Query 021039
Match_columns 318
No_of_seqs 254 out of 1613
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 07:08:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021039.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021039hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1311 DHHC-type Zn-finger pr 100.0 1.2E-44 2.7E-49 340.4 14.0 194 111-306 79-278 (299)
2 KOG1315 Predicted DHHC-type Zn 100.0 2.4E-41 5.2E-46 314.5 14.2 193 99-293 57-257 (307)
3 KOG1314 DHHC-type Zn-finger pr 100.0 4.5E-40 9.8E-45 302.9 8.8 188 99-304 59-275 (414)
4 PF01529 zf-DHHC: DHHC palmito 100.0 6.4E-40 1.4E-44 284.4 8.2 169 103-271 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 2.2E-37 4.7E-42 277.3 8.6 169 147-317 102-297 (309)
6 COG5273 Uncharacterized protei 100.0 2.2E-33 4.8E-38 264.0 10.3 160 100-269 68-231 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 3.6E-31 7.7E-36 238.5 10.6 98 103-209 113-210 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 1.1E-29 2.5E-34 250.1 6.5 189 101-303 381-598 (600)
9 COG5273 Uncharacterized protei 93.6 0.75 1.6E-05 43.8 10.6 136 145-291 121-277 (309)
10 PF01529 zf-DHHC: DHHC palmito 91.9 0.7 1.5E-05 39.4 7.4 48 145-203 60-107 (174)
11 KOG1311 DHHC-type Zn-finger pr 90.5 0.59 1.3E-05 44.0 6.0 42 160-201 112-164 (299)
12 PF13240 zinc_ribbon_2: zinc-r 78.7 1 2.3E-05 25.8 0.9 21 149-169 1-21 (23)
13 PRK04136 rpl40e 50S ribosomal 74.2 1.8 3.8E-05 29.5 1.2 25 146-170 13-37 (48)
14 KOG0509 Ankyrin repeat and DHH 72.7 1.6 3.5E-05 44.7 1.0 57 146-203 324-381 (600)
15 PF13248 zf-ribbon_3: zinc-rib 67.4 2.7 5.8E-05 24.6 0.8 22 148-169 3-24 (26)
16 PTZ00303 phosphatidylinositol 61.9 4.1 8.8E-05 43.1 1.4 22 148-169 461-489 (1374)
17 PF06906 DUF1272: Protein of u 57.1 5.4 0.00012 28.1 0.9 36 149-187 7-50 (57)
18 PF12773 DZR: Double zinc ribb 55.1 8.8 0.00019 25.7 1.8 34 147-180 12-48 (50)
19 PF10571 UPF0547: Uncharacteri 53.5 7.2 0.00016 23.0 0.9 22 148-169 1-22 (26)
20 PF01020 Ribosomal_L40e: Ribos 51.6 10 0.00022 26.2 1.6 25 146-170 16-42 (52)
21 KOG1315 Predicted DHHC-type Zn 51.3 45 0.00098 31.8 6.4 32 145-176 121-152 (307)
22 PF01363 FYVE: FYVE zinc finge 49.5 8 0.00017 27.8 0.9 27 146-172 8-36 (69)
23 COG1552 RPL40A Ribosomal prote 48.3 3.9 8.4E-05 27.9 -0.9 25 146-170 13-37 (50)
24 KOG1842 FYVE finger-containing 44.3 6.4 0.00014 39.0 -0.4 26 146-171 179-206 (505)
25 PF00641 zf-RanBP: Zn-finger i 43.8 11 0.00024 22.6 0.7 21 149-169 6-26 (30)
26 smart00064 FYVE Protein presen 40.7 17 0.00038 25.9 1.5 25 147-171 10-36 (68)
27 KOG3183 Predicted Zn-finger pr 35.8 17 0.00037 33.2 1.0 34 148-182 9-49 (250)
28 PF07649 C1_3: C1-like domain; 34.7 16 0.00034 22.0 0.4 21 149-169 2-23 (30)
29 PF09889 DUF2116: Uncharacteri 34.3 24 0.00051 25.2 1.3 23 147-169 3-26 (59)
30 PF08600 Rsm1: Rsm1-like; Int 32.3 23 0.00049 27.4 1.0 13 174-186 54-66 (91)
31 TIGR00155 pqiA_fam integral me 32.1 3.7E+02 0.008 26.6 9.7 33 146-178 214-247 (403)
32 PRK15103 paraquat-inducible me 31.6 2E+02 0.0044 28.5 7.8 33 146-178 220-252 (419)
33 KOG1314 DHHC-type Zn-finger pr 29.8 73 0.0016 31.0 4.1 83 98-199 62-146 (414)
34 KOG3415 Putative Rab5-interact 28.4 55 0.0012 26.5 2.6 27 45-71 30-56 (129)
35 cd00065 FYVE FYVE domain; Zinc 28.2 38 0.00082 23.0 1.5 22 149-170 4-27 (57)
36 cd01995 ExsB ExsB is a transcr 27.1 21 0.00046 30.1 0.1 23 149-174 142-164 (169)
37 PF02150 RNA_POL_M_15KD: RNA p 26.4 25 0.00054 22.2 0.3 7 148-154 2-8 (35)
38 TIGR02484 CitB CitB domain pro 23.7 4E+02 0.0086 26.2 8.0 15 162-180 48-62 (372)
39 smart00661 RPOL9 RNA polymeras 22.1 45 0.00097 22.3 0.9 8 149-156 2-9 (52)
40 COG2093 DNA-directed RNA polym 21.1 54 0.0012 23.7 1.1 23 147-169 4-26 (64)
41 KOG4753 Predicted membrane pro 20.6 2.3E+02 0.005 23.1 4.8 64 8-76 9-73 (124)
42 KOG3249 Uncharacterized conser 20.5 5E+02 0.011 22.5 7.0 17 103-119 132-148 (181)
No 1
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.2e-44 Score=340.42 Aligned_cols=194 Identities=37% Similarity=0.758 Sum_probs=146.5
Q ss_pred cCCCCcCCCCCCcccccCCCCCCccceEEEcccccceeeccccccccCCCCccCCCCCccccccccccccccccccccch
Q 021039 111 TDPGIIPRNDQANIEDVGTSDGTRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIGQCIALRNY 190 (318)
Q Consensus 111 ~DPG~ip~~~~~~~~~~~~~~~~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N~ 190 (318)
+|||++|++.+...+.. .+..+.+....+|.+.+++||.+|+.+||||||||++||+||+||||||+|+|||||+|||
T Consensus 79 sdpg~~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNy 156 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDP--ERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNY 156 (299)
T ss_pred CCCceecCcccCCCCCc--cccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCch
Confidence 59999999742222211 1334455667788889999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhhheeeeccccccccccc-----cccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcceee
Q 021039 191 RFYLSFVISALVLFAYLFAFSVWRIHAKSKSGLLGML-----KNCPETVALVSFSFAAIWFLAGLAIFHIYLITVNQTAY 265 (318)
Q Consensus 191 r~Fl~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~l~~l~~~h~~li~~n~Tt~ 265 (318)
