Query 021332
Match_columns 314
No_of_seqs 289 out of 1607
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 09:24:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021332.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021332hhsearch_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 2.4E-42 5.3E-47 315.6 12.3 219 77-313 14-258 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 4.7E-41 1E-45 303.3 13.9 206 101-312 47-262 (414)
3 PF01529 zf-DHHC: DHHC palmito 100.0 2.5E-40 5.4E-45 283.7 11.9 157 117-273 2-174 (174)
4 KOG1311 DHHC-type Zn-finger pr 100.0 1.1E-39 2.3E-44 303.1 16.7 192 107-314 58-267 (299)
5 COG5273 Uncharacterized protei 100.0 8.6E-37 1.9E-41 282.6 16.9 211 100-313 54-280 (309)
6 KOG0509 Ankyrin repeat and DHH 100.0 2.2E-36 4.7E-41 292.2 17.8 274 18-311 279-583 (600)
7 KOG1313 DHHC-type Zn-finger pr 100.0 8E-37 1.7E-41 268.1 11.9 180 114-314 80-277 (309)
8 KOG1312 DHHC-type Zn-finger pr 100.0 1.8E-33 4E-38 248.1 10.4 106 109-215 105-215 (341)
9 KOG1311 DHHC-type Zn-finger pr 89.7 1.2 2.7E-05 41.3 7.3 30 161-190 113-142 (299)
10 COG5273 Uncharacterized protei 89.0 3 6.5E-05 39.1 9.3 119 147-276 123-248 (309)
11 PRK04136 rpl40e 50S ribosomal 87.7 0.29 6.3E-06 32.3 1.2 28 142-169 9-36 (48)
12 PF13240 zinc_ribbon_2: zinc-r 87.1 0.39 8.5E-06 26.8 1.3 21 149-169 1-21 (23)
13 PF01529 zf-DHHC: DHHC palmito 85.9 12 0.00027 31.2 10.7 48 146-204 61-108 (174)
14 PF13248 zf-ribbon_3: zinc-rib 82.8 0.84 1.8E-05 26.2 1.4 23 147-169 2-24 (26)
15 PF12773 DZR: Double zinc ribb 77.6 2.2 4.7E-05 28.2 2.4 35 146-180 11-48 (50)
16 PTZ00303 phosphatidylinositol 76.9 1.6 3.6E-05 45.1 2.2 22 148-169 461-489 (1374)
17 KOG0509 Ankyrin repeat and DHH 72.9 3.9 8.5E-05 41.3 3.7 85 115-201 290-379 (600)
18 COG1552 RPL40A Ribosomal prote 69.9 0.5 1.1E-05 31.3 -2.2 29 142-170 9-37 (50)
19 PF10571 UPF0547: Uncharacteri 69.0 3.4 7.5E-05 23.7 1.4 22 148-169 1-22 (26)
20 PF06906 DUF1272: Protein of u 66.3 3 6.6E-05 28.6 1.0 37 148-187 6-50 (57)
21 PF09726 Macoilin: Transmembra 65.9 44 0.00095 35.0 9.7 22 77-98 96-117 (697)
22 COG3336 Predicted membrane pro 60.7 35 0.00075 31.6 7.0 30 100-129 154-184 (299)
23 KOG1842 FYVE finger-containing 57.8 3.6 7.9E-05 39.9 0.2 28 144-171 177-206 (505)
24 PF12773 DZR: Double zinc ribb 53.1 13 0.00027 24.4 2.2 23 146-168 28-50 (50)
25 PF01020 Ribosomal_L40e: Ribos 51.5 6.7 0.00015 26.5 0.6 26 145-170 15-42 (52)
26 KOG3183 Predicted Zn-finger pr 51.4 6.7 0.00015 35.0 0.8 13 170-182 37-49 (250)
27 smart00064 FYVE Protein presen 46.7 17 0.00038 25.4 2.2 25 147-171 10-36 (68)
28 PF00641 zf-RanBP: Zn-finger i 46.7 6.3 0.00014 23.1 -0.0 20 150-169 7-26 (30)
29 PF01363 FYVE: FYVE zinc finge 43.9 9 0.00019 27.0 0.4 26 147-172 9-36 (69)
30 PF08600 Rsm1: Rsm1-like; Int 42.2 13 0.00029 28.1 1.1 15 172-186 52-66 (91)
31 TIGR00155 pqiA_fam integral me 40.5 37 0.0008 33.1 4.2 32 147-178 215-247 (403)
32 PRK13743 conjugal transfer pro 40.2 2E+02 0.0044 23.3 7.7 75 189-264 37-117 (141)
33 KOG1398 Uncharacterized conser 39.8 12 0.00025 36.0 0.5 29 157-191 10-38 (460)
34 KOG1315 Predicted DHHC-type Zn 38.4 12 0.00027 35.0 0.5 44 147-201 123-166 (307)
35 COG0348 NapH Polyferredoxin [E 38.0 3.8E+02 0.0082 25.8 10.7 25 109-133 159-183 (386)
36 KOG1729 FYVE finger containing 36.2 12 0.00026 34.7 -0.0 27 147-173 168-197 (288)
37 COG4986 ABC-type anion transpo 34.4 2.8E+02 0.0061 27.4 8.8 96 28-127 6-107 (523)
38 KOG1819 FYVE finger-containing 32.4 15 0.00032 36.4 -0.0 23 147-169 901-925 (990)
39 PF00751 DM: DM DNA binding do 30.9 14 0.00031 24.4 -0.3 15 168-182 12-28 (47)
40 PF07010 Endomucin: Endomucin; 30.3 92 0.002 27.8 4.5 30 106-135 198-227 (259)
41 PF09889 DUF2116: Uncharacteri 30.2 53 0.0011 22.9 2.4 22 148-169 4-26 (59)
42 COG2093 DNA-directed RNA polym 29.0 30 0.00066 24.3 1.1 22 148-169 5-26 (64)
43 PHA02690 hypothetical protein; 28.7 2.4E+02 0.0053 20.8 6.4 50 6-57 27-80 (90)
44 KOG4085 Uncharacterized conser 28.6 51 0.0011 27.2 2.5 61 4-69 87-147 (175)
45 KOG1818 Membrane trafficking a 27.6 24 0.00052 36.1 0.6 23 147-169 165-189 (634)
46 PF13842 Tnp_zf-ribbon_2: DDE_ 27.3 51 0.0011 19.8 1.8 19 150-168 3-23 (32)
47 PF03083 MtN3_slv: Sugar efflu 26.6 1.5E+02 0.0033 21.6 4.7 29 71-99 31-59 (87)
48 PF02150 RNA_POL_M_15KD: RNA p 25.8 16 0.00035 22.4 -0.7 23 148-170 2-29 (35)
49 PF11674 DUF3270: Protein of u 25.7 3E+02 0.0065 20.9 6.2 20 44-63 64-83 (90)
50 PF01437 PSI: Plexin repeat; 25.5 16 0.00035 24.2 -0.8 18 165-182 6-23 (51)
51 cd00065 FYVE FYVE domain; Zinc 25.3 34 0.00074 22.8 0.8 24 148-171 3-28 (57)
52 TIGR02972 TMAO_torE trimethyla 25.3 72 0.0016 21.1 2.3 15 21-35 13-27 (47)
53 PLN00186 ribosomal protein S26 25.2 29 0.00062 27.2 0.4 15 160-174 19-33 (109)
54 smart00547 ZnF_RBZ Zinc finger 24.6 42 0.00091 18.6 1.0 21 149-169 4-24 (26)
55 PF01534 Frizzled: Frizzled/Sm 24.5 5.7E+02 0.012 24.1 9.1 29 238-267 229-257 (328)
56 smart00301 DM Doublesex DNA-bi 24.2 46 0.00099 22.8 1.2 6 177-182 23-28 (54)
57 smart00423 PSI domain found in 24.0 28 0.00061 22.4 0.2 17 165-181 5-21 (46)
58 PRK14559 putative protein seri 23.9 61 0.0013 33.7 2.6 38 147-186 15-52 (645)
59 PRK09335 30S ribosomal protein 23.7 31 0.00068 26.4 0.4 20 160-179 19-38 (95)
60 smart00661 RPOL9 RNA polymeras 22.6 56 0.0012 21.3 1.5 22 148-169 1-28 (52)
61 PRK14559 putative protein seri 22.5 52 0.0011 34.2 1.8 24 148-171 2-25 (645)
62 PTZ00172 40S ribosomal protein 22.3 35 0.00075 26.7 0.4 16 160-175 19-34 (108)
63 COG5183 SSM4 Protein involved 20.9 1.7E+02 0.0036 31.2 5.0 31 12-42 1072-1102(1175)
64 KOG1710 MYND Zn-finger and ank 20.8 41 0.00089 31.3 0.6 22 146-169 318-339 (396)
65 PF01283 Ribosomal_S26e: Ribos 20.7 47 0.001 26.3 0.8 20 160-179 19-38 (113)
66 KOG3611 Semaphorins [Signal tr 20.5 35 0.00076 35.9 0.2 35 161-195 491-533 (737)
67 PRK00432 30S ribosomal protein 20.1 71 0.0015 21.3 1.5 24 146-169 19-45 (50)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.4e-42 Score=315.61 Aligned_cols=219 Identities=18% Similarity=0.275 Sum_probs=159.3
Q ss_pred hhhHHHHHHHHHHHHHHHhhccc--------hhhHHHHHHHHHHHHHHHHHHHHHhcCCCccCCCCCCchhhh-------
Q 021332 77 APAFVFFNILFIWGFYIAVVRQA--------VSSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDKLV------- 141 (314)
Q Consensus 77 ~P~~~~f~~~~~w~~~~~~~~~~--------~~~~~~i~~~~~~~l~~~~~~~~~~~dPG~vp~~~~~~~~~~------- 141 (314)
.|. +++.+...|.+|+++.... ......++++.++++..|+|++++++|||.+|.....+.+..
