Query psy13205
Match_columns 267
No_of_seqs 213 out of 1917
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 22:50:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13205.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13205hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1311|consensus 100.0 7.2E-40 1.6E-44 292.0 17.6 189 45-267 58-269 (299)
2 KOG1315|consensus 100.0 2.7E-38 5.8E-43 277.3 11.1 179 45-264 51-258 (307)
3 PF01529 zf-DHHC: DHHC palmito 100.0 4.1E-36 9E-41 247.5 10.6 148 55-241 2-174 (174)
4 KOG1314|consensus 100.0 8.9E-35 1.9E-39 252.2 9.2 186 44-264 52-263 (414)
5 KOG1313|consensus 100.0 2.3E-34 4.9E-39 242.5 9.9 184 50-261 78-273 (309)
6 COG5273 Uncharacterized protei 100.0 4E-32 8.6E-37 241.3 16.5 159 40-240 56-232 (309)
7 KOG1312|consensus 100.0 3.8E-28 8.2E-33 206.0 11.0 82 54-135 112-205 (341)
8 KOG0509|consensus 99.9 4.9E-28 1.1E-32 225.0 9.0 96 50-145 378-487 (600)
9 KOG1311|consensus 99.8 9.9E-21 2.1E-25 168.9 9.7 72 91-190 112-183 (299)
10 KOG1315|consensus 99.8 1.9E-19 4.1E-24 158.4 10.1 123 91-243 108-231 (307)
11 KOG1313|consensus 99.8 3.5E-19 7.6E-24 150.8 4.1 72 90-189 100-171 (309)
12 COG5273 Uncharacterized protei 99.8 2.5E-18 5.5E-23 153.0 8.8 61 88-176 105-165 (309)
13 PF01529 zf-DHHC: DHHC palmito 99.7 4E-18 8.8E-23 140.2 5.9 84 88-199 44-127 (174)
14 KOG1314|consensus 99.6 4.6E-17 1E-21 142.2 2.5 58 93-178 92-149 (414)
15 KOG1312|consensus 99.5 4E-15 8.6E-20 127.0 1.5 123 91-241 147-291 (341)
16 KOG0509|consensus 99.5 5.9E-14 1.3E-18 131.5 5.2 143 90-261 417-582 (600)
17 PF12773 DZR: Double zinc ribb 93.3 0.063 1.4E-06 34.4 2.1 40 74-113 8-50 (50)
18 PF13240 zinc_ribbon_2: zinc-r 90.5 0.13 2.8E-06 27.5 0.8 21 80-100 1-21 (23)
19 PF13248 zf-ribbon_3: zinc-rib 87.6 0.26 5.6E-06 27.1 0.8 22 79-100 3-24 (26)
20 PF10571 UPF0547: Uncharacteri 81.0 0.84 1.8E-05 25.2 0.9 22 79-100 1-22 (26)
21 PF12773 DZR: Double zinc ribb 75.7 2.1 4.6E-05 27.1 1.8 35 81-115 1-38 (50)
22 PRK04136 rpl40e 50S ribosomal 72.4 2.1 4.6E-05 27.1 1.1 24 77-100 13-36 (48)
23 PRK14559 putative protein seri 70.7 3.3 7.1E-05 41.1 2.6 43 74-118 11-53 (645)
24 PF09889 DUF2116: Uncharacteri 70.5 4.2 9.1E-05 27.1 2.3 17 93-109 4-20 (59)
25 PF06906 DUF1272: Protein of u 59.0 4.8 0.0001 26.4 0.9 34 80-113 7-48 (57)
26 PTZ00303 phosphatidylinositol 58.0 6.1 0.00013 39.6 1.8 22 79-100 461-489 (1374)
27 smart00423 PSI domain found in 50.3 7.1 0.00015 24.2 0.6 22 96-117 5-29 (46)
28 PF00641 zf-RanBP: Zn-finger i 49.0 13 0.00028 20.8 1.5 25 78-102 4-28 (30)
29 PF01020 Ribosomal_L40e: Ribos 49.0 13 0.00028 24.0 1.6 25 77-101 16-42 (52)
30 PRK14559 putative protein seri 48.2 13 0.00027 37.0 2.2 37 79-117 2-38 (645)
31 COG2093 DNA-directed RNA polym 43.9 13 0.00028 25.0 1.1 22 79-100 5-26 (64)
32 PF01363 FYVE: FYVE zinc finge 41.7 12 0.00025 25.3 0.7 10 91-100 24-33 (69)
33 COG1552 RPL40A Ribosomal prote 40.7 5.5 0.00012 25.3 -1.0 24 77-100 13-36 (50)
34 PF11023 DUF2614: Protein of u 39.3 82 0.0018 23.9 4.8 21 80-100 71-93 (114)
35 PF09297 zf-NADH-PPase: NADH p 38.4 18 0.0004 20.5 1.1 23 78-100 3-29 (32)
36 PF01437 PSI: Plexin repeat; 37.1 7.3 0.00016 24.8 -0.9 23 96-118 6-31 (51)
37 KOG4399|consensus 37.0 11 0.00023 32.9 -0.2 40 79-119 262-304 (325)
38 smart00661 RPOL9 RNA polymeras 35.0 21 0.00045 22.5 1.0 21 79-99 1-27 (52)
39 TIGR00155 pqiA_fam integral me 33.5 90 0.0019 29.2 5.3 31 78-108 215-246 (403)
40 KOG1819|consensus 33.0 15 0.00033 35.0 0.1 22 79-100 902-925 (990)
41 PF03503 Chlam_OMP3: Chlamydia 32.9 39 0.00084 21.4 1.9 31 79-109 24-54 (55)
42 PRK02935 hypothetical protein; 32.9 98 0.0021 23.2 4.3 21 80-100 72-94 (110)
43 PRK15103 paraquat-inducible me 32.6 40 0.00088 31.7 2.9 30 78-107 221-250 (419)
44 KOG1842|consensus 32.2 12 0.00027 35.0 -0.6 25 77-101 179-205 (505)
45 smart00064 FYVE Protein presen 31.9 36 0.00079 22.7 1.9 22 79-100 11-34 (68)
46 PTZ00303 phosphatidylinositol 31.1 32 0.00069 34.9 2.0 29 86-114 452-489 (1374)
47 PF02150 RNA_POL_M_15KD: RNA p 31.0 20 0.00042 21.1 0.3 9 79-87 2-10 (35)
48 COG2888 Predicted Zn-ribbon RN 30.8 27 0.00059 23.3 1.0 37 78-114 9-49 (61)
49 KOG1729|consensus 30.8 17 0.00036 32.4 0.0 29 86-114 161-193 (288)
50 PF07649 C1_3: C1-like domain; 30.6 22 0.00048 19.8 0.5 21 80-100 2-23 (30)
51 PRK14890 putative Zn-ribbon RN 29.6 33 0.00073 22.8 1.3 36 78-113 7-46 (59)
52 PRK14714 DNA polymerase II lar 29.3 45 0.00098 35.6 2.8 22 94-115 694-718 (1337)
53 PRK00432 30S ribosomal protein 27.8 38 0.00082 21.7 1.3 23 77-99 19-44 (50)
54 cd00065 FYVE FYVE domain; Zinc 25.9 46 0.001 21.2 1.5 11 90-100 16-26 (57)
55 COG4068 Uncharacterized protei 25.8 80 0.0017 21.0 2.5 19 92-110 8-26 (64)
56 KOG4399|consensus 25.6 16 0.00035 31.8 -0.9 32 72-103 198-229 (325)
57 PLN00186 ribosomal protein S26 25.4 33 0.00071 25.8 0.8 20 91-110 19-38 (109)
58 smart00547 ZnF_RBZ Zinc finger 25.0 36 0.00078 18.0 0.7 22 79-100 3-24 (26)
59 PRK09335 30S ribosomal protein 24.7 32 0.00069 25.2 0.6 22 91-112 19-40 (95)
60 PF13842 Tnp_zf-ribbon_2: DDE_ 24.4 55 0.0012 18.8 1.4 7 93-99 17-23 (32)
61 PTZ00172 40S ribosomal protein 22.6 38 0.00083 25.4 0.7 20 91-110 19-38 (108)
62 PRK03681 hypA hydrogenase nick 22.1 46 0.001 25.2 1.1 25 76-100 68-95 (114)
63 KOG3183|consensus 21.4 42 0.00092 28.9 0.8 14 101-114 37-50 (250)
No 1
>KOG1311|consensus
Probab=100.00 E-value=7.2e-40 Score=291.98 Aligned_cols=189 Identities=38% Similarity=0.705 Sum_probs=131.5
Q ss_pred HHHHHHHHHHHHHHhhhh---cCCCCCCCC--C-----------------CccccceecCccccccCCCCccCcCCCccc
Q psy13205 45 IQAVITFFVLANFTLATF---MDPGAIPKV--N-----------------GITVRMKWCVTCKFYRPPRCSHCSVCNYCI 102 (267)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~---~dPG~ip~~--~-----------------~~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv 102 (267)
...++....+.+...+.. +|||.+|+. . +...++++|.+|+..||+|||||++||+||
T Consensus 58 ~~~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV 137 (299)
T KOG1311|consen 58 LGAIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCV 137 (299)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccc
Confidence 334444444555544444 499999883 1 112358999999999999999999999999
Q ss_pred cCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHHHHHHHHHHHH
Q psy13205 103 ETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFA 182 (267)
Q Consensus 103 ~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~~~~~~~~~~~ 182 (267)