|||+.|+++..+++++.+++....+............ ......+++.+++++++++++.|+.+|++++.+|+||+
T Consensus 157 r~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~ 236 (299)
T KOG1311|consen 157 RYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTY 236 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchh
Confidence 9999999999888888877665553322111110000 11112233334556666677889999999999999999
Q ss_pred eehhh-ccCCCCCCCCHhHHHHHHHhcCCCCCCCccccceee
Q 021039 266 ENFRQ-RYADSQNPYDKGIVSNFKDVLFGPVPPSRVDFRAEV 306 (318)
Q Consensus 266 E~~~~-~~~~~~npyd~G~~~N~~evf~~p~~~~~~~~~~~~ 306 (318)
|++++ +.....+|||+|.++|++++|+++.++...+.....
T Consensus 237 e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~ 278 (299)
T KOG1311|consen 237 ESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARS 278 (299)
T ss_pred hhhhccccccccCCCchhHHHHHHHHhCCCCCcccccccccC
Confidence 99885 222224899999999999999999988888777644
No 2
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.4e-41 Score=314.54 Aligned_cols=193 Identities=28% Similarity=0.533 Sum_probs=137.8
Q ss_pred HHHHHHhhhheecCCCCcCCCCCCcccccCCCCC----CccceEEEcccccceeeccccccccCCCCccCCCCCcccccc
Q 021039 99 NNVFINLILVSTTDPGIIPRNDQANIEDVGTSDG----TRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKF 174 (318)
Q Consensus 99 ~~~~~~~~~~~~~DPG~ip~~~~~~~~~~~~~~~----~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~ 174 (318)
...+.+++.+.++|||.+|..+....++.+..+. ++.......+.....|+|.+|+.+||+||||||+|+|||+||
T Consensus 57 ~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKm 136 (307)
T KOG1315|consen 57 IMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKM 136 (307)
T ss_pred HHHHHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhcc
Confidence 4456789999999999999888765544422221 123334445556689999999999999999999999999999
Q ss_pred ccccccccccccccchhHHHHHHHHHHHHHHHHHHhhheeeeccccccccccccccchhhHHHHHHHHHHHHHHHHHHHH
Q 021039 175 DHHCPWIGQCIALRNYRFYLSFVISALVLFAYLFAFSVWRIHAKSKSGLLGMLKNCPETVALVSFSFAAIWFLAGLAIFH 254 (318)
Q Consensus 175 DHHC~Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~h 254 (318)
||||||+|||||.+|||+|++|++|+.+++++.++.....+......+...........++++++++.+.+.+.+|+++|
T Consensus 137 DHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h 216 (307)
T KOG1315|consen 137 DHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFH 216 (307)
T ss_pred ccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999987765544332221100000000001122333444555556667799999
Q ss_pred HHHHHhcceeeeehhhcc-C---CCCCCCCHhHHHHHHHhcCC
Q 021039 255 IYLITVNQTAYENFRQRY-A---DSQNPYDKGIVSNFKDVLFG 293 (318)
Q Consensus 255 ~~li~~n~Tt~E~~~~~~-~---~~~npyd~G~~~N~~evf~~ 293 (318)
++||++|+||+|.++... . ...+.|+. ..|++|+|++
T Consensus 217 ~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~--~~n~~~vfg~ 257 (307)
T KOG1315|consen 217 TYLILKNKTTIEAYKSPVFRSGLHNKNGFNL--YVNFREVFGS 257 (307)
T ss_pred HHHHHcCchhHhhhccccccccccccCCcce--eecHHHHhCC
Confidence 999999999999987642 1 23466666 6899999843
No 3
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.5e-40 Score=302.92 Aligned_cols=188 Identities=26% Similarity=0.519 Sum_probs=134.6
Q ss_pred HHHHHHhhhheecCCCCcCCCCCCcccccCCCCCCccceEEEcccccceeeccccccccCCCCccCCCCCcccccccccc
Q 021039 99 NNVFINLILVSTTDPGIIPRNDQANIEDVGTSDGTRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHC 178 (318)
Q Consensus 99 ~~~~~~~~~~~~~DPG~ip~~~~~~~~~~~~~~~~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC 178 (318)
..++.||+.+++++||++|++|++.... .+...+||..|+.+|+||||||+.|||||.+|||||
T Consensus 59 ~m~~~ny~~A~~~gPG~vp~~wkPe~~~----------------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHC 122 (414)
T KOG1314|consen 59 SMILYNYFNAIFTGPGFVPLGWKPENPK----------------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHC 122 (414)
T ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCCCh----------------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCC
Confidence 5678999999999999999999864321 124578999999999999999999999999999999
Q ss_pred ccccccccccchhHHHHHHHHHHHHHHHHH----------HhhheeeeccccccccccccccchhhHHHHH----HHHHH
Q 021039 179 PWIGQCIALRNYRFYLSFVISALVLFAYLF----------AFSVWRIHAKSKSGLLGMLKNCPETVALVSF----SFAAI 244 (318)
Q Consensus 179 ~Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ 244 (318)
||+|||||..||.||+.||++..++|+-.. ++..|++... ...+..+.. .+..++..++ +++.+
T Consensus 123 PWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g-~~hlp~v~f-t~~~li~~vfslgla~gv~ 200 (414)
T KOG1314|consen 123 PWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYG-LRHLPIVFF-TLSSLIALVFSLGLAIGVV 200 (414)
T ss_pred cchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcc-cccCceeec-cHHHHHHHHHHhHHHHHHH
Confidence 999999999999999999999887654321 2222211110 001111111 0112222222 33344
Q ss_pred HHHHHHHHHHHHHHHhcceeeeehh-------h-ccC-----CCCCCCCHhHHHHHHHhcCCCCC--CCccccce
Q 021039 245 WFLAGLAIFHIYLITVNQTAYENFR-------Q-RYA-----DSQNPYDKGIVSNFKDVLFGPVP--PSRVDFRA 304 (318)
Q Consensus 245 ~~l~~l~~~h~~li~~n~Tt~E~~~-------~-~~~-----~~~npyd~G~~~N~~evf~~p~~--~~~~~~~~ 304 (318)
+.++.|+..|+..|.+|+|.+|.+- . .+. ....|||.||..|+++||++... ++++.|..
