Query 021813
Match_columns 307
No_of_seqs 206 out of 1693
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:52:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021813.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021813hhsearch_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-57 4.6E-62 412.9 18.0 264 11-284 3-271 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 4E-50 8.7E-55 360.6 11.3 245 19-304 12-281 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 7E-44 1.5E-48 329.7 22.9 208 84-301 79-293 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 4.7E-41 1E-45 287.0 13.4 172 76-249 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 2E-39 4.3E-44 283.5 15.0 179 122-303 100-307 (309)
6 COG5273 Uncharacterized protei 100.0 1.4E-38 3E-43 293.3 15.7 222 63-304 58-306 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 3.3E-31 7.1E-36 233.1 10.3 103 73-188 110-212 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 1.1E-28 2.4E-33 238.0 7.8 177 76-271 383-585 (600)
9 PF01529 zf-DHHC: DHHC palmito 92.5 3 6.6E-05 34.8 11.9 57 119-186 57-113 (174)
10 KOG1311 DHHC-type Zn-finger pr 91.9 0.87 1.9E-05 42.1 8.4 44 137-180 112-166 (299)
11 COG5273 Uncharacterized protei 87.5 12 0.00026 35.0 12.2 32 122-153 121-152 (309)
12 PF13240 zinc_ribbon_2: zinc-r 86.3 0.42 9E-06 26.6 1.2 21 126-146 1-21 (23)
13 PRK04136 rpl40e 50S ribosomal 85.3 0.51 1.1E-05 31.1 1.3 25 122-146 12-36 (48)
14 PF13248 zf-ribbon_3: zinc-rib 77.8 1.3 2.9E-05 25.2 1.1 22 125-146 3-24 (26)
15 PTZ00303 phosphatidylinositol 77.2 1.5 3.3E-05 45.1 2.1 22 125-146 461-489 (1374)
16 KOG0509 Ankyrin repeat and DHH 71.4 2.4 5.1E-05 42.7 1.8 57 122-179 323-379 (600)
17 PF06906 DUF1272: Protein of u 69.9 2.1 4.6E-05 29.2 0.8 37 125-164 6-50 (57)
18 PF12773 DZR: Double zinc ribb 68.1 5.1 0.00011 26.3 2.4 35 123-157 11-48 (50)
19 PF01020 Ribosomal_L40e: Ribos 66.0 4.1 8.9E-05 27.3 1.5 25 123-147 16-42 (52)
20 COG1552 RPL40A Ribosomal prote 65.5 1.6 3.4E-05 28.9 -0.5 24 123-146 13-36 (50)
21 KOG1315 Predicted DHHC-type Zn 63.8 83 0.0018 29.4 10.2 30 137-166 108-137 (307)
22 PF10571 UPF0547: Uncharacteri 60.2 5.4 0.00012 22.8 1.1 22 125-146 1-22 (26)
23 PF00641 zf-RanBP: Zn-finger i 55.7 5.1 0.00011 23.4 0.6 21 126-146 6-26 (30)
24 PF12773 DZR: Double zinc ribb 54.5 9.6 0.00021 24.9 1.8 25 121-145 26-50 (50)
25 smart00064 FYVE Protein presen 52.4 11 0.00024 26.4 1.9 24 125-148 11-36 (68)
26 PF01363 FYVE: FYVE zinc finge 47.8 5.1 0.00011 28.2 -0.4 25 124-148 9-35 (69)
27 KOG3183 Predicted Zn-finger pr 44.0 11 0.00023 33.7 0.9 13 147-159 37-49 (250)
28 KOG1842 FYVE finger-containing 39.6 8.6 0.00019 37.3 -0.4 26 122-147 178-205 (505)
29 PF09297 zf-NADH-PPase: NADH p 39.1 13 0.00028 22.1 0.5 23 124-146 3-29 (32)
30 PF07649 C1_3: C1-like domain; 37.8 11 0.00025 21.9 0.1 21 126-146 2-23 (30)
31 PF02150 RNA_POL_M_15KD: RNA p 35.8 13 0.00028 22.8 0.1 7 125-131 2-8 (35)
32 KOG1314 DHHC-type Zn-finger pr 35.0 1.3E+02 0.0029 28.5 6.6 90 66-178 58-148 (414)
33 COG2093 DNA-directed RNA polym 34.3 22 0.00049 24.9 1.1 23 124-146 4-26 (64)
34 PHA02680 ORF090 IMV phosphoryl 33.0 2.1E+02 0.0046 21.5 7.0 25 225-249 60-84 (91)
35 cd00065 FYVE FYVE domain; Zinc 30.8 25 0.00054 23.4 0.9 24 125-148 3-28 (57)
36 PF07282 OrfB_Zn_ribbon: Putat 30.4 30 0.00066 24.1 1.4 26 122-147 26-55 (69)
37 PF03107 C1_2: C1 domain; Int 29.5 33 0.00073 20.0 1.2 20 126-145 2-22 (30)
38 PF00751 DM: DM DNA binding do 29.1 21 0.00045 23.6 0.3 15 145-159 12-28 (47)
39 smart00547 ZnF_RBZ Zinc finger 29.1 30 0.00065 19.2 0.9 21 126-146 4-24 (26)
40 PLN00186 ribosomal protein S26 28.8 22 0.00049 27.7 0.4 19 137-155 19-37 (109)
41 PF09889 DUF2116: Uncharacteri 28.8 80 0.0017 21.9 3.1 22 125-146 4-26 (59)
42 PRK09335 30S ribosomal protein 27.5 24 0.00052 26.9 0.4 21 137-157 19-39 (95)
43 PRK13130 H/ACA RNA-protein com 26.8 45 0.00098 22.9 1.6 22 123-146 4-25 (56)
44 PF08600 Rsm1: Rsm1-like; Int 25.7 33 0.00071 25.9 0.9 10 153-162 56-65 (91)
45 PTZ00172 40S ribosomal protein 25.5 27 0.00059 27.2 0.4 19 137-155 19-37 (108)
46 PRK03681 hypA hydrogenase nick 25.3 38 0.00083 26.6 1.2 25 122-146 68-95 (114)
47 KOG3611 Semaphorins [Signal tr 25.2 24 0.00053 36.9 0.1 39 138-176 491-537 (737)
48 KOG1398 Uncharacterized conser 24.5 33 0.00072 32.9 0.8 27 133-165 9-35 (460)
49 PF01437 PSI: Plexin repeat; 24.4 15 0.00032 24.3 -1.1 17 142-158 6-22 (51)
50 smart00661 RPOL9 RNA polymeras 23.8 38 0.00083 22.1 0.8 6 126-131 2-7 (52)