.||||||+|+|||||+||||+|+.|++++++.+++.++....+...++
T Consensus 138 ~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~-------------------------------- 185 (299)
T KOG1311|consen 138 LRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRA-------------------------------- 185 (299)
T ss_pred cccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------------------------
Confidence 999999999999999999999999999887777554433221100000
Q ss_pred HHHhhHhhccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhc-ccCCCCCCCChhHhhhccccc
Q psy13205 183 LCLIYVMINKNSLSDTEAIISLVIMSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTG-KFKGGYNPFSHGCWHNCCYGL 261 (267)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~-~~~~~~npy~~G~~~N~~~~~ 261 (267)
..... ...............++..+.++.....+.++.+|++++.+|+||+|++++ +.+.+++|||+|.++|+++++
T Consensus 186 ~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~ 263 (299)
T KOG1311|consen 186 DNLKV--NLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVF 263 (299)
T ss_pred ccccc--cccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHh
Confidence 00000 000001112222333344455666666778999999999999999999986 333335999999999999999
Q ss_pred cccCCC
Q psy13205 262 CGPMYP 267 (267)
Q Consensus 262 ~~p~~~ 267 (267)
++|.++
T Consensus 264 ~~~~~~ 269 (299)
T KOG1311|consen 264 GGPLPL 269 (299)
T ss_pred CCCCCc
Confidence 999875
No 2
>KOG1315|consensus
Probab=100.00 E-value=2.7e-38 Score=277.27 Aligned_cols=179 Identities=30% Similarity=0.596 Sum_probs=128.6
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCCCCC------------CC-------------ccccceecCccccccCCCCccCcCCC
Q psy13205 45 IQAVITFFVLANFTLATFMDPGAIPKV------------NG-------------ITVRMKWCVTCKFYRPPRCSHCSVCN 99 (267)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~~dPG~ip~~------------~~-------------~~~~~~~C~~C~~~kP~Rs~hC~~C~ 99 (267)
....+......+|.+++++|||.+|.. ++ ...+.|+|.+|+.+||||||||++|+
T Consensus 51 ~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~ 130 (307)
T KOG1315|consen 51 LFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCN 130 (307)
T ss_pred HHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhh
Confidence 345566677888999999999999871 11 12367999999999999999999999
Q ss_pred ccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHHHHHHHHH
Q psy13205 100 YCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMAS 179 (267)
Q Consensus 100 ~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~~~~~~~~ 179 (267)
|||+||||||+|+|||||.+|||+|++|++|..+++.+.......
T Consensus 131 rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~----------------------------------- 175 (307)
T KOG1315|consen 131 RCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLI----------------------------------- 175 (307)
T ss_pred hhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------
Confidence 999999999999999999999999999999999888543332111
Q ss_pred HHHHHHhhHhhccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhcc-c---CCCCCCCChhHhh
Q psy13205 180 IFALCLIYVMINKNSLSDTEAIISLVIMSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTGK-F---KGGYNPFSHGCWH 255 (267)
Q Consensus 180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~-~---~~~~npy~~G~~~ 255 (267)
.....+ ......+........+...+...+.+.+.+++++|++|+++|+||+|..+.+ + ....|.++. ..
T Consensus 176 --~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~--~~ 249 (307)
T KOG1315|consen 176 --GFTKYF--QGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGFNL--YV 249 (307)
T ss_pred --HHHHHH--hccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCcce--ee
Confidence 001111 1111111212233344444455555666679999999999999999998875 2 233566666 77
Q ss_pred hcccccccc
Q psy13205 256 NCCYGLCGP 264 (267)
Q Consensus 256 N~~~~~~~p 264 (267)
|++|+|.+.
T Consensus 250 n~~~vfg~~ 258 (307)
T KOG1315|consen 250 NFREVFGSN 258 (307)
T ss_pred cHHHHhCCC
Confidence 888886653
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=4.1e-36 Score=247.47 Aligned_cols=148 Identities=39% Similarity=0.757 Sum_probs=109.3
Q ss_pred HHHHhhhhcCCCCCCCC-----------------------CCccccceecCccccccCCCCccCcCCCccccCccccCcc
Q psy13205 55 ANFTLATFMDPGAIPKV-----------------------NGITVRMKWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPW 111 (267)
Q Consensus 55 ~~~~~~~~~dPG~ip~~-----------------------~~~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w 111 (267)
.+|+++.++|||++|+. ++...+.++|.+|+.+||+|||||+.||+||+++||||+|
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 46788999999999885 1223567999999999999999999999999999999999
Q ss_pred ccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHHHHHHHHHHHHHHHhhHhhc
Q psy13205 112 VNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYVMIN 191 (267)
Q Consensus 112 ~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~ 191 (267)
+|+|||++|||+|++|+++..+..++.....+.+ +......
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~---------------------------------------~~~~~~~ 122 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYY---------------------------------------LVRYIPS 122 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHH---------------------------------------HHHHhhc
Confidence 9999999999999999999888764433221111 0000000
Q ss_pred cCCCCch--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhcc
Q psy13205 192 KNSLSDT--EAIISLVIMSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTGK 241 (267)
Q Consensus 192 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~ 241 (267)
....... .....++.+.+.++.+++++.++++|++++++|+||+|.+++|
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 123 ISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred ccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 1111101 1111144555566677778889999999999999999999865
No 4
>KOG1314|consensus
Probab=100.00 E-value=8.9e-35 Score=252.24 Aligned_cols=186 Identities=25% Similarity=0.414 Sum_probs=129.6
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCCCCCC----CC-ccccceecCccccccCCCCccCcCCCccccCccccCccccccccc
Q psy13205 44 PIQAVITFFVLANFTLATFMDPGAIPKV----NG-ITVRMKWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNCIGR 118 (267)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~dPG~ip~~----~~-~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~ 118 (267)
+.+.+.....++||+.+++++||++|.. +. ...-.+||.+|+.+|+||||||+.|||||.+|||||||+|||||.