T Consensus 201 la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~~~~gdg~~wPv 275 (414)
T KOG1314|consen 201 LALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNKKEEGDGIEWPV 275 (414)
T ss_pred HHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhccccCCCCccccc
Confidence 5567788999999999999999863 1 111 12379999988899999976533 57888873
No 4
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=6.4e-40 Score=284.39 Aligned_cols=169 Identities=33% Similarity=0.658 Sum_probs=118.1
Q ss_pred HHhhhheecCCCCcCCCCCCcccccC--CCCCCccceEEEcccccceeeccccccccCCCCccCCCCCcccccccccccc
Q 021039 103 INLILVSTTDPGIIPRNDQANIEDVG--TSDGTRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPW 180 (318)
Q Consensus 103 ~~~~~~~~~DPG~ip~~~~~~~~~~~--~~~~~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~W 180 (318)
++|+++.++|||++|+......+... ..+.........++...+.++|.+|+..||+|||||+.||+||+||||||+|
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 46788999999999988221111111 1111112222334456778999999999999999999999999999999999
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHHHhhheeeecccccc-ccc-cccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 021039 181 IGQCIALRNYRFYLSFVISALVLFAYLFAFSVWRIHAKSKSG-LLG-MLKNCPETVALVSFSFAAIWFLAGLAIFHIYLI 258 (318)
Q Consensus 181 l~nCVG~~N~r~Fl~fl~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~l~~l~~~h~~li 258 (318)
+|||||.+|||+|++|+++..+++++.+...+..+....... ... ........+++++++++..++++.|+++|++++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999998887777654443332211110 000 000000113445556666677889999999999
Q ss_pred Hhcceeeeehhhc
Q 021039 259 TVNQTAYENFRQR 271 (318)
Q Consensus 259 ~~n~Tt~E~~~~~ 271 (318)
++|+||+|.++++
T Consensus 162 ~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 162 LRNITTYERIKRK 174 (174)
T ss_pred HcCCcHHHHHHcC
Confidence 9999999998763
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2.2e-37 Score=277.28 Aligned_cols=169 Identities=25% Similarity=0.497 Sum_probs=125.1
Q ss_pred eeeccccccccCCCCccCCCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHHHHhhhee--eecc---ccc
Q 021039 147 LKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIGQCIALRNYRFYLSFVISALVLFAYLFAFSVWR--IHAK---SKS 221 (318)
Q Consensus 147 ~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~~~~~~~--~~~~---~~~ 221 (318)
..+|.+|..+||||+||||+||+||++|||||||+|||||..|||||++|++++.+++.|..+...+. -+.. ...
T Consensus 102 ~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~t 181 (309)
T KOG1313|consen 102 DSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEIT 181 (309)
T ss_pred ccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhcc
Confidence 47999999999999999999999999999999999999999999999999999999988876543211 1100 000
Q ss_pred ----c---------ccccccccc--hhhHHHHHHHHHHHHHHHHHHHHHHHHHhcceeeeehhh-----cc--CCCCCCC
Q 021039 222 ----G---------LLGMLKNCP--ETVALVSFSFAAIWFLAGLAIFHIYLITVNQTAYENFRQ-----RY--ADSQNPY 279 (318)
Q Consensus 222 ----~---------~~~~~~~~~--~~~~~~~~~~~~~~~l~~l~~~h~~li~~n~Tt~E~~~~-----~~--~~~~npy 279 (318)
+ +........ ...-+.+++..+++.++.|..+|.++|.+|.|.+|+... ++ +.++||+
T Consensus 182 ay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~~ 261 (309)
T KOG1313|consen 182 AYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNPT 261 (309)
T ss_pred cccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCCc
Confidence 0 000000000 011123344445667788999999999999999998632 21 2346999
Q ss_pred CHhHHHHHHHhcCCCCCCCccccceeeccccCcccccC
Q 021039 280 DKGIVSNFKDVLFGPVPPSRVDFRAEVTSSWHIKATRR 317 (318)
Q Consensus 280 d~G~~~N~~evf~~p~~~~~~~~~~~~~~~~~~~~~~~ 317 (318)
+.|.++||+.++.- -..+-.|++...|+.+++.+++
T Consensus 262 n~g~k~nWr~fLg~--~~~r~~wk~v~lPt~~~p~~~~ 297 (309)
T KOG1313|consen 262 NFGGKANWRNFLGL--FRGRHFWKTVLLPTIRKPVKYG 297 (309)
T ss_pred ccchHHHHHHhhcc--ccCCceeEEEeccccccccccC
Confidence 99999999999844 3445678888999999988765
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=2.2e-33 Score=263.97 Aligned_cols=160 Identities=28% Similarity=0.589 Sum_probs=109.4
Q ss_pred HHHHHhhhheecCCCCcCCCCCCc-ccccCCCCCCccceEEEcccccceeeccccccccCCCCccCCCCCcccccccccc
Q 021039 100 NVFINLILVSTTDPGIIPRNDQAN-IEDVGTSDGTRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHC 178 (318)
Q Consensus 100 ~~~~~~~~~~~~DPG~ip~~~~~~-~~~~~~~~~~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC 178 (318)
.+.+.++...++|||..+++.... ..+. .+.....|.....++|.+|+.+||+|||||+.||+||+||||||
T Consensus 68 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC 140 (309)
T COG5273 68 LASFSYLLLLVSDPGYLGENITLSGYRET-------ISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHC 140 (309)
T ss_pred hHHHhhHHHhhcCCCccCccccccchhhh-------hhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccC
Confidence 455778889999999998654321 1111 01122345566789999999999999999999999999999999
Q ss_pred ccccccccccchhHHHHHHHHHHHHHHHHHHhhheeeeccccc-cccccccccchhhHH--HHHHHHHHHHHHHHHHHHH
Q 021039 179 PWIGQCIALRNYRFYLSFVISALVLFAYLFAFSVWRIHAKSKS-GLLGMLKNCPETVAL--VSFSFAAIWFLAGLAIFHI 255 (318)
Q Consensus 179 ~Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~l~~l~~~h~ 255 (318)
+|+|||||.+|||+|+.|+++.....+++++.....+....+. ....... ..++. ..++...++++..++.+|.