51 PF03842 Silic_transp: Silicon 23.6 7E+02 0.015 24.4 9.4 16 168-183 171-186 (512)
52 PRK00432 30S ribosomal protein 23.0 47 0.001 22.1 1.1 24 123-146 19-45 (50)
53 PRK12286 rpmF 50S ribosomal pr 23.0 58 0.0013 22.3 1.6 23 122-146 25-48 (57)
54 smart00423 PSI domain found in 22.5 32 0.00069 22.1 0.2 23 127-149 7-29 (46)
55 PF07010 Endomucin: Endomucin; 21.7 1.8E+02 0.0038 26.0 4.6 23 68-90 201-223 (259)
56 PRK14559 putative protein seri 21.5 64 0.0014 33.3 2.3 21 126-146 29-49 (645)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.1e-57 Score=412.94 Aligned_cols=264 Identities=40% Similarity=0.732 Sum_probs=207.3
Q ss_pred hhhhhccccccchhHHHHHHHHHHhhheeeEeeeecccccccCCCchHHHHHHHHHHHHHHHHHHHHHhHhcccCCCCCC
Q 021813 11 NVFKFCTALRGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVP 90 (307)
Q Consensus 11 ~~~~~~~~~r~~g~i~~~~v~~li~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~i~f~~l~~~~~~~y~~~~~~dPG~vp 90 (307)
+..++++..| +++++++.+.+++.||+++...+++....+ ..+.+.+++++.++++.+|+|++++++|||.+|
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 3344444445 889999999999999999998887755332 456677889999999999999999999999999
Q ss_pred CCCCCCchhhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCcccCcccccccccCccccccccccchHHH
Q 021813 91 PNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYF 170 (307)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F 170 (307)
.++.++.++++..+..............+.++..|+|.+|+.+|||||||||+|+|||+||||||||+|||||.+|||+|
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 99988765543322211110011122345577899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHhhcC
Q 021813 171 LLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYEKKT 250 (307)
Q Consensus 171 ~lFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~ 250 (307)
++|++|+.+.+.+..+.....+...+... ...++.....+++.+++.+.+++.+.+|+++|++||++|+||+|.++...
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 99999999999988887777777766222 22222333445555677788888888899999999999999999998753
Q ss_pred C-----CCCCCchhHHHHHhhhhCCCcccceeccccCcc
Q 021813 251 T-----PKWRYDLGRKKNFEQVFGTDKRYWFIPAYSDED 284 (307)
Q Consensus 251 ~-----~~~~yd~G~~~N~~~vfG~~~~~W~~P~~~~~~ 284 (307)
. ..+.++. ..|++|+||+++..|++|..++..
T Consensus 235 ~~~~~~~~~~~~~--~~n~~~vfg~~~~~wl~P~~~s~~ 271 (307)
T KOG1315|consen 235 FRSGLHNKNGFNL--YVNFREVFGSNLLYWLLPIDSSWG 271 (307)
T ss_pred ccccccccCCcce--eecHHHHhCCCceEEeccccCccc
Confidence 3 3344544 579999999999999999988754
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4e-50 Score=360.63 Aligned_cols=245 Identities=29% Similarity=0.547 Sum_probs=182.0
Q ss_pred cccchhHHHHHHHHHHhhheeeEeeeecccccccCCCchHHHHHHHHHHHHHHHHHHHHHhHhcccCCCCCCCCCCCCch
Q 021813 19 LRGLGSIMILLVLGVVGVTYYAVVLTNYGPALYDGGLDSVTAVAVLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALD 98 (307)
Q Consensus 19 ~r~~g~i~~~~v~~li~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~i~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~ 98 (307)
+..+|++..+.++.+++...-......|.| .++..+....+.|-....|++++|+.+++++||++|++|+|+..
T Consensus 12 ~~hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~ 85 (414)
T KOG1314|consen 12 FLHWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENP 85 (414)
T ss_pred eeccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Confidence 445788877777666655443333345556 45556667777788889999999999999999999999998542
Q ss_pred hhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCcccCcccccccccCccccccccccchHHHHHHHHHHH
Q 021813 99 EERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTF 178 (307)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~ 178 (307)
.+ ..-.+||.+|+.+|+||||||+.|||||++|||||||+|||||..||.||+.||++..
T Consensus 86 ~D--------------------~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~i 145 (414)
T KOG1314|consen 86 KD--------------------EMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSI 145 (414)
T ss_pred hh--------------------HHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHH
Confidence 21 2345899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH----HHh----cCCCCCC---CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHh
Q 021813 179 LETSLVTLSLLPHFI----SFF----SEGEIPG---TPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYE 247 (307)
Q Consensus 179 l~~~~~~~~~~~~~~----~~~----~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~ 247 (307)
++|+...+.+..+++ ..| .....+. +...++.+++++.++++..+.+..|++.|+..|.+|+|.||.+.