T Consensus 52 i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~ 131 (414)
T KOG1314|consen 52 ITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGW 131 (414)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccc
Confidence 3455567778999999999999999882 22 224578999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHHHHHHHHHHHHHHHhhHh---hccCCC
Q psy13205 119 RNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYVM---INKNSL 195 (267)
Q Consensus 119 ~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~---~~~~~~ 195 (267)
.||.+|+.||++..++++-... +. ..+..-.++..+ .....+
T Consensus 132 aNh~~F~~FLlf~ivG~ih~ti--------------------------I~---------~~~~~~~Iy~~W~~~~g~~hl 176 (414)
T KOG1314|consen 132 ANHAYFLRFLLFSIVGCIHGTI--------------------------IL---------VCAQYRGIYFRWYIKYGLRHL 176 (414)
T ss_pred cccHHHHHHHHHHHHhccccee--------------------------ee---------hhHHHHHHHHHHHhhcccccC
Confidence 9999999999987665421000 00 011111121111 111111
Q ss_pred C-----chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhc-c-------c-CC--C--CCCCChhHhhhc
Q psy13205 196 S-----DTEAIISLVIMSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTG-K-------F-KG--G--YNPFSHGCWHNC 257 (267)
Q Consensus 196 ~-----~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~-~-------~-~~--~--~npy~~G~~~N~ 257 (267)
. ....+..++.+.+.....+.++.|+..|+..|.+|+|.+|.... | + .+ + -.|||.|+..|.
T Consensus 177 p~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~ 256 (414)
T KOG1314|consen 177 PIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINL 256 (414)
T ss_pred ceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccH
Confidence 1 12223333444455555666778888999999999999997541 1 0 11 1 369999966699
Q ss_pred ccccccc
Q psy13205 258 CYGLCGP 264 (267)
Q Consensus 258 ~~~~~~p 264 (267)
+|||++.
T Consensus 257 r~vf~~~ 263 (414)
T KOG1314|consen 257 REVFFQN 263 (414)
T ss_pred HHHhhhc
Confidence 9999875
No 5
>KOG1313|consensus
Probab=100.00 E-value=2.3e-34 Score=242.52 Aligned_cols=184 Identities=29% Similarity=0.460 Sum_probs=125.5
Q ss_pred HHHHHHHHHhhhhcCCCCCCCCCCccccceecCccccccCCCCccCcCCCccccCccccCccccccccccchHHHHHHHH
Q psy13205 50 TFFVLANFTLATFMDPGAIPKVNGITVRMKWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLV 129 (267)
Q Consensus 50 ~~~~~~~~~~~~~~dPG~ip~~~~~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~ 129 (267)
..++++.|+++..+. |..++..+...+|.+|..+||||+|||+.|||||++|||||||+|||||..|||+|++|++
T Consensus 78 l~nvi~hy~ka~t~p----Pvgn~~~~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~ 153 (309)
T KOG1313|consen 78 LSNVIFHYYKARTKP----PVGNPGLENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLF 153 (309)
T ss_pred HHHHHHhheeecccC----CcCCCCCccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHH
Confidence 334455566666554 4566677779999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhhccCCCccccc-----cccccccchhhHHHHHHHHHHHHHHHHHHhhHhhccCCCCchhHHHHH
Q psy13205 130 TLSLHMASIFALCLIYTFDHHCPWVNN-----CIGRRNYRYFFFFLVTLSLHMASIFALCLIYVMINKNSLSDTEAIISL 204 (267)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~DHHC~Wi~~-----CVG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (267)
|+++++++...++.+.-.||-=+|-.. =+++.-.. .-+.... .........
T Consensus 154 ~ltlat~~~~i~~~~~w~~~le~~~~~tay~~d~~h~~Pp---------------------~~i~r~~---~~i~~t~~~ 209 (309)
T KOG1313|consen 154 YLTLATSYAAIMCVYTWIDHLEPIEEITAYASDVAHVAPP---------------------PSILRVY---KNITRTSIA 209 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHhcchHhhcccccCcccccCCC---------------------hhhhhhh---hhhhHHHHH
Confidence 999999886666544323332222110 00000000 0000000 000011112
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhccc-------CCCCCCCChhHhhhccccc
Q psy13205 205 VIMSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTGKF-------KGGYNPFSHGCWHNCCYGL 261 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~~~-------~~~~npy~~G~~~N~~~~~ 261 (267)
..+.+.+..+++++.+..+|.++|++|.|++|+..... +.++||++.|..+||+.++
T Consensus 210 ~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~~n~g~k~nWr~fL 273 (309)
T KOG1313|consen 210 NLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNPTNFGGKANWRNFL 273 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCCcccchHHHHHHhh
Confidence 24445555667788899999999999999999875432 2347999999988887654
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=4e-32 Score=241.26 Aligned_cols=159 Identities=34% Similarity=0.600 Sum_probs=114.9
Q ss_pred ccHHHHHHHHHHHHHHHHHhhhhcCCCCCCC---------------CCCccccceecCccccccCCCCccCcCCCccccC
Q psy13205 40 PWVIPIQAVITFFVLANFTLATFMDPGAIPK---------------VNGITVRMKWCVTCKFYRPPRCSHCSVCNYCIET 104 (267)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~dPG~ip~---------------~~~~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~ 104 (267)
........++.......++....+|||..++ ..+..+..++|++|+.+||+|||||+.||+||++
T Consensus 56 ~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k 135 (309)
T COG5273 56 VLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLK 135 (309)
T ss_pred hhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhc
Confidence 4444455666777888889999999999974 2345567899999999999999999999999999
Q ss_pred ccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHHHHHHHHHHHHHH
Q psy13205 105 FDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALC 184 (267)
Q Consensus 105 ~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~~~~~~~~~~~~~ 184 (267)
+||||+|+|||||++|||+|++|++++..++..++....
T Consensus 136 ~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~----------------------------------------- 174 (309)
T COG5273 136 FDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTA----------------------------------------- 174 (309)
T ss_pred cCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------------
Confidence 999999999999999999999999998777644332211
Q ss_pred HhhHhhccCCCCchhHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHhCcchhhhhhc
Q psy13205 185 LIYVMINKNSLSDTEAIISLVI---MSLIAILFIPIFGLTGFHMVLVARGRTTNEQVTG 240 (267)
Q Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~~~h~~li~~n~TT~E~~~~ 240 (267)
+......+............+ .......++.+..++.++.+++..|+|+.|..+.
T Consensus 175 -~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~ 232 (309)
T COG5273 175 -YYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQI 232 (309)
T ss_pred -HHHHhhccccCChHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHh
Confidence 111111111111112211111 2334445666778889999999999999997654
No 7
>KOG1312|consensus
Probab=99.95 E-value=3.8e-28 Score=205.99 Aligned_cols=82 Identities=50% Similarity=0.970 Sum_probs=71.4
Q ss_pred HHHHHhhhhcCCCCCCCCCC------------ccccceecCccccccCCCCccCcCCCccccCccccCccccccccccch
Q psy13205 54 LANFTLATFMDPGAIPKVNG------------ITVRMKWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNCIGRRNY 121 (267)
Q Consensus 54 ~~~~~~~~~~dPG~ip~~~~------------~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~ 121 (267)
...+.+++.+|||.+.+++. ...+...|++|+.+||+|||||+.|||||.|+||||.|+|||||++|.