T Consensus 141 ~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~li~~~~~~~~~~f~~~~~~~~~~~ 217 (309)
T COG5273 141 PWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAI---CFLIFGCSLLGVVFFIITTLLLLFLI 217 (309)
T ss_pred cccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHH---HHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998776665554433332221111 0000000 00111 1222333445677889999
Q ss_pred HHHHhcceeeeehh
Q 021039 256 YLITVNQTAYENFR 269 (318)
Q Consensus 256 ~li~~n~Tt~E~~~ 269 (318)
+++..|+|++|..+
T Consensus 218 ~~~~~~~t~~e~~~ 231 (309)
T COG5273 218 YLILNNLTTIEFIQ 231 (309)
T ss_pred HHHHhhHHHHHHHH
Confidence 99999999998753
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=3.6e-31 Score=238.53 Aligned_cols=98 Identities=38% Similarity=0.789 Sum_probs=78.2
Q ss_pred HHhhhheecCCCCcCCCCCCcccccCCCCCCccceEEEcccccceeeccccccccCCCCccCCCCCcccccccccccccc
Q 021039 103 INLILVSTTDPGIIPRNDQANIEDVGTSDGTRSKRVMINGVEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIG 182 (318)
Q Consensus 103 ~~~~~~~~~DPG~ip~~~~~~~~~~~~~~~~~~~~v~~~g~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~ 182 (318)
+.+.+++.+|||.+.+.......+..+.|. ++ ..+...|+||++.||.||||||+|||||+||||||.|+|
T Consensus 113 i~f~ltc~snpg~i~k~n~s~~~~~ypYDy-----~i----f~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiN 183 (341)
T KOG1312|consen 113 IFFTLTCGSNPGIITKANESLFLHVYPYDY-----VI----FPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWIN 183 (341)
T ss_pred HHHhhhhcCCCCccchhhhccceeccCccc-----ee----ecCCCccccccCCCccccccchHHHHHHHHhccceEeee
Confidence 556678999999998754433222222221 11 124479999999999999999999999999999999999
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHH
Q 021039 183 QCIALRNYRFYLSFVISALVLFAYLFA 209 (318)
Q Consensus 183 nCVG~~N~r~Fl~fl~~~~~~~~~~~~ 209 (318)
||||++|+|||++|+++...++.|.++
T Consensus 184 NCIG~~N~ryF~lFLL~~i~l~~yaiv 210 (341)
T KOG1312|consen 184 NCIGAWNIRYFLLFLLTLISLATYAIV 210 (341)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999998777777664
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.96 E-value=1.1e-29 Score=250.09 Aligned_cols=189 Identities=25% Similarity=0.545 Sum_probs=118.4
Q ss_pred HHHHhhhheecCCCCcCCCCCCcccccCCCCCCccceEEEcccccce-eeccccccccCCCCccCCCCCccccccccccc
Q 021039 101 VFINLILVSTTDPGIIPRNDQANIEDVGTSDGTRSKRVMINGVEMKL-KYCRICKIFRPPRSCHCAVCDNCVEKFDHHCP 179 (318)
Q Consensus 101 ~~~~~~~~~~~DPG~ip~~~~~~~~~~~~~~~~~~~~v~~~g~~~~~-~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~ 179 (318)
.|+.+.+...+|||++|.......+... ...-.|..... +||.+|.++||.|||||++|||||.|||||||
T Consensus 381 ~~~~f~~~~rsDPg~i~~~~~~~~~tIs--------~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCP 452 (600)
T KOG0509|consen 381 YFITFGLFLRSDPGFIPTSTEVGRETIS--------QLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCP 452 (600)
T ss_pred HHHHHHHHhccCCCCCCCchhhHHHHHH--------HhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCC
Confidence 3455555666999999976654322210 01112222333 79999999999999999999999999999999
Q ss_pred cccccccccchhHHHHHHHHHHHHHHHHHHhhheeeeccccccccccccccchhhHHHHHHHHH--H-------------
Q 021039 180 WIGQCIALRNYRFYLSFVISALVLFAYLFAFSVWRIHAKSKSGLLGMLKNCPETVALVSFSFAA--I------------- 244 (318)
Q Consensus 180 Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~------------- 244 (318)
|++||||.+|||+|+.|++.....+.+.+....+++........ .... ...++..+.. .