T Consensus 14 ~~~-~~i~~~~~~~yy~~v~~~c~~~i~~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~ 92 (307)
T KOG1315|consen 14 IPV-LIILLVIGWTYYVYVAVLCILSISLTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGS 92 (307)
T ss_pred hhh-eeeeeeEEEEEEEeehhhhHHHHhhhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccC
Confidence 444 3555677888888766421 245678889999999999999999999999997643221110
Q ss_pred -----------cCCCCCCCCcccCCCCCCCccccccccceeecccccCcccccccccccHHHHHHHHHHHHHHHHHHHHH
Q 021332 142 -----------EGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVAC 210 (314)
Q Consensus 142 -----------~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~~~~~~~ 210 (314)
..+...++|.+|+.+||+|||||+.|+|||+||||||||+|||||.+|||+|++|+++..+.+......
T Consensus 93 ~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~ 172 (307)
T KOG1315|consen 93 DNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVT 172 (307)
T ss_pred cccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHH
Confidence 011236799999999999999999999999999999999999999999999999999999887655554
Q ss_pred HHHHhhhccCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHhhhhcCCccchhccCCCCCccc
Q 021332 211 SAQFVGKSQNFDKSQSENDWVVNLATSTMLFSILQLLWQAVFFMWHIYCVCFNVRTDEWVNWKKYPEFQVIESEPGESFT 290 (314)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~~~~ll~~q~~lI~~n~TT~E~~~~~r~~~~~~~~~~~~~~~~ 290 (314)
....+..... ++ ............+.++.++..++.++.++++|++||++|+||+|.++.+.+..
T Consensus 173 ~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~------------- 237 (307)
T KOG1315|consen 173 TLIGFTKYFQ-GG-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRS------------- 237 (307)
T ss_pred HHHHHHHHHh-cc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccc-------------
Confidence 4444433332 11 11122222233334555666667777799999999999999999997553222
Q ss_pred CCcccCCCCHhHHHHHHHhcCCC
Q 021332 291 RMRFTNPYDKGFLQNVKDFLSLR 313 (314)
Q Consensus 291 ~~~~~npfd~G~~~N~~~vfg~~ 313 (314)
+....|.|+. ..|++|+||.+
T Consensus 238 ~~~~~~~~~~--~~n~~~vfg~~ 258 (307)
T KOG1315|consen 238 GLHNKNGFNL--YVNFREVFGSN 258 (307)
T ss_pred cccccCCcce--eecHHHHhCCC
Confidence 2234566666 78999999876
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.7e-41 Score=303.31 Aligned_cols=206 Identities=17% Similarity=0.136 Sum_probs=149.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCccCCCCCCchhhhcCCCCCCCCcccCCCCCCCccccccccceeecccccCcc
Q 021332 101 SSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDKLVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPA 180 (314)
Q Consensus 101 ~~~~~i~~~~~~~l~~~~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpW 180 (314)
+....+.|.....|.+++|+.+++++||++|+...++... ++.-.+||..|+.+|+||||||+.|||||.+|||||||
T Consensus 47 g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~--D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPW 124 (414)
T KOG1314|consen 47 GVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK--DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPW 124 (414)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh--hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcc
Confidence 4556778888889999999999999999999987654321 11225799999999999999999999999999999999
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHH--H-HHH-----HHHh--hhccCCCCCCCCccHHHHHHHHHHHHHHHHHHHHH
Q 021332 181 FGNCIGQNNYFLFIVLLVGFLATEASY--V-ACS-----AQFV--GKSQNFDKSQSENDWVVNLATSTMLFSILQLLWQA 250 (314)
Q Consensus 181 i~nCVG~~N~r~F~lfl~~~~~~~~~~--~-~~~-----~~~~--~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~~~ 250 (314)
+|||||..||.+|..||+...++++-- + .++ +..+ ......-....-...+....++.+..++...+.++
T Consensus 125 innCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t 204 (414)
T KOG1314|consen 125 INNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALT 204 (414)
T ss_pred hhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHH
Confidence 999999999999999999888865311 1 111 1111 11111101112223344444555666677778889
Q ss_pred HHHHHHHHHHHhCchhHHhhhhcCCccchhccCCCCCcccCCcccCCCCHhHHHHHHHhcCC
Q 021332 251 VFFMWHIYCVCFNVRTDEWVNWKKYPEFQVIESEPGESFTRMRFTNPYDKGFLQNVKDFLSL 312 (314)
Q Consensus 251 ~ll~~q~~lI~~n~TT~E~~~~~r~~~~~~~~~~~~~~~~~~~~~npfd~G~~~N~~~vfg~ 312 (314)
+|+..|+.+|.+|+|.+|...-+|...-+.... .+..++...|||.|+..|++|||..
T Consensus 205 ~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~----~d~~~~f~ypydlgWr~n~r~vf~~ 262 (414)
T KOG1314|consen 205 MLFFIQLKQILNNRTGIESWIVEKAMDRREYYF----NDDEGEFTYPYDLGWRINLREVFFQ 262 (414)
T ss_pred HHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhc----cCCCCceeeeccccccccHHHHhhh
Confidence 999999999999999999987433322221111 2334678899999988899999854
No 3
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=100.00 E-value=2.5e-40 Score=283.67 Aligned_cols=157 Identities=19% Similarity=0.280 Sum_probs=118.1
Q ss_pred HHHHHHHhcCCCccCCCC-CCchh---------------hhcCCCCCCCCcccCCCCCCCccccccccceeecccccCcc
Q 021332 117 IGLCSIMSKDPGLITNEF-PHLDK---------------LVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPA 180 (314)
Q Consensus 117 ~~~~~~~~~dPG~vp~~~-~~~~~---------------~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpW 180 (314)
++|++++++|||++|+.. +..++ ..+.....++|.+|+.+||+|||||+.||+||.|+||||||
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 578999999999999881 11100 01122347899999999999999999999999999999999
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 021332 181 FGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVNLATSTMLFSILQLLWQAVFFMWHIYCV 260 (314)
Q Consensus 181 i~nCVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~~~~ll~~q~~lI 260 (314)
+|||||.+|||+|++|+++..++++......+.++....................++.++.+++.+++++.+++.|++++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999888776666555555443322211111111111124456677888899999999999999
Q ss_pred HhCchhHHhhhhc
Q 021332 261 CFNVRTDEWVNWK 273 (314)
Q Consensus 261 ~~n~TT~E~~~~~ 273 (314)
++|+||+|.+|+|
T Consensus 162 ~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 162 LRNITTYERIKRK 174 (174)
T ss_pred HcCCcHHHHHHcC
Confidence 9999999999754
No 4
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.1e-39 Score=303.09 Aligned_cols=192 Identities=24% Similarity=0.282 Sum_probs=131.5
Q ss_pred HHHHHHHHHHHHHHHHHh---cCCCccCCCC--CCchh-hhc---------CCCCCCCCcccCCCCCCCcccccccccee
Q 021332 107 LFNIEVAMIIIGLCSIMS---KDPGLITNEF--PHLDK-LVE---------GSELGVDPDNENSLSRKRVRYCKICKAHV 171 (314)
Q Consensus 107 ~~~~~~~l~~~~~~~~~~---~dPG~vp~~~--~~~~~-~~~---------~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV 171 (314)
...++....+.....+.. +|||.+|+.. +.+.. +.. .+...++|.+|+..||+|||||+.||+||
T Consensus 58 ~~~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV 137 (299)
T KOG1311|consen 58 LGAIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCV 137 (299)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccc
Confidence 333344433444444433 4999999952 21111 110 01126899999999999999999999999
Q ss_pred ecccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhh-ccCCCCCCC--CccHHHHHHHHHHHHHHHHHHH
Q 021332 172 EGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGK-SQNFDKSQS--ENDWVVNLATSTMLFSILQLLW 248 (314)
Q Consensus 172 ~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~i~~~~~~~~~~i~ 248 (314)
.||||||||+|||||++|||+|+.|++++.++.+.........+.. ......... .........+.+.+.+++.+..