T Consensus 146 vG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi 225 (414)
T KOG1314|consen 146 VGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWI 225 (414)
T ss_pred HhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHH
Confidence 988764443332222 222 1111111 11223333444445555666677788899999999999999874
Q ss_pred hc--------------CCCCCCCchhHHHHHhhhhCCCcccceeccccCcccCCCCCCCCccCCCCCCCCC
Q 021813 248 KK--------------TTPKWRYDLGRKKNFEQVFGTDKRYWFIPAYSDEDIRKMPALQGLEYPSKPDFDS 304 (307)
Q Consensus 248 ~~--------------~~~~~~yd~G~~~N~~~vfG~~~~~W~~P~~~~~~~~~~~~~~G~~~~~~~~~~~ 304 (307)
.+ .....|||+|++.|+++||-.. ..+.|||.+||+.++|+|
T Consensus 226 ~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~---------------~~~~gdg~~wPv~~gc~q 281 (414)
T KOG1314|consen 226 VEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQN---------------KKEEGDGIEWPVVEGCVQ 281 (414)
T ss_pred HHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhc---------------cccCCCCccccccCcccc
Confidence 11 1234799999999999999854 225699999999999987
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=7e-44 Score=329.65 Aligned_cols=208 Identities=31% Similarity=0.584 Sum_probs=148.8
Q ss_pred cCCCCCCCCCCCCchhhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCcccCcccccccccCcccccccc
Q 021813 84 TDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVG 163 (307)
Q Consensus 84 ~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG 163 (307)
+|||.+|++..+..+. .++.+.. .....++...+.+||.+|+.+||||||||++||+||.||||||||+|||||
T Consensus 79 sdpg~~p~~~~~~~~~--~~~~~~~----~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG 152 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIED--PERAPLY----KNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIG 152 (299)
T ss_pred CCCceecCcccCCCCC--ccccccC----CCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceEC
Confidence 5999999753111111 1111111 112234556789999999999999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CC--CCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 021813 164 ALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGE--IP--GTPGTLATTFLAFVLNLAFALSVLGFLIMHISLVSAN 239 (307)
Q Consensus 164 ~~N~r~F~lFl~~~~l~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n 239 (307)
++|||+|+.|+++..+++++..+.....+........ .. ..+......++..++++.+...+++++.+|+++|.+|
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 9999999999999999888877766655554332211 11 1122222333334566667777778999999999999
Q ss_pred cchHHHHhh-cCCCC-CCCchhHHHHHhhhhCCCc-ccceeccccCcccCCCCCCCCccCCCCCC
Q 021813 240 TTTIEAYEK-KTTPK-WRYDLGRKKNFEQVFGTDK-RYWFIPAYSDEDIRKMPALQGLEYPSKPD 301 (307)
Q Consensus 240 ~Tt~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~~~-~~W~~P~~~~~~~~~~~~~~G~~~~~~~~ 301 (307)
+||+|.+++ +.+.. ++||.|..+|++++||.+. ..|.-|...+. ....||-.++..+.
T Consensus 233 ~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~~----~~p~~~~~~~~~~~ 293 (299)
T KOG1311|consen 233 STTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARSG----PLPHDGEGGPPTPH 293 (299)
T ss_pred cchhhhhhccccccccCCCchhHHHHHHHHhCCCCCcccccccccCC----CCCCCCCCCCcccc
Confidence 999999884 33334 8999999999999999985 57888876542 22246666654443
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=4.7e-41 Score=286.95 Aligned_cols=172 Identities=32% Similarity=0.626 Sum_probs=122.7
Q ss_pred HHHhHhcccCCCCCCCCCCCCchhhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCcccCcccccccccC
Q 021813 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHC 155 (307)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC 155 (307)
++|++++++|||++|+....+.+.+ .+ ..............+..++.++|.+|+..||+|||||+.||+||+||||||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC 79 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQ-EE-KEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHC 79 (174)
T ss_pred EEehhhheECCcccCCccccccccc-cc-cccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccc
Confidence 5688999999999997621111110 00 000001111122334577889999999999999999999999999999999
Q ss_pred ccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-CchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 021813 156 VWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTP-GTLATTFLAFVLNLAFALSVLGFLIMHIS 234 (307)
Q Consensus 156 pwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~l~~~h~~ 234 (307)
||+|||||++|||+|++|+++..+.+++.....+..+............. ......++.+++++++.++++.+++.|++
T Consensus 80 ~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 159 (174)
T PF01529_consen 80 PWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLY 159 (174)
T ss_pred hhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998887776665555543322111111 11111134445566777788889999999
Q ss_pred HHHhCcchHHHHhhc
Q 021813 235 LVSANTTTIEAYEKK 249 (307)
Q Consensus 235 li~~n~Tt~E~~~~~ 249 (307)
+|++|+||+|.++++
T Consensus 160 ~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 160 LILRNITTYERIKRK 174 (174)
T ss_pred HHHcCCcHHHHHHcC
Confidence 999999999999874
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2e-39 Score=283.46 Aligned_cols=179 Identities=31% Similarity=0.598 Sum_probs=131.2
Q ss_pred CCceeccccCcccCCCCCCCcccCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CC
Q 021813 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSE-GE 200 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~~~~~~~~~~~~~-~~ 200 (307)
+...+|.+|..+||||+||||.|||||++|||||||+|||||.+|||||++|++|+.+++.++.+......+..... .+
T Consensus 100 ~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~ 179 (309)
T KOG1313|consen 100 ENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEE 179 (309)
T ss_pred ccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhh
Confidence 34589999999999999999999999999999999999999999999999999999999998766544444432111 11
Q ss_pred CC---C------CCCch---------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHhhc--------CCCCC
Q 021813 201 IP---G------TPGTL---------ATTFLAFVLNLAFALSVLGFLIMHISLVSANTTTIEAYEKK--------TTPKW 254 (307)
Q Consensus 201 ~~---~------~~~~~---------~~~~l~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~--------~~~~~ 254 (307)
+. + .|... ....-+.+++..+.++++.+..||.++|.+|.|++|..... +...|
T Consensus 180 ~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~ 259 (309)
T KOG1313|consen 180 ITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSN 259 (309)
T ss_pred cccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCC
Confidence 11 0 11110 01112334556667777888999999999999999986431 12368
Q ss_pred CCchhHHHHHhhhhCCCc--ccceeccccCcccCCCCCCCCccCCCCCCCC
Q 021813 255 RYDLGRKKNFEQVFGTDK--RYWFIPAYSDEDIRKMPALQGLEYPSKPDFD 303 (307)
Q Consensus 255 ~yd~G~~~N~~~vfG~~~--~~W~~P~~~~~~~~~~~~~~G~~~~~~~~~~ 303 (307)
|++.|.+.||+.++|-.. -.|..-..|+ .+.|.+.|..++++|..|
T Consensus 260 ~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt---~~~p~~~~~~~~~~da~~ 307 (309)
T KOG1313|consen 260 PTNFGGKANWRNFLGLFRGRHFWKTVLLPT---IRKPVKYGDSKEKSDAYD 307 (309)
T ss_pred CcccchHHHHHHhhccccCCceeEEEeccc---cccccccCCcccccchhh
Confidence 999999999999999773 2454422222 234668999999777654
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=1.4e-38 Score=293.27 Aligned_cols=222 Identities=32% Similarity=0.573 Sum_probs=155.7
Q ss_pred HHHHHHHHHHHHHHHHhHhcccCCCCCCCCCCCCchhhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCc
Q 021813 63 VLILFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCS 142 (307)
Q Consensus 63 ~~i~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~ 142 (307)
..+.+.+...+...+|++.+++|||..+++-.....++..+ ....++..+..++|.+|+.+||||||||+
T Consensus 58 ~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~C~~C~~~KP~RS~HC~ 127 (309)
T COG5273 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETIS----------RLLDDGKFGTENFCSTCNIYKPPRSHHCS 127 (309)
T ss_pred hhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhh----------hhhhcCccccceeccccccccCCCCccch
Confidence 34455666778888999999999999985422211111111 11233556788999999999999999999
Q ss_pred ccCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCch-hHHHHH-HHHHHH
Q 021813 143 VCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTL-ATTFLA-FVLNLA 220 (307)
Q Consensus 143 ~C~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~-~~~~~~ 220 (307)
.|||||+||||||||+|||||++|||+|++|++++...+..+.+.....+..... ....+... ...+.+ ..+...