T Consensus 453 wi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~~-----~~~~-~l~~~~~~~~~~~~~~~~~~n~~~~~ 526 (600)
T KOG0509|consen 453 WIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENAST-----IYVG-FLIAVQAFRIPKPVTGNLLGNEDLNP 526 (600)
T ss_pred ccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHH-----HHHH-HHHHHHHHhCCccceeeeeecccccc
Confidence 99999999999999999998876665555443333221110000 0000 0000000000 0
Q ss_pred HH-HHHHHHHHHHHHHhcceeeeehhhc-c-------CCCCCCCCHhHHHHHHHhc----CCCCCCCccccc
Q 021039 245 WF-LAGLAIFHIYLITVNQTAYENFRQR-Y-------ADSQNPYDKGIVSNFKDVL----FGPVPPSRVDFR 303 (318)
Q Consensus 245 ~~-l~~l~~~h~~li~~n~Tt~E~~~~~-~-------~~~~npyd~G~~~N~~evf----~~p~~~~~~~~~ 303 (318)
.+ .......|...++.+.||+|.++.+ + ...++|+++|+.+|+.+|+ ++...+++++|.
T Consensus 527 t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g~~~Nl~df~~~~~~~~~~~~~~~~~ 598 (600)
T KOG0509|consen 527 TWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPGPIRNLVDFFLCSDCNLPLNDRFLWD 598 (600)
T ss_pred ccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCchhhhcchheeecccCcCcchhhcccC
Confidence 00 0111223344578899999988532 2 1246999999999999998 444445666665
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=93.56 E-value=0.75 Score=43.78 Aligned_cols=136 Identities=19% Similarity=0.303 Sum_probs=74.9
Q ss_pred cceeeccccccccCCCCccCCCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHHHH-hhh--eeeeccccc
Q 021039 145 MKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIGQCIALRNYRFYLSFVISALVLFAYLFA-FSV--WRIHAKSKS 221 (318)
Q Consensus 145 ~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N~r~Fl~fl~~~~~~~~~~~~-~~~--~~~~~~~~~ 221 (318)
.+.++|..|+.=....-|||.-=|+||-+.-| |=.-.|++++....+..++... ... .........
T Consensus 121 ~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 (309)
T COG5273 121 PRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSL 189 (309)
T ss_pred CCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHH
Confidence 46799999999999999999999999998655 5567788887554433332222 111 111111111
Q ss_pred cccccccccchh-hHHHHHH-----HHHHHHHHHHHHHHHHHHHhcceeeeehhhccC------------CCCCCCCHhH
Q 021039 222 GLLGMLKNCPET-VALVSFS-----FAAIWFLAGLAIFHIYLITVNQTAYENFRQRYA------------DSQNPYDKGI 283 (318)
Q Consensus 222 ~~~~~~~~~~~~-~~~~~~~-----~~~~~~l~~l~~~h~~li~~n~Tt~E~~~~~~~------------~~~npyd~G~ 283 (318)
.....+...+.. ....++. .....++..+.....+.+.++.++-|...-.+. +...|++.|.
T Consensus 190 ~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 269 (309)
T COG5273 190 AICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGI 269 (309)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCc
Confidence 101011111111 1111111 111122334555667778888887775421111 1237888888
Q ss_pred HHHHHHhc
Q 021039 284 VSNFKDVL 291 (318)
Q Consensus 284 ~~N~~evf 291 (318)
-+|+..++
T Consensus 270 ~~~~~~i~ 277 (309)
T COG5273 270 GQNLSTIK 277 (309)
T ss_pred cccceeec
Confidence 88888876
No 10
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=91.92 E-value=0.7 Score=39.42 Aligned_cols=48 Identities=21% Similarity=0.500 Sum_probs=37.5
Q ss_pred cceeeccccccccCCCCccCCCCCccccccccccccccccccccchhHHHHHHHHHHHH
Q 021039 145 MKLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIGQCIALRNYRFYLSFVISALVL 203 (318)
Q Consensus 145 ~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N~r~Fl~fl~~~~~~ 203 (318)
.+.++|..|+.-...+-|||..-|+||-+.-| +-+=.|+++.....+.
T Consensus 60 ~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~ 107 (174)
T PF01529_consen 60 PRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLY 107 (174)
T ss_pred CcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999998766 4455677666544433
No 11
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=90.55 E-value=0.59 Score=43.98 Aligned_cols=42 Identities=21% Similarity=0.362 Sum_probs=33.6
Q ss_pred CCccCCCCCccccccccccccccccccccc-----------hhHHHHHHHHHH
Q 021039 160 RSCHCAVCDNCVEKFDHHCPWIGQCIALRN-----------YRFYLSFVISAL 201 (318)
Q Consensus 160 Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N-----------~r~Fl~fl~~~~ 201 (318)
+-++|..|+..+.++-|||..-|+||-..- +|-+-.|+.+++
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 378899999999999999999999998774 456667775544
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=78.71 E-value=1 Score=25.78 Aligned_cols=21 Identities=24% Similarity=0.592 Sum_probs=17.5
Q ss_pred eccccccccCCCCccCCCCCc
Q 021039 149 YCRICKIFRPPRSCHCAVCDN 169 (318)
Q Consensus 149 ~C~tC~~~kP~Rs~HCs~C~~ 169 (318)
||+.|...-++.+..|..|+.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688888888888888888874
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=74.24 E-value=1.8 Score=29.46 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=22.1
Q ss_pred ceeeccccccccCCCCccCCCCCcc
Q 021039 146 KLKYCRICKIFRPPRSCHCAVCDNC 170 (318)
Q Consensus 146 ~~~~C~tC~~~kP~Rs~HCs~C~~C 170 (318)
..+.|..|...-|+|+..|+.|+.=
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~~ 37 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGYK 37 (48)
T ss_pred cccchhcccCCCCccccccccCCCC
Confidence 3579999999999999999999863
No 14
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=72.68 E-value=1.6 Score=44.71 Aligned_cols=57 Identities=19% Similarity=0.053 Sum_probs=48.1