T Consensus 138 ~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 217 (299)
T KOG1311|consen 138 LRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAF 217 (299)
T ss_pred cccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999997777655444433333222 221111111 2222223334455677777788
Q ss_pred HHHHHHHHHHHHHhCchhHHhhhhcCCccchhccCCCCCcccCCcccCCCCHhHHHHHHHhcCCCC
Q 021332 249 QAVFFMWHIYCVCFNVRTDEWVNWKKYPEFQVIESEPGESFTRMRFTNPYDKGFLQNVKDFLSLRR 314 (314)
Q Consensus 249 ~~~ll~~q~~lI~~n~TT~E~~~~~r~~~~~~~~~~~~~~~~~~~~~npfd~G~~~N~~~vfg~~r 314 (314)
++.|+.+|++++.+|+||+|.++. ++ .....+|||+|.++|+++++|+++
T Consensus 218 ~~~l~~fh~~li~~~~Tt~e~~~~--~~--------------~~~~~~~~~~g~~~n~~~~~~~~~ 267 (299)
T KOG1311|consen 218 TSALLCFHIYLIKSGSTTYESIKS--LD--------------FVSRSNPYDLGLLKNLQEVFGGPL 267 (299)
T ss_pred HHHHHHhheeeEecCcchhhhhhc--cc--------------cccccCCCchhHHHHHHHHhCCCC
Confidence 888999999999999999999865 11 011269999999999999998863
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=8.6e-37 Score=282.59 Aligned_cols=211 Identities=19% Similarity=0.284 Sum_probs=150.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhcCCCccCCCCCCch--h-----hhc-CCCCCCCCcccCCCCCCCcccccccccee
Q 021332 100 VSSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLD--K-----LVE-GSELGVDPDNENSLSRKRVRYCKICKAHV 171 (314)
Q Consensus 100 ~~~~~~i~~~~~~~l~~~~~~~~~~~dPG~vp~~~~~~~--~-----~~~-~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV 171 (314)
......+.+.+...+...+|++.+++|||+.+++....+ + ... ....+++|.+|+.+||+|||||+.||+||
T Consensus 54 ~~~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV 133 (309)
T COG5273 54 LVVLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCV 133 (309)
T ss_pred chhhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchh
Confidence 345677788888889999999999999999986533221 1 111 22347899999999999999999999999
Q ss_pred ecccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCccHHHH-HHHHHHHHHHHHHHHHH
Q 021332 172 EGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVN-LATSTMLFSILQLLWQA 250 (314)
Q Consensus 172 ~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~~~~~~~~~i~~~ 250 (314)
+||||||||+|||||.+|||+|++|+++....++........++........ ....... ++......+...++.+.
T Consensus 134 ~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~li~~~~~~~~~~f~~~~ 210 (309)
T COG5273 134 LKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRH---DTSLAICFLIFGCSLLGVVFFIITT 210 (309)
T ss_pred hccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccC---ChHHHHHHHHHhhhHHHHHHHHHHH
Confidence 9999999999999999999999999999988777666666666655543221 1111111 12222344455566777
Q ss_pred HHHHHHHHHHHhCchhHHhhhhcCCccchhccC-CCCC------cccCCcccCCCCHhHHHHHHHhcCCC
Q 021332 251 VFFMWHIYCVCFNVRTDEWVNWKKYPEFQVIES-EPGE------SFTRMRFTNPYDKGFLQNVKDFLSLR 313 (314)
Q Consensus 251 ~ll~~q~~lI~~n~TT~E~~~~~r~~~~~~~~~-~~~~------~~~~~~~~npfd~G~~~N~~~vfg~~ 313 (314)
.++.++.+++..|+||+|..+..|..+...... ..++ .....+..+|++.|.-+|+..+++.+
T Consensus 211 ~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~i~~~~ 280 (309)
T COG5273 211 LLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLSTIKGSN 280 (309)
T ss_pred HHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccceeecCCC
Confidence 889999999999999999998766655422111 0000 11122356788888888888877653
No 6
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=100.00 E-value=2.2e-36 Score=292.24 Aligned_cols=274 Identities=23% Similarity=0.339 Sum_probs=180.9
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHH------Hh-hhccccchhhHH-HHHHHHHH
Q 021332 18 CRCIISCILVLLTQLTLSLVPRFFAASPFIVQFALSGLVLLLVQTLCGWC------RR-LLGVCASAPAFV-FFNILFIW 89 (314)
Q Consensus 18 ~~~~~~~~~f~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~-~~~~~~~~P~~~-~f~~~~~w 89 (314)
++..++...|. .+.+.+.+.+.+|.++.+..+ ...+....+.+.+ .+ ..+.....|++. ++.++.+|
T Consensus 279 ~~~~~~~~~f~----~~~~~~~~~~~~~g~i~~~~~-~w~i~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw 353 (600)
T KOG0509|consen 279 GSKLAALIFFI----FLGLFYFISSWLPGVIFLINS-LWLIKGLALGKLVLTCLCATRKIVGFLLRPPLLSGFFLSTLFW 353 (600)
T ss_pred hhHHHHHHHHH----HHHHHHHHHhhccchhhhhhh-HHHHhhhhhhhhhhheeccchhhccccccchhHHHHHHHHHHH
Confidence 33344444444 777788888888888877776 3322222333221 11 222333456655 78889999
Q ss_pred HHHHHhhccch--hhHHHHHHHHHHHHHHHHHHHHHhcCCCccCCCCCCchhhh-----cCCCC-C-CCCcccCCCCCCC
Q 021332 90 GFYIAVVRQAV--SSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDKLV-----EGSEL-G-VDPDNENSLSRKR 160 (314)
Q Consensus 90 ~~~~~~~~~~~--~~~~~i~~~~~~~l~~~~~~~~~~~dPG~vp~~~~~~~~~~-----~~~~~-~-~~C~~C~~~kP~R 160 (314)
.++.|...... .+.....+.+..+..++.+++...+|||++|...+...+.. .++++ + +||.+|.++||.|
T Consensus 354 ~~~~w~~~i~~~~~~~~~~~~i~~~l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~clirKp~r 433 (600)
T KOG0509|consen 354 FYYFWFSKITPYTLFDFHYCFIISVLAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLTCLIRKPLR 433 (600)
T ss_pred HHHhhheeccchhhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceeeeeeecCCc
Confidence 99999873222 22222333333344445566666699999998876554332 23333 4 5999999999999
Q ss_pred ccccccccceeecccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCccHHHHHHHHHHH
Q 021332 161 VRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVNLATSTML 240 (314)
Q Consensus 161 s~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 240 (314)
||||+.|||||+||||||||++||||.+|||+|+.|++.+...+.+++.....|+....... ..+... ++.+..