T Consensus 112 ~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ 191 (341)
T KOG1312|consen 112 LIFFTLTCGSNPGIITKANESLFLHVYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINNCIGAWNI 191 (341)
T ss_pred HHHHhhhhcCCCCccchhhhccceeccCccceeecCCCccccccCCCccccccchHHHHHHHHhccceEeeecccccchH
Confidence 45667789999999988543 224458999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy13205 122 RYFFFFLVTLSLHM 135 (267)
Q Consensus 122 r~F~~fl~~~~~~~ 135 (267)
|||++|+++....+
T Consensus 192 ryF~lFLL~~i~l~ 205 (341)
T KOG1312|consen 192 RYFLLFLLTLISLA 205 (341)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999874444
No 8
>KOG0509|consensus
Probab=99.95 E-value=4.9e-28 Score=224.96 Aligned_cols=96 Identities=44% Similarity=0.921 Sum_probs=79.1
Q ss_pred HHHHHHHHHhhhhcCCCCCCCCC-------------Cccccc-eecCccccccCCCCccCcCCCccccCccccCcccccc
Q psy13205 50 TFFVLANFTLATFMDPGAIPKVN-------------GITVRM-KWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNC 115 (267)
Q Consensus 50 ~~~~~~~~~~~~~~dPG~ip~~~-------------~~~~~~-~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~C 115 (267)
.+..+..+.+...+|||++|..+ +..+.. +||.+|.++||.|||||++|||||.++||||||++||
T Consensus 378 ~l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~nc 457 (600)
T KOG0509|consen 378 VLAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNC 457 (600)
T ss_pred HHHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCccccc
Confidence 33444556666779999998832 334455 6999999999999999999999999999999999999
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHhhhh
Q psy13205 116 IGRRNYRYFFFFLVTLSLHMASIFALCLIY 145 (267)
Q Consensus 116 Ig~~N~r~F~~fl~~~~~~~~~~~~~~~~~ 145 (267)
||.+|||+|+.|++.+...+.+.+..+..|
T Consensus 458 VG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y 487 (600)
T KOG0509|consen 458 VGLKNHRLFVFFLLTLLTVIVFYLYLCLYY 487 (600)
T ss_pred cCccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999998877776655555555
No 9
>KOG1311|consensus
Probab=99.83 E-value=9.9e-21 Score=168.87 Aligned_cols=72 Identities=43% Similarity=0.927 Sum_probs=65.2
Q ss_pred CCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHH
Q psy13205 91 RCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFL 170 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl 170 (267)
+.++|+.|+..+|+|.|||+.||+||.+ +||||||+|||||++|||+|+.|+
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~r----------------------------fDHHC~WvnnCVG~rNyr~F~~f~ 163 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLR----------------------------FDHHCPWLNNCIGERNYRYFVLFL 163 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccc----------------------------cCCCCCCccceECCCchHHHHHHH
Confidence 3799999999999999999999999998 899999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhHhh
Q psy13205 171 VTLSLHMASIFALCLIYVMI 190 (267)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~ 190 (267)
++..+.+....+.....+..
T Consensus 164 ~~~~l~~i~~~~~~~~~~~~ 183 (299)
T KOG1311|consen 164 FYLALGVLLALAFLFYELLQ 183 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 98888887777776666554
No 10
>KOG1315|consensus
Probab=99.80 E-value=1.9e-19 Score=158.44 Aligned_cols=123 Identities=26% Similarity=0.524 Sum_probs=86.1
Q ss_pred CCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHH
Q psy13205 91 RCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFL 170 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl 170 (267)
+.+.|.+|+..+|+|.|||+.|++||.+ |||||||+|||||.+|||+|++|+
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLK----------------------------mDHHCpWi~nCVgf~NyKfF~lfl 159 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLK----------------------------MDHHCPWINNCVGFRNYKFFLLFL 159 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhc----------------------------cccCCcceeceecccchHHHHHHH
Confidence 7899999999999999999999999998 999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhHhhccCCCCchhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhCcchhhhhhcccC
Q psy13205 171 VTLSLHMASIFALCLIYVMINKNSLSDTEAIISLVIMSLIAILFIP-IFGLTGFHMVLVARGRTTNEQVTGKFK 243 (267)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~h~~li~~n~TT~E~~~~~~~ 243 (267)
+|..+.+.......+..+....... ..........+.+..++.++ ...+.++-.+.+. -...+|...+.++
T Consensus 160 ~y~~l~~~~~lv~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~-Li~~N~TTiE~~~ 231 (307)
T KOG1315|consen 160 FYTNLYSIYVLVTTLIGFTKYFQGG-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTY-LILKNKTTIEAYK 231 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHcCchhHhhhc
Confidence 9999988777777776666544222 22222223333333333333 3334443333333 4455555554444
No 11
>KOG1313|consensus
Probab=99.76 E-value=3.5e-19 Score=150.83 Aligned_cols=72 Identities=42% Similarity=0.942 Sum_probs=64.8
Q ss_pred CCCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHH
Q psy13205 90 PRCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFF 169 (267)
Q Consensus 90 ~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~f 169 (267)
+.-..|..|+.-++++.|||+.||+||.+ |||||||+|||||..|||||++|
T Consensus 100 ~~~SfC~KC~~pK~prTHHCsiC~kCVL~----------------------------MDHHCPwinnCVG~~NHryFFlF 151 (309)
T KOG1313|consen 100 ENDSFCNKCNYPKSPRTHHCSICNKCVLK----------------------------MDHHCPWINNCVGAHNHRYFFLF 151 (309)
T ss_pred ccccHHhhcCCCCCCCcchhhHHhhHhhc----------------------------cccCCchhhcccccccchhHHHH
Confidence 35678999999999999999999999987 99999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhHh
Q psy13205 170 LVTLSLHMASIFALCLIYVM 189 (267)
Q Consensus 170 l~~~~~~~~~~~~~~~~~~~ 189 (267)
++++++++..+..+..+.+.
T Consensus 152 l~~ltlat~~~~i~~~~~w~ 171 (309)
T KOG1313|consen 152 LFYLTLATSYAAIMCVYTWI 171 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999998887776555444
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.75 E-value=2.5e-18 Score=153.03 Aligned_cols=61 Identities=46% Similarity=1.025 Sum_probs=56.3
Q ss_pred cCCCCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhh
Q psy13205 88 RPPRCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFF 167 (267)
Q Consensus 88 kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi 167 (267)
+-.+.+.|++|+..+|+|.|||+.||+||.+ |||||||+|||||++|||+|+
T Consensus 105 ~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k----------------------------~DHHC~Wi~nCVG~~N~r~F~ 156 (309)
T COG5273 105 KFGTENFCSTCNIYKPPRSHHCSICNRCVLK----------------------------FDHHCPWINNCVGFRNYRFFY 156 (309)
T ss_pred ccccceeccccccccCCCCccchhhcchhhc----------------------------cCccCcccccccCcchHHHHH
Confidence 3457899999999999999999999999998 999999999999999999999
Q ss_pred HHHHHHHHH
Q psy13205 168 FFLVTLSLH 176 (267)
Q Consensus 168 ~fl~~~~~~ 176 (267)
+|+++....
T Consensus 157 ~Fl~~~~~~ 165 (309)
T COG5273 157 QFLLYTILV 165 (309)
T ss_pred HHHHHHHHH
Confidence 999987644
No 13
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.73 E-value=4e-18 Score=140.18 Aligned_cols=84 Identities=43% Similarity=0.827 Sum_probs=71.9
Q ss_pred cCCCCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhh
Q psy13205 88 RPPRCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFF 167 (267)
Q Consensus 88 kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi 167 (267)
...+.++|+.|+.-+|.|.|||+.||+||.+ +||||+|+|+|||++|+|+|+
T Consensus 44 ~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~----------------------------~DHHC~w~~~cIG~~N~~~F~ 95 (174)
T PF01529_consen 44 ENGELKYCSTCKIIKPPRSHHCRVCNRCVLR----------------------------FDHHCPWLGNCIGRRNHRYFL 95 (174)
T ss_pred cCCCCEECcccCCcCCCcceecccccccccc----------------------------ccccchhhccccccccHHHHH
Confidence 4457899999999999999999999999998 899999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhHhhccCCCCchh
Q psy13205 168 FFLVTLSLHMASIFALCLIYVMINKNSLSDTE 199 (267)
Q Consensus 168 ~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (267)
+|+++..+.........+..+...........
T Consensus 96 ~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (174)
T PF01529_consen 96 LFLLYLCLYCLYFFILSLYYLVRYIPSISFSS 127 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 99999998888777777777665544443333
No 14
>KOG1314|consensus
Probab=99.64 E-value=4.6e-17 Score=142.22 Aligned_cols=58 Identities=38% Similarity=0.869 Sum_probs=53.7
Q ss_pred ccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHHHH
Q psy13205 93 SHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFLVT 172 (267)
Q Consensus 93 ~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl~~ 172 (267)
.+|..|+..+++|+|||+-||+||-+ |||||||+|||||..||.+|..||++
T Consensus 92 qfCk~CqgYKapRSHHCrkCnrCvmk----------------------------MDHHCPWinnCVG~aNh~~F~~FLlf 143 (414)
T KOG1314|consen 92 QFCKKCQGYKAPRSHHCRKCNRCVMK----------------------------MDHHCPWINNCVGWANHAYFLRFLLF 143 (414)
T ss_pred HHHhhccCcCCCccccchHHHHHHHh----------------------------hccCCcchhhcccccccHHHHHHHHH
Confidence 57999999999999999999999887 99999999999999999999999998
Q ss_pred HHHHHH
Q psy13205 173 LSLHMA 178 (267)
Q Consensus 173 ~~~~~~ 178 (267)
..+++.
