Query 022535
Match_columns 295
No_of_seqs 184 out of 1694
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 04:17:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022535.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022535hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315 Predicted DHHC-type Zn 100.0 2.1E-56 4.6E-61 400.4 17.8 259 11-279 3-266 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 5.9E-47 1.3E-51 335.2 11.6 245 20-294 13-282 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 1.8E-44 3.9E-49 329.2 19.4 192 84-281 79-277 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 6.5E-42 1.4E-46 288.6 13.3 172 76-249 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 4.2E-39 9.1E-44 277.1 12.7 149 123-271 101-276 (309)
6 COG5273 Uncharacterized protei 100.0 8E-39 1.7E-43 290.7 14.4 202 65-279 60-288 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 1.8E-31 3.9E-36 231.2 9.1 100 76-188 113-212 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 8E-29 1.7E-33 235.5 7.0 177 76-271 383-585 (600)
9 PF01529 zf-DHHC: DHHC palmito 94.9 0.6 1.3E-05 38.7 11.7 57 119-186 57-113 (174)
10 KOG1311 DHHC-type Zn-finger pr 89.6 2.1 4.5E-05 39.1 8.6 42 137-178 112-164 (299)
11 PRK04136 rpl40e 50S ribosomal 88.2 0.29 6.2E-06 31.7 1.3 24 123-146 13-36 (48)
12 COG5273 Uncharacterized protei 87.5 1.8 3.9E-05 39.8 6.7 55 119-184 118-172 (309)
13 PF13240 zinc_ribbon_2: zinc-r 87.4 0.32 7E-06 26.6 1.1 21 126-146 1-21 (23)
14 PF13248 zf-ribbon_3: zinc-rib 82.0 0.78 1.7E-05 25.7 1.1 22 125-146 3-24 (26)
15 PTZ00303 phosphatidylinositol 81.8 0.92 2E-05 46.0 2.2 23 124-146 460-489 (1374)
16 KOG1315 Predicted DHHC-type Zn 81.6 7.6 0.00016 35.7 7.9 35 119-153 118-152 (307)
17 COG1552 RPL40A Ribosomal prote 75.0 0.61 1.3E-05 30.3 -0.9 24 123-146 13-36 (50)
18 PF01020 Ribosomal_L40e: Ribos 73.7 2.3 5E-05 28.1 1.6 26 122-147 15-42 (52)
19 PF12773 DZR: Double zinc ribb 72.6 3.7 8.1E-05 26.6 2.5 35 123-157 11-48 (50)
20 KOG0509 Ankyrin repeat and DHH 71.3 2 4.4E-05 42.5 1.3 55 122-177 323-377 (600)
21 PF10571 UPF0547: Uncharacteri 71.0 2.5 5.4E-05 23.8 1.1 22 125-146 1-22 (26)
22 PF06906 DUF1272: Protein of u 70.6 2.1 4.5E-05 28.8 0.8 37 125-164 6-50 (57)
23 PF01363 FYVE: FYVE zinc finge 66.8 2.2 4.7E-05 29.7 0.4 27 123-149 8-36 (69)
24 smart00064 FYVE Protein presen 61.6 6.4 0.00014 27.2 2.0 25 124-148 10-36 (68)
25 PF12773 DZR: Double zinc ribb 61.1 6.4 0.00014 25.4 1.8 25 121-145 26-50 (50)
26 PF00641 zf-RanBP: Zn-finger i 57.6 4.5 9.7E-05 23.3 0.5 21 126-146 6-26 (30)
27 KOG3183 Predicted Zn-finger pr 56.7 5 0.00011 35.1 0.9 12 148-159 38-49 (250)
28 PHA02680 ORF090 IMV phosphoryl 53.8 84 0.0018 23.2 6.6 25 225-249 60-84 (91)
29 KOG1842 FYVE finger-containing 48.9 5.1 0.00011 38.3 -0.3 28 121-148 177-206 (505)
30 KOG1313 DHHC-type Zn-finger pr 48.6 90 0.0019 28.2 7.3 90 69-184 76-165 (309)
31 PF12172 DUF35_N: Rubredoxin-l 47.1 8.6 0.00019 23.2 0.6 22 123-145 10-32 (37)
32 PF07010 Endomucin: Endomucin; 44.5 55 0.0012 28.7 5.2 26 65-90 198-223 (259)
33 PF07649 C1_3: C1-like domain; 43.6 9.7 0.00021 21.9 0.4 21 126-146 2-23 (30)
34 cd00065 FYVE FYVE domain; Zinc 42.6 18 0.00039 23.8 1.7 24 125-148 3-28 (57)
35 PF09297 zf-NADH-PPase: NADH p 40.8 15 0.00032 21.5 0.9 23 124-146 3-29 (32)
36 COG2093 DNA-directed RNA polym 38.0 18 0.0004 24.8 1.1 23 124-146 4-26 (64)
37 PLN00186 ribosomal protein S26 38.0 14 0.0003 28.4 0.6 17 137-153 19-35 (109)
38 PF07282 OrfB_Zn_ribbon: Putat 37.6 22 0.00048 24.5 1.6 26 122-147 26-55 (69)
39 KOG1314 DHHC-type Zn-finger pr 37.6 1.1E+02 0.0024 28.6 6.4 90 66-177 58-147 (414)
40 PF03107 C1_2: C1 domain; Int 36.9 24 0.00052 20.3 1.4 20 126-145 2-22 (30)
41 PRK09335 30S ribosomal protein 36.7 15 0.00032 27.5 0.6 20 137-156 19-38 (95)
42 KOG1818 Membrane trafficking a 36.5 14 0.00031 37.1 0.6 24 123-146 164-189 (634)
43 KOG1398 Uncharacterized conser 34.4 11 0.00024 35.5 -0.5 25 134-164 10-34 (460)
44 PTZ00172 40S ribosomal protein 34.1 17 0.00036 27.9 0.5 19 137-155 19-37 (108)
45 PF02150 RNA_POL_M_15KD: RNA p 33.9 14 0.00031 22.2 0.1 7 125-131 2-8 (35)
46 smart00547 ZnF_RBZ Zinc finger 31.6 25 0.00055 19.1 0.9 21 126-146 4-24 (26)
47 PF03842 Silic_transp: Silicon 29.8 5.2E+02 0.011 25.0 9.9 19 168-186 171-189 (512)
48 smart00661 RPOL9 RNA polymeras 27.9 33 0.00071 22.1 1.1 6 126-131 2-7 (52)
49 PRK14559 putative protein seri 27.3 43 0.00093 34.1 2.2 21 126-146 29-49 (645)
50 PF07818 HCNGP: HCNGP-like pro 27.1 74 0.0016 23.9 3.0 33 237-272 25-57 (96)
51 PF08600 Rsm1: Rsm1-like; Int 26.3 33 0.00072 25.4 1.0 11 153-163 56-66 (91)
52 PF14127 DUF4294: Domain of un 26.1 61 0.0013 26.7 2.5 32 237-271 103-134 (157)
53 PRK03681 hypA hydrogenase nick 26.0 37 0.0008 26.3 1.2 25 122-146 68-95 (114)
54 PF01283 Ribosomal_S26e: Ribos 25.9 24 0.00052 27.4 0.1 21 137-157 19-39 (113)
55 PHA02942 putative transposase; 25.2 46 0.001 31.6 2.0 25 122-146 323-350 (383)
56 PRK13130 H/ACA RNA-protein com 24.7 54 0.0012 22.1 1.7 22 123-146 4-25 (56)
57 PF00130 C1_1: Phorbol esters/ 24.7 63 0.0014 20.8 2.0 34 122-155 9-50 (53)
58 COG0603 Predicted PP-loop supe 24.4 26 0.00055 30.7 0.0 20 133-152 187-206 (222)
59 KOG3611 Semaphorins [Signal tr 24.2 27 0.00058 36.1 0.2 38 138-175 491-536 (737)