T Consensus 128 ~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~li~~~~~~~~~ 204 (309)
T COG5273 128 ICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFS---IRHDTSLAICFLIFGCSLLGVV 204 (309)
T ss_pred hhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc---ccCChHHHHHHHHHhhhHHHHH
Confidence 9999999999999999999999999999999999977776655544433333221 12222222 111111 233344
Q ss_pred HHHHHHHHHHHHHHHHHhCcchHHHHhhcCC------------C-------------CCCCchhHHHHHhhhhCCCcccc
Q 021813 221 FALSVLGFLIMHISLVSANTTTIEAYEKKTT------------P-------------KWRYDLGRKKNFEQVFGTDKRYW 275 (307)
Q Consensus 221 ~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~------------~-------------~~~yd~G~~~N~~~vfG~~~~~W 275 (307)
+.+.+..++.++.+++..|+||+|..+..+. . ..|++.|..+|+..++|.+...|
T Consensus 205 ~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~i~~~~~~~~ 284 (309)
T COG5273 205 FFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLSTIKGSNALYW 284 (309)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccceeecCCCceee
Confidence 4555667888999999999999998764321 1 24778888999999999999999
Q ss_pred eeccccCcccCCCCCCCCccCCCCCCCCC
Q 021813 276 FIPAYSDEDIRKMPALQGLEYPSKPDFDS 304 (307)
Q Consensus 276 ~~P~~~~~~~~~~~~~~G~~~~~~~~~~~ 304 (307)
..|...+. .++..++.+.+...
T Consensus 285 ~~~~~~~~-------~~~~~~~~~~~~~~ 306 (309)
T COG5273 285 LTPLHTNY-------CNSYDFSLRSDTLA 306 (309)
T ss_pred ccccccCC-------CCccCcccchhhcc
Confidence 99943321 37777777765443
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=3.3e-31 Score=233.08 Aligned_cols=103 Identities=32% Similarity=0.670 Sum_probs=78.1
Q ss_pred HHHHHHhHhcccCCCCCCCCCCCCchhhhccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCcccCccccccc
Q 021813 73 MLLWSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMD 152 (307)
Q Consensus 73 ~~~~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 152 (307)
+-..++..++.+|||.+.+. ...+..++.|.+..- ......|+||+..||.||||||.|||||.|+|
T Consensus 110 vp~i~f~ltc~snpg~i~k~----n~s~~~~~ypYDy~i---------f~k~~kCSTCki~KPARSKHCsiCNrCV~rfD 176 (341)
T KOG1312|consen 110 VPLIFFTLTCGSNPGIITKA----NESLFLHVYPYDYVI---------FPKNVKCSTCKIRKPARSKHCSICNRCVHRFD 176 (341)
T ss_pred HHHHHHhhhhcCCCCccchh----hhccceeccCcccee---------ecCCCccccccCCCccccccchHHHHHHHHhc
Confidence 33445678899999999742 111222333332211 22236899999999999999999999999999
Q ss_pred ccCccccccccccchHHHHHHHHHHHHHHHHHHHHH
Q 021813 153 HHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSL 188 (307)
Q Consensus 153 HHCpwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~~~ 188 (307)
|||.|+|||||.+|.|||++||++...++.++.+.+
T Consensus 177 HHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrl 212 (341)
T KOG1312|consen 177 HHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRL 212 (341)
T ss_pred cceEeeecccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999876666655443
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=1.1e-28 Score=237.99 Aligned_cols=177 Identities=25% Similarity=0.373 Sum_probs=110.0
Q ss_pred HHHhHhcccCCCCCCCCCCCCchhhhccCCCCCccccCCCcCCCCCCCc-eeccccCcccCCCCCCCcccCccccccccc
Q 021813 76 WSYFSVVLTDAGSVPPNWRPALDEERGEADPLNASEFSGAQSDPLNPRI-RYCRKCNQLKPPRCHHCSVCGRCILKMDHH 154 (307)
Q Consensus 76 ~~y~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHH 154 (307)
.++.+..-+|||.+|..-... .+... ++ .+.++.+.. +||.+|.+.||.|||||++|||||.|||||
T Consensus 383 ~~f~~~~rsDPg~i~~~~~~~--~~tIs--~l--------~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHh 450 (600)
T KOG0509|consen 383 ITFGLFLRSDPGFIPTSTEVG--RETIS--QL--------IDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHH 450 (600)
T ss_pred HHHHHHhccCCCCCCCchhhH--HHHHH--Hh--------hccccccccccceeeeeeecCCccchhhhhHHHHhccccC
Confidence 344555569999998531111 00000 00 111223333 799999999999999999999999999999
Q ss_pred CccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHH---------H---
Q 021813 155 CVWVVNCVGALNYKYFLLFLLYTFLETSLVTLSLLPHFISFFSEGEIPGTPGTLATTFLAFVLNLAF---------A--- 222 (307)
Q Consensus 155 Cpwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---------~--- 222 (307)
|||++||||.+|||+|+.|++.....+.+.+......+.. .+... ... ..++.++..+.. .