Q ss_pred ceeeccccccccCCCCccCCCCCccccccccccccccccccccchh-HHHHHHHHHHHH
Q 021039 146 KLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHCPWIGQCIALRNYR-FYLSFVISALVL 203 (318)
Q Consensus 146 ~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC~Wl~nCVG~~N~r-~Fl~fl~~~~~~ 203 (318)
....|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-. +++.|+++.+++
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~~ 381 (600)
T KOG0509|consen 324 LTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLAY 381 (600)
T ss_pred hheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHHH
Confidence 3578899999999999999999999999999999999 99999976 445555555443
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=67.42 E-value=2.7 Score=24.65 Aligned_cols=22 Identities=23% Similarity=0.614 Sum_probs=17.7
Q ss_pred eeccccccccCCCCccCCCCCc
Q 021039 148 KYCRICKIFRPPRSCHCAVCDN 169 (318)
Q Consensus 148 ~~C~tC~~~kP~Rs~HCs~C~~ 169 (318)
++|..|...-++-++.|..|+.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 5788888877888888888874
No 16
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=61.87 E-value=4.1 Score=43.12 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=18.1
Q ss_pred eeccccccccC-------CCCccCCCCCc
Q 021039 148 KYCRICKIFRP-------PRSCHCAVCDN 169 (318)
Q Consensus 148 ~~C~tC~~~kP-------~Rs~HCs~C~~ 169 (318)
..|..|+..-. -|-|||+.|++
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999997764 39999999987
No 17
>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=57.06 E-value=5.4 Score=28.08 Aligned_cols=36 Identities=33% Similarity=0.880 Sum_probs=27.0
Q ss_pred eccccccccCCCC-------ccCCCCCcccccc-ccccccccccccc
Q 021039 149 YCRICKIFRPPRS-------CHCAVCDNCVEKF-DHHCPWIGQCIAL 187 (318)
Q Consensus 149 ~C~tC~~~kP~Rs-------~HCs~C~~CV~r~-DHHC~Wl~nCVG~ 187 (318)
-|..|...-|+-+ +-|..|..|+..+ +++|| ||=|.
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 4666666555543 6789999999998 99999 77664
No 18
>PF12773 DZR: Double zinc ribbon
Probab=55.15 E-value=8.8 Score=25.74 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=23.8
Q ss_pred eeeccccccccC---CCCccCCCCCcccccccccccc
Q 021039 147 LKYCRICKIFRP---PRSCHCAVCDNCVEKFDHHCPW 180 (318)
Q Consensus 147 ~~~C~tC~~~kP---~Rs~HCs~C~~CV~r~DHHC~W 180 (318)
.+||..|...-+ .....|..|+.=+...+.+|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 578888876665 3366788887777777777764
No 19
>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=53.51 E-value=7.2 Score=23.03 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=18.0
Q ss_pred eeccccccccCCCCccCCCCCc
Q 021039 148 KYCRICKIFRPPRSCHCAVCDN 169 (318)
Q Consensus 148 ~~C~tC~~~kP~Rs~HCs~C~~ 169 (318)
|.|+.|....|.-++-|..||.
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 20
>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=51.59 E-value=10 Score=26.23 Aligned_cols=25 Identities=32% Similarity=0.765 Sum_probs=17.0
Q ss_pred ceeeccccccccCCCCccCCC--CCcc
Q 021039 146 KLKYCRICKIFRPPRSCHCAV--CDNC 170 (318)
Q Consensus 146 ~~~~C~tC~~~kP~Rs~HCs~--C~~C 170 (318)
....|..|...-|+|+..|+. ||++
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 357999999999999999998 8764
No 21
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=51.26 E-value=45 Score=31.75 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=27.3
Q ss_pred cceeeccccccccCCCCccCCCCCcccccccc
Q 021039 145 MKLKYCRICKIFRPPRSCHCAVCDNCVEKFDH 176 (318)
Q Consensus 145 ~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DH 176 (318)
.+.++|+.|+.=.-..-|||..=|+||--.++
T Consensus 121 dRaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny 152 (307)
T KOG1315|consen 121 DRAHHCSVCNRCVLKMDHHCPWINNCVGFRNY 152 (307)
T ss_pred CccccchhhhhhhhccccCCcceeceecccch
Confidence 56789999988778889999999999987655
No 22
>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=49.49 E-value=8 Score=27.78 Aligned_cols=27 Identities=30% Similarity=0.504 Sum_probs=12.8
Q ss_pred ceeeccccccc--cCCCCccCCCCCcccc
Q 021039 146 KLKYCRICKIF--RPPRSCHCAVCDNCVE 172 (318)
Q Consensus 146 ~~~~C~tC~~~--kP~Rs~HCs~C~~CV~ 172 (318)
+...|..|... --.|-|||+.||+-|=
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 34678877732 2358999999998553
No 23
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=48.30 E-value=3.9 Score=27.92 Aligned_cols=25 Identities=36% Similarity=0.778 Sum_probs=21.7
Q ss_pred ceeeccccccccCCCCccCCCCCcc
Q 021039 146 KLKYCRICKIFRPPRSCHCAVCDNC 170 (318)
Q Consensus 146 ~~~~C~tC~~~kP~Rs~HCs~C~~C 170 (318)
..+.|..|...-|+|+--|+.|+.=
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccCC
Confidence 3578999999999999999988653
No 24
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=44.31 E-value=6.4 Score=38.99 Aligned_cols=26 Identities=23% Similarity=0.683 Sum_probs=20.1
Q ss_pred ceeecccccccc--CCCCccCCCCCccc
Q 021039 146 KLKYCRICKIFR--PPRSCHCAVCDNCV 171 (318)
Q Consensus 146 ~~~~C~tC~~~k--P~Rs~HCs~C~~CV 171 (318)
...+|+.|...= --|-|||+.||+-+
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHH
Confidence 468999998543 34899999999844
No 25
>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=43.75 E-value=11 Score=22.62 Aligned_cols=21 Identities=24% Similarity=0.831 Sum_probs=15.0
Q ss_pred eccccccccCCCCccCCCCCc
Q 021039 149 YCRICKIFRPPRSCHCAVCDN 169 (318)
Q Consensus 149 ~C~tC~~~kP~Rs~HCs~C~~ 169 (318)
.|..|...-+++..+|..|+.
