Query 022225
Match_columns 300
No_of_seqs 187 out of 1693
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:58:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022225hhsearch_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 5.3E-59 1.1E-63 416.7 17.6 265 4-286 5-272 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 1.2E-50 2.6E-55 357.8 13.6 239 14-300 14-276 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 1E-43 2.2E-48 324.2 23.3 166 118-283 107-278 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 3.7E-41 8.1E-46 284.0 13.2 173 69-250 2-174 (174)
5 KOG1313 DHHC-type Zn-finger pr 100.0 1.1E-39 2.4E-44 280.1 16.1 174 123-299 101-302 (309)
6 COG5273 Uncharacterized protei 100.0 8.5E-39 1.8E-43 290.3 18.1 217 55-299 57-300 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 9.9E-31 2.1E-35 226.1 12.4 105 64-188 108-212 (341)
8 KOG0509 Ankyrin repeat and DHH 99.9 1.8E-27 3.9E-32 226.0 8.8 144 121-272 416-585 (600)
9 KOG1311 DHHC-type Zn-finger pr 93.3 0.34 7.4E-06 44.2 7.6 58 137-194 112-180 (299)
10 PF01529 zf-DHHC: DHHC palmito 92.2 3.2 6.9E-05 34.2 11.5 53 120-183 58-110 (174)
11 PF13240 zinc_ribbon_2: zinc-r 84.1 0.61 1.3E-05 25.4 1.1 21 126-146 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 83.1 0.65 1.4E-05 30.0 1.1 25 122-146 12-36 (48)
13 PF13248 zf-ribbon_3: zinc-rib 78.0 1.3 2.8E-05 24.7 1.1 23 124-146 2-24 (26)
14 PTZ00303 phosphatidylinositol 76.2 1.4 3.1E-05 44.7 1.6 23 124-146 460-489 (1374)
15 COG5273 Uncharacterized protei 74.9 52 0.0011 30.3 11.3 30 137-166 108-137 (309)
16 KOG0509 Ankyrin repeat and DHH 70.3 3.4 7.5E-05 40.9 2.6 54 122-176 323-376 (600)
17 PF06906 DUF1272: Protein of u 68.3 2.8 6.1E-05 28.1 1.1 36 126-164 7-50 (57)
18 PF12773 DZR: Double zinc ribb 65.0 5.9 0.00013 25.6 2.2 33 124-156 12-47 (50)
19 PF01363 FYVE: FYVE zinc finge 64.6 2.2 4.7E-05 29.7 0.0 26 123-148 8-35 (69)
20 COG1552 RPL40A Ribosomal prote 62.6 1.6 3.6E-05 28.2 -0.8 25 122-146 12-36 (50)
21 PF01020 Ribosomal_L40e: Ribos 59.8 4 8.6E-05 26.9 0.6 25 123-147 16-42 (52)
22 smart00064 FYVE Protein presen 59.2 6.2 0.00013 27.2 1.6 24 125-148 11-36 (68)
23 PF10571 UPF0547: Uncharacteri 58.6 5.3 0.00011 22.4 0.9 22 125-146 1-22 (26)
24 PF12773 DZR: Double zinc ribb 54.4 8.9 0.00019 24.7 1.6 25 121-145 26-50 (50)
25 KOG1842 FYVE finger-containing 52.3 4 8.7E-05 38.9 -0.4 28 121-148 177-206 (505)
26 KOG1315 Predicted DHHC-type Zn 50.0 2.1E+02 0.0045 26.3 13.7 52 137-188 108-170 (307)
27 KOG3183 Predicted Zn-finger pr 44.2 8.8 0.00019 33.6 0.4 16 145-160 35-50 (250)
28 PF00641 zf-RanBP: Zn-finger i 44.0 6.9 0.00015 22.4 -0.2 22 125-146 5-26 (30)
29 cd00065 FYVE FYVE domain; Zinc 38.7 18 0.0004 23.7 1.3 22 126-147 4-27 (57)
30 TIGR02745 ccoG_rdxA_fixG cytoc 37.0 81 0.0018 30.5 5.8 10 140-149 256-265 (434)
31 CHL00031 psbT photosystem II p 36.5 75 0.0016 18.8 3.4 16 69-84 16-31 (33)
32 PF07649 C1_3: C1-like domain; 36.4 9.6 0.00021 21.8 -0.4 21 126-146 2-23 (30)
33 PF03842 Silic_transp: Silicon 36.1 3.9E+02 0.0084 25.8 9.7 16 168-183 171-186 (512)
34 PRK11875 psbT photosystem II r 35.0 96 0.0021 18.1 3.6 15 69-83 16-30 (31)
35 PF00751 DM: DM DNA binding do 34.1 20 0.00043 23.2 0.8 22 138-159 2-28 (47)
36 PF03107 C1_2: C1 domain; Int 33.5 21 0.00044 20.5 0.7 20 126-145 2-22 (30)
37 PF02150 RNA_POL_M_15KD: RNA p 33.5 8.6 0.00019 23.1 -0.9 7 125-131 2-8 (35)
38 COG2093 DNA-directed RNA polym 31.9 23 0.00049 24.3 0.8 23 124-146 4-26 (64)
39 PF07010 Endomucin: Endomucin; 30.7 1.2E+02 0.0026 26.6 5.1 26 58-83 198-223 (259)
40 KOG1818 Membrane trafficking a 30.5 20 0.00044 36.0 0.6 25 122-146 163-189 (634)
41 PF07282 OrfB_Zn_ribbon: Putat 30.3 25 0.00054 24.2 0.9 27 121-147 25-55 (69)
42 PF01437 PSI: Plexin repeat; 30.0 18 0.00039 23.5 0.1 18 142-159 6-23 (51)
43 PF08600 Rsm1: Rsm1-like; Int 29.1 22 0.00048 26.3 0.5 39 124-162 19-65 (91)
44 KOG1841 Smad anchor for recept 28.9 27 0.0006 37.3 1.2 40 123-174 556-597 (1287)
45 PRK03681 hypA hydrogenase nick 26.7 29 0.00063 26.9 0.7 25 122-146 68-95 (114)
46 smart00661 RPOL9 RNA polymeras 26.6 26 0.00056 22.5 0.4 6 126-131 2-7 (52)
47 smart00423 PSI domain found in 26.5 37 0.00081 21.3 1.1 17 142-158 5-21 (46)
48 COG0603 Predicted PP-loop supe 25.9 28 0.0006 30.4 0.5 19 133-151 187-205 (222)
49 PRK00432 30S ribosomal protein 25.8 31 0.00067 22.6 0.6 24 123-146 19-45 (50)
50 KOG3611 Semaphorins [Signal tr 25.7 27 0.00059 36.1 0.5 38 139-176 492-537 (737)
51 PHA02680 ORF090 IMV phosphoryl 25.0 2.9E+02 0.0062 20.4 7.2 37 210-249 47-83 (91)
52 KOG1729 FYVE finger containing 24.8 16 0.00035 33.2 -1.1 27 124-150 168-197 (288)
53 smart00547 ZnF_RBZ Zinc finger 24.5 34 0.00073 18.6 0.6 21 126-146 4-24 (26)
54 PRK15103 paraquat-inducible me 24.4 6.4E+02 0.014 24.2 11.7 33 123-155 220-252 (419)
55 PRK14559 putative protein seri 23.7 50 0.0011 33.7 2.0 22 125-146 28-49 (645)
56 PLN00186 ribosomal protein S26 23.4 28 0.0006 26.7 0.1 20 137-156 19-38 (109)
57 PRK10747 putative protoheme IX 23.2 2.5E+02 0.0055 26.4 6.6 47 34-83 27-73 (398)
58 TIGR00540 hemY_coli hemY prote 23.2 2.2E+02 0.0047 26.9 6.2 47 34-83 27-73 (409)
59 PRK09335 30S ribosomal protein 21.9 30 0.00064 25.9 -0.0 21 137-157 19-39 (95)
60 TIGR00155 pqiA_fam integral me 21.7 7.1E+02 0.015 23.8 13.4 32 124-155 215-247 (403)
61 PRK12286 rpmF 50S ribosomal pr 21.5 56 0.0012 22.0 1.3 22 122-145 25-47 (57)