T Consensus 451 CPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~----~~~~~--~~~-~~~l~~~~~~~~~~~~~~~~~~n~~ 523 (600)
T KOG0509|consen 451 CPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMN----LENAS--TIY-VGFLIAVQAFRIPKPVTGNLLGNED 523 (600)
T ss_pred CCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhh----cchhH--HHH-HHHHHHHHHHhCCccceeeeeeccc
Confidence 9999999999999999999998877666555443322221 11100 000 001111100000 0
Q ss_pred ---HHHH-HHHHHHHHHHHhCcchHHHHhhcC---------CCCCCCchhHHHHHhhhhCCC
Q 021813 223 ---LSVL-GFLIMHISLVSANTTTIEAYEKKT---------TPKWRYDLGRKKNFEQVFGTD 271 (307)
Q Consensus 223 ---~~~~-~l~~~h~~li~~n~Tt~E~~~~~~---------~~~~~yd~G~~~N~~~vfG~~ 271 (307)
.... .-...|-..++.+.||+|.++..+ ..++|++.|+++|+.+++-.+
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 0000 011223345889999999986532 246899999999999988755
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=92.49 E-value=3 Score=34.83 Aligned_cols=57 Identities=33% Similarity=0.553 Sum_probs=40.2
Q ss_pred CCCCCceeccccCcccCCCCCCCcccCcccccccccCccccccccccchHHHHHHHHHHHHHHHHHHH
Q 021813 119 PLNPRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFLETSLVTL 186 (307)
Q Consensus 119 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~l~~~~~~~ 186 (307)
....+.++|+.|+.--..+-|||.--|.||.+-.| +-+=.|+++..-..+.......
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 34567788999988888888999999999888776 3344666666555555544333
No 10
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=91.87 E-value=0.87 Score=42.10 Aligned_cols=44 Identities=23% Similarity=0.480 Sum_probs=38.2
Q ss_pred CCCCCcccCcccccccccCccccccccccch-----------HHHHHHHHHHHHH
Q 021813 137 RCHHCSVCGRCILKMDHHCVWVVNCVGALNY-----------KYFLLFLLYTFLE 180 (307)
Q Consensus 137 Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~-----------r~F~lFl~~~~l~ 180 (307)
+.++|+.|+..+...-|||+.-|+||-+.-| |-+-.|+.++...
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~ 166 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYL 166 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHH
Confidence 4899999999999999999999999988765 7788999766633
No 11
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=87.47 E-value=12 Score=34.96 Aligned_cols=32 Identities=28% Similarity=0.506 Sum_probs=17.1
Q ss_pred CCceeccccCcccCCCCCCCcccCcccccccc
Q 021813 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDH 153 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DH 153 (307)
++.+.|+.|+.=-...-|||.-=|+||-+-.|
T Consensus 121 ~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~ 152 (309)
T COG5273 121 PRSHHCSICNRCVLKFDHHCPWINNCVGFRNY 152 (309)
T ss_pred CCCccchhhcchhhccCccCcccccccCcchH
Confidence 34455555555555555555555555555444
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.30 E-value=0.42 Score=26.60 Aligned_cols=21 Identities=29% Similarity=0.842 Sum_probs=18.2
Q ss_pred eccccCcccCCCCCCCcccCc
Q 021813 126 YCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
+|..|...-++.+..|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688999888899999999875
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=85.25 E-value=0.51 Score=31.11 Aligned_cols=25 Identities=32% Similarity=0.754 Sum_probs=22.1
Q ss_pred CCceeccccCcccCCCCCCCcccCc
Q 021813 122 PRIRYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
.....|.+|...-|+||..|+.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3457899999999999999999875
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=77.83 E-value=1.3 Score=25.24 Aligned_cols=22 Identities=27% Similarity=0.854 Sum_probs=18.4
Q ss_pred eeccccCcccCCCCCCCcccCc
Q 021813 125 RYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
++|..|...-++.++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6788998877888888988875
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=77.19 E-value=1.5 Score=45.13 Aligned_cols=22 Identities=36% Similarity=0.880 Sum_probs=18.4
Q ss_pred eeccccCcccC-------CCCCCCcccCc
Q 021813 125 RYCRKCNQLKP-------PRCHHCSVCGR 146 (307)
Q Consensus 125 ~~C~~C~~~kP-------~Rs~HC~~C~~ 146 (307)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 67999997664 39999999987
No 16
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=71.39 E-value=2.4 Score=42.67 Aligned_cols=57 Identities=7% Similarity=-0.102 Sum_probs=48.3
Q ss_pred CCceeccccCcccCCCCCCCcccCcccccccccCccccccccccchHHHHHHHHHHHH
Q 021813 122 PRIRYCRKCNQLKPPRCHHCSVCGRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTFL 179 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~l 179 (307)
.-...|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-..|.+..+...+
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l 379 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVL 379 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHH
Confidence 34577899999999999999999999999999999999 9999998877655444333
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=69.92 E-value=2.1 Score=29.20 Aligned_cols=37 Identities=32% Similarity=0.859 Sum_probs=28.3
Q ss_pred eeccccCcccCCCC-------CCCcccCcccccc-cccCccccccccc
Q 021813 125 RYCRKCNQLKPPRC-------HHCSVCGRCILKM-DHHCVWVVNCVGA 164 (307)
Q Consensus 125 ~~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHHCpwi~nCIG~ 164 (307)
.-|..|+.--|+-| +-|..|..|+..+ +++|| ||=|.