60 PF01437 PSI: Plexin repeat; 23.6 17 0.00036 23.7 -1.0 17 142-158 6-22 (51)
61 PRK00432 30S ribosomal protein 23.3 52 0.0011 21.5 1.4 24 123-146 19-45 (50)
62 PRK14559 putative protein seri 22.7 48 0.001 33.8 1.6 42 121-164 12-53 (645)
63 PRK12286 rpmF 50S ribosomal pr 22.4 72 0.0016 21.5 1.9 23 122-146 25-48 (57)
64 COG4640 Predicted membrane pro 21.8 47 0.001 31.5 1.2 26 124-149 1-26 (465)
65 PF07754 DUF1610: Domain of un 21.5 69 0.0015 17.7 1.4 19 127-145 1-23 (24)
66 PF13842 Tnp_zf-ribbon_2: DDE_ 21.3 68 0.0015 18.8 1.4 7 125-131 17-23 (32)
67 KOG0003 Ubiquitin/60s ribosoma 20.3 15 0.00032 28.2 -1.9 26 121-146 90-115 (128)
68 smart00423 PSI domain found in 20.2 35 0.00077 21.5 0.1 24 126-149 6-29 (46)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.1e-56 Score=400.44 Aligned_cols=259 Identities=39% Similarity=0.691 Sum_probs=203.0
Q ss_pred hhhhhcccccchhHHHHHHHHhhhceeeeEEEEeecccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022535 11 NVFKFCTALRGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVP 90 (295)
Q Consensus 11 ~~~~~~~~~r~~g~i~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~~y~~~~~~dPG~vp 90 (295)
+..++++..| +++++++.+.+++.||+++...+.+....+ ..+...+++++.+++|.+|+|++++++|||.+|
T Consensus 3 ~~~~~~~~~r---~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~----~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp 75 (307)
T KOG1315|consen 3 GSRRFSKCLR---WIPVLIILLVIGWTYYVYVAVLCILSISLT----IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVP 75 (307)
T ss_pred Ccccchhhhc---chhheeeeeeEEEEEEEeehhhhHHHHhhh----hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCc
Confidence 3444444446 899999999999999999998887765332 455667789999999999999999999999999
Q ss_pred CCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCccccccccccccccccccccchHHH
Q 022535 91 PNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYF 170 (295)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~F 170 (295)
..+.++.++++..+................++..|+|.+|+.+|||||||||+|+|||+||||||||+|||||.+|||+|
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF 155 (307)
T KOG1315|consen 76 DSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFF 155 (307)
T ss_pred cccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHH
Confidence 99888765443322111100001112234567899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchHHhHhccC
Q 022535 171 LLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYEKKT 250 (295)
Q Consensus 171 ilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l~~~~l~~~hl~li~~n~TT~E~~~~~~ 250 (295)
++|++|+.+++.+..+.....+...+... ...++.....+++.+++.+.|++.+.+|+++|++||++|+||+|.++...
T Consensus 156 ~lfl~y~~l~~~~~lv~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~ 234 (307)
T KOG1315|consen 156 LLFLFYTNLYSIYVLVTTLIGFTKYFQGG-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPV 234 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhcccc
Confidence 99999999999998887777777766332 22223333445555667778888888899999999999999999998753
Q ss_pred C-----CCCCCchhHHhHHHHhcCCCchhhcccc
Q 022535 251 T-----PKWRYDLGRKKNFEQVVAFCFLLLCSLI 279 (295)
Q Consensus 251 ~-----~~~~yd~G~~~N~~~vfG~~~~~w~~~~ 279 (295)
. .++.+++ .+|++|+||+++..|..|+
T Consensus 235 ~~~~~~~~~~~~~--~~n~~~vfg~~~~~wl~P~ 266 (307)
T KOG1315|consen 235 FRSGLHNKNGFNL--YVNFREVFGSNLLYWLLPI 266 (307)
T ss_pred ccccccccCCcce--eecHHHHhCCCceEEeccc
Confidence 2 3445555 6799999999999999999
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.9e-47 Score=335.18 Aligned_cols=245 Identities=27% Similarity=0.507 Sum_probs=168.2
Q ss_pred cchhHHHHHHHHhhhceeeeEEEEeecccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchh
Q 022535 20 RGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDE 99 (295)
Q Consensus 20 r~~g~i~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~ 99 (295)
.+.|++..+-+..+++...-......|.| ..+..+....+.|.+...|.+++|+.+++++||++|++|.|+...
T Consensus 13 ~hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~ 86 (414)
T KOG1314|consen 13 LHWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK 86 (414)
T ss_pred eccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh
Confidence 34566655555554443332222334555 344455566677777889999999999999999999999985432
Q ss_pred hhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCccccccccccccccccccccchHHHHHHHHHHHH
Q 022535 100 ERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFL 179 (295)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l 179 (295)
+ ..-.+||.+|+.+|+||||||+.|||||.+|||||||+|||||..||.+|+.||++..+
T Consensus 87 D--------------------~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~iv 146 (414)
T KOG1314|consen 87 D--------------------EMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIV 146 (414)
T ss_pred h--------------------HHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHH
Confidence 1 23468999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH----HHHHHh----cCCCCCCC---CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchHHhHhc
Q 022535 180 ETSLVTLSLLP----HFISFF----SEGEIPGT---PGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYEK 248 (295)
Q Consensus 180 ~~~~~~~~~~~----~~~~~~----~~~~~~~~---~~~~~~~~l~~~l~~~~~l~~~~l~~~hl~li~~n~TT~E~~~~ 248 (295)
+|+-..+.+.. .++..| +....+.. +..++.+++++.++++..+.++.|++.|+..|.+|+|.||.+..