T Consensus 144 ~ivG~i 149 (414)
T KOG1314|consen 144 SIVGCI 149 (414)
T ss_pred HHHhcc
Confidence 766543
No 15
>KOG1312|consensus
Probab=99.51 E-value=4e-15 Score=127.03 Aligned_cols=123 Identities=33% Similarity=0.575 Sum_probs=81.3
Q ss_pred CCccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhHHH
Q psy13205 91 RCSHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFFFL 170 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~fl 170 (267)
...-||+|+--+|.|+.||+.||.||.+ +||||.|+|||||..|.|||+.|+
T Consensus 147 k~~kCSTCki~KPARSKHCsiCNrCV~r----------------------------fDHHCiWiNNCIG~~N~ryF~lFL 198 (341)
T KOG1312|consen 147 KNVKCSTCKIRKPARSKHCSICNRCVHR----------------------------FDHHCIWINNCIGAWNIRYFLLFL 198 (341)
T ss_pred CCCccccccCCCccccccchHHHHHHHH----------------------------hccceEeeecccccchHHHHHHHH
Confidence 4578999999999999999999999998 999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhHhhccCCCCc-----------hhHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHH
Q psy13205 171 VTLSLHMASIFALCLIYVMINKNSLSD-----------TEAIISLVIMSLIA-----------ILFIPIFGLTGFHMVLV 228 (267)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~-----------~~~~~~~~l~~~h~~li 228 (267)
+.....+........+..+.......+ ......++...+.+ ..+..+++...+-.|+.
T Consensus 199 L~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g~~ks~~~L~~yl~la~~~~v~~l~~~~~~~~~~~Y~~f~~y~~ 278 (341)
T KOG1312|consen 199 LTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHGHVKSTVFLIQYLFLAFPRIVFMLGFVVVLSFLGGYLLFVLYLA 278 (341)
T ss_pred HHHHHHHHHHHHHHHheehhhccccchheeeeeeeecchhhHHHHHHHHHHHhccceeeeehhhhhhHhHHHHHHHHHHH
Confidence 987555444433322221211111110 00011111111110 01122445566777889
Q ss_pred HhCcchhhhhhcc
Q psy13205 229 ARGRTTNEQVTGK 241 (267)
Q Consensus 229 ~~n~TT~E~~~~~ 241 (267)
+.|+||.|+.+++
T Consensus 279 ~t~~~~~~W~~~d 291 (341)
T KOG1312|consen 279 ATNQTTNEWYRGD 291 (341)
T ss_pred hccCCchhhhccc
Confidence 9999999988764
No 16
>KOG0509|consensus
Probab=99.45 E-value=5.9e-14 Score=131.46 Aligned_cols=143 Identities=31% Similarity=0.441 Sum_probs=99.2
Q ss_pred CCC-ccCcCCCccccCccccCccccccccccchHHHHHHHHHHHHHHHHHHHHhhhhhccCCCccccccccccccchhhH
Q psy13205 90 PRC-SHCSVCNYCIETFDHHCPWVNNCIGRRNYRYFFFFLVTLSLHMASIFALCLIYTFDHHCPWVNNCIGRRNYRYFFF 168 (267)
Q Consensus 90 ~Rs-~hC~~C~~cv~~~DHHC~w~~~CIg~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~DHHC~Wi~~CVG~~N~~~Fi~ 168 (267)
++. ++|..|-..+|.|++||+.||+||.+ |||||||++||||.+|+++|+.
T Consensus 417 ~~en~FC~~clirKp~rSkhc~vcnrcVar----------------------------fDHhCPwi~ncVG~kNh~~F~~ 468 (600)
T KOG0509|consen 417 DLENRFCLTCLIRKPLRSKHCSVCNRCVAR----------------------------FDHHCPWIGNCVGLKNHRLFVF 468 (600)
T ss_pred cccccceeeeeeecCCccchhhhhHHHHhc----------------------------cccCCCccccccCccchHHHHH
Confidence 355 79999999999999999999999998 9999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhHhhccCCCCchhHHHHHHHHHHHHH--H----HH-------HHHHHH-HHHHHHHHhCcch
Q psy13205 169 FLVTLSLHMASIFALCLIYVMINKNSLSDTEAIISLVIMSLIAI--L----FI-------PIFGLT-GFHMVLVARGRTT 234 (267)
Q Consensus 169 fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~----~~-------~~~~l~-~~h~~li~~n~TT 234 (267)
|++.....+.+.+....+++.............+..+.. +... + +. ...... .-|...++.+.||
T Consensus 469 Fl~~l~~~~~~~l~~~~~y~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt 547 (600)
T KOG0509|consen 469 FLLTLLTVIVFYLYLCLYYIMNLENASTIYVGFLIAVQA-FRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTT 547 (600)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHH-HhCCccceeeeeeccccccccccccccccccceeeecccH
Confidence 999988887777777776655332211111111111100 0000 0 00 001111 1233357889999
Q ss_pred hhhhhcccCC--------CCCCCChhHhhhccccc
Q psy13205 235 NEQVTGKFKG--------GYNPFSHGCWHNCCYGL 261 (267)
Q Consensus 235 ~E~~~~~~~~--------~~npy~~G~~~N~~~~~ 261 (267)
+|+++.++++ .++|+++|..+|+.+++
T Consensus 548 ~e~~n~~r~~~~~~~~~~~~~~~s~g~~~Nl~df~ 582 (600)
T KOG0509|consen 548 NEQINVKRYEHLGIKRGPTRSPFSPGPIRNLVDFF 582 (600)
T ss_pred HHHHHHHHhhccccccCcCCCCCCchhhhcchhee
Confidence 9998775432 26899999999998875
No 17
>PF12773 DZR: Double zinc ribbon
Probab=93.34 E-value=0.063 Score=34.36 Aligned_cols=40 Identities=20% Similarity=0.343 Sum_probs=32.1
Q ss_pred ccccceecCccccccC---CCCccCcCCCccccCccccCcccc
Q psy13205 74 ITVRMKWCVTCKFYRP---PRCSHCSVCNYCIETFDHHCPWVN 113 (267)
Q Consensus 74 ~~~~~~~C~~C~~~kP---~Rs~hC~~C~~cv~~~DHHC~w~~ 113 (267)
..++.+||..|....+ ...+.|+.|+.-+.+.+.+|+.+|
T Consensus 8 ~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCccccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456789999998777 346789999999999999998775
No 18
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.45 E-value=0.13 Score=27.51 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=17.0
Q ss_pred ecCccccccCCCCccCcCCCc
Q psy13205 80 WCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 80 ~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
+|+.|...-++.++.|+.|+.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588888888888888888875
No 19
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.56 E-value=0.26 Score=27.09 Aligned_cols=22 Identities=23% Similarity=0.635 Sum_probs=15.1
Q ss_pred eecCccccccCCCCccCcCCCc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
++|+.|....++.+++|+.|+.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 4677777766777777777664
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=80.98 E-value=0.84 Score=25.15 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=15.7
Q ss_pred eecCccccccCCCCccCcCCCc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
+.|+.|....|..++.|+.|+.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 3577777777777777777763
No 21
>PF12773 DZR: Double zinc ribbon
Probab=75.73 E-value=2.1 Score=27.10 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=23.1
Q ss_pred cCccccccCCCCccCcCCCccccCc---cccCcccccc
Q psy13205 81 CVTCKFYRPPRCSHCSVCNYCIETF---DHHCPWVNNC 115 (267)
Q Consensus 81 C~~C~~~kP~Rs~hC~~C~~cv~~~---DHHC~w~~~C 115 (267)
|++|+...++.+++|..|+.-+... ...|+-++.=
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CCCcCCcCCccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 6677777777777777777766622 3456666553
No 22
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=72.41 E-value=2.1 Score=27.13 Aligned_cols=24 Identities=33% Similarity=0.845 Sum_probs=21.5
Q ss_pred cceecCccccccCCCCccCcCCCc
Q psy13205 77 RMKWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 77 ~~~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
..+.|..|...-|+|+.-|+.|+.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 467899999999999999998875
No 23
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=70.68 E-value=3.3 Score=41.05 Aligned_cols=43 Identities=19% Similarity=0.414 Sum_probs=35.6
Q ss_pred ccccceecCccccccCCCCccCcCCCccccCccccCccccccccc
Q psy13205 74 ITVRMKWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNCIGR 118 (267)
Q Consensus 74 ~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg~ 118 (267)
...+.+||.+|+..-+ .+.|..|+.=+++-..+|+-||.=.|.
