+||==|.-.|
T Consensus 12 ~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 12 PNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCccc
Confidence 345689999986543 36799999888888888884444443
No 53
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=30.21 E-value=1.2e+02 Score=26.88 Aligned_cols=110 Identities=18% Similarity=0.258 Sum_probs=69.2
Q ss_pred CCCcCceeccccccccCCCCccCcccCcccccCCcccccccceeccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025960 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSE 198 (245)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHhCpwi~nCIG~~N~k~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~ 198 (245)
+++++..-|+.|+.---.=-|||.-=|.||--..| +-.-.|+.++.-...++...........+.-.++
T Consensus 111 pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~ 179 (309)
T KOG1313|consen 111 PKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE 179 (309)
T ss_pred CCCCCcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh
Confidence 55667788988887666667999999999998888 6777888888766666665545444444443333
Q ss_pred CC-CCCC--------------------hh-H---HHHHHHHHHHHHHHHHHHHHHHHhHhhhhhcC
Q 025960 199 GE-IPGT--------------------PG-T---LATTFLAFGMASLTYHSDLCNRLHQHFYVING 239 (245)
Q Consensus 199 ~~-~~~~--------------------~~-~---~~~~~l~fvl~~~~~h~~l~~~~~tt~~~~~~ 239 (245)
.+ .+++ .+ . ++..++..+..+...|..++.++-|.+|...+
T Consensus 180 ~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~ 245 (309)
T KOG1313|consen 180 ITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLIN 245 (309)
T ss_pred cccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHH
Confidence 11 1110 01 1 11111222333567788888888888877654
No 54
>PLN00186 ribosomal protein S26; Provisional
Probab=29.83 E-value=23 Score=26.66 Aligned_cols=15 Identities=40% Similarity=0.970 Sum_probs=12.0
Q ss_pred CCccCcccCcccccC
Q 025960 137 RCHHCSVCGRCILKM 151 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~ 151 (245)
+.-||..|++||.+=
T Consensus 19 ~~V~C~nCgr~vPKD 33 (109)
T PLN00186 19 KRIRCSNCGKCVPKD 33 (109)
T ss_pred cceeeCCCccccccc
Confidence 355899999999874
No 55
>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=29.46 E-value=14 Score=23.46 Aligned_cols=17 Identities=29% Similarity=0.913 Sum_probs=11.8
Q ss_pred cccCcccccCCcccccc
Q 025960 142 SVCGRCILKMDHHCVWV 158 (245)
Q Consensus 142 ~~C~~CV~~~DHhCpwi 158 (245)
..|+.|+...|-+|.|=
T Consensus 6 ~sC~~Cl~~~dp~CgWc 22 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWC 22 (51)
T ss_dssp SSHHHHHHSTCTTEEEE
T ss_pred CcHHHHHcCCCcCcccc
Confidence 56677777777777764
No 56
>PF14965 BRI3BP: Negative regulator of p53/TP53
Probab=29.23 E-value=3.2e+02 Score=22.43 Aligned_cols=19 Identities=21% Similarity=0.209 Sum_probs=13.6
Q ss_pred ccceeccCchHHHHHHHHH
Q 025960 158 VVNCVGALNYKYFLLFLLY 176 (245)
Q Consensus 158 i~nCIG~~N~k~F~~fl~~ 176 (245)
+.+++|++|.+.=.-|+.-
T Consensus 12 l~s~~G~e~v~~~~efls~ 30 (177)
T PF14965_consen 12 LESWLGEENVRAVAEFLSR 30 (177)
T ss_pred HHHHhChHHHHHHHHHHHH
Confidence 5678999999875555543
No 57
>PHA02942 putative transposase; Provisional
Probab=28.90 E-value=34 Score=31.56 Aligned_cols=24 Identities=33% Similarity=0.721 Sum_probs=17.9
Q ss_pred CceeccccccccC---CCCccCcccCc
Q 025960 123 RIRYCRKCNQLKP---PRCHHCSVCGR 146 (245)
Q Consensus 123 ~~~~C~~C~~~kP---~Rs~HC~~C~~ 146 (245)
..+.|+.|+...+ .|.+.|..||.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCC
Confidence 5688999986644 37778888776
No 58
>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=28.60 E-value=37 Score=19.09 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=11.8
Q ss_pred eccccccccCCC-CccCcccC
Q 025960 126 YCRKCNQLKPPR-CHHCSVCG 145 (245)
Q Consensus 126 ~C~~C~~~kP~R-s~HC~~C~ 145 (245)
.|..|+..-... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 366665555555 66776665
No 59
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=28.05 E-value=24 Score=25.92 Aligned_cols=20 Identities=30% Similarity=0.687 Sum_probs=14.7
Q ss_pred CCccCcccCcccccCCcccc