T Consensus 147 G~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~ 226 (414)
T KOG1314|consen 147 GCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIV 226 (414)
T ss_pred hcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHH
Confidence 77654433222 222222 22222221 22233334444445555566677888999999999999999741
Q ss_pred c--------------CCCCCCCchhHHhHHHHhcCCCchhhcccccccccccccccCCCC
Q 022535 249 K--------------TTPKWRYDLGRKKNFEQVVAFCFLLLCSLISLLVSFAYFSDSLKY 294 (295)
Q Consensus 249 ~--------------~~~~~~yd~G~~~N~~~vfG~~~~~w~~~~~~~~~~~~~~~~~~~ 294 (295)
+ .....|||+|++.|++|||-.+.- +=+||..||...+--+|
T Consensus 227 ~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~~----~~gdg~~wPv~~gc~qy 282 (414)
T KOG1314|consen 227 EKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNKK----EEGDGIEWPVVEGCVQY 282 (414)
T ss_pred HHHHHHHHhhccCCCCceeeeccccccccHHHHhhhccc----cCCCCccccccCccccc
Confidence 1 112469999999999999933311 44555555554443333
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.8e-44 Score=329.17 Aligned_cols=192 Identities=31% Similarity=0.561 Sum_probs=140.0
Q ss_pred cCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCcccccccccccccccccc
Q 022535 84 TDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVG 163 (295)
Q Consensus 84 ~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG 163 (295)
+|||.+|++..+..+.. ++.++.. +...++...+.+||.+|+.+|||||||||+||+||+||||||||+|||||
T Consensus 79 sdpg~~p~~~~~~~~~~--~~~~~~~----~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG 152 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDP--ERAPLYK----NVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIG 152 (299)
T ss_pred CCCceecCcccCCCCCc--cccccCC----CcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceEC
Confidence 59999998631111110 1111111 12334556789999999999999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC----CCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 022535 164 ALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPG----TPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSAN 239 (295)
Q Consensus 164 ~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~l~~~l~~~~~l~~~~l~~~hl~li~~n 239 (295)
++|||+|+.|+++..+++++..+.....+.....+..... .+......++..++++.+...+++|+.+|++++.+|
T Consensus 153 ~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~ 232 (299)
T KOG1311|consen 153 ERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSG 232 (299)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecC
Confidence 9999999999999999888887766555544332221111 112222233333556666677778999999999999
Q ss_pred cchHHhHhc-cCCC-CCCCchhHHhHHHHhcCCCchh-hcccccc
Q 022535 240 TTTIEAYEK-KTTP-KWRYDLGRKKNFEQVVAFCFLL-LCSLISL 281 (295)
Q Consensus 240 ~TT~E~~~~-~~~~-~~~yd~G~~~N~~~vfG~~~~~-w~~~~~~ 281 (295)
+||+|..+. +... .++||+|.++|++++||.+..+ |+.|...
T Consensus 233 ~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~ 277 (299)
T KOG1311|consen 233 STTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFAR 277 (299)
T ss_pred cchhhhhhccccccccCCCchhHHHHHHHHhCCCCCccccccccc
Confidence 999999884 2223 3899999999999999887655 8888743
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=6.5e-42 Score=288.57 Aligned_cols=172 Identities=32% Similarity=0.623 Sum_probs=122.8
Q ss_pred HHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCcccccccccc
Q 022535 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (295)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHC 155 (295)
++|++++++|||++|+....+.+. ..+. .............+..++.++|.+|+..||+|||||+.||+||+||||||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC 79 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQR-QEEK-EEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHC 79 (174)
T ss_pred EEehhhheECCcccCCcccccccc-cccc-ccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccc
Confidence 468899999999999762211111 1010 00111111123345678899999999999999999999999999999999
Q ss_pred ccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-CchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 022535 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP-GTLATTFLAFVLNLAFALSVLGFLIMHIS 234 (295)
Q Consensus 156 pWi~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~l~~~~l~~~hl~ 234 (295)
||+|||||++|||+|++|+++..+.+++..+..+..+............. ......++.+++++++.++++++++.|++
T Consensus 80 ~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 159 (174)
T PF01529_consen 80 PWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLY 159 (174)
T ss_pred hhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998888776655555443322111111 11111134445566677778889999999
Q ss_pred HHhhCcchHHhHhcc
Q 022535 235 LVSANTTTIEAYEKK 249 (295)
Q Consensus 235 li~~n~TT~E~~~~~ 249 (295)
++++|+||+|.++++
T Consensus 160 ~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 160 LILRNITTYERIKRK 174 (174)
T ss_pred HHHcCCcHHHHHHcC
Confidence 999999999999875
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.2e-39 Score=277.15 Aligned_cols=149 Identities=34% Similarity=0.648 Sum_probs=112.9
Q ss_pred CceeccccCcccCCCCccCCccCccccccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---cCC
Q 022535 123 RIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFF---SEG 199 (295)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~---~~~ 199 (295)
...+|.+|..+||||+||||.|||||+||||||||+|||||.+|||||++|++|+.+++.+..+...+..++.. .+.
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ 180 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEI 180 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhc
Confidence 45899999999999999999999999999999999999999999999999999999999997765444444321 111
Q ss_pred C-CCC------CCCchh---------hHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchHHhHhc----c----CCCCCC
Q 022535 200 E-IPG------TPGTLA---------TTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYEK----K----TTPKWR 255 (295)
Q Consensus 200 ~-~~~------~~~~~~---------~~~l~~~l~~~~~l~~~~l~~~hl~li~~n~TT~E~~~~----~----~~~~~~ 255 (295)
+ .+. .|.... .+.-..++++.+.+.++.+..||.++|.+|.|++|+... + +..+||
T Consensus 181 tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~ 260 (309)
T KOG1313|consen 181 TAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNP 260 (309)
T ss_pred ccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCC
Confidence 0 100 011110 012234455556667778889999999999999998642 1 123789
Q ss_pred CchhHHhHHHHhcCCC
Q 022535 256 YDLGRKKNFEQVVAFC 271 (295)
Q Consensus 256 yd~G~~~N~~~vfG~~ 271 (295)
||.|.++|++.++|-.
T Consensus 261 ~n~g~k~nWr~fLg~~ 276 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLF 276 (309)
T ss_pred cccchHHHHHHhhccc
Confidence 9999999999998754
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=8e-39 Score=290.74 Aligned_cols=202 Identities=33% Similarity=0.550 Sum_probs=145.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCcc
Q 022535 65 ILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVC 144 (295)
Q Consensus 65 ~~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C 144 (295)
+.+.+...+....|++..++|||+.+++-....-++..++ ...++..+..++|.+|+.+||||||||+.|
T Consensus 60 i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~C~~C~~~KP~RS~HC~~C 129 (309)
T COG5273 60 ILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISR----------LLDDGKFGTENFCSTCNIYKPPRSHHCSIC 129 (309)
T ss_pred hhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhh----------hhhcCccccceeccccccccCCCCccchhh
Confidence 3455556677888999999999999865333222221111 122355678899999999999999999999
Q ss_pred CccccccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCch-hhHHHH-HHHHHHHH
Q 022535 145 GRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTL-ATTFLA-FVLNLAFA 222 (295)
Q Consensus 145 ~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~-~~l~~~~~ 222 (295)
||||+||||||||+|||||.+|||+|++|++++...+..+.......+..... ....+... ..++.+ ..+.+.+.
T Consensus 130 n~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~li~~~~~~~~~~f 206 (309)
T COG5273 130 NRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFS---IRHDTSLAICFLIFGCSLLGVVFF 206 (309)
T ss_pred cchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---ccCChHHHHHHHHHhhhHHHHHHH
Confidence 99999999999999999999999999999999977776665544333333221 12222222 111221 23344445
Q ss_pred HHHHHHHHHHHHHHhhCcchHHhHhccCC------------C-------------CCCCchhHHhHHHHhcCCCchhhcc
Q 022535 223 LSVLGFLIMHISLVSANTTTIEAYEKKTT------------P-------------KWRYDLGRKKNFEQVVAFCFLLLCS 277 (295)
Q Consensus 223 l~~~~l~~~hl~li~~n~TT~E~~~~~~~------------~-------------~~~yd~G~~~N~~~vfG~~~~~w~~ 277 (295)
+.++.++..+.+++..|+|++|..+..+. . -.|++.|.-+|++.++|.+...|..