T Consensus 11 n~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 11 NPNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CCCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCcccc
Confidence 3456789999986543 468999999999999999999998887
No 24
>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=70.47 E-value=4.2 Score=27.14 Aligned_cols=17 Identities=35% Similarity=0.805 Sum_probs=8.6
Q ss_pred ccCcCCCccccCccccC
Q psy13205 93 SHCSVCNYCIETFDHHC 109 (267)
Q Consensus 93 ~hC~~C~~cv~~~DHHC 109 (267)
+||.+|+.-++.-...|
T Consensus 4 kHC~~CG~~Ip~~~~fC 20 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFC 20 (59)
T ss_pred CcCCcCCCcCCcchhhh
Confidence 35555555555544444
No 25
>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=59.00 E-value=4.8 Score=26.42 Aligned_cols=34 Identities=32% Similarity=0.749 Sum_probs=26.7
Q ss_pred ecCccccccCCCC-------ccCcCCCccccCc-cccCcccc
Q psy13205 80 WCVTCKFYRPPRC-------SHCSVCNYCIETF-DHHCPWVN 113 (267)
Q Consensus 80 ~C~~C~~~kP~Rs-------~hC~~C~~cv~~~-DHHC~w~~ 113 (267)
-|..|+..-|+.| .-|..|..|+..+ +++||=+|
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCg 48 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCG 48 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCC
Confidence 4777777777655 5688999999998 99998554
No 26
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=58.04 E-value=6.1 Score=39.63 Aligned_cols=22 Identities=27% Similarity=0.609 Sum_probs=16.5
Q ss_pred eecCccccccC-------CCCccCcCCCc
Q psy13205 79 KWCVTCKFYRP-------PRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP-------~Rs~hC~~C~~ 100 (267)
.-|..|+..-. .|-|||+.|++
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 45888887664 38899988876
No 27
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=50.31 E-value=7.1 Score=24.24 Aligned_cols=22 Identities=27% Similarity=0.886 Sum_probs=15.2
Q ss_pred cCCCccccCccccCccc---ccccc
Q psy13205 96 SVCNYCIETFDHHCPWV---NNCIG 117 (267)
Q Consensus 96 ~~C~~cv~~~DHHC~w~---~~CIg 117 (267)
+.|..|+...|-||.|+ ++|+.
T Consensus 5 ~sC~~C~~~~~~~C~Wc~~~~~C~~ 29 (46)
T smart00423 5 TSCSECLLARDPYCAWCSSQGRCTS 29 (46)
T ss_pred CcHHHHHcCCCCCCCccCCCCcccC
Confidence 45777777777788887 44554
No 28
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=49.04 E-value=13 Score=20.83 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=18.3
Q ss_pred ceecCccccccCCCCccCcCCCccc
Q psy13205 78 MKWCVTCKFYRPPRCSHCSVCNYCI 102 (267)
Q Consensus 78 ~~~C~~C~~~kP~Rs~hC~~C~~cv 102 (267)
.-.|..|...-++++.+|..|+.-.
T Consensus 4 ~W~C~~C~~~N~~~~~~C~~C~~~r 28 (30)
T PF00641_consen 4 DWKCPSCTFMNPASRSKCVACGAPR 28 (30)
T ss_dssp SEEETTTTEEEESSSSB-TTT--BT
T ss_pred CccCCCCcCCchHHhhhhhCcCCCC
Confidence 4579999999999999999987643
No 29
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=48.98 E-value=13 Score=24.05 Aligned_cols=25 Identities=28% Similarity=0.671 Sum_probs=16.5
Q ss_pred cceecCccccccCCCCccCcC--CCcc
Q psy13205 77 RMKWCVTCKFYRPPRCSHCSV--CNYC 101 (267)
Q Consensus 77 ~~~~C~~C~~~kP~Rs~hC~~--C~~c 101 (267)
+...|.+|..+-|+|+..|+. |+..
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 467899999999999999998 7653
No 30
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=48.21 E-value=13 Score=37.04 Aligned_cols=37 Identities=22% Similarity=0.596 Sum_probs=27.0
Q ss_pred eecCccccccCCCCccCcCCCccccCccccCcccccccc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNYCIETFDHHCPWVNNCIG 117 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC~w~~~CIg 117 (267)
..|+.|+...|+.+++|..|+.-... ..|+-||.=+.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~--~~Cp~CG~~~~ 38 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTH--KPCPQCGTEVP 38 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCC--CcCCCCCCCCC
Confidence 47899999999999999988775532 35776665443
No 31
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=43.95 E-value=13 Score=25.02 Aligned_cols=22 Identities=36% Similarity=0.770 Sum_probs=15.6
Q ss_pred eecCccccccCCCCccCcCCCc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
+-|..|+...|+.+.-|++|+.
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred HHHhhccccCCCCCccCCCCCC
Confidence 4577777777777777777765
No 32
>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=41.66 E-value=12 Score=25.32 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=3.1
Q ss_pred CCccCcCCCc
Q psy13205 91 RCSHCSVCNY 100 (267)
Q Consensus 91 Rs~hC~~C~~ 100 (267)
|-|||+.|++
T Consensus 24 rrhhCr~CG~ 33 (69)
T PF01363_consen 24 RRHHCRNCGR 33 (69)
T ss_dssp -EEE-TTT--
T ss_pred eeEccCCCCC
Confidence 4455555544
No 33
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=40.71 E-value=5.5 Score=25.34 Aligned_cols=24 Identities=38% Similarity=0.930 Sum_probs=20.7
Q ss_pred cceecCccccccCCCCccCcCCCc
Q psy13205 77 RMKWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 77 ~~~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
..+.|..|...-|+|+.-|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 356899999999999999998864
No 34
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=39.28 E-value=82 Score=23.88 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=12.6
Q ss_pred ecCcccccc--CCCCccCcCCCc
Q psy13205 80 WCVTCKFYR--PPRCSHCSVCNY 100 (267)
Q Consensus 80 ~C~~C~~~k--P~Rs~hC~~C~~ 100 (267)
.|++|+... -.|..-|-.|+.
T Consensus 71 ~CP~C~K~TKmLGr~D~CM~C~~ 93 (114)
T PF11023_consen 71 ECPNCGKQTKMLGRVDACMHCKE 93 (114)
T ss_pred ECCCCCChHhhhchhhccCcCCC
Confidence 488888654 345555555554
No 35
>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=38.39 E-value=18 Score=20.54 Aligned_cols=23 Identities=17% Similarity=0.501 Sum_probs=11.4
Q ss_pred ceecCcccccc----CCCCccCcCCCc
Q psy13205 78 MKWCVTCKFYR----PPRCSHCSVCNY 100 (267)
Q Consensus 78 ~~~C~~C~~~k----P~Rs~hC~~C~~ 100 (267)
.+||+.|.... -.+++.|+.|+.
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 57888887642 235667776654
No 36
>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=37.15 E-value=7.3 Score=24.84 Aligned_cols=23 Identities=26% Similarity=0.934 Sum_probs=16.2
Q ss_pred cCCCccccCccccCcccc---ccccc
Q psy13205 96 SVCNYCIETFDHHCPWVN---NCIGR 118 (267)
Q Consensus 96 ~~C~~cv~~~DHHC~w~~---~CIg~ 118 (267)
..|..|+..+|-+|.|+. +|+-.