Q 025960 137 RCHHCSVCGRCILKMDHHCV 156 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhCp 156 (245)
+.-+|..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 35579999999998654443
No 60
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=27.82 E-value=5.1e+02 Score=24.24 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=23.3
Q ss_pred CceeccccccccCCCCccCcccCcccccCCc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSVCGRCILKMDH 153 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DH 153 (245)
...-|+.|+..-|....+|..||.-..+.++
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~ 250 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRR 250 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCC
Confidence 3556999998877777789888887655444
No 61
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.65 E-value=47 Score=21.94 Aligned_cols=24 Identities=38% Similarity=0.963 Sum_probs=15.9
Q ss_pred CcCceeccccccccCCCCcc-CcccCc
Q 025960 121 NPRIRYCRKCNQLKPPRCHH-CSVCGR 146 (245)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~H-C~~C~~ 146 (245)
......|+.|+..+.+ || |..||.
T Consensus 24 ~~~l~~C~~CG~~~~~--H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP--HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC--eEECCCCCc
Confidence 3445779999866544 55 777764
No 62
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.56 E-value=31 Score=18.37 Aligned_cols=21 Identities=29% Similarity=0.675 Sum_probs=14.2
Q ss_pred eccccccccCCCCccCcccCc
Q 025960 126 YCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 367777777777777776653
No 63
>PF07062 Clc-like: Clc-like; InterPro: IPR010761 Clc proteins are a nine-member gene family of chloride channels that have diverse roles in the plasma membrane and in intracellular organelles, especially membrane excitability and the maintenance of osmotic balance [, ]. This family contains a number of Clc-like proteins that are approximately 250 residues long and their homologues. ; GO: 0016021 integral to membrane
Probab=27.34 E-value=3.8e+02 Score=22.64 Aligned_cols=10 Identities=30% Similarity=0.378 Sum_probs=7.4
Q ss_pred cCcccccCCc
Q 025960 144 CGRCILKMDH 153 (245)
Q Consensus 144 C~~CV~~~DH 153 (245)
-.+|+.|||+
T Consensus 64 ~~~C~ykFd~ 73 (211)
T PF07062_consen 64 PLHCTYKFDY 73 (211)
T ss_pred CceEEEEcCc
Confidence 3678889884
No 64
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=27.06 E-value=61 Score=34.08 Aligned_cols=24 Identities=33% Similarity=0.760 Sum_probs=16.4
Q ss_pred ceeccccc--cccCCCCccCcccCcc
Q 025960 124 IRYCRKCN--QLKPPRCHHCSVCGRC 147 (245)
Q Consensus 124 ~~~C~~C~--~~kP~Rs~HC~~C~~C 147 (245)
..-|..|. -.--.|-||||.||+-
T Consensus 557 ~pncm~clqkft~ikrrhhcRacgkV 582 (1287)
T KOG1841|consen 557 APNCMDCLQKFTPIKRRHHCRACGKV 582 (1287)
T ss_pred CchHHHHHhhcccccccccchhccce
Confidence 34455555 3445699999999983
No 65
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=26.74 E-value=27 Score=26.29 Aligned_cols=16 Identities=44% Similarity=0.947 Sum_probs=12.3
Q ss_pred CCccCcccCcccccCC
Q 025960 137 RCHHCSVCGRCILKMD 152 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~D 152 (245)
+.-+|..|++||.+=-
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDK 34 (108)
T ss_pred ccEEeCCccccccccc
Confidence 3457999999998743
No 66
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=26.48 E-value=76 Score=21.20 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=16.6
Q ss_pred ceeccccccccCCCCccCc-ccCc
Q 025960 124 IRYCRKCNQLKPPRCHHCS-VCGR 146 (245)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~-~C~~ 146 (245)
.+-|..|+..-|+--..|| .|++
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 3668888888888777885 5544
No 67
>COG4640 Predicted membrane protein [Function unknown]
Probab=25.53 E-value=35 Score=31.66 Aligned_cols=26 Identities=27% Similarity=0.744 Sum_probs=20.6
Q ss_pred eeccccccccCCCCccCcccCccccc
Q 025960 125 RYCRKCNQLKPPRCHHCSVCGRCILK 150 (245)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~CV~~ 150 (245)
++|..|+..+-+-+..|..||.=+-.