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 34777776666654 6788999999999 99998 77664
No 18
>PF12773 DZR: Double zinc ribbon
Probab=68.09 E-value=5.1 Score=26.31 Aligned_cols=35 Identities=20% Similarity=0.485 Sum_probs=22.2
Q ss_pred CceeccccCcccC---CCCCCCcccCcccccccccCcc
Q 021813 123 RIRYCRKCNQLKP---PRCHHCSVCGRCILKMDHHCVW 157 (307)
Q Consensus 123 ~~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHHCpw 157 (307)
..++|..|...-+ .....|+.|+.=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 3467777766554 3355677777766666666653
No 19
>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=65.96 E-value=4.1 Score=27.35 Aligned_cols=25 Identities=40% Similarity=0.931 Sum_probs=17.1
Q ss_pred CceeccccCcccCCCCCCCcc--cCcc
Q 021813 123 RIRYCRKCNQLKPPRCHHCSV--CGRC 147 (307)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 147 (307)
....|.+|...-||||..|+. ||.+
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 458899999999999999998 8765
No 20
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=65.48 E-value=1.6 Score=28.88 Aligned_cols=24 Identities=38% Similarity=1.029 Sum_probs=21.3
Q ss_pred CceeccccCcccCCCCCCCcccCc
Q 021813 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
..+.|.+|...-|+|+..|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 457899999999999999998864
No 21
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=63.79 E-value=83 Score=29.36 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=16.5
Q ss_pred CCCCCcccCcccccccccCccccccccccc
Q 021813 137 RCHHCSVCGRCILKMDHHCVWVVNCVGALN 166 (307)
Q Consensus 137 Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~N 166 (307)
+.+-|..|+.-....-|||.--+.||.+.-
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmD 137 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMD 137 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccc
Confidence 444555555555555555555555555443
No 22
>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=60.23 E-value=5.4 Score=22.83 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=17.5
Q ss_pred eeccccCcccCCCCCCCcccCc
Q 021813 125 RYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
+.|..|...-|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4588888888888888888874
No 23
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=55.72 E-value=5.1 Score=23.43 Aligned_cols=21 Identities=29% Similarity=0.882 Sum_probs=15.2
Q ss_pred eccccCcccCCCCCCCcccCc
Q 021813 126 YCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
.|..|...-++++.+|..|+.
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 24
>PF12773 DZR: Double zinc ribbon
Probab=54.53 E-value=9.6 Score=24.93 Aligned_cols=25 Identities=28% Similarity=0.894 Sum_probs=21.6
Q ss_pred CCCceeccccCcccCCCCCCCcccC
Q 021813 121 NPRIRYCRKCNQLKPPRCHHCSVCG 145 (307)
Q Consensus 121 ~~~~~~C~~C~~~kP~Rs~HC~~C~ 145 (307)
.....+|..|....++.++.|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456899999999999999999986
No 25
>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 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=47.82 E-value=5.1 Score=28.22 Aligned_cols=25 Identities=36% Similarity=0.790 Sum_probs=12.2
Q ss_pred ceeccccCcc--cCCCCCCCcccCccc
Q 021813 124 IRYCRKCNQL--KPPRCHHCSVCGRCI 148 (307)
Q Consensus 124 ~~~C~~C~~~--kP~Rs~HC~~C~~CV 148 (307)
...|..|... --.|-|||+.||+-|
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 4678888632 237899999999854
No 27
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=44.04 E-value=11 Score=33.68 Aligned_cols=13 Identities=23% Similarity=0.189 Sum_probs=10.4
Q ss_pred ccccccccCcccc
Q 021813 147 CILKMDHHCVWVV 159 (307)
Q Consensus 147 CV~~~DHHCpwi~ 159 (307)
=..+.+|||||..
T Consensus 37 Hrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 37 HRSYESHHCPKGL 49 (250)
T ss_pred cchHhhcCCCccc
Confidence 3578899999875
No 28
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=39.61 E-value=8.6 Score=37.30 Aligned_cols=26 Identities=35% Similarity=1.012 Sum_probs=20.0
Q ss_pred CCceeccccCcc--cCCCCCCCcccCcc
Q 021813 122 PRIRYCRKCNQL--KPPRCHHCSVCGRC 147 (307)
Q Consensus 122 ~~~~~C~~C~~~--kP~Rs~HC~~C~~C 147 (307)
....+|..|... ---|-|||+.||+-
T Consensus 178 s~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred CcccccccccchhhhHHHhhhhhhcchH
Confidence 457899999743 24589999999983
No 29
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=39.12 E-value=13 Score=22.13 Aligned_cols=23 Identities=26% Similarity=0.813 Sum_probs=10.8
Q ss_pred ceeccccCcc----cCCCCCCCcccCc
Q 021813 124 IRYCRKCNQL----KPPRCHHCSVCGR 146 (307)
Q Consensus 124 ~~~C~~C~~~----kP~Rs~HC~~C~~ 146 (307)
.+||..|... .-.++..|..|+.
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 3788888742 2345666666653
No 30
>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=37.75 E-value=11 Score=21.92 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=8.2
Q ss_pred eccccCcccCC-CCCCCcccCc
Q 021813 126 YCRKCNQLKPP-RCHHCSVCGR 146 (307)
Q Consensus 126 ~C~~C~~~kP~-Rs~HC~~C~~ 146 (307)
.|..|+..... ...+|+.|+-
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 6777887764
No 31
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=35.78 E-value=13 Score=22.82 Aligned_cols=7 Identities=43% Similarity=1.592 Sum_probs=4.1
Q ss_pred eeccccC
Q 021813 125 RYCRKCN 131 (307)
Q Consensus 125 ~~C~~C~ 131 (307)
++|.+|.
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 5677775
No 32
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=35.04 E-value=1.3e+02 Score=28.54 Aligned_cols=90 Identities=22% Similarity=0.236 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHhHhcccCCCCCCCCCCCCchhhh-ccCCCCCccccCCCcCCCCCCCceeccccCcccCCCCCCCccc
Q 021813 66 LFHCLLVMLLWSYFSVVLTDAGSVPPNWRPALDEER-GEADPLNASEFSGAQSDPLNPRIRYCRKCNQLKPPRCHHCSVC 144 (307)
Q Consensus 66 ~f~~l~~~~~~~y~~~~~~dPG~vp~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C 144 (307)
.+.+++..+...+.--=+..||.-|++-. +..-.+ -..-+ .-+.++...|++|+.=--.=-|||.--
T Consensus 58 ~~m~~~ny~~A~~~gPG~vp~~wkPe~~~-D~~~lqfCk~Cq-----------gYKapRSHHCrkCnrCvmkMDHHCPWi 125 (414)
T KOG1314|consen 58 TSMILYNYFNAIFTGPGFVPLGWKPENPK-DEMFLQFCKKCQ-----------GYKAPRSHHCRKCNRCVMKMDHHCPWI 125 (414)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCCCCCCCh-hHHHHHHHhhcc-----------CcCCCccccchHHHHHHHhhccCCcch
Confidence 34445555555667788999999986532 222111 01000 011245588999986555556999999
Q ss_pred CcccccccccCccccccccccchHHHHHHHHHHH
Q 021813 145 GRCILKMDHHCVWVVNCVGALNYKYFLLFLLYTF 178 (307)
Q Consensus 145 ~~CV~~~DHHCpwi~nCIG~~N~r~F~lFl~~~~ 178 (307)
|.||---.| .-.-+|++|...+.