62 smart00109 C1 Protein kinase C 21.4 72 0.0016 19.7 1.7 25 122-146 9-35 (49)
63 PTZ00172 40S ribosomal protein 20.3 33 0.00072 26.2 -0.0 20 137-156 19-38 (108)
64 KOG1398 Uncharacterized conser 20.2 32 0.0007 32.5 -0.2 26 134-165 10-35 (460)
65 PRK02935 hypothetical protein; 20.1 4.1E+02 0.0089 20.4 5.7 10 122-131 84-93 (110)
66 PHA02942 putative transposase; 20.1 50 0.0011 31.3 1.1 26 121-146 322-350 (383)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.3e-59 Score=416.71 Aligned_cols=265 Identities=35% Similarity=0.677 Sum_probs=209.6
Q ss_pred chhhhcccccchhHHHHHHHHHHHHhheeeEEeeeeccccccCcccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022225 4 NLFKLCSGLKVLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVP 83 (300)
Q Consensus 4 ~~~~~c~~~r~~g~~~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~sy~~~~~~dPG~vp 83 (300)
..+++|+ | +++++++.++++|+||++++..+.+... .+..+.+.+++++.+++|.+|+|++++++|||.+|
T Consensus 5 ~~~~~~~--r---~~~~~~i~~~~~~~yy~~v~~~c~~~i~----~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp 75 (307)
T KOG1315|consen 5 RRFSKCL--R---WIPVLIILLVIGWTYYVYVAVLCILSIS----LTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVP 75 (307)
T ss_pred ccchhhh--c---chhheeeeeeEEEEEEEeehhhhHHHHh----hhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCc
Confidence 3444554 6 8889999999999999999998876542 23567788899999999999999999999999999
Q ss_pred CCCCCCCcCCCCCcCCccccCCCCCCCCCCCCCCCCCCcCeecccccccCCCCCCCCCcchhhhhcCCCccccccccccc
Q 022225 84 ENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVG 163 (300)
Q Consensus 84 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG 163 (300)
.++.++.++.+....+...+ .......++.++..|+|++|+.+|||||||||.|+|||+||||||||+|||||
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVg 148 (307)
T KOG1315|consen 76 DSYRPSVEDEDSLENGSDNE-------RDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVG 148 (307)
T ss_pred cccCCCcCccccccccCccc-------ccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceec
Confidence 99988876443221111100 11223445788899999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCchh
Q 022225 164 ARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTS 243 (300)
Q Consensus 164 ~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt 243 (300)
.+|||+|++|++|+.+.+.+..+.....+..++.. . ...++.....+.+.+++++.+++.+.+++++|+++|++|+||
T Consensus 149 f~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TT 226 (307)
T KOG1315|consen 149 FRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQG-G-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTT 226 (307)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-c-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchh
Confidence 99999999999999999998887777777776632 1 222233333444556677788888888999999999999999
Q ss_pred HHHHhhcCCcCCCCchhH---HHHHHhhcCCCccceEeecccCCCC
Q 022225 244 IEVYEKKRTVRWKYDLGR---KKNFEQVFGTNKALWFFPLFSKEDS 286 (300)
Q Consensus 244 ~E~~~~~~~~~~~yd~G~---~~N~~~vfG~~~~~W~~P~~~~~~~ 286 (300)
+|.++.+....+.++.+- ..|++|+||+++..|++|+.++...
T Consensus 227 iE~~~~~~~~~~~~~~~~~~~~~n~~~vfg~~~~~wl~P~~~s~~~ 272 (307)
T KOG1315|consen 227 IEAYKSPVFRSGLHNKNGFNLYVNFREVFGSNLLYWLLPIDSSWGD 272 (307)
T ss_pred HhhhccccccccccccCCcceeecHHHHhCCCceEEeccccCcccc
Confidence 999987643333344333 5699999999999999999887753
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-50 Score=357.85 Aligned_cols=239 Identities=29% Similarity=0.537 Sum_probs=180.9
Q ss_pred chhHHHHHHHHHHHHhheeeEEeeeeccccccCcccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCC
Q 022225 14 VLGYFMILLVAAIIAVSYYAVVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSS 93 (300)
Q Consensus 14 ~~g~~~~~~v~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~ 93 (300)
++|++..+.++.++....-..-..+|.| .+++.+...-+.|.+...|++++|+.+++++||++|++|.|+...
T Consensus 14 hwGpi~alsiit~i~~~~~~~n~lww~p------~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~- 86 (414)
T KOG1314|consen 14 HWGPITALSIITIITSTTGYMNSLWWFP------LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK- 86 (414)
T ss_pred ccccHHHHHHHHHHHHHHHHhhhhhhcc------ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh-
Confidence 4677777766666665444443345555 367788888889999999999999999999999999999987651
Q ss_pred CCCcCCccccCCCCCCCCCCCCCCCCCCcCeecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHH
Q 022225 94 SSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLF 173 (300)
Q Consensus 94 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~F 173 (300)
.....+||++|+.+|+||||||+.|||||.+|||||||+|||||..||.||+.|
T Consensus 87 --------------------------D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~F 140 (414)
T KOG1314|consen 87 --------------------------DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRF 140 (414)
T ss_pred --------------------------hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHH
Confidence 234578999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH----HHHHhhc--cc-CC---CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCchh
Q 022225 174 LLYTFLETTMDTLVLLPS----FIKFFGK--AK-NH---SSSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTS 243 (300)
Q Consensus 174 l~~~~l~~~~~~~~~~~~----~~~~~~~--~~-~~---~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt 243 (300)
|++..++|+..++.+... ++..|.. .. .. ..++..+...++++.++++..+++..|+..|+..|.+|+|.