T Consensus 2 ~fC~kcG~qk~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 2 KFCPKCGSQKAEDDVQCTQCGHKFTS 27 (465)
T ss_pred CcccccccccccccccccccCCcCCc
Confidence 68999998888888888888875443
No 68
>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=25.19 E-value=27 Score=20.54 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=12.6
Q ss_pred cCceeccccccc-cCCCCccCcccC
Q 025960 122 PRIRYCRKCNQL-KPPRCHHCSVCG 145 (245)
Q Consensus 122 ~~~~~C~~C~~~-kP~Rs~HC~~C~ 145 (245)
...+.|..|+.. =||| ..|..|+
T Consensus 9 l~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEEEE-TTT--EEES---SEETTTT
T ss_pred EEEEEcCCCCCEecCCC-cCCCCcC
Confidence 345789999877 4555 7777775
No 69
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=24.93 E-value=30 Score=21.32 Aligned_cols=15 Identities=40% Similarity=1.214 Sum_probs=7.0
Q ss_pred ccCcccccCCccccc
Q 025960 143 VCGRCILKMDHHCVW 157 (245)
Q Consensus 143 ~C~~CV~~~DHhCpw 157 (245)
.|..|+...|-||.|
T Consensus 6 sC~~C~~~~~~~C~W 20 (46)
T smart00423 6 SCSECLLARDPYCAW 20 (46)
T ss_pred cHHHHHcCCCCCCCc
Confidence 344444444444444
No 70
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=24.01 E-value=29 Score=29.62 Aligned_cols=19 Identities=26% Similarity=0.740 Sum_probs=15.3
Q ss_pred ccCCCCccCcccCcccccC
Q 025960 133 LKPPRCHHCSVCGRCILKM 151 (245)
Q Consensus 133 ~kP~Rs~HC~~C~~CV~~~ 151 (245)
+++.+..||..|..|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 4666666999999999874
No 71
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.94 E-value=53 Score=21.71 Aligned_cols=22 Identities=41% Similarity=0.895 Sum_probs=14.6
Q ss_pred CceeccccccccCCCCccCcccCc
Q 025960 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
..+.|..|+++-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4577777777665 566776664
No 72
>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=22.68 E-value=64 Score=21.11 Aligned_cols=23 Identities=30% Similarity=0.814 Sum_probs=15.0
Q ss_pred cCceeccccccccCCCCcc-CcccCc
Q 025960 122 PRIRYCRKCNQLKPPRCHH-CSVCGR 146 (245)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H-C~~C~~ 146 (245)
.....|+.|+. +-++|| |..||.
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 34566999985 445566 777764
No 73
>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=22.42 E-value=61 Score=17.57 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=4.8
Q ss_pred ccccccccCCC
Q 025960 127 CRKCNQLKPPR 137 (245)
Q Consensus 127 C~~C~~~kP~R 137 (245)
|..|+..-.+|
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 44454444444
No 74
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=21.78 E-value=36 Score=34.28 Aligned_cols=37 Identities=27% Similarity=0.614 Sum_probs=28.2
Q ss_pred CccCc---ccCcccccCCccccccc---cee--ccCchHHHHHHH
Q 025960 138 CHHCS---VCGRCILKMDHHCVWVV---NCV--GALNYKYFLLFL 174 (245)
Q Consensus 138 s~HC~---~C~~CV~~~DHhCpwi~---nCI--G~~N~k~F~~fl 174 (245)
-|+|+ .|..|++..|-||.|-+ .|+ +..|.|.+.+=+
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 89998888999999998 786 445666665544
No 75
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=21.74 E-value=53 Score=27.26 Aligned_cols=24 Identities=46% Similarity=0.838 Sum_probs=18.1
Q ss_pred CcCceeccccccccCCCCccCcccCc
Q 025960 121 NPRIRYCRKCNQLKPPRCHHCSVCGR 146 (245)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (245)
.....||.+|+.+-+.|. |+.||.