T Consensus 207 ~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ 286 (309)
T COG5273 207 IITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLSTIKGSNALYWLT 286 (309)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccceeecCCCceeecc
Confidence 55677888999999999999998764321 0 2478899999999999999999988
Q ss_pred cc
Q 022535 278 LI 279 (295)
Q Consensus 278 ~~ 279 (295)
|.
T Consensus 287 ~~ 288 (309)
T COG5273 287 PL 288 (309)
T ss_pred cc
Confidence 84
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=1.8e-31 Score=231.18 Aligned_cols=100 Identities=32% Similarity=0.685 Sum_probs=76.0
Q ss_pred HHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCcccccccccc
Q 022535 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (295)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHC 155 (295)
.++..++.+|||.+.+... .+..++-|-+. ........|++|+..||.||||||.|||||.|+||||
T Consensus 113 i~f~ltc~snpg~i~k~n~----s~~~~~ypYDy---------~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHC 179 (341)
T KOG1312|consen 113 IFFTLTCGSNPGIITKANE----SLFLHVYPYDY---------VIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHC 179 (341)
T ss_pred HHHhhhhcCCCCccchhhh----ccceeccCccc---------eeecCCCccccccCCCccccccchHHHHHHHHhccce
Confidence 3456788999999974210 11111222211 1123347899999999999999999999999999999
Q ss_pred ccccccccccchHHHHHHHHHHHHHHHHHHHHH
Q 022535 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSL 188 (295)
Q Consensus 156 pWi~nCIG~~N~k~FilFl~~~~l~~~~~~~~~ 188 (295)
.|+|||||++|.|||++||++....+.++.+-+
T Consensus 180 iWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrl 212 (341)
T KOG1312|consen 180 IWINNCIGAWNIRYFLLFLLTLISLATYAIVRL 212 (341)
T ss_pred EeeecccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999877777665543
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=8e-29 Score=235.48 Aligned_cols=177 Identities=25% Similarity=0.387 Sum_probs=109.6
Q ss_pred HHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCc-eeccccCcccCCCCccCCccCccccccccc
Q 022535 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRI-RYCRKCNQLKPPRCHHCSVCGRCILKMDHH 154 (295)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHH 154 (295)
.++.+...+|||++|...... .+...+ ..+.++.+.. ++|.+|.++||.|||||++|||||.|||||
T Consensus 383 ~~f~~~~rsDPg~i~~~~~~~--~~tIs~----------l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHh 450 (600)
T KOG0509|consen 383 ITFGLFLRSDPGFIPTSTEVG--RETISQ----------LIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHH 450 (600)
T ss_pred HHHHHHhccCCCCCCCchhhH--HHHHHH----------hhccccccccccceeeeeeecCCccchhhhhHHHHhccccC
Confidence 345566679999999542221 111111 0111233344 799999999999999999999999999999
Q ss_pred cccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHH---------H---
Q 022535 155 CVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTLATTFLAFVLNLAF---------A--- 222 (295)
Q Consensus 155 CpWi~nCIG~~N~k~FilFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~---------~--- 222 (295)
|||++||||.+|||+|+.|++.+...+.+.+..... ++.... ... .....++..+..+.. .
T Consensus 451 CPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~----y~~~~~--~~~-~~~~~~l~~~~~~~~~~~~~~~~~~n~~ 523 (600)
T KOG0509|consen 451 CPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLY----YIMNLE--NAS-TIYVGFLIAVQAFRIPKPVTGNLLGNED 523 (600)
T ss_pred CCccccccCccchHHHHHHHHHHHHHHHHHHHHHHH----HHhhcc--hhH-HHHHHHHHHHHHHhCCccceeeeeeccc
Confidence 999999999999999999999876666554433222 221111 100 000001111100000 0
Q ss_pred ----HHHHHHHHHHHHHHhhCcchHHhHhccCC---------CCCCCchhHHhHHHHhcCCC
Q 022535 223 ----LSVLGFLIMHISLVSANTTTIEAYEKKTT---------PKWRYDLGRKKNFEQVVAFC 271 (295)
Q Consensus 223 ----l~~~~l~~~hl~li~~n~TT~E~~~~~~~---------~~~~yd~G~~~N~~~vfG~~ 271 (295)
.....-...|-..++.+.||+|+++.++. .+.|++.|+.+|+.+++=.+
T Consensus 524 ~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 524 LNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPGPIRNLVDFFLCS 585 (600)
T ss_pred cccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCchhhhcchheeecc
Confidence 00000111233357899999999875433 36799999999999998443
No 9
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=94.87 E-value=0.6 Score=38.66 Aligned_cols=57 Identities=33% Similarity=0.553 Sum_probs=43.8
Q ss_pred CCCCCceeccccCcccCCCCccCCccCccccccccccccccccccccchHHHHHHHHHHHHHHHHHHH
Q 022535 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTL 186 (295)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l~~~~~~~ 186 (295)
.+..+.++|..|+.--..+-|||.--|.||.+.-| +-+=.|+++..-..+.......
T Consensus 57 ~kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~~~~ 113 (174)
T PF01529_consen 57 IKPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFILSL 113 (174)
T ss_pred cCCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999999999999998776 5566777766655555554433
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=89.65 E-value=2.1 Score=39.06 Aligned_cols=42 Identities=24% Similarity=0.525 Sum_probs=36.8
Q ss_pred CCccCCccCccccccccccccccccccccch-----------HHHHHHHHHHH
Q 022535 137 RCHHCSVCGRCILKMDHHCVWVVNCVGALNY-----------KYFLLFLLYTF 178 (295)
Q Consensus 137 Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~-----------k~FilFl~~~~ 178 (295)
+.++|..|+.-+...-|||+.=|+||-+.-| |.+-.|+.+++
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 4899999999999999999999999988765 67778996666
No 11
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=88.18 E-value=0.29 Score=31.72 Aligned_cols=24 Identities=33% Similarity=0.838 Sum_probs=21.9
Q ss_pred CceeccccCcccCCCCccCCccCc
Q 022535 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
....|.+|...-|+||..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 458899999999999999999886
No 12
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=87.53 E-value=1.8 Score=39.83 Aligned_cols=55 Identities=25% Similarity=0.369 Sum_probs=44.3
Q ss_pred CCCCCceeccccCcccCCCCccCCccCccccccccccccccccccccchHHHHHHHHHHHHHHHHH
Q 022535 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLV 184 (295)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l~~~~~ 184 (295)
.+.++.+.|+.|+.--...-|||.--|+||-+.-| +=.-.|++++....+..++.