T Consensus 141 Llf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~ 220 (414)
T KOG1314|consen 141 LLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTG 220 (414)
T ss_pred HHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcc
Confidence 999999887654433322 2222311 11 11 11223344444455556666777788889999999999999
Q ss_pred HHHHhhc--------------CCcCCCCchhHHHHHHhhcCCCccceEeecccCCCCCCCCCCCCccccCC
Q 022225 244 IEVYEKK--------------RTVRWKYDLGRKKNFEQVFGTNKALWFFPLFSKEDSDSIPALHGLDFPTC 300 (300)
Q Consensus 244 ~E~~~~~--------------~~~~~~yd~G~~~N~~~vfG~~~~~W~~P~~~~~~~~~~~~~~G~~~~~~ 300 (300)
||.+..+ .....|||+|++.|+++||-... .+.|||..||+.
T Consensus 221 IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~~~---------------~~~gdg~~wPv~ 276 (414)
T KOG1314|consen 221 IESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQNK---------------KEEGDGIEWPVV 276 (414)
T ss_pred hHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhhcc---------------ccCCCCcccccc
Confidence 9997411 12457999999999999998753 134899999973
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1e-43 Score=324.24 Aligned_cols=166 Identities=34% Similarity=0.642 Sum_probs=130.6
Q ss_pred CCCCcCeecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022225 118 RGPSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFG 197 (300)
Q Consensus 118 ~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~~ 197 (300)
++...+.+||.+|+.+||||||||+.||+||+||||||||+|||||++|||+|++|++++.+.+++........+.....
T Consensus 107 ~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~ 186 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRAD 186 (299)
T ss_pred CCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 46778899999999999999999999999999999999999999999999999999999888888876665555444222
Q ss_pred ccc-CCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCchhHHHHhh-cCCcC-CCCchhHHHHHHhhcCCC
Q 022225 198 KAK-NHS--SSPANLAIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK-KRTVR-WKYDLGRKKNFEQVFGTN 272 (300)
Q Consensus 198 ~~~-~~~--~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~~ 272 (300)
+.. ... ..+......++..++++.+...++.++.+|++++.+|+||+|..++ +.... ++||+|.++|++++||.+
T Consensus 187 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~ 266 (299)
T KOG1311|consen 187 NLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGP 266 (299)
T ss_pred cccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCCC
Confidence 211 111 1222223333444556666677778999999999999999999874 33334 899999999999999998
Q ss_pred c-cceEeecccC
Q 022225 273 K-ALWFFPLFSK 283 (300)
Q Consensus 273 ~-~~W~~P~~~~ 283 (300)
. ..|.-|...+
T Consensus 267 ~~~~~~~p~~~~ 278 (299)
T KOG1311|consen 267 LPLSWLSPFARS 278 (299)
T ss_pred CCcccccccccC
Confidence 5 6899988764
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=3.7e-41 Score=283.98 Aligned_cols=173 Identities=30% Similarity=0.589 Sum_probs=122.6
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCcCCCCCcCCccccCCCCCCCCCCCCCCCCCCcCeecccccccCCCCCCCCCcchhhhh
Q 022225 69 WSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSVCQRCV 148 (300)
Q Consensus 69 ~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~C~~CV 148 (300)
++|++++++|||++|+....+.+.. ++. +... .........+...+.++|.+|+..||+|||||+.||+||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~----~~~-~~~~----~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 72 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQ----EEK-EEEQ----NQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCV 72 (174)
T ss_pred EEehhhheECCcccCCccccccccc----ccc-cccc----chhhhhhccccCCCCEECcccCCcCCCcceecccccccc
Confidence 5788999999999998722111111 000 0000 001111223567889999999999999999999999999
Q ss_pred cCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 022225 149 LKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANLAIVFLAFVINLAFALSLLC 228 (300)
Q Consensus 149 ~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 228 (300)
+||||||||+|||||++|||+|++|+++..+.+++.....+..+....................++.++++++++++++.
T Consensus 73 ~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (174)
T PF01529_consen 73 LRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGF 152 (174)
T ss_pred ccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998888776655555554432211111111111113444556667778888
Q ss_pred HHHHHHHhHhcCchhHHHHhhc
Q 022225 229 FIVMHSSLVSSNTTSIEVYEKK 250 (300)
Q Consensus 229 l~~~~l~~i~~n~Tt~E~~~~~ 250 (300)
+++.|++++++|+||+|.+++|
T Consensus 153 l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 153 LLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHcCCcHHHHHHcC
Confidence 9999999999999999999875
No 5
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.1e-39 Score=280.13 Aligned_cols=174 Identities=31% Similarity=0.606 Sum_probs=124.9
Q ss_pred CeecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hcc
Q 022225 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFF---GKA 199 (300)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~---~~~ 199 (300)
...+|.+|+.+||||+||||.|||||+||||||||+|||||.+|||||++|++|+.+++.++.+...+.+++.. ++.
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 35799999999999999999999999999999999999999999999999999999999987655444444322 111
Q ss_pred cCCCC-----C-ChhHH---------HHHHHHHHHHHHHHHHHHHHHHHHHhHhcCchhHHHHhh----cC----CcCCC
Q 022225 200 KNHSS-----S-PANLA---------IVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK----KR----TVRWK 256 (300)
Q Consensus 200 ~~~~~-----~-~~~~~---------~~~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~----~~----~~~~~ 256 (300)
..... . |.... -+.-...+++.+.++++.+..+|.++|.+|.|++|+... |+ ..+||
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 10000 0 11110 011122344455667778889999999999999998632 11 24689
Q ss_pred CchhHHHHHHhhcCCCc--cceEeecccCCCCCCCCCCCCccccC
Q 022225 257 YDLGRKKNFEQVFGTNK--ALWFFPLFSKEDSDSIPALHGLDFPT 299 (300)
Q Consensus 257 yd~G~~~N~~~vfG~~~--~~W~~P~~~~~~~~~~~~~~G~~~~~ 299 (300)
++.|.++||+.++|-.. -.|..=+-|+ .+.|.+.|.++|.
T Consensus 261 ~n~g~k~nWr~fLg~~~~r~~wk~v~lPt---~~~p~~~~~~~~~ 302 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLFRGRHFWKTVLLPT---IRKPVKYGDSKEK 302 (309)
T ss_pred cccchHHHHHHhhccccCCceeEEEeccc---cccccccCCcccc
Confidence 99999999999999863 3565422222 1456678888773
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=8.5e-39 Score=290.31 Aligned_cols=217 Identities=33% Similarity=0.598 Sum_probs=153.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCcCCccccCCCCCCCCCCCCCCCCCCcCeecccccccCC
Q 022225 55 SIIILFHILLVMLVWSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGK 134 (300)
Q Consensus 55 ~~~~~f~~l~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~k 134 (300)
+..+.+.+.+.+...+|++.+++|||..+++-....- .+..+ .....++.+..++|.+|+.+|
T Consensus 57 ~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~------~~~~~-----------~~~~~~~~~~~~~C~~C~~~K 119 (309)
T COG5273 57 LFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGY------RETIS-----------RLLDDGKFGTENFCSTCNIYK 119 (309)
T ss_pred hhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccch------hhhhh-----------hhhhcCccccceecccccccc
Confidence 4445566677788889999999999998864221111 11111 112236778999999999999
Q ss_pred CCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCChhH-H-HH
Q 022225 135 PPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKAKNHSSSPANL-A-IV 212 (300)
Q Consensus 135 P~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~ 212 (300)
|+|||||+.|||||+||||||||+|||||.+|||+|++|++++...+.+........+...+ .....+..+ . .+
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~li 195 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIF----SIRHDTSLAICFLI 195 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc----cccCChHHHHHHHH
Confidence 99999999999999999999999999999999999999999987777665544433333222 122223222 1 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhcCchhHHHHhhcCC-------------------------cCCCCchhHHHHHHh
Q 022225 213 FLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEKKRT-------------------------VRWKYDLGRKKNFEQ 267 (300)
Q Consensus 213 ~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~~~~-------------------------~~~~yd~G~~~N~~~ 267 (300)
+....+...+.+.+..++..+.+++..|+|++|..+..+. ..+|++.|..+|++.