T Consensus 6 ~sC~~Cl~~~dp~CgWc~~~~~C~~~ 31 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWCSSENRCVSG 31 (51)
T ss_dssp SSHHHHHHSTCTTEEEETTTTEEEEC
T ss_pred CcHHHHHcCCCcCccccCCCCcccCC
Confidence 667778888888888874 46543
No 37
>KOG4399|consensus
Probab=36.98 E-value=11 Score=32.88 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=19.1
Q ss_pred eecCccccccCCCCccCcCCCcc---ccCccccCcccccccccc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNYC---IETFDHHCPWVNNCIGRR 119 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~c---v~~~DHHC~w~~~CIg~~ 119 (267)
++|..|+...-.| .||..|+.| ..+...||.-+.+|+-+.
T Consensus 262 ~~C~iC~~~~~~R-~~C~~~kA~~~~~Q~K~N~~~~~~~~~q~~ 304 (325)
T KOG4399|consen 262 HGCFICGELDHKR-STCPNIKAVRKQKQRKSNKMKMETTKGQSM 304 (325)
T ss_pred cceeecccccccc-ccCccHHHHHHHHhcccchhhhhhhhhhhh
Confidence 4455555555555 444444332 223445555555665543
No 38
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.02 E-value=21 Score=22.51 Aligned_cols=21 Identities=29% Similarity=0.694 Sum_probs=11.7
Q ss_pred eecCccccccCCC------CccCcCCC
Q psy13205 79 KWCVTCKFYRPPR------CSHCSVCN 99 (267)
Q Consensus 79 ~~C~~C~~~kP~R------s~hC~~C~ 99 (267)
+||+.|+....++ ...|+.|+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg 27 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCC
Confidence 4777776654332 23466665
No 39
>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=33.47 E-value=90 Score=29.20 Aligned_cols=31 Identities=16% Similarity=0.440 Sum_probs=17.1
Q ss_pred ceecCcccc-ccCCCCccCcCCCccccCcccc
Q psy13205 78 MKWCVTCKF-YRPPRCSHCSVCNYCIETFDHH 108 (267)
Q Consensus 78 ~~~C~~C~~-~kP~Rs~hC~~C~~cv~~~DHH 108 (267)
..-|++|+. .+|....+|..|+.-..++.++
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~ 246 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRN 246 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCC
Confidence 445777776 3344445566666655444443
No 40
>KOG1819|consensus
Probab=32.96 E-value=15 Score=34.96 Aligned_cols=22 Identities=27% Similarity=0.667 Sum_probs=14.2
Q ss_pred eecCccccccC--CCCccCcCCCc
Q psy13205 79 KWCVTCKFYRP--PRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP--~Rs~hC~~C~~ 100 (267)
..|-.|+.+-. .|-|||+.|+.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 45666664322 37788888876
No 41
>PF03503 Chlam_OMP3: Chlamydia cysteine-rich outer membrane protein 3; InterPro: IPR003517 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP2 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP3 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=32.91 E-value=39 Score=21.44 Aligned_cols=31 Identities=19% Similarity=0.539 Sum_probs=19.9
Q ss_pred eecCccccccCCCCccCcCCCccccCccccC
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNYCIETFDHHC 109 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~cv~~~DHHC 109 (267)
+-|.-|+..|-+++--|+-|+..+|.-+.-|
T Consensus 24 ~sc~pc~~~kkd~~~g~n~cg~y~pscskpc 54 (55)
T PF03503_consen 24 KSCNPCEVNKKDVSCGCNPCGSYTPSCSKPC 54 (55)
T ss_pred CcccccccccccccCCccccccccccccCCC
Confidence 4566677767777777777777666544433
No 42
>PRK02935 hypothetical protein; Provisional
Probab=32.88 E-value=98 Score=23.18 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=12.8
Q ss_pred ecCcccccc--CCCCccCcCCCc
Q psy13205 80 WCVTCKFYR--PPRCSHCSVCNY 100 (267)
Q Consensus 80 ~C~~C~~~k--P~Rs~hC~~C~~ 100 (267)
.|++|+... -.|..-|-.|+.
T Consensus 72 ~CP~C~K~TKmLGrvD~CM~C~~ 94 (110)
T PRK02935 72 ICPSCEKPTKMLGRVDACMHCNQ 94 (110)
T ss_pred ECCCCCchhhhccceeecCcCCC
Confidence 788887542 235556666655
No 43
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=32.60 E-value=40 Score=31.67 Aligned_cols=30 Identities=17% Similarity=0.335 Sum_probs=16.6
Q ss_pred ceecCccccccCCCCccCcCCCccccCccc
Q psy13205 78 MKWCVTCKFYRPPRCSHCSVCNYCIETFDH 107 (267)
Q Consensus 78 ~~~C~~C~~~kP~Rs~hC~~C~~cv~~~DH 107 (267)
..-|+.|+...|.+..+|..|+.-..++++
T Consensus 221 l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~ 250 (419)
T PRK15103 221 LRSCSCCTAILPADQPVCPRCHTKGYVRRR 250 (419)
T ss_pred CCcCCCCCCCCCCCCCCCCCCCCcCcCCCC
Confidence 344666666655555556666555544443
No 44
>KOG1842|consensus
Probab=32.16 E-value=12 Score=35.01 Aligned_cols=25 Identities=24% Similarity=0.663 Sum_probs=16.8
Q ss_pred cceecCcccccc--CCCCccCcCCCcc
Q psy13205 77 RMKWCVTCKFYR--PPRCSHCSVCNYC 101 (267)
Q Consensus 77 ~~~~C~~C~~~k--P~Rs~hC~~C~~c 101 (267)
...+|+.|...= -.|-|||+.|++-
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchH
Confidence 357898887542 3467777777774
No 45
>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 PTZ00303 phosphatidylinositol kinase; Provisional
Probab=31.12 E-value=32 Score=34.86 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=20.6
Q ss_pred cccCCC--CccCcCCCcccc-------CccccCccccc
Q psy13205 86 FYRPPR--CSHCSVCNYCIE-------TFDHHCPWVNN 114 (267)
Q Consensus 86 ~~kP~R--s~hC~~C~~cv~-------~~DHHC~w~~~ 114 (267)
.+.|+. ++.|..|++--- .|-|||+-||.
T Consensus 452 vWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 452 SWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCCCCcccCCcccCcCCcccccccccccccccccCCcc
Confidence 345554 477999977553 48999998876
No 47
>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=31.05 E-value=20 Score=21.11 Aligned_cols=9 Identities=22% Similarity=0.859 Sum_probs=5.9
Q ss_pred eecCccccc
Q psy13205 79 KWCVTCKFY 87 (267)
Q Consensus 79 ~~C~~C~~~ 87 (267)
+||++|+..
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 578888764
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.79 E-value=27 Score=23.27 Aligned_cols=37 Identities=19% Similarity=0.250 Sum_probs=28.2
Q ss_pred ceecCccccccCCCC----ccCcCCCccccCccccCccccc
Q psy13205 78 MKWCVTCKFYRPPRC----SHCSVCNYCIETFDHHCPWVNN 114 (267)
Q Consensus 78 ~~~C~~C~~~kP~Rs----~hC~~C~~cv~~~DHHC~w~~~ 114 (267)
...|.+|+..-+++. .-|..|+.=+..|++-|+-.++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~ 49 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGN 49 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcCC
Confidence 457999998886653 4499999888888888876654
No 49
>KOG1729|consensus
Probab=30.78 E-value=17 Score=32.40 Aligned_cols=29 Identities=24% Similarity=0.657 Sum_probs=14.8
Q ss_pred cccCC-CCccCcCCCc---cccCccccCccccc
Q psy13205 86 FYRPP-RCSHCSVCNY---CIETFDHHCPWVNN 114 (267)
Q Consensus 86 ~~kP~-Rs~hC~~C~~---cv~~~DHHC~w~~~ 114 (267)
.+.|+ .+-+|.+|++ =.-.|-|||+-||.