T Consensus 434 Skhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~-----~~~~~~-l~~~~~ 507 (600)
T KOG0509|consen 434 SKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENAS-----TIYVGF-LIAVQA 507 (600)
T ss_pred cchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhH-----HHHHHH-HHHHHH
Confidence 99999999999999999999999999999999999999999988888887777776543311 001100 000000
Q ss_pred HHH-------------HHHHHHHHHHHHH-HHHHHhCchhHHhhhhcCCccchhccCCCCCcccCCcccCCCCHhHHHHH
Q 021332 241 FSI-------------LQLLWQAVFFMWH-IYCVCFNVRTDEWVNWKKYPEFQVIESEPGESFTRMRFTNPYDKGFLQNV 306 (314)
Q Consensus 241 ~~~-------------~~~i~~~~ll~~q-~~lI~~n~TT~E~~~~~r~~~~~~~~~~~~~~~~~~~~~npfd~G~~~N~ 306 (314)
+.. +.-.|......-| -..++.++||+|.++.+|+++++.+ +.+.++|++.|..+|+
T Consensus 508 ~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~---------~~~~~~~~s~g~~~Nl 578 (600)
T KOG0509|consen 508 FRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIK---------RGPTRSPFSPGPIRNL 578 (600)
T ss_pred HhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccc---------cCcCCCCCCchhhhcc
Confidence 000 0012333333333 3457999999999999999988743 3446899999999999
Q ss_pred HHhcC
Q 021332 307 KDFLS 311 (314)
Q Consensus 307 ~~vfg 311 (314)
.+|+-
T Consensus 579 ~df~~ 583 (600)
T KOG0509|consen 579 VDFFL 583 (600)
T ss_pred hheee
Confidence 99873
No 7
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=8e-37 Score=268.13 Aligned_cols=180 Identities=20% Similarity=0.217 Sum_probs=128.1
Q ss_pred HHHHHHHHHHhcCCCccCCCCCCchhhhcCCCCCCCCcccCCCCCCCccccccccceeecccccCcccccccccccHHHH
Q 021332 114 MIIIGLCSIMSKDPGLITNEFPHLDKLVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLF 193 (314)
Q Consensus 114 l~~~~~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F 193 (314)
-+.+.|+++....| +- + .+.....+|.+|..+||||+|||+.||+||+||||||||+|||||.+|||||
T Consensus 80 nvi~hy~ka~t~pP--vg--n-------~~~~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryF 148 (309)
T KOG1313|consen 80 NVIFHYYKARTKPP--VG--N-------PGLENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYF 148 (309)
T ss_pred HHHHhheeecccCC--cC--C-------CCCccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhH
Confidence 34455777777665 11 1 1122357999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccC-C-------CCCCCCcc-H---------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 021332 194 IVLLVGFLATEASYVACSAQFVGKSQN-F-------DKSQSEND-W---------VVNLATSTMLFSILQLLWQAVFFMW 255 (314)
Q Consensus 194 ~lfl~~~~~~~~~~~~~~~~~~~~~~~-~-------~~~~~~~~-~---------~~~~~i~~~~~~~~~~i~~~~ll~~ 255 (314)
++|++++++++....+...+.+..... . ++.....+ . ...-+..+.+.+...++.++.+..+
T Consensus 149 FlFl~~ltlat~~~~i~~~~~w~~~le~~~~~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W 228 (309)
T KOG1313|consen 149 FLFLFYLTLATSYAAIMCVYTWIDHLEPIEEITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAW 228 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcchHhhcccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999987665543333332211 1 11111111 1 1112334556666777888999999
Q ss_pred HHHHHHhCchhHHhhhhcCCccchhccCCCCCcccCCcccCCCCHhHHHHHHHhcCCCC
Q 021332 256 HIYCVCFNVRTDEWVNWKKYPEFQVIESEPGESFTRMRFTNPYDKGFLQNVKDFLSLRR 314 (314)
Q Consensus 256 q~~lI~~n~TT~E~~~~~r~~~~~~~~~~~~~~~~~~~~~npfd~G~~~N~~~vfg~~r 314 (314)
|.++|.+|.|.+|.....+.++... .+...||++.|.++|||.++|-.|
T Consensus 229 ~~vlI~~G~tsi~~~~~~~e~k~~~----------a~~R~~~~n~g~k~nWr~fLg~~~ 277 (309)
T KOG1313|consen 229 HAVLISRGETSIEQLINIKERKRYL----------AHLRSNPTNFGGKANWRNFLGLFR 277 (309)
T ss_pred hheeeehhhhhHHHHHHHHHhHhHH----------HhccCCCcccchHHHHHHhhcccc
Confidence 9999999999999987543222110 122389999999999999998654
No 8
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.8e-33 Score=248.14 Aligned_cols=106 Identities=26% Similarity=0.404 Sum_probs=81.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCCCCCCch-hh---hcCCCC-CCCCcccCCCCCCCccccccccceeecccccCccccc
Q 021332 109 NIEVAMIIIGLCSIMSKDPGLITNEFPHLD-KL---VEGSEL-GVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGN 183 (314)
Q Consensus 109 ~~~~~l~~~~~~~~~~~dPG~vp~~~~~~~-~~---~~~~~~-~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~n 183 (314)
..+.++-..+++.++.+|||.+.+++.... +. ++.-+. ...|+||+++||.|||||+.|||||.||||||.|+||
T Consensus 105 ~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfDHHCiWiNN 184 (341)
T KOG1312|consen 105 YLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFDHHCIWINN 184 (341)
T ss_pred HHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceeecCCCccccccCCCccccccchHHHHHHHHhccceEeeec
Confidence 334455667788999999999998754322 11 111222 4789999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 021332 184 CIGQNNYFLFIVLLVGFLATEASYVACSAQFV 215 (314)
Q Consensus 184 CVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~ 215 (314)
|||++|.|||++|+++... .+.+......|+
T Consensus 185 CIG~~N~ryF~lFLL~~i~-l~~yaivrlgfi 215 (341)
T KOG1312|consen 185 CIGAWNIRYFLLFLLTLIS-LATYAIVRLGFI 215 (341)
T ss_pred ccccchHHHHHHHHHHHHH-HHHHHHHHHHhe
Confidence 9999999999999998843 345554444443
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=89.66 E-value=1.2 Score=41.27 Aligned_cols=30 Identities=23% Similarity=0.577 Sum_probs=22.9
Q ss_pred ccccccccceeecccccCcccccccccccH
Q 021332 161 VRYCKICKAHVEGFDHHCPAFGNCIGQNNY 190 (314)
Q Consensus 161 s~HC~~C~~CV~r~DHHCpWi~nCVG~~N~ 190 (314)
.|+|..|+..+.++-|||+.-|+||-..=|
T Consensus 113 ~~~C~~C~~~rPpRs~HCsvC~~CV~rfDH 142 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPRSSHCSVCNNCVLRFDH 142 (299)
T ss_pred eEEcCcCcccCCCCcccchhhcccccccCC
Confidence 677888888888888888888888776654
No 10
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=89.02 E-value=3 Score=39.09 Aligned_cols=119 Identities=11% Similarity=-0.067 Sum_probs=78.1
Q ss_pred CCCCcccCCCCCCCccccccccceeecccccCcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCC-
Q 021332 147 GVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQ- 225 (314)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 225 (314)
.+.|..|+.=-...-|||.-=|.||.+..| +=.-.|++++....+..+....................
T Consensus 123 S~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (309)
T COG5273 123 SHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAI 191 (309)
T ss_pred CccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHH
Confidence 678999998899999999999999998665 55678888886555444433332222222111111111
Q ss_pred -----CCccHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhHHhhhhcCCc
Q 021332 226 -----SENDWVV-NLATSTMLFSILQLLWQAVFFMWHIYCVCFNVRTDEWVNWKKYP 276 (314)
Q Consensus 226 -----~~~~~~~-~~~i~~~~~~~~~~i~~~~ll~~q~~lI~~n~TT~E~~~~~r~~ 276 (314)
.+..... .+++..+++...+..|+......+.+++.++.++-|...-.+.+
T Consensus 192 ~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~ 248 (309)
T COG5273 192 CFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRES 248 (309)
T ss_pred HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccC
Confidence 1112222 23444556666677788888999999999999999988766555
No 11
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=87.72 E-value=0.29 Score=32.35 Aligned_cols=28 Identities=14% Similarity=-0.010 Sum_probs=24.0
Q ss_pred cCCCCCCCCcccCCCCCCCccccccccc
Q 021332 142 EGSELGVDPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 142 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
+...+...|..|..+-|+|+..|+.|+.
T Consensus 9 k~~~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 9 KRVFNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred HHhhcccchhcccCCCCccccccccCCC
Confidence 3445678999999999999999999886
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.08 E-value=0.39 Score=26.82 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=18.5
Q ss_pred CCcccCCCCCCCccccccccc
Q 021332 149 DPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
+|+.|...-++.++.|..|+.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999875
No 13
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=85.92 E-value=12 Score=31.19 Aligned_cols=48 Identities=13% Similarity=0.078 Sum_probs=33.3
Q ss_pred CCCCCcccCCCCCCCccccccccceeecccccCcccccccccccHHHHHHHHHHHHHHH
Q 021332 146 LGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATE 204 (314)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~~~~ 204 (314)
..+.|..|+.-...+-|||.--|.||.+..| +.+=.|+++.....+..