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 275 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLST 275 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCcccccee
Confidence 1112344445556667888999999999999998653221 125788999999999
Q ss_pred hcCCCccceEeecccCCCCCCCCCCCCccccC
Q 022225 268 VFGTNKALWFFPLFSKEDSDSIPALHGLDFPT 299 (300)
Q Consensus 268 vfG~~~~~W~~P~~~~~~~~~~~~~~G~~~~~ 299 (300)
++|.....|..|..... .++.+|+.
T Consensus 276 i~~~~~~~~~~~~~~~~-------~~~~~~~~ 300 (309)
T COG5273 276 IKGSNALYWLTPLHTNY-------CNSYDFSL 300 (309)
T ss_pred ecCCCceeeccccccCC-------CCccCccc
Confidence 99999999999843322 35666554
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=9.9e-31 Score=226.10 Aligned_cols=105 Identities=32% Similarity=0.621 Sum_probs=78.9
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCcCCccccCCCCCCCCCCCCCCCCCCcCeecccccccCCCCCCCCCcc
Q 022225 64 LVMLVWSYVMVVFWDPGSVPENWRSVSVSSSSSSGVNLEAGTSSQSLDNVGPDARGPSRSVGFCDRCQNGKPPRCHHCSV 143 (300)
Q Consensus 64 ~~~~~~sy~~~~~~dPG~vp~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~RshHC~~ 143 (300)
.++-..++..+..+|||.+.++... +..+.-|.+ .....+...|++|+..||.||+|||.
T Consensus 108 vivp~i~f~ltc~snpg~i~k~n~s----------~~~~~ypYD----------y~if~k~~kCSTCki~KPARSKHCsi 167 (341)
T KOG1312|consen 108 VIVPLIFFTLTCGSNPGIITKANES----------LFLHVYPYD----------YVIFPKNVKCSTCKIRKPARSKHCSI 167 (341)
T ss_pred HHHHHHHHhhhhcCCCCccchhhhc----------cceeccCcc----------ceeecCCCccccccCCCccccccchH
Confidence 3334455677889999998753110 111111221 01223447899999999999999999
Q ss_pred hhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHH
Q 022225 144 CQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVL 188 (300)
Q Consensus 144 C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~ 188 (300)
|||||.|+||||.|+|||||.+|.|||++|+++....+.++.+.+
T Consensus 168 CNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrl 212 (341)
T KOG1312|consen 168 CNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRL 212 (341)
T ss_pred HHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999877777765544
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.94 E-value=1.8e-27 Score=225.99 Aligned_cols=144 Identities=29% Similarity=0.487 Sum_probs=93.4
Q ss_pred CcCe-ecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022225 121 SRSV-GFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTMDTLVLLPSFIKFFGKA 199 (300)
Q Consensus 121 ~~~~-~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~~~~~~~~~~~~~~~~~ 199 (300)
.... +||.+|...||.|||||++|||||.|+||||||++||||.+|||+|+.|++.+...+.+.... ...++...
T Consensus 416 f~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~----~~~y~~~~ 491 (600)
T KOG0509|consen 416 FDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYL----CLYYIMNL 491 (600)
T ss_pred ccccccceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHH----HHHHHhhc
Confidence 3344 799999999999999999999999999999999999999999999999998766555443222 22233221
Q ss_pred cCCCCCChhHHHHHHHHHHHHHH--HH-------------HHHHH-HHHHHHhHhcCchhHHHHhhcC---------CcC
Q 022225 200 KNHSSSPANLAIVFLAFVINLAF--AL-------------SLLCF-IVMHSSLVSSNTTSIEVYEKKR---------TVR 254 (300)
Q Consensus 200 ~~~~~~~~~~~~~~l~~~~~~~~--~~-------------~~~~l-~~~~l~~i~~n~Tt~E~~~~~~---------~~~ 254 (300)
.... .....++..+..+.. .+ ..... ...|-..++.+.||+|.++.++ ..+
T Consensus 492 ~~~~----~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~ 567 (600)
T KOG0509|consen 492 ENAS----TIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTR 567 (600)
T ss_pred chhH----HHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCC
Confidence 1110 000111111110000 00 00000 1122334688999999986543 246
Q ss_pred CCCchhHHHHHHhhcCCC
Q 022225 255 WKYDLGRKKNFEQVFGTN 272 (300)
Q Consensus 255 ~~yd~G~~~N~~~vfG~~ 272 (300)
.|++.|+++|+.+++=.+
T Consensus 568 ~~~s~g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 568 SPFSPGPIRNLVDFFLCS 585 (600)
T ss_pred CCCCchhhhcchheeecc
Confidence 799999999999987654
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=93.25 E-value=0.34 Score=44.19 Aligned_cols=58 Identities=24% Similarity=0.372 Sum_probs=40.5
Q ss_pred CCCCCcchhhhhcCCCccccccccccccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022225 137 RCHHCSVCQRCVLKMDHHCVWVVNCVGARNY-----------KSFLLFLLYTFLETTMDTLVLLPSFIK 194 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~-----------k~Fi~Fl~~~~l~~~~~~~~~~~~~~~ 194 (300)
+.++|..|+..+...-|||+.-|+||-..-| |-+-.|+.+++...+.....+....+.
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~ 180 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYE 180 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999999999988754 678888866653333333333333333
No 10
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=92.15 E-value=3.2 Score=34.24 Aligned_cols=53 Identities=25% Similarity=0.420 Sum_probs=35.9
Q ss_pred CCcCeecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHHHHHHHHH
Q 022225 120 PSRSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLYTFLETTM 183 (300)
Q Consensus 120 ~~~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~~~l~~~~ 183 (300)
...+.+.|+.|+.--..+-|||.--|.||.+.-| +..=.|+++..-..+....