T Consensus 11 k~~iyWCe~cNlPl~~~~--c~~cg~ 34 (202)
T COG5270 11 KFPIYWCEKCNLPLLGRR--CSVCGS 34 (202)
T ss_pred ccceeehhhCCCcccccc--ccccCC
Confidence 456799999998777654 777773
No 76
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.13 E-value=37 Score=33.38 Aligned_cols=23 Identities=35% Similarity=0.808 Sum_probs=16.6
Q ss_pred ceeccccccc--cCCCCccCcccCc
Q 025960 124 IRYCRKCNQL--KPPRCHHCSVCGR 146 (245)
Q Consensus 124 ~~~C~~C~~~--kP~Rs~HC~~C~~ 146 (245)
..-|.+|... --.|.|||+.||+
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccceeeeeeeeccccccccccch
Confidence 3568888642 1239999999998
No 77
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=20.65 E-value=3.7e+02 Score=20.04 Aligned_cols=56 Identities=13% Similarity=0.146 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025960 176 YTFLETSLVTLSLLPHFISFFSEGEIPGTPGTLATTFLAFGMASLTYHSDLCNRLH 231 (245)
Q Consensus 176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~fvl~~~~~h~~l~~~~~ 231 (245)
|..+..........+...+...+--.-..+..+...+...++-...+|.+.....+
T Consensus 36 Wl~~~i~~l~~~ifP~~~~~vA~~lGi~~~~n~lf~~~i~~ll~~~~~l~~~is~l 91 (115)
T PF10066_consen 36 WLVFSIILLILSIFPNILDWVAKLLGIGRPPNLLFYLGILFLLVIIFSLYVRISRL 91 (115)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444555566667777666655222223333444444444445566665554443
No 78
>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=20.59 E-value=38 Score=25.78 Aligned_cols=19 Identities=32% Similarity=0.646 Sum_probs=11.7
Q ss_pred CCccCcccCcccccCCccc
Q 025960 137 RCHHCSVCGRCILKMDHHC 155 (245)
Q Consensus 137 Rs~HC~~C~~CV~~~DHhC 155 (245)
+.-+|..|++||.+----.
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIK 37 (113)
T ss_dssp -EEE-TTTB-EEECCCSEE
T ss_pred cCEeeCcccccCcCCceEE
Confidence 4568999999999854433
No 79
>KOG4004 consensus Matricellular protein Osteonectin/SPARC/BM-40 [Extracellular structures]
Probab=20.57 E-value=49 Score=27.91 Aligned_cols=15 Identities=33% Similarity=0.543 Sum_probs=9.7
Q ss_pred Cccccccccee-ccCc
Q 025960 152 DHHCVWVVNCV-GALN 166 (245)
Q Consensus 152 DHhCpwi~nCI-G~~N 166 (245)
||||.|--||+ |.+|
T Consensus 55 dh~Cg~gk~C~vd~~~ 70 (259)
T KOG4004|consen 55 DHKCGPGKNCLVDLQT 70 (259)
T ss_pred cccCCCCceeeecCCC
Confidence 77777777763 5444
No 80
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=20.48 E-value=71 Score=18.38 Aligned_cols=7 Identities=43% Similarity=1.246 Sum_probs=3.2
Q ss_pred eeccccc
Q 025960 125 RYCRKCN 131 (245)
Q Consensus 125 ~~C~~C~ 131 (245)
.+|.+|+
T Consensus 17 ~~C~~C~ 23 (32)
T PF13842_consen 17 YMCSKCD 23 (32)
T ss_pred EEccCCC
Confidence 3455543
No 81
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.02 E-value=54 Score=28.98 Aligned_cols=24 Identities=33% Similarity=0.940 Sum_probs=17.0
Q ss_pred CceeccccccccCCC----CccCcccCc
Q 025960 123 RIRYCRKCNQLKPPR----CHHCSVCGR 146 (245)
Q Consensus 123 ~~~~C~~C~~~kP~R----s~HC~~C~~ 146 (245)
..|||..|+...-+| +..|+.||.
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCC
Confidence 458899998655544 667888865
Done!