T Consensus 61 Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~ 108 (174)
T PF01529_consen 61 RSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYF 108 (174)
T ss_pred cceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHH
Confidence 3567888888888888888888888887666 34456666665443333
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.80 E-value=0.84 Score=26.17 Aligned_cols=23 Identities=17% Similarity=0.260 Sum_probs=19.0
Q ss_pred CCCCcccCCCCCCCccccccccc
Q 021332 147 GVDPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
..+|+.|...-++.++.|..||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 36799999888888999998875
No 15
>PF12773 DZR: Double zinc ribbon
Probab=77.64 E-value=2.2 Score=28.23 Aligned_cols=35 Identities=14% Similarity=0.152 Sum_probs=26.0
Q ss_pred CCCCCcccCCCCC---CCccccccccceeecccccCcc
Q 021332 146 LGVDPDNENSLSR---KRVRYCKICKAHVEGFDHHCPA 180 (314)
Q Consensus 146 ~~~~C~~C~~~kP---~Rs~HC~~C~~CV~r~DHHCpW 180 (314)
+.+||+.|...-+ ...+.|..|+.=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 4678888877665 3466788888888888888774
No 16
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=76.92 E-value=1.6 Score=45.11 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=18.0
Q ss_pred CCCcccCCCCC-------CCccccccccc
Q 021332 148 VDPDNENSLSR-------KRVRYCKICKA 169 (314)
Q Consensus 148 ~~C~~C~~~kP-------~Rs~HC~~C~~ 169 (314)
..|..|+..-. .|-||||.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999987664 39999999977
No 17
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=72.93 E-value=3.9 Score=41.31 Aligned_cols=85 Identities=16% Similarity=-0.060 Sum_probs=60.7
Q ss_pred HHHHHHHHHhcCCCccCCCCCCchhhhc---CC-CCCCCCcccCCCCCCCccccccccceeecccccCcccccccccccH
Q 021332 115 IIIGLCSIMSKDPGLITNEFPHLDKLVE---GS-ELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNY 190 (314)
Q Consensus 115 ~~~~~~~~~~~dPG~vp~~~~~~~~~~~---~~-~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~ 190 (314)
....++..+..+||++-.... ..-... .+ .....|.+|....+.+-.++..+-.++..+++||+|+. +|+-+|-
T Consensus 290 ~~~~~~~~~~~~~g~i~~~~~-~w~i~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~ 367 (600)
T KOG0509|consen 290 FLGLFYFISSWLPGVIFLINS-LWLIKGLALGKLVLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTL 367 (600)
T ss_pred HHHHHHHHHhhccchhhhhhh-HHHHhhhhhhhhhhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhh
Confidence 334455677778998876544 111111 11 12567899999999999999999999999999999999 9999998
Q ss_pred HHHH-HHHHHHH
Q 021332 191 FLFI-VLLVGFL 201 (314)
Q Consensus 191 r~F~-lfl~~~~ 201 (314)
..+- .++++.+
T Consensus 368 ~~~~~~~i~~~l 379 (600)
T KOG0509|consen 368 FDFHYCFIISVL 379 (600)
T ss_pred hhhHHHHHHHHH
Confidence 7543 3444433
No 18
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=69.91 E-value=0.5 Score=31.34 Aligned_cols=29 Identities=10% Similarity=-0.011 Sum_probs=24.0
Q ss_pred cCCCCCCCCcccCCCCCCCccccccccce
Q 021332 142 EGSELGVDPDNENSLSRKRVRYCKICKAH 170 (314)
Q Consensus 142 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~C 170 (314)
+..++...|..|..+-|+|+.-|+.|+.=
T Consensus 9 ~r~~~kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 9 KRLFNKKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHhhHHHHHHhcCCCCcchhHHhhccCC
Confidence 34456778999999999999999988753
No 19
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=68.99 E-value=3.4 Score=23.75 Aligned_cols=22 Identities=9% Similarity=0.229 Sum_probs=18.4
Q ss_pred CCCcccCCCCCCCccccccccc
Q 021332 148 VDPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
+.|+.|....|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 3589999999999999988874
No 20
>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=66.32 E-value=3 Score=28.58 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=27.9
Q ss_pred CCCcccCCCCCCC-------ccccccccceeecc-cccCccccccccc
Q 021332 148 VDPDNENSLSRKR-------VRYCKICKAHVEGF-DHHCPAFGNCIGQ 187 (314)
Q Consensus 148 ~~C~~C~~~kP~R-------s~HC~~C~~CV~r~-DHHCpWi~nCVG~ 187 (314)
.-|..|..--|+- |.-|..|..|+... +++|| ||=|.
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 3466776666655 46788999999988 99999 77665
No 21
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=65.88 E-value=44 Score=35.02 Aligned_cols=22 Identities=14% Similarity=0.332 Sum_probs=15.8
Q ss_pred hhhHHHHHHHHHHHHHHHhhcc
Q 021332 77 APAFVFFNILFIWGFYIAVVRQ 98 (314)
Q Consensus 77 ~P~~~~f~~~~~w~~~~~~~~~ 98 (314)
..++++++.+..|+.|+|-+..
T Consensus 96 ~~~~~~~~~~~v~~~~~~~~~~ 117 (697)
T PF09726_consen 96 VHWLFFAASTYVWVQYVWHTDR 117 (697)
T ss_pred HHHHHHHHhHHHHHHHhhhccC
Confidence 3445577778899998887754
No 22
>COG3336 Predicted membrane protein [Function unknown]
Probab=60.71 E-value=35 Score=31.62 Aligned_cols=30 Identities=23% Similarity=0.174 Sum_probs=24.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhc-CCCc
Q 021332 100 VSSLIGGLFNIEVAMIIIGLCSIMSK-DPGL 129 (314)
Q Consensus 100 ~~~~~~i~~~~~~~l~~~~~~~~~~~-dPG~ 129 (314)
.++..+.+.+..++...|.|+..+.. |||.
T Consensus 154 ~~p~~H~lm~~~~f~~aylfww~mI~~dpg~ 184 (299)
T COG3336 154 TSPTLHLLMNLLFFLSAYLFWWAMIGPDPGP 184 (299)
T ss_pred hcccHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 35778888888888888888888776 9984
No 23
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=57.79 E-value=3.6 Score=39.92 Aligned_cols=28 Identities=11% Similarity=0.110 Sum_probs=20.8
Q ss_pred CCCCCCCcccCCCC--CCCcccccccccee
Q 021332 144 SELGVDPDNENSLS--RKRVRYCKICKAHV 171 (314)
Q Consensus 144 ~~~~~~C~~C~~~k--P~Rs~HC~~C~~CV 171 (314)
+....+|+.|...- -.|-|||+.||+-+
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 34478999997543 34789999999844
No 24
>PF12773 DZR: Double zinc ribbon
Probab=53.11 E-value=13 Score=24.45 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=20.5
Q ss_pred CCCCCcccCCCCCCCcccccccc
Q 021332 146 LGVDPDNENSLSRKRVRYCKICK 168 (314)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~C~ 168 (314)
...+|+.|....++.+++|..|+
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 36789999999999999999986
No 25
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=51.46 E-value=6.7 Score=26.46 Aligned_cols=26 Identities=12% Similarity=0.037 Sum_probs=17.3
Q ss_pred CCCCCCcccCCCCCCCcccccc--ccce
Q 021332 145 ELGVDPDNENSLSRKRVRYCKI--CKAH 170 (314)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~--C~~C 170 (314)
.+...|..|..+-|+|+..|+. ||.+
T Consensus 15 ~~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 15 CDKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp TS-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred ccceecccccCcCCCCccceecccCCCC
Confidence 3467899999999999999998 8764
No 26
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=51.37 E-value=6.7 Score=35.02 Aligned_cols=13 Identities=38% Similarity=0.460 Sum_probs=10.3
Q ss_pred eeecccccCcccc
Q 021332 170 HVEGFDHHCPAFG 182 (314)
Q Consensus 170 CV~r~DHHCpWi~ 182 (314)
=..+.+|||||..
T Consensus 37 Hrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 37 HRSYESHHCPKGL 49 (250)
T ss_pred cchHhhcCCCccc
Confidence 4577899999975
No 27
>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 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=46.65 E-value=6.3 Score=23.12 Aligned_cols=20 Identities=15% Similarity=0.193 Sum_probs=14.5
Q ss_pred CcccCCCCCCCccccccccc
Q 021332 150 PDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 150 C~~C~~~kP~Rs~HC~~C~~ 169 (314)
|..|...-++++.+|..|+.
T Consensus 7 C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 7 CPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp ETTTTEEEESSSSB-TTT--
T ss_pred CCCCcCCchHHhhhhhCcCC
Confidence 88888888888888888864
No 29
>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=43.94 E-value=9 Score=27.03 Aligned_cols=26 Identities=15% Similarity=0.083 Sum_probs=12.5
Q ss_pred CCCCcccCCC--CCCCccccccccceee
Q 021332 147 GVDPDNENSL--SRKRVRYCKICKAHVE 172 (314)
Q Consensus 147 ~~~C~~C~~~--kP~Rs~HC~~C~~CV~ 172 (314)
...|..|... --.|-|||+.||+.|=
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEEC
Confidence 4567777642 2368899999998663
No 30
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=42.19 E-value=13 Score=28.11 Aligned_cols=15 Identities=20% Similarity=0.317 Sum_probs=10.5
Q ss_pred ecccccCcccccccc
Q 021332 172 EGFDHHCPAFGNCIG 186 (314)
Q Consensus 172 ~r~DHHCpWi~nCVG 186 (314)
..+-.||||++.-..