T Consensus 58 kp~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~~ 110 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFFI 110 (174)
T ss_pred CCCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHHH
Confidence 3456778888888888888888888888887655 2233566655544444444
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.12 E-value=0.61 Score=25.39 Aligned_cols=21 Identities=19% Similarity=0.683 Sum_probs=17.5
Q ss_pred cccccccCCCCCCCCCcchhh
Q 022225 126 FCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 126 ~C~~C~~~kP~RshHC~~C~~ 146 (300)
+|.+|...-++.+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688888888888888888874
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=83.06 E-value=0.65 Score=29.99 Aligned_cols=25 Identities=28% Similarity=0.630 Sum_probs=22.1
Q ss_pred cCeecccccccCCCCCCCCCcchhh
Q 022225 122 RSVGFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~C~~ 146 (300)
-....|.+|...-|+|+..|+.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3467899999999999999998875
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=78.05 E-value=1.3 Score=24.74 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=18.6
Q ss_pred eecccccccCCCCCCCCCcchhh
Q 022225 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~ 146 (300)
.++|..|...-++.++.|..||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 35788999877888888888874
No 14
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=76.21 E-value=1.4 Score=44.70 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=18.5
Q ss_pred eecccccccCCC-------CCCCCCcchhh
Q 022225 124 VGFCDRCQNGKP-------PRCHHCSVCQR 146 (300)
Q Consensus 124 ~~~C~~C~~~kP-------~RshHC~~C~~ 146 (300)
...|..|+..-. -|-|||+.||+
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCcc
Confidence 367999997664 39999999987
No 15
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=74.90 E-value=52 Score=30.27 Aligned_cols=30 Identities=27% Similarity=0.479 Sum_probs=15.8
Q ss_pred CCCCCcchhhhhcCCCcccccccccccccc
Q 022225 137 RCHHCSVCQRCVLKMDHHCVWVVNCVGARN 166 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCpwi~nCIG~~N 166 (300)
+.+.|+.|+.-....-|||.--|.||-...
T Consensus 108 ~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~D 137 (309)
T COG5273 108 TENFCSTCNIYKPPRSHHCSICNRCVLKFD 137 (309)
T ss_pred cceeccccccccCCCCccchhhcchhhccC
Confidence 344455555555555555555555555443
No 16
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=70.25 E-value=3.4 Score=40.93 Aligned_cols=54 Identities=6% Similarity=-0.128 Sum_probs=46.9
Q ss_pred cCeecccccccCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHHHH
Q 022225 122 RSVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFLLY 176 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl~~ 176 (300)
.....|.+|....+.+..++..+-.++..+++||+|+. +|+..|...+....+.
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~ 376 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFII 376 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHH
Confidence 45567899999999999999999999999999999999 9999998866554443
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=68.26 E-value=2.8 Score=28.05 Aligned_cols=36 Identities=33% Similarity=0.923 Sum_probs=27.0
Q ss_pred cccccccCCCCCC-------CCCcchhhhhcCC-Ccccccccccccc
Q 022225 126 FCDRCQNGKPPRC-------HHCSVCQRCVLKM-DHHCVWVVNCVGA 164 (300)
Q Consensus 126 ~C~~C~~~kP~Rs-------hHC~~C~~CV~~~-DHHCpwi~nCIG~ 164 (300)
-|..|+.--|+-+ +-|..|..|+..+ +++|| ||=|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 3666665555543 7789999999999 99998 66654
No 18
>PF12773 DZR: Double zinc ribbon
Probab=65.00 E-value=5.9 Score=25.56 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=19.9
Q ss_pred eecccccccCCC---CCCCCCcchhhhhcCCCcccc
Q 022225 124 VGFCDRCQNGKP---PRCHHCSVCQRCVLKMDHHCV 156 (300)
Q Consensus 124 ~~~C~~C~~~kP---~RshHC~~C~~CV~~~DHHCp 156 (300)
.++|..|...-+ .....|..|+.=+...+.+|+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 566666665544 335566666666666666665
No 19
>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=64.59 E-value=2.2 Score=29.68 Aligned_cols=26 Identities=35% Similarity=0.632 Sum_probs=12.4
Q ss_pred CeecccccccC--CCCCCCCCcchhhhh
Q 022225 123 SVGFCDRCQNG--KPPRCHHCSVCQRCV 148 (300)
Q Consensus 123 ~~~~C~~C~~~--kP~RshHC~~C~~CV 148 (300)
+...|..|+.- --.|-|||+.||+.|
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 34567777732 347889999999854
No 20
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=62.57 E-value=1.6 Score=28.23 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=21.4
Q ss_pred cCeecccccccCCCCCCCCCcchhh
Q 022225 122 RSVGFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~RshHC~~C~~ 146 (300)
...+.|.+|...-|+|+-.|+.|+.
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccC
Confidence 3457899999999999999998864
No 21
>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=59.82 E-value=4 Score=26.88 Aligned_cols=25 Identities=28% Similarity=0.782 Sum_probs=16.9
Q ss_pred CeecccccccCCCCCCCCCcc--hhhh
Q 022225 123 SVGFCDRCQNGKPPRCHHCSV--CQRC 147 (300)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~--C~~C 147 (300)
....|.+|...-|+|+-.|+. ||.+
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 457899999999999999998 8764
No 22
>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 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=58.56 E-value=5.3 Score=22.41 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=17.6
Q ss_pred ecccccccCCCCCCCCCcchhh
Q 022225 125 GFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~ 146 (300)
+.|..|...-|.-+.-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4688888888888888888774
No 24
>PF12773 DZR: Double zinc ribbon
Probab=54.40 E-value=8.9 Score=24.67 Aligned_cols=25 Identities=28% Similarity=0.805 Sum_probs=21.8
Q ss_pred CcCeecccccccCCCCCCCCCcchh
Q 022225 121 SRSVGFCDRCQNGKPPRCHHCSVCQ 145 (300)
Q Consensus 121 ~~~~~~C~~C~~~kP~RshHC~~C~ 145 (300)
.....+|.+|....++.+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 4556899999999999999999886
No 25
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=52.31 E-value=4 Score=38.89 Aligned_cols=28 Identities=43% Similarity=0.953 Sum_probs=21.4
Q ss_pred CcCeecccccccC--CCCCCCCCcchhhhh
Q 022225 121 SRSVGFCDRCQNG--KPPRCHHCSVCQRCV 148 (300)
Q Consensus 121 ~~~~~~C~~C~~~--kP~RshHC~~C~~CV 148 (300)
.....+|+.|... ---|-|||+.||+-+
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 3467899999843 456899999999843
No 26
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=50.01 E-value=2.1e+02 Score=26.34 Aligned_cols=52 Identities=25% Similarity=0.509 Sum_probs=30.0
Q ss_pred CCCCCcchhhhhcCCCccccccccccccccH-----------HHHHHHHHHHHHHHHHHHHHH
Q 022225 137 RCHHCSVCQRCVLKMDHHCVWVVNCVGARNY-----------KSFLLFLLYTFLETTMDTLVL 188 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~-----------k~Fi~Fl~~~~l~~~~~~~~~ 188 (300)
+.+.|..|+.-....-|||.--+.||...-| +-+=.|+++++-+.++....+
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~l 170 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVL 170 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHH
Confidence 5566777777677777777777777766533 344445555444444443333
No 27
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=44.20 E-value=8.8 Score=33.61 Aligned_cols=16 Identities=19% Similarity=0.144 Sum_probs=11.7
Q ss_pred hhhhcCCCcccccccc
Q 022225 145 QRCVLKMDHHCVWVVN 160 (300)
Q Consensus 145 ~~CV~~~DHHCpwi~n 160 (300)
-.=..+.+|||||...