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 588888888888888888863
No 26
>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 KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=35.84 E-value=17 Score=33.15 Aligned_cols=34 Identities=29% Similarity=0.498 Sum_probs=20.1
Q ss_pred eecc--ccccccCCCCccCCCCCc-----ccccccccccccc
Q 021039 148 KYCR--ICKIFRPPRSCHCAVCDN-----CVEKFDHHCPWIG 182 (318)
Q Consensus 148 ~~C~--tC~~~kP~Rs~HCs~C~~-----CV~r~DHHC~Wl~ 182 (318)
++|. .|+..- -=..||..|+- =..+.+|||||..
T Consensus 9 kHCs~~~CkqlD-FLPf~Cd~C~~~FC~eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 9 KHCSVPYCKQLD-FLPFKCDGCSGIFCLEHRSYESHHCPKGL 49 (250)
T ss_pred cccCcchhhhcc-ccceeeCCccchhhhccchHhhcCCCccc
Confidence 5665 555311 11345666543 3577899999975
No 28
>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=34.71 E-value=16 Score=21.96 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=8.4
Q ss_pred eccccccccCC-CCccCCCCCc
Q 021039 149 YCRICKIFRPP-RSCHCAVCDN 169 (318)
Q Consensus 149 ~C~tC~~~kP~-Rs~HCs~C~~ 169 (318)
.|..|+..... ..++|..||-
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 47777766665 6788888863
No 29
>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=34.29 E-value=24 Score=25.20 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=16.9
Q ss_pred eeeccccccccCCCCccCC-CCCc
Q 021039 147 LKYCRICKIFRPPRSCHCA-VCDN 169 (318)
Q Consensus 147 ~~~C~tC~~~kP~Rs~HCs-~C~~ 169 (318)
.++|..|...-|+--..|| .|+.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 4678888888888777786 5544
No 30
>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=32.32 E-value=23 Score=27.38 Aligned_cols=13 Identities=23% Similarity=0.864 Sum_probs=9.5
Q ss_pred ccccccccccccc
Q 021039 174 FDHHCPWIGQCIA 186 (318)
Q Consensus 174 ~DHHC~Wl~nCVG 186 (318)
+-.||||++.-..
T Consensus 54 Hr~~CPwv~~~~q 66 (91)
T PF08600_consen 54 HREYCPWVNPSTQ 66 (91)
T ss_pred ccccCCccCCccc
Confidence 3468999997653
No 31
>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=32.12 E-value=3.7e+02 Score=26.55 Aligned_cols=33 Identities=21% Similarity=0.489 Sum_probs=23.1
Q ss_pred ceeecccccc-ccCCCCccCCCCCcccccccccc
Q 021039 146 KLKYCRICKI-FRPPRSCHCAVCDNCVEKFDHHC 178 (318)
Q Consensus 146 ~~~~C~tC~~-~kP~Rs~HCs~C~~CV~r~DHHC 178 (318)
...-|+.|+. .+|....+|..|+.-..+..++.
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 3456999997 45555678888888776665543
No 32
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=31.59 E-value=2e+02 Score=28.53 Aligned_cols=33 Identities=18% Similarity=0.368 Sum_probs=24.8
Q ss_pred ceeeccccccccCCCCccCCCCCcccccccccc
Q 021039 146 KLKYCRICKIFRPPRSCHCAVCDNCVEKFDHHC 178 (318)
Q Consensus 146 ~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~DHHC 178 (318)
...-|+.|+...|....||..|+.-..+..++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 456799999887777778999888776655543
No 33
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=29.84 E-value=73 Score=30.96 Aligned_cols=83 Identities=22% Similarity=0.259 Sum_probs=51.3
Q ss_pred HHHHHHHhhh-heecCCCCcCCCCCCcccccCCCCCCccceEEEcc-cccceeeccccccccCCCCccCCCCCccccccc
Q 021039 98 GNNVFINLIL-VSTTDPGIIPRNDQANIEDVGTSDGTRSKRVMING-VEMKLKYCRICKIFRPPRSCHCAVCDNCVEKFD 175 (318)
Q Consensus 98 ~~~~~~~~~~-~~~~DPG~ip~~~~~~~~~~~~~~~~~~~~v~~~g-~~~~~~~C~tC~~~kP~Rs~HCs~C~~CV~r~D 175 (318)
..+.|.+.+. --+..+|.-|.+.....--..= ..-+| +..+.++|.+|+.-.-.--|||.--|+||--..
T Consensus 62 ~~ny~~A~~~gPG~vp~~wkPe~~~D~~~lqfC--------k~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aN 133 (414)
T KOG1314|consen 62 LYNYFNAIFTGPGFVPLGWKPENPKDEMFLQFC--------KKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWAN 133 (414)
T ss_pred HHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHH--------hhccCcCCCccccchHHHHHHHhhccCCcchhhcccccc
Confidence 3455544443 3567789999776653211000 00000 123568999999777777899999999997655
Q ss_pred cccccccccccccchhHHHHHHHH
Q 021039 176 HHCPWIGQCIALRNYRFYLSFVIS 199 (318)
Q Consensus 176 HHC~Wl~nCVG~~N~r~Fl~fl~~ 199 (318)
| .-.-+|++|...