T Consensus 52 ~eHr~~CPwv~~~~q 66 (91)
T PF08600_consen 52 EEHREYCPWVNPSTQ 66 (91)
T ss_pred ccccccCCccCCccc
Confidence 334578999987653
No 31
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=40.55 E-value=37 Score=33.07 Aligned_cols=32 Identities=6% Similarity=0.020 Sum_probs=22.8
Q ss_pred CCCCcccCC-CCCCCccccccccceeecccccC
Q 021332 147 GVDPDNENS-LSRKRVRYCKICKAHVEGFDHHC 178 (314)
Q Consensus 147 ~~~C~~C~~-~kP~Rs~HC~~C~~CV~r~DHHC 178 (314)
..-|+.|.. .+|....+|.+|+.-..+.+++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 345999997 45556678888888776666653
No 32
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=40.18 E-value=2e+02 Score=23.33 Aligned_cols=75 Identities=9% Similarity=-0.029 Sum_probs=36.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH---HhhhccCCCCCCCCccHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 021332 189 NYFLFIVLLVGFLATEASYVACSAQ---FVGKSQNFDKSQSENDWVVN---LATSTMLFSILQLLWQAVFFMWHIYCVCF 262 (314)
Q Consensus 189 N~r~F~lfl~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~---~~i~~~~~~~~~~i~~~~ll~~q~~lI~~ 262 (314)
--+||-+|++.++.++.++.+.-.. -++....+++. ......++ .++-.++|++..+.+++.+..--.-++..
T Consensus 37 ~~~Y~~LfiVFl~AG~vLw~vM~~iFd~CIDsWkAdpeL-nn~rymWNilMYaIPy~L~Ala~GFlv~~~~~p~~~~i~~ 115 (141)
T PRK13743 37 SDIYFDLFIVFLTAGIVLWVIMHSIFDACIDSWKADPEL-NNFRYMWNILMYVIPYTLWALAAGFLVAGVRNPLCELING 115 (141)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhcChhh-hhHHHHHHHHHHHHHHHHHHHHhchhhhhhhhHHHHHHhc
Confidence 3478999999988887766553211 12222222222 11222222 23445566666555555444433334444
Q ss_pred Cc
Q 021332 263 NV 264 (314)
Q Consensus 263 n~ 264 (314)
|.
T Consensus 116 ~~ 117 (141)
T PRK13743 116 GI 117 (141)
T ss_pred ce
Confidence 43
No 33
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.81 E-value=12 Score=36.03 Aligned_cols=29 Identities=31% Similarity=0.433 Sum_probs=20.2
Q ss_pred CCCCccccccccceeecccccCcccccccccccHH
Q 021332 157 SRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYF 191 (314)
Q Consensus 157 kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r 191 (314)
+-.|-.||..|+. +|| +|..||||.-=.-
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga~~~~ 38 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGALCQS 38 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHHHHHH
Confidence 4445567777764 788 7999999974433
No 34
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=38.37 E-value=12 Score=34.96 Aligned_cols=44 Identities=14% Similarity=0.019 Sum_probs=32.9
Q ss_pred CCCCcccCCCCCCCccccccccceeecccccCcccccccccccHHHHHHHHHHHH
Q 021332 147 GVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFL 201 (314)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG~~N~r~F~lfl~~~~ 201 (314)
.+-|..|+.=--..-|||.-=|.||.-.++ +=.-.|+.+.....
T Consensus 123 aHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny-----------KfF~lfl~y~~l~~ 166 (307)
T KOG1315|consen 123 AHHCSVCNRCVLKMDHHCPWINNCVGFRNY-----------KFFLLFLFYTNLYS 166 (307)
T ss_pred cccchhhhhhhhccccCCcceeceecccch-----------HHHHHHHHHHHHHH
Confidence 677888887677788999999999986554 44556666666444
No 35
>COG0348 NapH Polyferredoxin [Energy production and conversion]
Probab=37.98 E-value=3.8e+02 Score=25.85 Aligned_cols=25 Identities=0% Similarity=-0.216 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCCC
Q 021332 109 NIEVAMIIIGLCSIMSKDPGLITNE 133 (314)
Q Consensus 109 ~~~~~l~~~~~~~~~~~dPG~vp~~ 133 (314)
+.........+....+.++|++++.
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~rr~ 183 (386)
T COG0348 159 GRLAIGLFAVFAFLLLGFGLFVRRF 183 (386)
T ss_pred hHHHHHHHHHHHHHHHHcccccccc
Confidence 3344444555666777788888765
No 36
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=36.20 E-value=12 Score=34.74 Aligned_cols=27 Identities=15% Similarity=0.114 Sum_probs=18.5
Q ss_pred CCCCcccCC-CC--CCCccccccccceeec
Q 021332 147 GVDPDNENS-LS--RKRVRYCKICKAHVEG 173 (314)
Q Consensus 147 ~~~C~~C~~-~k--P~Rs~HC~~C~~CV~r 173 (314)
...|..|.. .. -.|-|||+.||.-|-.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 556777765 22 3488999998886654
No 37
>COG4986 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]
Probab=34.36 E-value=2.8e+02 Score=27.37 Aligned_cols=96 Identities=17% Similarity=0.174 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHH---HHHHHHHHhhhccccchhhHHHHHHHHHHHHHHHhhccchhhH-
Q 021332 28 LLTQLTLSLVPRFFAASPFIVQFALSGLVLLLV---QTLCGWCRRLLGVCASAPAFVFFNILFIWGFYIAVVRQAVSSL- 103 (314)
Q Consensus 28 ~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~P~~~~f~~~~~w~~~~~~~~~~~~~~- 103 (314)
+.|...|...-.++.. +.+.+..+..+++.. +..++.+-.....+++.|.+.+|..+++...+.. +......
T Consensus 6 ~i~la~LaT~gRm~~a--i~iSi~~~~~lAy~A~Ksk~~E~i~ip~ldVlqSVPVlgFfpi~l~~Fv~lf--pG~lGvEl 81 (523)
T COG4986 6 LIPLALLATAGRMLLA--ILISILTGWFLAYAAIKSKRFENIYIPVLDVLQSVPVLGFFPIVLIFFVYLF--PGPLGVEL 81 (523)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhhhhhHhhhhhHHHHHhcCchheehhhhhhhhhhhc--CcchhHHH
Confidence 3455555544444442 223344444444444 3444444445557788999777777665544433 3221111
Q ss_pred --HHHHHHHHHHHHHHHHHHHHhcCC
Q 021332 104 --IGGLFNIEVAMIIIGLCSIMSKDP 127 (314)
Q Consensus 104 --~~i~~~~~~~l~~~~~~~~~~~dP 127 (314)
.-.+|+....-...+.|++-.+=|
T Consensus 82 Aa~FlvFTs~aWNi~fs~YQsFkTvP 107 (523)
T COG4986 82 AADFLVFTSVAWNIWFSEYQSFKTVP 107 (523)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 223344444444555666555444
No 38
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=32.36 E-value=15 Score=36.39 Aligned_cols=23 Identities=13% Similarity=0.106 Sum_probs=15.0
Q ss_pred CCCCcccCCCC--CCCccccccccc
Q 021332 147 GVDPDNENSLS--RKRVRYCKICKA 169 (314)
Q Consensus 147 ~~~C~~C~~~k--P~Rs~HC~~C~~ 169 (314)
...|..|+.+- --|-|||+.||.
T Consensus 901 a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCc
Confidence 34577776432 237899998886
No 39
>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=30.92 E-value=14 Score=24.43 Aligned_cols=15 Identities=27% Similarity=0.215 Sum_probs=6.8
Q ss_pred cceeecccc--cCcccc
Q 021332 168 KAHVEGFDH--HCPAFG 182 (314)
Q Consensus 168 ~~CV~r~DH--HCpWi~ 182 (314)
|.-+..-+| +|||-+
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 455666667 688865
No 40
>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=30.31 E-value=92 Score=27.81 Aligned_cols=30 Identities=17% Similarity=0.082 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCCCCC
Q 021332 106 GLFNIEVAMIIIGLCSIMSKDPGLITNEFP 135 (314)
Q Consensus 106 i~~~~~~~l~~~~~~~~~~~dPG~vp~~~~ 135 (314)
++..++.++++-+|..|.-.|||...+...