T Consensus 35 ~eHrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 35 LEHRSYESHHCPKGLR 50 (250)
T ss_pred hccchHhhcCCCcccc
Confidence 3346788999999753
No 28
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=43.95 E-value=6.9 Score=22.43 Aligned_cols=22 Identities=23% Similarity=0.537 Sum_probs=14.5
Q ss_pred ecccccccCCCCCCCCCcchhh
Q 022225 125 GFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~ 146 (300)
-.|..|...-++++-+|..|+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--
T ss_pred ccCCCCcCCchHHhhhhhCcCC
Confidence 3478888777788888877764
No 29
>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=38.73 E-value=18 Score=23.72 Aligned_cols=22 Identities=36% Similarity=0.753 Sum_probs=13.7
Q ss_pred ccccccc--CCCCCCCCCcchhhh
Q 022225 126 FCDRCQN--GKPPRCHHCSVCQRC 147 (300)
Q Consensus 126 ~C~~C~~--~kP~RshHC~~C~~C 147 (300)
-|..|.. -.-.|.|||+.|++-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 3555552 134678888888774
No 30
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=37.04 E-value=81 Score=30.51 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=5.8
Q ss_pred CCcchhhhhc
Q 022225 140 HCSVCQRCVL 149 (300)
Q Consensus 140 HC~~C~~CV~ 149 (300)
.|..|++|+.
T Consensus 256 ~Ci~Cg~Cid 265 (434)
T TIGR02745 256 ECINCGLCID 265 (434)
T ss_pred hChhhhHHHH
Confidence 4666666654
No 31
>CHL00031 psbT photosystem II protein T
Probab=36.49 E-value=75 Score=18.82 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=12.1
Q ss_pred HHHHHHhhcCCCCCCC
Q 022225 69 WSYVMVVFWDPGSVPE 84 (300)
Q Consensus 69 ~sy~~~~~~dPG~vp~ 84 (300)
..++...|.||-.+++
T Consensus 16 ilFFAI~FRePPri~k 31 (33)
T CHL00031 16 IIFFAIFFREPPKVPT 31 (33)
T ss_pred HHHHhheecCCCCCCC
Confidence 3467788999988775
No 32
>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=36.36 E-value=9.6 Score=21.84 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=7.8
Q ss_pred cccccccCCCC-CCCCCcchhh
Q 022225 126 FCDRCQNGKPP-RCHHCSVCQR 146 (300)
Q Consensus 126 ~C~~C~~~kP~-RshHC~~C~~ 146 (300)
.|..|+..... ..++|..|+-
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 46667766555 6777777764
No 33
>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=36.08 E-value=3.9e+02 Score=25.76 Aligned_cols=16 Identities=31% Similarity=0.575 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 022225 168 KSFLLFLLYTFLETTM 183 (300)
Q Consensus 168 k~Fi~Fl~~~~l~~~~ 183 (300)
-||.+|.+|+.+..=.
T Consensus 171 nyFalFTlyvam~IEf 186 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEF 186 (512)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3899999998765433
No 34
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=34.96 E-value=96 Score=18.09 Aligned_cols=15 Identities=20% Similarity=0.461 Sum_probs=11.0
Q ss_pred HHHHHHhhcCCCCCC
Q 022225 69 WSYVMVVFWDPGSVP 83 (300)
Q Consensus 69 ~sy~~~~~~dPG~vp 83 (300)
..++...|.||-.++
T Consensus 16 iiFFAIfFRepPri~ 30 (31)
T PRK11875 16 TLFFAIAFRDPPKID 30 (31)
T ss_pred HHHHhhhccCCCCCC
Confidence 346678889997765
No 35
>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=34.13 E-value=20 Score=23.20 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=8.6
Q ss_pred CCCCcch---hhhhcCCCc--cccccc
Q 022225 138 CHHCSVC---QRCVLKMDH--HCVWVV 159 (300)
Q Consensus 138 shHC~~C---~~CV~~~DH--HCpwi~ 159 (300)
..+|..| |.=+..-+| .|||-+
T Consensus 2 ~p~C~RCrnHG~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 2 SPTCARCRNHGVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp -SS-HHHHTTT---TTTT-GGG-TTTT
T ss_pred CCcCcchhcCCcccchhhhccccCcCC
Confidence 3445555 335555666 688754
No 36
>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=33.55 E-value=21 Score=20.51 Aligned_cols=20 Identities=35% Similarity=0.771 Sum_probs=12.0
Q ss_pred cccccccCCCCC-CCCCcchh
Q 022225 126 FCDRCQNGKPPR-CHHCSVCQ 145 (300)
Q Consensus 126 ~C~~C~~~kP~R-shHC~~C~ 145 (300)
+|..|...-... .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 366665554455 67776665
No 37
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=33.54 E-value=8.6 Score=23.15 Aligned_cols=7 Identities=43% Similarity=1.317 Sum_probs=4.0
Q ss_pred ecccccc
Q 022225 125 GFCDRCQ 131 (300)
Q Consensus 125 ~~C~~C~ 131 (300)
++|.+|+
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 4666666
No 38
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=31.94 E-value=23 Score=24.34 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=19.9
Q ss_pred eecccccccCCCCCCCCCcchhh
Q 022225 124 VGFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 124 ~~~C~~C~~~kP~RshHC~~C~~ 146 (300)
.+-|..|+..-|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 35699999999999999999876
No 39
>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=30.70 E-value=1.2e+02 Score=26.58 Aligned_cols=26 Identities=31% Similarity=0.368 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022225 58 ILFHILLVMLVWSYVMVVFWDPGSVP 83 (300)
Q Consensus 58 ~~f~~l~~~~~~sy~~~~~~dPG~vp 83 (300)
++..++.+.++-.|.+|--+|||..-
T Consensus 198 iVitl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 198 IVITLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 34444555556667788889999743
No 40
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.52 E-value=20 Score=36.00 Aligned_cols=25 Identities=32% Similarity=0.619 Sum_probs=18.7
Q ss_pred cCeecccccccC--CCCCCCCCcchhh
Q 022225 122 RSVGFCDRCQNG--KPPRCHHCSVCQR 146 (300)
Q Consensus 122 ~~~~~C~~C~~~--kP~RshHC~~C~~ 146 (300)
....-|.+|... ---|.|||+.||+
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccccceeeeeeeeccccccccccch
Confidence 344678999833 3349999999998
No 41
>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=30.31 E-value=25 Score=24.20 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=19.0
Q ss_pred CcCeecccccccCC----CCCCCCCcchhhh
Q 022225 121 SRSVGFCDRCQNGK----PPRCHHCSVCQRC 147 (300)
Q Consensus 121 ~~~~~~C~~C~~~k----P~RshHC~~C~~C 147 (300)
....+.|+.|.... ..|.++|..||.-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCE
Confidence 34677899998654 4467788888764
No 42
>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=30.04 E-value=18 Score=23.49 Aligned_cols=18 Identities=28% Similarity=0.822 Sum_probs=14.5
Q ss_pred cchhhhhcCCCccccccc
Q 022225 142 SVCQRCVLKMDHHCVWVV 159 (300)
Q Consensus 142 ~~C~~CV~~~DHHCpwi~ 159 (300)
..|+.|+...|-+|.|-.