T Consensus 118 ~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~ 172 (309)
T COG5273 118 YKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLS 172 (309)
T ss_pred ccCCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHH
Confidence 44678899999999999999999999999998776 66778888886555444443
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.38 E-value=0.32 Score=26.57 Aligned_cols=21 Identities=29% Similarity=0.842 Sum_probs=17.9
Q ss_pred eccccCcccCCCCccCCccCc
Q 022535 126 YCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~r 146 (295)
+|..|...-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 588898888899999998875
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.00 E-value=0.78 Score=25.75 Aligned_cols=22 Identities=27% Similarity=0.854 Sum_probs=18.4
Q ss_pred eeccccCcccCCCCccCCccCc
Q 022535 125 RYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
++|..|...-++.++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6788898877888888988875
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=81.81 E-value=0.92 Score=46.05 Aligned_cols=23 Identities=35% Similarity=0.816 Sum_probs=18.8
Q ss_pred ceeccccCcccC-------CCCccCCccCc
Q 022535 124 IRYCRKCNQLKP-------PRCHHCSVCGR 146 (295)
Q Consensus 124 ~~~C~~C~~~kP-------~Rs~HC~~C~r 146 (295)
.+.|..|+..-. -|-||||.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999997664 39999999987
No 16
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=81.64 E-value=7.6 Score=35.67 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=26.1
Q ss_pred CCCCCceeccccCcccCCCCccCCccCcccccccc
Q 022535 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDH 153 (295)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DH 153 (295)
-+.++.+.|+.|+.=--..-|||.--|+||.-.++
T Consensus 118 iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny 152 (307)
T KOG1315|consen 118 IKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNY 152 (307)
T ss_pred ccCCccccchhhhhhhhccccCCcceeceecccch
Confidence 34567788888876666777888888888876554
No 17
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=75.03 E-value=0.61 Score=30.30 Aligned_cols=24 Identities=38% Similarity=1.029 Sum_probs=21.4
Q ss_pred CceeccccCcccCCCCccCCccCc
Q 022535 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
..+.|.+|...-|+|+--|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 457899999999999999998875
No 18
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=73.68 E-value=2.3 Score=28.06 Aligned_cols=26 Identities=38% Similarity=0.856 Sum_probs=17.6
Q ss_pred CCceeccccCcccCCCCccCCc--cCcc
Q 022535 122 PRIRYCRKCNQLKPPRCHHCSV--CGRC 147 (295)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~--C~rC 147 (295)
.+...|.+|...-|+||..|+. ||.+
T Consensus 15 ~~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 15 CDKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp TS-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred ccceecccccCcCCCCccceecccCCCC
Confidence 3458999999999999999998 8765
No 19
>PF12773 DZR: Double zinc ribbon
Probab=72.65 E-value=3.7 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.485 Sum_probs=21.7
Q ss_pred CceeccccCcccC---CCCccCCccCcccccccccccc
Q 022535 123 RIRYCRKCNQLKP---PRCHHCSVCGRCILKMDHHCVW 157 (295)
Q Consensus 123 ~~~~C~~C~~~kP---~Rs~HC~~C~rCV~r~DHHCpW 157 (295)
+.++|..|...-+ .....|+.|++=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 4567777765544 3355677777766666666653
No 20
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=71.31 E-value=2 Score=42.54 Aligned_cols=55 Identities=5% Similarity=-0.130 Sum_probs=47.4
Q ss_pred CCceeccccCcccCCCCccCCccCccccccccccccccccccccchHHHHHHHHHH
Q 022535 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYT 177 (295)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~ 177 (295)
.....|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-..+-+..+..
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~ 377 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIIS 377 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHH
Confidence 45578889999999999999999999999999999999 99999988665544433
No 21
>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=70.96 E-value=2.5 Score=23.82 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=18.2
Q ss_pred eeccccCcccCCCCccCCccCc
Q 022535 125 RYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
|.|..|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688899888988888888874
No 22
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=70.62 E-value=2.1 Score=28.78 Aligned_cols=37 Identities=32% Similarity=0.859 Sum_probs=27.7
Q ss_pred eeccccCcccCCCC-------ccCCccCcccccc-ccccccccccccc
Q 022535 125 RYCRKCNQLKPPRC-------HHCSVCGRCILKM-DHHCVWVVNCVGA 164 (295)
Q Consensus 125 ~~C~~C~~~kP~Rs-------~HC~~C~rCV~r~-DHHCpWi~nCIG~ 164 (295)
.-|..|+.--|+-| +-|-.|..|+..+ +++|| ||=|.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 34666666555554 6688999999999 99999 77664
No 23
>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=66.83 E-value=2.2 Score=29.71 Aligned_cols=27 Identities=33% Similarity=0.719 Sum_probs=13.0
Q ss_pred CceeccccCcc--cCCCCccCCccCcccc
Q 022535 123 RIRYCRKCNQL--KPPRCHHCSVCGRCIL 149 (295)
Q Consensus 123 ~~~~C~~C~~~--kP~Rs~HC~~C~rCV~ 149 (295)
+...|..|... --.|-|||+.||+-|=
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 34678878632 2478999999998553
No 24
>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 PF12773 DZR: Double zinc ribbon
Probab=61.13 E-value=6.4 Score=25.41 Aligned_cols=25 Identities=28% Similarity=0.894 Sum_probs=21.9
Q ss_pred CCCceeccccCcccCCCCccCCccC
Q 022535 121 NPRIRYCRKCNQLKPPRCHHCSVCG 145 (295)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~ 145 (295)
.....+|..|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456899999999999999999986
No 26
>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=57.64 E-value=4.5 Score=23.30 Aligned_cols=21 Identities=29% Similarity=0.882 Sum_probs=15.0
Q ss_pred eccccCcccCCCCccCCccCc
Q 022535 126 YCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~r 146 (295)
.|..|...-++++.+|..|+.
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 588888888888888888864
No 27
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=56.73 E-value=5 Score=35.14 Aligned_cols=12 Identities=25% Similarity=0.241 Sum_probs=9.8
Q ss_pred cccccccccccc
Q 022535 148 ILKMDHHCVWVV 159 (295)
Q Consensus 148 V~r~DHHCpWi~ 159 (295)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 567899999875
No 28
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=53.84 E-value=84 Score=23.17 Aligned_cols=25 Identities=12% Similarity=0.325 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHhhCcchHHhHhcc
Q 022535 225 VLGFLIMHISLVSANTTTIEAYEKK 249 (295)
Q Consensus 225 ~~~l~~~hl~li~~n~TT~E~~~~~ 249 (295)
+++++++..|--+++.++.|+++..
T Consensus 60 ~lGilifs~y~~C~~~~~~~r~n~s 84 (91)
T PHA02680 60 LLGLFVFSMYRKCSGSMPYERLNNT 84 (91)
T ss_pred HHHHHHHHHhcccCCCceeecccCC
Confidence 4456677777777888888887654
No 29
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=48.91 E-value=5.1 Score=38.25 Aligned_cols=28 Identities=32% Similarity=0.996 Sum_probs=21.5
Q ss_pred CCCceeccccCcc--cCCCCccCCccCccc
Q 022535 121 NPRIRYCRKCNQL--KPPRCHHCSVCGRCI 148 (295)
Q Consensus 121 ~~~~~~C~~C~~~--kP~Rs~HC~~C~rCV 148 (295)
.....+|..|... ---|-|||+.||+-+
T Consensus 177 Ds~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 177 DSSVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred CCcccccccccchhhhHHHhhhhhhcchHH
Confidence 3467899999743 356899999999844
No 30
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=48.62 E-value=90 Score=28.24 Aligned_cols=90 Identities=22% Similarity=0.451 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccCccc
Q 022535 69 CLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCI 148 (295)
Q Consensus 69 ~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~rCV 148 (295)
.++..+.+.|+++....|-..|. .+. ..+-+.-..++.++...|+.|+.---.=-|||.-=|+||
T Consensus 76 ~~l~nvi~hy~ka~t~pPvgn~~-----~~~----------~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCV 140 (309)
T KOG1313|consen 76 YLLSNVIFHYYKARTKPPVGNPG-----LEN----------DSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCV 140 (309)
T ss_pred HHHHHHHHhheeecccCCcCCCC-----Ccc----------ccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhccc
Confidence 44556667788888777622221 100 011111234667788999999976666779999999999
Q ss_pred cccccccccccccccccchHHHHHHHHHHHHHHHHH
Q 022535 149 LKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLV 184 (295)
Q Consensus 149 ~r~DHHCpWi~nCIG~~N~k~FilFl~~~~l~~~~~ 184 (295)
--..| +=.=.|+.++.-+.....+.