T Consensus 126 nnCVG~aNh-----------~~F~~FLlf~ivG~ 148 (414)
T KOG1314|consen 126 NNCVGWANH-----------AYFLRFLLFSIVGC 148 (414)
T ss_pred hhccccccc-----------HHHHHHHHHHHHhc
Confidence 999986555 44678999888744
No 33
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=34.25 E-value=22 Score=24.86 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=20.3
Q ss_pred ceeccccCcccCCCCCCCcccCc
Q 021813 124 IRYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 124 ~~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
.+-|..|+..-|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 36699999999999999999986
No 34
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=32.99 E-value=2.1e+02 Score=21.46 Aligned_cols=25 Identities=12% Similarity=0.325 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhCcchHHHHhhc
Q 021813 225 VLGFLIMHISLVSANTTTIEAYEKK 249 (307)
Q Consensus 225 ~~~l~~~h~~li~~n~Tt~E~~~~~ 249 (307)
+++++++..|-=+++.++.|++++.
T Consensus 60 ~lGilifs~y~~C~~~~~~~r~n~s 84 (91)
T PHA02680 60 LLGLFVFSMYRKCSGSMPYERLNNT 84 (91)
T ss_pred HHHHHHHHHhcccCCCceeecccCC
Confidence 4456677777677788888877553
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=30.82 E-value=25 Score=23.43 Aligned_cols=24 Identities=38% Similarity=0.862 Sum_probs=16.0
Q ss_pred eeccccCc--ccCCCCCCCcccCccc
Q 021813 125 RYCRKCNQ--LKPPRCHHCSVCGRCI 148 (307)
Q Consensus 125 ~~C~~C~~--~kP~Rs~HC~~C~~CV 148 (307)
+-|..|.. -.-.|.|||+.|++-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 34666653 2356889999998843
No 36
>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=30.40 E-value=30 Score=24.15 Aligned_cols=26 Identities=23% Similarity=0.567 Sum_probs=18.8
Q ss_pred CCceeccccCccc----CCCCCCCcccCcc
Q 021813 122 PRIRYCRKCNQLK----PPRCHHCSVCGRC 147 (307)
Q Consensus 122 ~~~~~C~~C~~~k----P~Rs~HC~~C~~C 147 (307)
...+.|+.|.... ..|.++|..||.-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCCE
Confidence 3568899997554 4577788888764
No 37
>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=29.50 E-value=33 Score=19.99 Aligned_cols=20 Identities=30% Similarity=0.692 Sum_probs=12.3
Q ss_pred eccccCcccCCC-CCCCcccC
Q 021813 126 YCRKCNQLKPPR-CHHCSVCG 145 (307)
Q Consensus 126 ~C~~C~~~kP~R-s~HC~~C~ 145 (307)
.|..|...-... .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 366666555555 67776666
No 38
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=29.12 E-value=21 Score=23.57 Aligned_cols=15 Identities=20% Similarity=0.293 Sum_probs=6.3
Q ss_pred Ccccccccc--cCcccc
Q 021813 145 GRCILKMDH--HCVWVV 159 (307)
Q Consensus 145 ~~CV~~~DH--HCpwi~ 159 (307)
|.=+..-+| +|||-+
T Consensus 12 G~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 12 GVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp T---TTTT-GGG-TTTT
T ss_pred CcccchhhhccccCcCC
Confidence 445666666 688764
No 39
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=29.09 E-value=30 Score=19.16 Aligned_cols=21 Identities=29% Similarity=0.675 Sum_probs=16.0
Q ss_pred eccccCcccCCCCCCCcccCc
Q 021813 126 YCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477888888888888887764
No 40
>PLN00186 ribosomal protein S26; Provisional
Probab=28.82 E-value=22 Score=27.67 Aligned_cols=19 Identities=32% Similarity=0.674 Sum_probs=14.0
Q ss_pred CCCCCcccCcccccccccC
Q 021813 137 RCHHCSVCGRCILKMDHHC 155 (307)
Q Consensus 137 Rs~HC~~C~~CV~~~DHHC 155 (307)
+.-||..|++||++=---+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIK 37 (109)
T ss_pred cceeeCCCcccccccceEE
Confidence 4568999999999744433
No 41
>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=28.80 E-value=80 Score=21.87 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=12.7
Q ss_pred eeccccCcccCCCCCCCc-ccCc
Q 021813 125 RYCRKCNQLKPPRCHHCS-VCGR 146 (307)
Q Consensus 125 ~~C~~C~~~kP~Rs~HC~-~C~~ 146 (307)
+.|..|...-|+--..|| .|++
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 556666666666555564 4544
No 42
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=27.47 E-value=24 Score=26.85 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=16.0
Q ss_pred CCCCCcccCcccccccccCcc
Q 021813 137 RCHHCSVCGRCILKMDHHCVW 157 (307)
Q Consensus 137 Rs~HC~~C~~CV~~~DHHCpw 157 (307)
+.-+|..|++||++----+.+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEE
Confidence 455899999999986665543
No 43
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.75 E-value=45 Score=22.86 Aligned_cols=22 Identities=41% Similarity=0.895 Sum_probs=17.2
Q ss_pred CceeccccCcccCCCCCCCcccCc
Q 021813 123 RIRYCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 123 ~~~~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
..+.|..|.++-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 5688999988877 777888875
No 44
>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=25.74 E-value=33 Score=25.85 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=8.0
Q ss_pred ccCccccccc
Q 021813 153 HHCVWVVNCV 162 (307)
Q Consensus 153 HHCpwi~nCI 162 (307)
.||||++.-.