T Consensus 6 ~sC~~Cl~~~dp~CgWc~ 23 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWCS 23 (51)
T ss_dssp SSHHHHHHSTCTTEEEET
T ss_pred CcHHHHHcCCCcCccccC
Confidence 678888888888888843
No 43
>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=29.15 E-value=22 Score=26.33 Aligned_cols=39 Identities=15% Similarity=0.222 Sum_probs=19.7
Q ss_pred eecccccc------cCCCCCCCCCcchh--hhhcCCCcccccccccc
Q 022225 124 VGFCDRCQ------NGKPPRCHHCSVCQ--RCVLKMDHHCVWVVNCV 162 (300)
Q Consensus 124 ~~~C~~C~------~~kP~RshHC~~C~--~CV~~~DHHCpwi~nCI 162 (300)
.-.|..|. .++|.....-..-. .=+..+-.||||++.-.
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr~~CPwv~~~~ 65 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHREYCPWVNPST 65 (91)
T ss_pred eEEccccCcEeeeeecccCccCCCCcCCCCCCcccccccCCccCCcc
Confidence 56677776 34554433222000 01223336899998754
No 44
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=28.92 E-value=27 Score=37.29 Aligned_cols=40 Identities=33% Similarity=0.521 Sum_probs=27.0
Q ss_pred Ceecccccc--cCCCCCCCCCcchhhhhcCCCccccccccccccccHHHHHHHH
Q 022225 123 SVGFCDRCQ--NGKPPRCHHCSVCQRCVLKMDHHCVWVVNCVGARNYKSFLLFL 174 (300)
Q Consensus 123 ~~~~C~~C~--~~kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~N~k~Fi~Fl 174 (300)
...-|..|+ ..--.|-||||.||+- .-+.| -|.|.++-|+
T Consensus 556 e~pncm~clqkft~ikrrhhcRacgkV---------lcgvc---cnek~~leyl 597 (1287)
T KOG1841|consen 556 EAPNCMDCLQKFTPIKRRHHCRACGKV---------LCGVC---CNEKSALEYL 597 (1287)
T ss_pred cCchHHHHHhhcccccccccchhccce---------eehhh---cchhhhhhhc
Confidence 445566666 5567799999999983 11333 4667777776
No 45
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.66 E-value=29 Score=26.88 Aligned_cols=25 Identities=20% Similarity=0.579 Sum_probs=18.0
Q ss_pred cCeecccccccCCCCCCCC---Ccchhh
Q 022225 122 RSVGFCDRCQNGKPPRCHH---CSVCQR 146 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~RshH---C~~C~~ 146 (300)
...-+|..|+..-|...++ |..||.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 4567899999887765444 887774
No 46
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.62 E-value=26 Score=22.54 Aligned_cols=6 Identities=50% Similarity=1.719 Sum_probs=2.9
Q ss_pred cccccc
Q 022225 126 FCDRCQ 131 (300)
Q Consensus 126 ~C~~C~ 131 (300)
+|+.|.
T Consensus 2 FCp~Cg 7 (52)
T smart00661 2 FCPKCG 7 (52)
T ss_pred CCCCCC
Confidence 455554
No 47
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=26.51 E-value=37 Score=21.33 Aligned_cols=17 Identities=35% Similarity=1.077 Sum_probs=9.8
Q ss_pred cchhhhhcCCCcccccc
Q 022225 142 SVCQRCVLKMDHHCVWV 158 (300)
Q Consensus 142 ~~C~~CV~~~DHHCpwi 158 (300)
+.|..|+...|-||-|=
T Consensus 5 ~sC~~C~~~~~~~C~Wc 21 (46)
T smart00423 5 TSCSECLLARDPYCAWC 21 (46)
T ss_pred CcHHHHHcCCCCCCCcc
Confidence 34566666666666654
No 48
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=25.91 E-value=28 Score=30.44 Aligned_cols=19 Identities=32% Similarity=0.719 Sum_probs=15.4
Q ss_pred CCCCCCCCCcchhhhhcCC
Q 022225 133 GKPPRCHHCSVCQRCVLKM 151 (300)
Q Consensus 133 ~kP~RshHC~~C~~CV~~~ 151 (300)
|++.+..||..|..|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 5666666999999999873
No 49
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.78 E-value=31 Score=22.55 Aligned_cols=24 Identities=29% Similarity=0.588 Sum_probs=14.8
Q ss_pred Ceeccccccc-CC--CCCCCCCcchhh
Q 022225 123 SVGFCDRCQN-GK--PPRCHHCSVCQR 146 (300)
Q Consensus 123 ~~~~C~~C~~-~k--P~RshHC~~C~~ 146 (300)
..++|+.|.. .- -....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3568999986 22 223566777763
No 50
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=25.72 E-value=27 Score=36.09 Aligned_cols=38 Identities=29% Similarity=0.570 Sum_probs=29.9
Q ss_pred CCCc---chhhhhcCCCccccccc---ccccc--ccHHHHHHHHHH
Q 022225 139 HHCS---VCQRCVLKMDHHCVWVV---NCVGA--RNYKSFLLFLLY 176 (300)
Q Consensus 139 hHC~---~C~~CV~~~DHHCpwi~---nCIG~--~N~k~Fi~Fl~~ 176 (300)
|+|+ .|..|++..|-||.|-+ .|+-. .|.|.+.+=+-.
T Consensus 492 ~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~~ 537 (737)
T KOG3611|consen 492 ARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVSS 537 (737)
T ss_pred hHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhcc
Confidence 7788 89888888999999988 78743 567777776654
No 51
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=25.04 E-value=2.9e+02 Score=20.40 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCchhHHHHhh
Q 022225 210 AIVFLAFVINLAFALSLLCFIVMHSSLVSSNTTSIEVYEK 249 (300)
Q Consensus 210 ~~~~l~~~~~~~~~~~~~~l~~~~l~~i~~n~Tt~E~~~~ 249 (300)
++.+++|++.+ +.+++++++.+|--+++.+..|+++.