T Consensus 141 G~~NH-----------ryFFlFl~~ltlat~~~~i~ 165 (309)
T KOG1313|consen 141 GAHNH-----------RYFFLFLFYLTLATSYAAIM 165 (309)
T ss_pred ccccc-----------hhHHHHHHHHHHHHHHHHHH
Confidence 99888 66778888886655555444
No 31
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=47.14 E-value=8.6 Score=23.24 Aligned_cols=22 Identities=41% Similarity=1.078 Sum_probs=12.5
Q ss_pred CceeccccCccc-CCCCccCCccC
Q 022535 123 RIRYCRKCNQLK-PPRCHHCSVCG 145 (295)
Q Consensus 123 ~~~~C~~C~~~k-P~Rs~HC~~C~ 145 (295)
..+.|..|..+. ||| ..|..|+
T Consensus 10 ~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEEE-TTT--EEES---SEETTTT
T ss_pred EEEEcCCCCCEecCCC-cCCCCcC
Confidence 457899998775 777 7777775
No 32
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=44.49 E-value=55 Score=28.66 Aligned_cols=26 Identities=23% Similarity=0.203 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022535 65 ILFHCLLVMLLWSYFSVVLTDAGSVP 90 (295)
Q Consensus 65 ~~f~~l~~~~~~~y~~~~~~dPG~vp 90 (295)
++..++.+.++-.|..|...|||..-
T Consensus 198 iVitl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 198 IVITLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 34444555556678889999999743
No 33
>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=43.59 E-value=9.7 Score=21.87 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=8.3
Q ss_pred eccccCcccCC-CCccCCccCc
Q 022535 126 YCRKCNQLKPP-RCHHCSVCGR 146 (295)
Q Consensus 126 ~C~~C~~~kP~-Rs~HC~~C~r 146 (295)
.|..|+..... ...+|+.|+-
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 47777766655 6778888764
No 34
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=42.62 E-value=18 Score=23.78 Aligned_cols=24 Identities=38% Similarity=0.862 Sum_probs=15.1
Q ss_pred eeccccCc--ccCCCCccCCccCccc
Q 022535 125 RYCRKCNQ--LKPPRCHHCSVCGRCI 148 (295)
Q Consensus 125 ~~C~~C~~--~kP~Rs~HC~~C~rCV 148 (295)
+-|..|.. -.-.|.|||+.||+-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 34555642 2356788999988743
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=40.81 E-value=15 Score=21.46 Aligned_cols=23 Identities=26% Similarity=0.829 Sum_probs=10.8
Q ss_pred ceeccccCc----ccCCCCccCCccCc
Q 022535 124 IRYCRKCNQ----LKPPRCHHCSVCGR 146 (295)
Q Consensus 124 ~~~C~~C~~----~kP~Rs~HC~~C~r 146 (295)
.+||..|.. ..-.++..|..|+.
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 478888863 23346666666653
No 36
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.01 E-value=18 Score=24.85 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=20.6
Q ss_pred ceeccccCcccCCCCccCCccCc
Q 022535 124 IRYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
.+-|..|+..-|+.+.-|.+|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999986
No 37
>PLN00186 ribosomal protein S26; Provisional
Probab=38.00 E-value=14 Score=28.38 Aligned_cols=17 Identities=35% Similarity=0.851 Sum_probs=13.3
Q ss_pred CCccCCccCcccccccc
Q 022535 137 RCHHCSVCGRCILKMDH 153 (295)
Q Consensus 137 Rs~HC~~C~rCV~r~DH 153 (295)
+.-||..|++||.+---
T Consensus 19 ~~V~C~nCgr~vPKDKA 35 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKA 35 (109)
T ss_pred cceeeCCCcccccccce
Confidence 45589999999998443
No 38
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.63 E-value=22 Score=24.52 Aligned_cols=26 Identities=23% Similarity=0.567 Sum_probs=19.3
Q ss_pred CCceeccccCccc----CCCCccCCccCcc
Q 022535 122 PRIRYCRKCNQLK----PPRCHHCSVCGRC 147 (295)
Q Consensus 122 ~~~~~C~~C~~~k----P~Rs~HC~~C~rC 147 (295)
...+.|+.|.... ..|.++|..||.-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCCE
Confidence 3678899997543 5578889998875
No 39
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=37.57 E-value=1.1e+02 Score=28.65 Aligned_cols=90 Identities=22% Similarity=0.256 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCchhhhccCCCCCccccCCCCCCCCCCCceeccccCcccCCCCccCCccC
Q 022535 66 LFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCG 145 (295)
Q Consensus 66 ~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~ 145 (295)
.+.+++..+...+.---+..||.-|++.....--+-...-+ .=+.++.+.|++|+.---.=-|||.=-|
T Consensus 58 ~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~lqfCk~Cq-----------gYKapRSHHCrkCnrCvmkMDHHCPWin 126 (414)
T KOG1314|consen 58 TSMILYNYFNAIFTGPGFVPLGWKPENPKDEMFLQFCKKCQ-----------GYKAPRSHHCRKCNRCVMKMDHHCPWIN 126 (414)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHhhcc-----------CcCCCccccchHHHHHHHhhccCCcchh
Confidence 44455555555667778899999997644432221111100 0123567899999866666679999999
Q ss_pred ccccccccccccccccccccchHHHHHHHHHH
Q 022535 146 RCILKMDHHCVWVVNCVGALNYKYFLLFLLYT 177 (295)
Q Consensus 146 rCV~r~DHHCpWi~nCIG~~N~k~FilFl~~~ 177 (295)
.||---.| .-.-+|++|....
T Consensus 127 nCVG~aNh-----------~~F~~FLlf~ivG 147 (414)
T KOG1314|consen 127 NCVGWANH-----------AYFLRFLLFSIVG 147 (414)
T ss_pred hccccccc-----------HHHHHHHHHHHHh
Confidence 99976555 4577888888763
No 40
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=36.95 E-value=24 Score=20.25 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=13.1
Q ss_pred eccccCcccCCC-CccCCccC
Q 022535 126 YCRKCNQLKPPR-CHHCSVCG 145 (295)
Q Consensus 126 ~C~~C~~~kP~R-s~HC~~C~ 145 (295)
.|..|+..-... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 466676555555 77787776
No 41
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=36.74 E-value=15 Score=27.54 Aligned_cols=20 Identities=30% Similarity=0.687 Sum_probs=15.4
Q ss_pred CCccCCccCccccccccccc
Q 022535 137 RCHHCSVCGRCILKMDHHCV 156 (295)
Q Consensus 137 Rs~HC~~C~rCV~r~DHHCp 156 (295)
+.-+|..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 45689999999998665554
No 42
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=36.49 E-value=14 Score=37.09 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=18.0
Q ss_pred CceeccccCcc--cCCCCccCCccCc
Q 022535 123 RIRYCRKCNQL--KPPRCHHCSVCGR 146 (295)
Q Consensus 123 ~~~~C~~C~~~--kP~Rs~HC~~C~r 146 (295)
+..-|.+|... ---|.|||+.||+
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccccceeeeeeeeccccccccccch
Confidence 34678999742 2349999999998
No 43
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.44 E-value=11 Score=35.50 Aligned_cols=25 Identities=40% Similarity=0.858 Sum_probs=19.0
Q ss_pred cCCCCccCCccCccccccccccccccccccc
Q 022535 134 KPPRCHHCSVCGRCILKMDHHCVWVVNCVGA 164 (295)
Q Consensus 134 kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~ 164 (295)
+-.|..||..|+. .|| +|+.||||.