T Consensus 198 iVitl~vf~LvgLyr~C~k~dPg~p~~g~~ 227 (259)
T PF07010_consen 198 IVITLSVFTLVGLYRMCWKTDPGTPENGPD 227 (259)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCCcccCCC
Confidence 344555566667788888999996554443
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=30.20 E-value=53 Score=22.86 Aligned_cols=22 Identities=9% Similarity=0.169 Sum_probs=15.1
Q ss_pred CCCcccCCCCCCCccccc-cccc
Q 021332 148 VDPDNENSLSRKRVRYCK-ICKA 169 (314)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~-~C~~ 169 (314)
+-|..|...-|+--..|+ .|+.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 457777777777777775 5544
No 42
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=29.00 E-value=30 Score=24.30 Aligned_cols=22 Identities=18% Similarity=0.418 Sum_probs=18.5
Q ss_pred CCCcccCCCCCCCccccccccc
Q 021332 148 VDPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
+-|..|....|+.++-|..|+.
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred HHHhhccccCCCCCccCCCCCC
Confidence 4588898889999999998876
No 43
>PHA02690 hypothetical protein; Provisional
Probab=28.68 E-value=2.4e+02 Score=20.80 Aligned_cols=50 Identities=28% Similarity=0.359 Sum_probs=28.5
Q ss_pred hhhhccccchhhhhhhhhhhHH---HHHHHHHHHHHHHhcCch-HHHHHHHHHHHH
Q 021332 6 EQRKLSASLPLICRCIISCILV---LLTQLTLSLVPRFFAASP-FIVQFALSGLVL 57 (314)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~f---~~p~~~l~~~~~~~~~~~-~~~~~~~~~~~~ 57 (314)
-||-.|-+-|..|+ ++.++| |+-|+++.+++.+..+=| +-..+.++.++.
T Consensus 27 IqrhlEgs~plLR~--~~RlLfDL~lTvfV~myiv~Rl~~RN~gacamlAlaAA~~ 80 (90)
T PHA02690 27 IQRHLEGSTPLLRQ--MWRLLFDLLLTVFVVMYIVFRLIWRNPGACAMLALAAAVY 80 (90)
T ss_pred HHHHHhcCCHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHcChhHHHHHHHHHHHH
Confidence 36777888899988 444443 444566666666665544 333333433333
No 44
>KOG4085 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.57 E-value=51 Score=27.23 Aligned_cols=61 Identities=15% Similarity=0.175 Sum_probs=48.3
Q ss_pred cchhhhccccchhhhhhhhhhhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHh
Q 021332 4 VNEQRKLSASLPLICRCIISCILVLLTQLTLSLVPRFFAASPFIVQFALSGLVLLLVQTLCGWCRR 69 (314)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~f~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (314)
+|+--++.-|+|.--|+...+..=+.|.++-...-.++++ ++.++-.+.||+-.+++..+|
T Consensus 87 ~n~iAekves~~lw~kA~~Y~aMavvPI~lc~~L~tllGs-----g~iFatGV~YG~mALGKKadr 147 (175)
T KOG4085|consen 87 ANTIAEKVESLRLWQKAVFYCAMAVVPIVLCLTLTTLLGS-----GIIFATGVLYGLMALGKKADR 147 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHHhCc-----chhhhhHHHHHHHHhcccccH
Confidence 6787888888888888888888888888776666666665 678888899999888876644
No 45
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.62 E-value=24 Score=36.14 Aligned_cols=23 Identities=13% Similarity=0.148 Sum_probs=17.4
Q ss_pred CCCCcccCCC--CCCCccccccccc
Q 021332 147 GVDPDNENSL--SRKRVRYCKICKA 169 (314)
Q Consensus 147 ~~~C~~C~~~--kP~Rs~HC~~C~~ 169 (314)
..-|..|... ---|+|||+.||+
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccceeeeeeeeccccccccccch
Confidence 5679999742 1239999999998
No 46
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.32 E-value=51 Score=19.78 Aligned_cols=19 Identities=21% Similarity=0.480 Sum_probs=10.0
Q ss_pred CcccCCCCCCC-cc-cccccc
Q 021332 150 PDNENSLSRKR-VR-YCKICK 168 (314)
Q Consensus 150 C~~C~~~kP~R-s~-HC~~C~ 168 (314)
|..|...+..+ ++ -|+.|+
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~ 23 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCD 23 (32)
T ss_pred CeECCcCCccceeEEEccCCC
Confidence 55555544444 33 366665
No 47
>PF03083 MtN3_slv: Sugar efflux transporter for intercellular exchange; InterPro: IPR004316 This family includes proteins such as Drosophila saliva [], MtN3 involved in root nodule development [] and proteins involved in activation and expression of recombination activation genes (RAGs) []. Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This signature maps to transmembrane helices which are found in two copies in most members of the family.; GO: 0016021 integral to membrane
Probab=26.61 E-value=1.5e+02 Score=21.58 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=20.9
Q ss_pred hccccchhhHHHHHHHHHHHHHHHhhccc
Q 021332 71 LGVCASAPAFVFFNILFIWGFYIAVVRQA 99 (314)
Q Consensus 71 ~~~~~~~P~~~~f~~~~~w~~~~~~~~~~ 99 (314)
.+.+...|++..+.....|..|-+...+.
T Consensus 31 ~~~~~~~~~~~~~~~~~~W~~YG~l~~d~ 59 (87)
T PF03083_consen 31 TGSVSFPPFLAMFFNCVLWLIYGILINDW 59 (87)
T ss_pred CCccceehhHHHhhhccHhhhhhhhcCCe
Confidence 33444566666788889999999887654
No 48
>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=25.81 E-value=16 Score=22.44 Aligned_cols=23 Identities=9% Similarity=0.163 Sum_probs=10.7
Q ss_pred CCCcccCC---CCCCCcc--ccccccce
Q 021332 148 VDPDNENS---LSRKRVR--YCKICKAH 170 (314)
Q Consensus 148 ~~C~~C~~---~kP~Rs~--HC~~C~~C 170 (314)
+||++|.- .+..+.+ .|+.|+.-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCc
Confidence 57888863 2222222 46666653
No 49
>PF11674 DUF3270: Protein of unknown function (DUF3270); InterPro: IPR021688 This family of proteins with unknown function appears to be restricted to Streptococcus.
Probab=25.71 E-value=3e+02 Score=20.88 Aligned_cols=20 Identities=25% Similarity=0.265 Sum_probs=14.9
Q ss_pred chHHHHHHHHHHHHHHHHHH
Q 021332 44 SPFIVQFALSGLVLLLVQTL 63 (314)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~ 63 (314)
++.+.|.++|.++.++...+
T Consensus 64 l~t~~Af~~Ai~~Sl~~~~~ 83 (90)
T PF11674_consen 64 LNTFWAFPLAILISLAITQL 83 (90)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 67778888888888776443
No 50
>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=25.48 E-value=16 Score=24.23 Aligned_cols=18 Identities=17% Similarity=0.302 Sum_probs=12.9
Q ss_pred ccccceeecccccCcccc
Q 021332 165 KICKAHVEGFDHHCPAFG 182 (314)
Q Consensus 165 ~~C~~CV~r~DHHCpWi~ 182 (314)
..|+.|+.-.|-+|.|-.
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 667777777777777753
No 51
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=25.34 E-value=34 Score=22.84 Aligned_cols=24 Identities=13% Similarity=0.149 Sum_probs=16.0
Q ss_pred CCCcccCC--CCCCCcccccccccee
Q 021332 148 VDPDNENS--LSRKRVRYCKICKAHV 171 (314)
Q Consensus 148 ~~C~~C~~--~kP~Rs~HC~~C~~CV 171 (314)
+.|..|.. -.-.|.|||+.|++-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 34666653 2346889999998754
No 52
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Probab=25.34 E-value=72 Score=21.14 Aligned_cols=15 Identities=27% Similarity=0.361 Sum_probs=7.5
Q ss_pred hhhhhHHHHHHHHHH
Q 021332 21 IISCILVLLTQLTLS 35 (314)
Q Consensus 21 ~~~~~~f~~p~~~l~ 35 (314)
|.-+..+++|.+.+.