T Consensus 47 alSii~FIlG~---vl~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 47 ALSVTCFIVGA---VLLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHhcccCCCceeecccC
Confidence 34445555443 33445677777777777777776654
No 52
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=24.84 E-value=16 Score=33.20 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=15.2
Q ss_pred eeccccccc---CCCCCCCCCcchhhhhcC
Q 022225 124 VGFCDRCQN---GKPPRCHHCSVCQRCVLK 150 (300)
Q Consensus 124 ~~~C~~C~~---~kP~RshHC~~C~~CV~~ 150 (300)
..-|..|.. ---.|-|||+.||+-|-.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 344555553 223466778777775443
No 53
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.55 E-value=34 Score=18.57 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=14.9
Q ss_pred cccccccCCCCCCCCCcchhh
Q 022225 126 FCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 126 ~C~~C~~~kP~RshHC~~C~~ 146 (300)
.|..|.....+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477777777777777777753
No 54
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.37 E-value=6.4e+02 Score=24.24 Aligned_cols=33 Identities=15% Similarity=0.298 Sum_probs=25.1
Q ss_pred CeecccccccCCCCCCCCCcchhhhhcCCCccc
Q 022225 123 SVGFCDRCQNGKPPRCHHCSVCQRCVLKMDHHC 155 (300)
Q Consensus 123 ~~~~C~~C~~~kP~RshHC~~C~~CV~~~DHHC 155 (300)
...-|+.|+..-|....||..|+.-..+.+++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 455699999887777778888888776665555
No 55
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.71 E-value=50 Score=33.66 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=13.2
Q ss_pred ecccccccCCCCCCCCCcchhh
Q 022225 125 GFCDRCQNGKPPRCHHCSVCQR 146 (300)
Q Consensus 125 ~~C~~C~~~kP~RshHC~~C~~ 146 (300)
+.|.+|...-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 4566666666666666666655
No 56
>PLN00186 ribosomal protein S26; Provisional
Probab=23.37 E-value=28 Score=26.68 Aligned_cols=20 Identities=30% Similarity=0.486 Sum_probs=14.7
Q ss_pred CCCCCcchhhhhcCCCcccc
Q 022225 137 RCHHCSVCQRCVLKMDHHCV 156 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCp 156 (300)
+.-||..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIKR 38 (109)
T ss_pred cceeeCCCcccccccceEEE
Confidence 34579999999998555443
No 57
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=23.21 E-value=2.5e+02 Score=26.41 Aligned_cols=47 Identities=15% Similarity=0.264 Sum_probs=23.2
Q ss_pred EEeeeeccccccCcccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022225 34 VVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVP 83 (300)
Q Consensus 34 ~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~sy~~~~~~dPG~vp 83 (300)
++.+.|.++-+.. |....+..++..++.+.+++-.++.++.-|+.+.
T Consensus 27 yv~i~~~~~~ie~---sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~ 73 (398)
T PRK10747 27 YVLIQTDNYNIET---SVTGLAIILILAMVVLFAIEWLLRRIFRTGARTR 73 (398)
T ss_pred eEEEEECCEEEEe---hHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhh
Confidence 5555665554333 2222232222223333344555677788888754
No 58
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=23.20 E-value=2.2e+02 Score=26.92 Aligned_cols=47 Identities=13% Similarity=0.169 Sum_probs=22.9
Q ss_pred EEeeeeccccccCcccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 022225 34 VVVITCGPQLLRGGVHSFFGFSIIILFHILLVMLVWSYVMVVFWDPGSVP 83 (300)
Q Consensus 34 ~~~~~~~p~~~~~~~~~~~~~~~~~~f~~l~~~~~~sy~~~~~~dPG~vp 83 (300)
++.+.|.++-... |....+.+++..+..+.+++-.++.++.-|+.+.
T Consensus 27 yv~i~~~~~~ie~---s~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~ 73 (409)
T TIGR00540 27 YVLIETANRIIEM---SITGLAIFFIIALAIIFAFEWGLRRFFRLGAHSR 73 (409)
T ss_pred eEEEEECCEEEEe---eHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHH
Confidence 5666666654333 2222222222222333334455677788887753
No 59
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=21.91 E-value=30 Score=25.90 Aligned_cols=21 Identities=29% Similarity=0.483 Sum_probs=16.1
Q ss_pred CCCCCcchhhhhcCCCccccc
Q 022225 137 RCHHCSVCQRCVLKMDHHCVW 157 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCpw 157 (300)
+.-+|..|++||.+----+.+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEE
Confidence 345799999999987666654
No 60
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=21.74 E-value=7.1e+02 Score=23.78 Aligned_cols=32 Identities=16% Similarity=0.393 Sum_probs=23.1
Q ss_pred eeccccccc-CCCCCCCCCcchhhhhcCCCccc
Q 022225 124 VGFCDRCQN-GKPPRCHHCSVCQRCVLKMDHHC 155 (300)
Q Consensus 124 ~~~C~~C~~-~kP~RshHC~~C~~CV~~~DHHC 155 (300)
..-|+.|+. .+|....||..|+.-..+..++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 456999997 56666677888888776666555
No 61
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.46 E-value=56 Score=21.99 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=14.6
Q ss_pred cCeecccccccCCCCCCCC-Ccchh
Q 022225 122 RSVGFCDRCQNGKPPRCHH-CSVCQ 145 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~RshH-C~~C~ 145 (300)
.....|..|...+. +|| |..||
T Consensus 25 ~~l~~C~~CG~~~~--~H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKL--PHRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccC--CeEECCCCC
Confidence 34567899986654 466 76666
No 62
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.38 E-value=72 Score=19.67 Aligned_cols=25 Identities=20% Similarity=0.384 Sum_probs=16.9
Q ss_pred cCeecccccccCCCC--CCCCCcchhh
Q 022225 122 RSVGFCDRCQNGKPP--RCHHCSVCQR 146 (300)
Q Consensus 122 ~~~~~C~~C~~~kP~--RshHC~~C~~ 146 (300)
....+|..|+..-+. .+..|+.|+.
T Consensus 9 ~~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 9 KKPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCCccccccccCcCCCCcCCCCCCc
Confidence 345689999855443 3788988843
No 63
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=20.30 E-value=33 Score=26.24 Aligned_cols=20 Identities=35% Similarity=0.507 Sum_probs=14.7
Q ss_pred CCCCCcchhhhhcCCCcccc
Q 022225 137 RCHHCSVCQRCVLKMDHHCV 156 (300)
Q Consensus 137 RshHC~~C~~CV~~~DHHCp 156 (300)
+.-||..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIKR 38 (108)
T ss_pred ccEEeCCccccccccceEEE
Confidence 34579999999998555554
No 64
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.22 E-value=32 Score=32.48 Aligned_cols=26 Identities=38% Similarity=0.808 Sum_probs=18.8
Q ss_pred CCCCCCCCcchhhhhcCCCccccccccccccc
Q 022225 134 KPPRCHHCSVCQRCVLKMDHHCVWVVNCVGAR 165 (300)
Q Consensus 134 kP~RshHC~~C~~CV~~~DHHCpwi~nCIG~~ 165 (300)
+-.|..||..|+. .|| +|..||||.-
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHHH
Confidence 3456667777775 566 7899999973
No 65
>PRK02935 hypothetical protein; Provisional
Probab=20.08 E-value=4.1e+02 Score=20.37 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=4.8
Q ss_pred cCeecccccc
Q 022225 122 RSVGFCDRCQ 131 (300)
Q Consensus 122 ~~~~~C~~C~ 131 (300)
++...|-.|+
T Consensus 84 GrvD~CM~C~ 93 (110)
T PRK02935 84 GRVDACMHCN 93 (110)
T ss_pred cceeecCcCC
Confidence 3344555555
No 66
>PHA02942 putative transposase; Provisional
Probab=20.06 E-value=50 Score=31.34 Aligned_cols=26 Identities=31% Similarity=0.577 Sum_probs=18.6
Q ss_pred CcCeecccccccCCC---CCCCCCcchhh
Q 022225 121 SRSVGFCDRCQNGKP---PRCHHCSVCQR 146 (300)
Q Consensus 121 ~~~~~~C~~C~~~kP---~RshHC~~C~~ 146 (300)
....+.|+.|....+ .|.+.|..||.
T Consensus 322 ~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 322 SYSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 346688999986644 37778877775
Done!