T Consensus 134 h-----------~~F~~FLlf~iv 146 (414)
T KOG1314|consen 134 H-----------AYFLRFLLFSIV 146 (414)
T ss_pred c-----------HHHHHHHHHHHH
Confidence 5 234678888665
No 34
>KOG3415 consensus Putative Rab5-interacting protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.40 E-value=55 Score=26.50 Aligned_cols=27 Identities=4% Similarity=0.044 Sum_probs=17.5
Q ss_pred CCcchhhhhhhhhhHHHHHHHHHHHHH
Q 021039 45 KPELHIKIAENFGNFFASLRENLLVVK 71 (318)
Q Consensus 45 ~~~~~~~~~~~~~~~~~~l~~~~~~i~ 71 (318)
+++.+|..+--++..+-|.++.+..++
T Consensus 30 ~~da~W~DKdellDViyW~rQVi~l~l 56 (129)
T KOG3415|consen 30 DSDAEWPDKDELLDVIYWIRQVIGLIL 56 (129)
T ss_pred CccccCCCHHHHHHHHHHHHHHHHHHH
Confidence 344578666677777777777665554
No 35
>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=28.20 E-value=38 Score=23.05 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=13.9
Q ss_pred ecccccc--ccCCCCccCCCCCcc
Q 021039 149 YCRICKI--FRPPRSCHCAVCDNC 170 (318)
Q Consensus 149 ~C~tC~~--~kP~Rs~HCs~C~~C 170 (318)
.|..|.. ..-.|.|||+.|++-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 4555542 234578899988874
No 36
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=27.11 E-value=21 Score=30.09 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=16.6
Q ss_pred eccccccccCCCCccCCCCCcccccc
Q 021039 149 YCRICKIFRPPRSCHCAVCDNCVEKF 174 (318)
Q Consensus 149 ~C~tC~~~kP~Rs~HCs~C~~CV~r~ 174 (318)
...+|... ...||..|..|+.|.
T Consensus 142 ~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 142 LTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred heeeccCC---CCCCCCCCHHHHHHH
Confidence 44566543 338999999999884
No 37
>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=26.45 E-value=25 Score=22.16 Aligned_cols=7 Identities=29% Similarity=1.241 Sum_probs=3.9
Q ss_pred eeccccc
Q 021039 148 KYCRICK 154 (318)
Q Consensus 148 ~~C~tC~ 154 (318)
+||++|.
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 4666666
No 38
>TIGR02484 CitB CitB domain protein. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the C-terminal domain of the R. capsulatus CobZ, which, in most other species exists as a separate gene adjacent to CobZ.
Probab=23.69 E-value=4e+02 Score=26.18 Aligned_cols=15 Identities=33% Similarity=1.021 Sum_probs=12.1
Q ss_pred ccCCCCCcccccccccccc
Q 021039 162 CHCAVCDNCVEKFDHHCPW 180 (318)
Q Consensus 162 ~HCs~C~~CV~r~DHHC~W 180 (318)
..|..|++| +|.||.
T Consensus 48 ~lChnC~~C----~~~CPy 62 (372)
T TIGR02484 48 HLCHDCQSC----WHDCQY 62 (372)
T ss_pred HHCcCcccc----cccCcC
Confidence 668888888 578887
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.10 E-value=45 Score=22.28 Aligned_cols=8 Identities=25% Similarity=0.949 Sum_probs=4.5
Q ss_pred eccccccc
Q 021039 149 YCRICKIF 156 (318)
Q Consensus 149 ~C~tC~~~ 156 (318)
||+.|...
T Consensus 2 FCp~Cg~~ 9 (52)
T smart00661 2 FCPKCGNM 9 (52)
T ss_pred CCCCCCCc
Confidence 56666543
No 40
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.08 E-value=54 Score=23.68 Aligned_cols=23 Identities=35% Similarity=0.790 Sum_probs=20.0
Q ss_pred eeeccccccccCCCCccCCCCCc
Q 021039 147 LKYCRICKIFRPPRSCHCAVCDN 169 (318)
Q Consensus 147 ~~~C~tC~~~kP~Rs~HCs~C~~ 169 (318)
.+-|..|+...|.-+.-|.+|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 36799999999999999999975
No 41
>KOG4753 consensus Predicted membrane protein [Function unknown]
Probab=20.61 E-value=2.3e+02 Score=23.13 Aligned_cols=64 Identities=14% Similarity=-0.018 Sum_probs=32.6
Q ss_pred cccCCCCcchHHhhhhhcCCCC-cccccccccCCCCCCCCcchhhhhhhhhhHHHHHHHHHHHHHhhhhh
Q 021039 8 LETCSSESDKEAMEQIALSESP-IQDIANSSTNNNIKGKPELHIKIAENFGNFFASLRENLLVVKRVVQN 76 (318)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~ 76 (318)
-.+.||+.++.+-+.-+.|... +.+ ..-|.|+-+-.|+++...++-.+..+...++.+..++..
T Consensus 9 ~~~~dss~~~~~y~~~~~s~~Dsd~~-----~~~~~~~s~tr~P~k~i~lavvL~~fg~Lli~lg~fl~~ 73 (124)
T KOG4753|consen 9 VGTRDSSRTSMAYSDHAFSISDSDIQ-----IDYSYKVSNTRHPVKEIALAVVLLVFGLLLIGLGFFLAG 73 (124)
T ss_pred eeccCCCccchhhcccccccccccce-----eecccccCCCCCchHHHHHHHHHHHHHHHHHHHHHHhee
Confidence 3466777777666554444442 222 233334444367777666665555554444444433333
No 42
>KOG3249 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.54 E-value=5e+02 Score=22.53 Aligned_cols=17 Identities=18% Similarity=0.268 Sum_probs=8.8
Q ss_pred HHhhhheecCCCCcCCC
Q 021039 103 INLILVSTTDPGIIPRN 119 (318)
Q Consensus 103 ~~~~~~~~~DPG~ip~~ 119 (318)
.+.+..++.+||--.++
T Consensus 132 lSlf~~iy~n~~~rk~g 148 (181)
T KOG3249|consen 132 LSLFSIIYLNTGKRKRG 148 (181)
T ss_pred HHHHHHheecCCCCCCC
Confidence 34444555567754444
Done!