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga 34 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGA 34 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHH
Confidence 4456667777765 577 899999997
No 44
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=34.11 E-value=17 Score=27.90 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=14.1
Q ss_pred CCccCCccCcccccccccc
Q 022535 137 RCHHCSVCGRCILKMDHHC 155 (295)
Q Consensus 137 Rs~HC~~C~rCV~r~DHHC 155 (295)
+.-||..|++||.+----+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIK 37 (108)
T ss_pred ccEEeCCccccccccceEE
Confidence 4458999999999844433
No 45
>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=33.90 E-value=14 Score=22.24 Aligned_cols=7 Identities=43% Similarity=1.592 Sum_probs=4.0
Q ss_pred eeccccC
Q 022535 125 RYCRKCN 131 (295)
Q Consensus 125 ~~C~~C~ 131 (295)
++|.+|.
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 5666775
No 46
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=31.60 E-value=25 Score=19.13 Aligned_cols=21 Identities=29% Similarity=0.675 Sum_probs=15.7
Q ss_pred eccccCcccCCCCccCCccCc
Q 022535 126 YCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~r 146 (295)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477787777777778877764
No 47
>PF03842 Silic_transp: Silicon transporter; InterPro: IPR004693 Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms, which make their "glass houses" out of silicon.
Probab=29.77 E-value=5.2e+02 Score=24.97 Aligned_cols=19 Identities=32% Similarity=0.662 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022535 168 KYFLLFLLYTFLETSLVTL 186 (295)
Q Consensus 168 k~FilFl~~~~l~~~~~~~ 186 (295)
.||.+|.+|+.+..-+.-+
T Consensus 171 nyFalFTlyvam~IEfsGv 189 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEFSGV 189 (512)
T ss_pred HHHHHHHHHHHHHHHHhhh
Confidence 5899999998876555433
No 48
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.90 E-value=33 Score=22.06 Aligned_cols=6 Identities=50% Similarity=1.708 Sum_probs=3.1
Q ss_pred eccccC
Q 022535 126 YCRKCN 131 (295)
Q Consensus 126 ~C~~C~ 131 (295)
+|..|.
T Consensus 2 FCp~Cg 7 (52)
T smart00661 2 FCPKCG 7 (52)
T ss_pred CCCCCC
Confidence 455554
No 49
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.31 E-value=43 Score=34.14 Aligned_cols=21 Identities=33% Similarity=0.814 Sum_probs=9.7
Q ss_pred eccccCcccCCCCccCCccCc
Q 022535 126 YCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~r 146 (295)
.|.+|...-|+.+++|..||.
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred cCCCCCCCCCcccccccccCC
Confidence 344444444444444444444
No 50
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=27.09 E-value=74 Score=23.91 Aligned_cols=33 Identities=0% Similarity=-0.115 Sum_probs=29.9
Q ss_pred hhCcchHHhHhccCCCCCCCchhHHhHHHHhcCCCc
Q 022535 237 SANTTTIEAYEKKTTPKWRYDLGRKKNFEQVVAFCF 272 (295)
Q Consensus 237 ~~n~TT~E~~~~~~~~~~~yd~G~~~N~~~vfG~~~ 272 (295)
.+|.+-++.+.+.+..+|| ++.+.+.+++|..-
T Consensus 25 ~~G~~fN~~L~~s~~frNP---~i~ekLi~~~~Ide 57 (96)
T PF07818_consen 25 RQGIHFNDRLQNSKSFRNP---SILEKLIEFFGIDE 57 (96)
T ss_pred HcCCCHHHHHHHccccCCh---HHHHHHHHHcCCCc
Confidence 4999999999999998999 89999999999875
No 51
>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=26.29 E-value=33 Score=25.43 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.6
Q ss_pred ccccccccccc
Q 022535 153 HHCVWVVNCVG 163 (295)
Q Consensus 153 HHCpWi~nCIG 163 (295)
.||||++.-..
T Consensus 56 ~~CPwv~~~~q 66 (91)
T PF08600_consen 56 EYCPWVNPSTQ 66 (91)
T ss_pred ccCCccCCccc
Confidence 68999997653
No 52
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=26.11 E-value=61 Score=26.74 Aligned_cols=32 Identities=9% Similarity=0.068 Sum_probs=27.4
Q ss_pred hhCcchHHhHhccCCCCCCCchhHHhHHHHhcCCC
Q 022535 237 SANTTTIEAYEKKTTPKWRYDLGRKKNFEQVVAFC 271 (295)
Q Consensus 237 ~~n~TT~E~~~~~~~~~~~yd~G~~~N~~~vfG~~ 271 (295)
-+|.|++|..+.-+ .++.-|+++.+..+||.+
T Consensus 103 etg~TsyelIK~~r---gg~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 103 ETGSTSYELIKELR---GGWRAFWYQTFAWLFGIS 134 (157)
T ss_pred hcCCcHHHHHHHhh---CChhHHHHHHHHHHhCcc
Confidence 58999999998765 478889999999999975
No 53
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.04 E-value=37 Score=26.33 Aligned_cols=25 Identities=20% Similarity=0.530 Sum_probs=18.2
Q ss_pred CCceeccccCcccCCCCcc---CCccCc
Q 022535 122 PRIRYCRKCNQLKPPRCHH---CSVCGR 146 (295)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H---C~~C~r 146 (295)
+..-+|..|+..-|...++ |..||.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 4567899999877765444 888874
No 54
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=25.95 E-value=24 Score=27.40 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=13.5
Q ss_pred CCccCCccCcccccccccccc
Q 022535 137 RCHHCSVCGRCILKMDHHCVW 157 (295)
Q Consensus 137 Rs~HC~~C~rCV~r~DHHCpW 157 (295)
+.-||..|++||.+----..+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKRF 39 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEEE
T ss_pred cCEeeCcccccCcCCceEEEE
Confidence 445899999999996655544
No 55
>PHA02942 putative transposase; Provisional
Probab=25.20 E-value=46 Score=31.58 Aligned_cols=25 Identities=32% Similarity=0.651 Sum_probs=19.1
Q ss_pred CCceeccccCcccC---CCCccCCccCc
Q 022535 122 PRIRYCRKCNQLKP---PRCHHCSVCGR 146 (295)
Q Consensus 122 ~~~~~C~~C~~~kP---~Rs~HC~~C~r 146 (295)
...+.|+.|....+ .|.+.|..||.