T Consensus 13 flfl~v~l~PiLsV~ 27 (47)
T TIGR02972 13 LGFIIVVLFPILSVA 27 (47)
T ss_pred HHHHHHHHHHHHHHH
Confidence 555555555554443
No 53
>PLN00186 ribosomal protein S26; Provisional
Probab=25.18 E-value=29 Score=27.21 Aligned_cols=15 Identities=20% Similarity=0.253 Sum_probs=12.3
Q ss_pred Cccccccccceeecc
Q 021332 160 RVRYCKICKAHVEGF 174 (314)
Q Consensus 160 Rs~HC~~C~~CV~r~ 174 (314)
+.-||..|++||.+=
T Consensus 19 ~~V~C~nCgr~vPKD 33 (109)
T PLN00186 19 KRIRCSNCGKCVPKD 33 (109)
T ss_pred cceeeCCCccccccc
Confidence 345899999999973
No 54
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.62 E-value=42 Score=18.63 Aligned_cols=21 Identities=19% Similarity=0.165 Sum_probs=16.5
Q ss_pred CCcccCCCCCCCccccccccc
Q 021332 149 DPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
.|..|...-..++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 488888888888888888864
No 55
>PF01534 Frizzled: Frizzled/Smoothened family membrane region; InterPro: IPR000539 The frizzled (fz) locus of Drosophila coordinates the cytoskeletons of epidermal cells, producing a parallel array of cuticular hairs and bristles [, ]. In fz mutants, the orientation of individual hairs with respect both to their neighbours and to the organism as a whole is altered. In the wild-type wing, all hairs point towards the distal tip []. In the developing wing, fz has 2 functions: it is required for the proximal-distal transmission of an intracellular polarity signal; and it is required for cells to respond to the polarity signal. Fz produces an mRNA that encodes an integral membrane protein with 7 putative transmembrane (TM) domains. This protein should contain both extracellular and cytoplasmic domains, which could function in the transmission and interpretation of polarity information []. This signature is usually found downstream of the Fz domain (IPR000024 from INTERPRO); GO: 0007166 cell surface receptor linked signaling pathway, 0016020 membrane
Probab=24.52 E-value=5.7e+02 Score=24.14 Aligned_cols=29 Identities=24% Similarity=0.218 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCchhH
Q 021332 238 TMLFSILQLLWQAVFFMWHIYCVCFNVRTD 267 (314)
Q Consensus 238 ~~~~~~~~~i~~~~ll~~q~~lI~~n~TT~ 267 (314)
..+++++..+.....++.|+|.- .|+...
T Consensus 229 iGiFsvly~vp~~~~i~c~~YE~-~~~~~W 257 (328)
T PF01534_consen 229 IGIFSVLYLVPALIVIACHFYEY-SNRPQW 257 (328)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HhhHHH
Confidence 45566666666667777788764 334343
No 56
>smart00301 DM Doublesex DNA-binding motif.
Probab=24.18 E-value=46 Score=22.75 Aligned_cols=6 Identities=33% Similarity=0.783 Sum_probs=4.5
Q ss_pred cCcccc
Q 021332 177 HCPAFG 182 (314)
Q Consensus 177 HCpWi~ 182 (314)
+|||-+
T Consensus 23 ~C~~r~ 28 (54)
T smart00301 23 ECPFRD 28 (54)
T ss_pred CCCCCC
Confidence 788875
No 57
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=24.02 E-value=28 Score=22.40 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=11.2
Q ss_pred ccccceeecccccCccc
Q 021332 165 KICKAHVEGFDHHCPAF 181 (314)
Q Consensus 165 ~~C~~CV~r~DHHCpWi 181 (314)
+.|..|+...|-||.|=
T Consensus 5 ~sC~~C~~~~~~~C~Wc 21 (46)
T smart00423 5 TSCSECLLARDPYCAWC 21 (46)
T ss_pred CcHHHHHcCCCCCCCcc
Confidence 45667777766667664
No 58
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.90 E-value=61 Score=33.66 Aligned_cols=38 Identities=21% Similarity=0.311 Sum_probs=20.3
Q ss_pred CCCCcccCCCCCCCccccccccceeecccccCcccccccc
Q 021332 147 GVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIG 186 (314)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWi~nCVG 186 (314)
.+||..|...- ..+.|..||.=+..-..+||=-|.-.|
T Consensus 15 akFC~~CG~~l--~~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 15 NRFCQKCGTSL--THKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CccccccCCCC--CCCcCCCCCCCCCcccccccccCCccc
Confidence 45666665332 234566666666666666654444333
No 59
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=23.72 E-value=31 Score=26.35 Aligned_cols=20 Identities=20% Similarity=0.311 Sum_probs=15.0
Q ss_pred CccccccccceeecccccCc
Q 021332 160 RVRYCKICKAHVEGFDHHCP 179 (314)
Q Consensus 160 Rs~HC~~C~~CV~r~DHHCp 179 (314)
+.-+|..|++||++----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 34589999999998655543
No 60
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.63 E-value=56 Score=21.33 Aligned_cols=22 Identities=9% Similarity=0.055 Sum_probs=11.3
Q ss_pred CCCcccCCCCCCC------ccccccccc
Q 021332 148 VDPDNENSLSRKR------VRYCKICKA 169 (314)
Q Consensus 148 ~~C~~C~~~kP~R------s~HC~~C~~ 169 (314)
+||+.|......+ -..|+.|+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCC
Confidence 3677775433222 234666663
No 61
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.54 E-value=52 Score=34.16 Aligned_cols=24 Identities=13% Similarity=0.268 Sum_probs=17.6
Q ss_pred CCCcccCCCCCCCcccccccccee
Q 021332 148 VDPDNENSLSRKRVRYCKICKAHV 171 (314)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~CV 171 (314)
..|+.|...-|+.+|.|..||.=.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l 25 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSL 25 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCC
Confidence 358888888888888887777643
No 62
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=22.29 E-value=35 Score=26.74 Aligned_cols=16 Identities=19% Similarity=0.256 Sum_probs=12.6
Q ss_pred Cccccccccceeeccc
Q 021332 160 RVRYCKICKAHVEGFD 175 (314)
Q Consensus 160 Rs~HC~~C~~CV~r~D 175 (314)
+.-||..|++||.+=-
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDK 34 (108)
T ss_pred ccEEeCCccccccccc
Confidence 3458999999999733
No 63
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=20.91 E-value=1.7e+02 Score=31.23 Aligned_cols=31 Identities=23% Similarity=0.255 Sum_probs=26.6
Q ss_pred ccchhhhhhhhhhhHHHHHHHHHHHHHHHhc
Q 021332 12 ASLPLICRCIISCILVLLTQLTLSLVPRFFA 42 (314)
Q Consensus 12 ~~~~~~~~~~~~~~~f~~p~~~l~~~~~~~~ 42 (314)
.-||++|+++.-....++|.++|++++.=.+
T Consensus 1072 ~~L~L~Kq~~l~~v~~vl~~iiL~~VF~~Vs 1102 (1175)
T COG5183 1072 MALELFKQGFLHMVIYVLPIIILSLVFLDVS 1102 (1175)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHhcc
Confidence 4589999999999999999999999887433
No 64
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=20.84 E-value=41 Score=31.28 Aligned_cols=22 Identities=23% Similarity=0.176 Sum_probs=16.6
Q ss_pred CCCCCcccCCCCCCCccccccccc
Q 021332 146 LGVDPDNENSLSRKRVRYCKICKA 169 (314)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~C~~ 169 (314)
+.+||.+|...+|. |-|+.|+.
T Consensus 318 d~~fCstCG~~ga~--KrCs~CKa 339 (396)
T KOG1710|consen 318 DCQFCSTCGHPGAK--KRCSQCKA 339 (396)
T ss_pred ecccccccCCCCcc--chhhhhHH
Confidence 47899999987764 67777763
No 65
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=20.65 E-value=47 Score=26.31 Aligned_cols=20 Identities=15% Similarity=0.081 Sum_probs=12.6
Q ss_pred CccccccccceeecccccCc
Q 021332 160 RVRYCKICKAHVEGFDHHCP 179 (314)
Q Consensus 160 Rs~HC~~C~~CV~r~DHHCp 179 (314)
+.-||..|++||++----..
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKR 38 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEE
T ss_pred cCEeeCcccccCcCCceEEE
Confidence 45689999999998554443
No 66
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=20.53 E-value=35 Score=35.89 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=26.8
Q ss_pred ccccc---cccceeecccccCcccc---ccc--ccccHHHHHH
Q 021332 161 VRYCK---ICKAHVEGFDHHCPAFG---NCI--GQNNYFLFIV 195 (314)
Q Consensus 161 s~HC~---~C~~CV~r~DHHCpWi~---nCV--G~~N~r~F~l 195 (314)
-|+|. .|..|++..|-||.|-+ .|+ +..|.|.+.+
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Q 533 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQ 533 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhh
Confidence 36777 88888878999999998 686 4556666654
No 67
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.09 E-value=71 Score=21.32 Aligned_cols=24 Identities=13% Similarity=-0.007 Sum_probs=14.7
Q ss_pred CCCCCcccCC-C--CCCCccccccccc
Q 021332 146 LGVDPDNENS-L--SRKRVRYCKICKA 169 (314)
Q Consensus 146 ~~~~C~~C~~-~--kP~Rs~HC~~C~~ 169 (314)
..++|+.|.. . .-....+|..|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3568999975 1 1223567777764
Done!