T Consensus 56 ~~CPwv~~~~ 65 (91)
T PF08600_consen 56 EYCPWVNPST 65 (91)
T ss_pred ccCCccCCcc
Confidence 6899998754
No 45
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=25.48 E-value=27 Score=27.21 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=14.0
Q ss_pred CCCCCcccCcccccccccC
Q 021813 137 RCHHCSVCGRCILKMDHHC 155 (307)
Q Consensus 137 Rs~HC~~C~~CV~~~DHHC 155 (307)
+.-||..|++||++=---+
T Consensus 19 ~~V~C~nCgr~vPKDKAIk 37 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIK 37 (108)
T ss_pred ccEEeCCccccccccceEE
Confidence 4558999999999744444
No 46
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.33 E-value=38 Score=26.62 Aligned_cols=25 Identities=20% Similarity=0.530 Sum_probs=17.9
Q ss_pred CCceeccccCcccCCCCCC---CcccCc
Q 021813 122 PRIRYCRKCNQLKPPRCHH---CSVCGR 146 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H---C~~C~~ 146 (307)
...-+|..|+..-|...++ |..|+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 3457899999877765444 888874
No 47
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=25.18 E-value=24 Score=36.90 Aligned_cols=39 Identities=26% Similarity=0.548 Sum_probs=30.5
Q ss_pred CCCCc---ccCcccccccccCcccc---ccc--cccchHHHHHHHHH
Q 021813 138 CHHCS---VCGRCILKMDHHCVWVV---NCV--GALNYKYFLLFLLY 176 (307)
Q Consensus 138 s~HC~---~C~~CV~~~DHHCpwi~---nCI--G~~N~r~F~lFl~~ 176 (307)
-|+|+ .|..|++..|-||.|-+ .|+ +..|.|.+.+=+-.
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~~ 537 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVSS 537 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhcc
Confidence 46788 89998888999999998 687 45577777776543
No 48
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.46 E-value=33 Score=32.90 Aligned_cols=27 Identities=41% Similarity=0.817 Sum_probs=19.9
Q ss_pred ccCCCCCCCcccCcccccccccCcccccccccc
Q 021813 133 LKPPRCHHCSVCGRCILKMDHHCVWVVNCVGAL 165 (307)
Q Consensus 133 ~kP~Rs~HC~~C~~CV~~~DHHCpwi~nCIG~~ 165 (307)
.+-.|..||..|+. .|| +|..||||.-
T Consensus 9 ~sl~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 9 RSLARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred hhhcCchHhhhhhh----ccC--CcccchhHHH
Confidence 34556677777765 677 8999999964
No 49
>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=24.42 E-value=15 Score=24.33 Aligned_cols=17 Identities=29% Similarity=0.913 Sum_probs=10.3
Q ss_pred cccCcccccccccCccc
Q 021813 142 SVCGRCILKMDHHCVWV 158 (307)
Q Consensus 142 ~~C~~CV~~~DHHCpwi 158 (307)
..|+.|+.-.|-+|.|-
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 50
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.79 E-value=38 Score=22.06 Aligned_cols=6 Identities=50% Similarity=1.708 Sum_probs=2.8
Q ss_pred eccccC
Q 021813 126 YCRKCN 131 (307)
Q Consensus 126 ~C~~C~ 131 (307)
+|..|.
T Consensus 2 FCp~Cg 7 (52)
T smart00661 2 FCPKCG 7 (52)
T ss_pred CCCCCC
Confidence 444454
No 51
>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=23.64 E-value=7e+02 Score=24.44 Aligned_cols=16 Identities=38% Similarity=0.791 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHH
Q 021813 168 KYFLLFLLYTFLETSL 183 (307)
Q Consensus 168 r~F~lFl~~~~l~~~~ 183 (307)
-||.+|.+|+.+..-+
T Consensus 171 nyFalFTlyvam~IEf 186 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEF 186 (512)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4899999998776544
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.02 E-value=47 Score=22.11 Aligned_cols=24 Identities=25% Similarity=0.845 Sum_probs=14.6
Q ss_pred CceeccccCc-ccC--CCCCCCcccCc
Q 021813 123 RIRYCRKCNQ-LKP--PRCHHCSVCGR 146 (307)
Q Consensus 123 ~~~~C~~C~~-~kP--~Rs~HC~~C~~ 146 (307)
..++|+.|.. .-. ....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3468999976 221 23556777763
No 53
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.95 E-value=58 Score=22.34 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=15.8
Q ss_pred CCceeccccCcccCCCCCC-CcccCc
Q 021813 122 PRIRYCRKCNQLKPPRCHH-CSVCGR 146 (307)
Q Consensus 122 ~~~~~C~~C~~~kP~Rs~H-C~~C~~ 146 (307)
.....|..|...+ ++|| |..||-
T Consensus 25 ~~l~~C~~CG~~~--~~H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPK--LPHRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCcc--CCeEECCCCCc
Confidence 4456799998665 4466 777764
No 54
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=22.46 E-value=32 Score=22.06 Aligned_cols=23 Identities=39% Similarity=0.960 Sum_probs=10.0
Q ss_pred ccccCcccCCCCCCCcccCcccc
Q 021813 127 CRKCNQLKPPRCHHCSVCGRCIL 149 (307)
Q Consensus 127 C~~C~~~kP~Rs~HC~~C~~CV~ 149 (307)
|..|...+++...-|..-++|+.
T Consensus 7 C~~C~~~~~~~C~Wc~~~~~C~~ 29 (46)
T smart00423 7 CSECLLARDPYCAWCSSQGRCTS 29 (46)
T ss_pred HHHHHcCCCCCCCccCCCCcccC
Confidence 55555554443333333344444
No 55
>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=21.69 E-value=1.8e+02 Score=25.99 Aligned_cols=23 Identities=22% Similarity=0.131 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHhHhcccCCCCCC
Q 021813 68 HCLLVMLLWSYFSVVLTDAGSVP 90 (307)
Q Consensus 68 ~~l~~~~~~~y~~~~~~dPG~vp 90 (307)
.++.+.++-.|.+|.-.|||...
T Consensus 201 tl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 201 TLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHhhcCCCCCcc
Confidence 33445555667889999999643
No 56
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.51 E-value=64 Score=33.33 Aligned_cols=21 Identities=33% Similarity=0.814 Sum_probs=10.2
Q ss_pred eccccCcccCCCCCCCcccCc
Q 021813 126 YCRKCNQLKPPRCHHCSVCGR 146 (307)
Q Consensus 126 ~C~~C~~~kP~Rs~HC~~C~~ 146 (307)
.|..|...-|+.+++|..||.
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred cCCCCCCCCCcccccccccCC
Confidence 344444444445555555444
Done!