T Consensus 323 yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 323 YSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 36788999986644 37788988887
No 56
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.72 E-value=54 Score=22.10 Aligned_cols=22 Identities=41% Similarity=0.895 Sum_probs=16.6
Q ss_pred CceeccccCcccCCCCccCCccCc
Q 022535 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
..+.|..|..+-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 5678888887766 677887775
No 57
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=24.69 E-value=63 Score=20.78 Aligned_cols=34 Identities=29% Similarity=0.785 Sum_probs=22.4
Q ss_pred CCceeccccCccc---CCCCccCCccCc-----ccccccccc
Q 022535 122 PRIRYCRKCNQLK---PPRCHHCSVCGR-----CILKMDHHC 155 (295)
Q Consensus 122 ~~~~~C~~C~~~k---P~Rs~HC~~C~r-----CV~r~DHHC 155 (295)
....+|..|+..- ...+.+|+.|+. |..+.+.-|
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 4568999998655 566788999964 666555544
No 58
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=24.37 E-value=26 Score=30.67 Aligned_cols=20 Identities=25% Similarity=0.698 Sum_probs=15.7
Q ss_pred ccCCCCccCCccCccccccc
Q 022535 133 LKPPRCHHCSVCGRCILKMD 152 (295)
Q Consensus 133 ~kP~Rs~HC~~C~rCV~r~D 152 (295)
+++.+..||..|..|++|.+
T Consensus 187 Y~g~~~~~CG~C~sC~~R~~ 206 (222)
T COG0603 187 YNGGEGDHCGECESCVLRER 206 (222)
T ss_pred eCCCCCCCCCCCHHHHHHHH
Confidence 35666669999999999843
No 59
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=24.23 E-value=27 Score=36.13 Aligned_cols=38 Identities=26% Similarity=0.579 Sum_probs=28.8
Q ss_pred CccCC---ccCcccccccccccccc---ccc--cccchHHHHHHHH
Q 022535 138 CHHCS---VCGRCILKMDHHCVWVV---NCV--GALNYKYFLLFLL 175 (295)
Q Consensus 138 s~HC~---~C~rCV~r~DHHCpWi~---nCI--G~~N~k~FilFl~ 175 (295)
-|+|+ .|..|++..|-||.|-+ .|+ +..|.|.+..=+-
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~ 536 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVS 536 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhc
Confidence 46788 89888888999999998 687 4446666665543
No 60
>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=23.57 E-value=17 Score=23.68 Aligned_cols=17 Identities=29% Similarity=0.913 Sum_probs=10.4
Q ss_pred CccCccccccccccccc
Q 022535 142 SVCGRCILKMDHHCVWV 158 (295)
Q Consensus 142 ~~C~rCV~r~DHHCpWi 158 (295)
..|+.|+...|-+|.|=
T Consensus 6 ~sC~~Cl~~~dp~CgWc 22 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWC 22 (51)
T ss_dssp SSHHHHHHSTCTTEEEE
T ss_pred CcHHHHHcCCCcCcccc
Confidence 45666666666666664
No 61
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.26 E-value=52 Score=21.51 Aligned_cols=24 Identities=25% Similarity=0.826 Sum_probs=14.8
Q ss_pred CceeccccCc-cc--CCCCccCCccCc
Q 022535 123 RIRYCRKCNQ-LK--PPRCHHCSVCGR 146 (295)
Q Consensus 123 ~~~~C~~C~~-~k--P~Rs~HC~~C~r 146 (295)
..++|..|.. .- -....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 4568999976 22 223567777764
No 62
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.75 E-value=48 Score=33.79 Aligned_cols=42 Identities=24% Similarity=0.506 Sum_probs=31.4
Q ss_pred CCCceeccccCcccCCCCccCCccCccccccccccccccccccc
Q 022535 121 NPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGA 164 (295)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~rCV~r~DHHCpWi~nCIG~ 164 (295)
....++|.+|...-+ .+.|..||.=+..-..+||==|.-.|.
T Consensus 12 ~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 12 PNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCcccc
Confidence 356789999975433 467999999899888999866655554
No 63
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.39 E-value=72 Score=21.52 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=15.7
Q ss_pred CCceeccccCcccCCCCcc-CCccCc
Q 022535 122 PRIRYCRKCNQLKPPRCHH-CSVCGR 146 (295)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H-C~~C~r 146 (295)
.....|..|...+ ++|| |..||.
T Consensus 25 ~~l~~C~~CG~~~--~~H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPK--LPHRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCcc--CCeEECCCCCc
Confidence 4557799998655 4466 777763
No 64
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.85 E-value=47 Score=31.51 Aligned_cols=26 Identities=27% Similarity=0.774 Sum_probs=21.7
Q ss_pred ceeccccCcccCCCCccCCccCcccc
Q 022535 124 IRYCRKCNQLKPPRCHHCSVCGRCIL 149 (295)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~rCV~ 149 (295)
+++|..|...+-+-+..|..||.=+-
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFT 26 (465)
T ss_pred CCcccccccccccccccccccCCcCC
Confidence 37899999999999999999887443
No 65
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=21.45 E-value=69 Score=17.66 Aligned_cols=19 Identities=37% Similarity=0.992 Sum_probs=9.6
Q ss_pred ccccCcccCCCC----ccCCccC
Q 022535 127 CRKCNQLKPPRC----HHCSVCG 145 (295)
Q Consensus 127 C~~C~~~kP~Rs----~HC~~C~ 145 (295)
|.+|...-.||- ..|..||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 455554444442 4466665
No 66
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.28 E-value=68 Score=18.83 Aligned_cols=7 Identities=43% Similarity=1.246 Sum_probs=3.1
Q ss_pred eeccccC
Q 022535 125 RYCRKCN 131 (295)
Q Consensus 125 ~~C~~C~ 131 (295)
-+|.+|+
T Consensus 17 ~~C~~C~ 23 (32)
T PF13842_consen 17 YMCSKCD 23 (32)
T ss_pred EEccCCC
Confidence 3444443
No 67
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=20.31 E-value=15 Score=28.18 Aligned_cols=26 Identities=31% Similarity=0.471 Sum_probs=21.5
Q ss_pred CCCceeccccCcccCCCCccCCccCc
Q 022535 121 NPRIRYCRKCNQLKPPRCHHCSVCGR 146 (295)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~r 146 (295)
+.+-..|.+|-..-|||+..|+.|..
T Consensus 90 ~~D~lICRkCYAR~g~~Ae~CRK~~~ 115 (128)
T KOG0003|consen 90 NCDKLICRKCYARLGPRAENCRKKKC 115 (128)
T ss_pred ccchHHHHHHHHhcCcHHHHhHHhhc
Confidence 34557899999999999999998753
No 68
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=20.21 E-value=35 Score=21.48 Aligned_cols=24 Identities=38% Similarity=0.894 Sum_probs=10.4
Q ss_pred eccccCcccCCCCccCCccCcccc
Q 022535 126 YCRKCNQLKPPRCHHCSVCGRCIL 149 (295)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~rCV~ 149 (295)
-|..|...+++...=|..-++|+.
T Consensus 6 sC~~C~~~~~~~C~Wc~~~~~C~~ 29 (46)
T smart00423 6 SCSECLLARDPYCAWCSSQGRCTS 29 (46)
T ss_pred cHHHHHcCCCCCCCccCCCCcccC
Confidence 355555555543333332244444
Done!