T Consensus 161 ~W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ 193 (288)
T KOG1729|consen 161 VWLPDSEATECMVCGCTEFTLSERRHHCRNCGD 193 (288)
T ss_pred cccCcccceecccCCCccccHHHHHHHHHhcch
Confidence 34555 5555655554 22234566665554
No 50
>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=30.62 E-value=22 Score=19.84 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=7.6
Q ss_pred ecCccccccCC-CCccCcCCCc
Q psy13205 80 WCVTCKFYRPP-RCSHCSVCNY 100 (267)
Q Consensus 80 ~C~~C~~~kP~-Rs~hC~~C~~ 100 (267)
.|..|+..... ...+|+.|+-
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 46667666555 5667777764
No 51
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=29.64 E-value=33 Score=22.81 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=24.5
Q ss_pred ceecCccccccCCCC----ccCcCCCccccCccccCcccc
Q psy13205 78 MKWCVTCKFYRPPRC----SHCSVCNYCIETFDHHCPWVN 113 (267)
Q Consensus 78 ~~~C~~C~~~kP~Rs----~hC~~C~~cv~~~DHHC~w~~ 113 (267)
...|.+|+..-.++. ..|..|+.-+..|...|+-.+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 457888887766554 458888887677766666443
No 52
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=29.29 E-value=45 Score=35.60 Aligned_cols=22 Identities=18% Similarity=0.372 Sum_probs=10.9
Q ss_pred cCcCCCccccCc---cccCcccccc
Q psy13205 94 HCSVCNYCIETF---DHHCPWVNNC 115 (267)
Q Consensus 94 hC~~C~~cv~~~---DHHC~w~~~C 115 (267)
+|..|+.=++.- .-+|+.|++=
T Consensus 694 ~CPsCGaev~~des~a~~CP~CGtp 718 (1337)
T PRK14714 694 VCPDCGAEVPPDESGRVECPRCDVE 718 (1337)
T ss_pred eCccCCCccCCCccccccCCCCCCc
Confidence 455554433321 2367777753
No 53
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.79 E-value=38 Score=21.66 Aligned_cols=23 Identities=26% Similarity=0.677 Sum_probs=13.7
Q ss_pred cceecCcccc-cc--CCCCccCcCCC
Q psy13205 77 RMKWCVTCKF-YR--PPRCSHCSVCN 99 (267)
Q Consensus 77 ~~~~C~~C~~-~k--P~Rs~hC~~C~ 99 (267)
..++|+.|.. .. -....+|..|+
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcC
Confidence 3568999876 22 12345666665
No 54
>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=25.91 E-value=46 Score=21.22 Aligned_cols=11 Identities=36% Similarity=0.806 Sum_probs=6.2
Q ss_pred CCCccCcCCCc
Q psy13205 90 PRCSHCSVCNY 100 (267)
Q Consensus 90 ~Rs~hC~~C~~ 100 (267)
.|.|||+.|++
T Consensus 16 ~rk~~Cr~Cg~ 26 (57)
T cd00065 16 RRRHHCRNCGR 26 (57)
T ss_pred ccccccCcCcC
Confidence 35566666555
No 55
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=25.79 E-value=80 Score=20.98 Aligned_cols=19 Identities=32% Similarity=0.730 Sum_probs=14.2
Q ss_pred CccCcCCCccccCccccCc
Q psy13205 92 CSHCSVCNYCIETFDHHCP 110 (267)
Q Consensus 92 s~hC~~C~~cv~~~DHHC~ 110 (267)
-+||.+|++-++.-..-|.
T Consensus 8 H~HC~VCg~aIp~de~~CS 26 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCS 26 (64)
T ss_pred CccccccCCcCCCccchHH
Confidence 4678888888877777776
No 56
>KOG4399|consensus
Probab=25.58 E-value=16 Score=31.79 Aligned_cols=32 Identities=25% Similarity=0.638 Sum_probs=20.9
Q ss_pred CCccccceecCccccccCCCCccCcCCCcccc
Q psy13205 72 NGITVRMKWCVTCKFYRPPRCSHCSVCNYCIE 103 (267)
Q Consensus 72 ~~~~~~~~~C~~C~~~kP~Rs~hC~~C~~cv~ 103 (267)
.+..++.+||+-|.++.-..-.||..|+.|..
T Consensus 198 ~~~EE~~~~~~~~~~Yv~~~~~H~~~~~S~~~ 229 (325)
T KOG4399|consen 198 LPTEEGYRFCSPCQRYVSLENQHCEHCNSCTS 229 (325)
T ss_pred cccccceEEEeehHHHHHHHhhhchhhccccc
Confidence 34556677888888777666666666655543
No 57
>PLN00186 ribosomal protein S26; Provisional
Probab=25.39 E-value=33 Score=25.78 Aligned_cols=20 Identities=20% Similarity=0.403 Sum_probs=14.8
Q ss_pred CCccCcCCCccccCccccCc
Q psy13205 91 RCSHCSVCNYCIETFDHHCP 110 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~ 110 (267)
+.-+|..|++|||+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIKR 38 (109)
T ss_pred cceeeCCCcccccccceEEE
Confidence 45689999999998544443
No 58
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.03 E-value=36 Score=18.04 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=16.5
Q ss_pred eecCccccccCCCCccCcCCCc
Q psy13205 79 KWCVTCKFYRPPRCSHCSVCNY 100 (267)
Q Consensus 79 ~~C~~C~~~kP~Rs~hC~~C~~ 100 (267)
-.|..|...-.+++..|..|+.
T Consensus 3 W~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 3 WECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred ccCCCCCCcChhhhccccccCC
Confidence 3578888777778888887764
No 59
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=24.73 E-value=32 Score=25.20 Aligned_cols=22 Identities=14% Similarity=0.252 Sum_probs=16.9
Q ss_pred CCccCcCCCccccCccccCccc
Q psy13205 91 RCSHCSVCNYCIETFDHHCPWV 112 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~w~ 112 (267)
+.-+|..|++|||+.---+.+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf~ 40 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVTK 40 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEEE
Confidence 4568999999999976666543
No 60
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=24.42 E-value=55 Score=18.77 Aligned_cols=7 Identities=43% Similarity=1.070 Sum_probs=4.2
Q ss_pred ccCcCCC
Q psy13205 93 SHCSVCN 99 (267)
Q Consensus 93 ~hC~~C~ 99 (267)
..|+.|+
T Consensus 17 ~~C~~C~ 23 (32)
T PF13842_consen 17 YMCSKCD 23 (32)
T ss_pred EEccCCC
Confidence 3477775
No 61
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=22.57 E-value=38 Score=25.40 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=15.0
Q ss_pred CCccCcCCCccccCccccCc
Q psy13205 91 RCSHCSVCNYCIETFDHHCP 110 (267)
Q Consensus 91 Rs~hC~~C~~cv~~~DHHC~ 110 (267)
+.-+|..|++|||+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIKR 38 (108)
T ss_pred ccEEeCCccccccccceEEE
Confidence 45689999999998554444
No 62
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.11 E-value=46 Score=25.16 Aligned_cols=25 Identities=28% Similarity=0.670 Sum_probs=14.6
Q ss_pred ccceecCccccccCCCCcc---CcCCCc
Q psy13205 76 VRMKWCVTCKFYRPPRCSH---CSVCNY 100 (267)
Q Consensus 76 ~~~~~C~~C~~~kP~Rs~h---C~~C~~ 100 (267)
+..-+|..|+..-|...++ |+.|+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 3456777777666554333 666653
No 63
>KOG3183|consensus
Probab=21.39 E-value=42 Score=28.88 Aligned_cols=14 Identities=29% Similarity=0.306 Sum_probs=10.0
Q ss_pred cccCccccCccccc
Q psy13205 101 CIETFDHHCPWVNN 114 (267)
Q Consensus 101 cv~~~DHHC~w~~~ 114 (267)
-....+|||||...
T Consensus 37 Hrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 37 HRSYESHHCPKGLR 50 (250)
T ss_pred cchHhhcCCCcccc
Confidence 45667888888654
Done!