Query 023696
Match_columns 278
No_of_seqs 221 out of 1587
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 05:57:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023696hhsearch_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 6.8E-42 1.5E-46 309.2 12.1 198 64-270 7-230 (307)
2 PF01529 zf-DHHC: DHHC palmito 100.0 8.6E-41 1.9E-45 281.9 11.1 157 117-273 2-174 (174)
3 KOG1314 DHHC-type Zn-finger pr 100.0 2.1E-37 4.5E-42 277.5 11.9 199 67-270 9-224 (414)
4 KOG1311 DHHC-type Zn-finger pr 100.0 5.2E-37 1.1E-41 280.6 14.2 162 110-271 61-240 (299)
5 COG5273 Uncharacterized protei 100.0 1.5E-35 3.2E-40 270.8 15.2 183 86-270 40-230 (309)
6 KOG1313 DHHC-type Zn-finger pr 100.0 3.1E-33 6.7E-38 243.7 8.9 149 111-270 77-243 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 1.5E-30 3.3E-35 228.0 9.5 103 101-203 97-204 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 4E-29 8.7E-34 239.3 12.5 191 82-278 346-560 (600)
9 KOG1311 DHHC-type Zn-finger pr 94.1 0.15 3.2E-06 46.6 6.8 42 160-201 112-164 (299)
10 PF01529 zf-DHHC: DHHC palmito 93.1 1.5 3.3E-05 36.3 10.7 51 144-205 59-109 (174)
11 COG5273 Uncharacterized protei 89.4 2.9 6.3E-05 38.6 9.4 117 143-270 119-242 (309)
12 PF13240 zinc_ribbon_2: zinc-r 89.3 0.22 4.9E-06 27.7 1.3 21 149-169 1-21 (23)
13 PRK04136 rpl40e 50S ribosomal 88.1 0.24 5.2E-06 32.6 1.0 26 144-169 11-36 (48)
14 PF13248 zf-ribbon_3: zinc-rib 87.6 0.35 7.6E-06 27.6 1.4 23 147-169 2-24 (26)
15 PF06906 DUF1272: Protein of u 85.2 0.41 8.9E-06 32.6 0.9 37 148-187 6-50 (57)
16 PTZ00303 phosphatidylinositol 81.1 1 2.2E-05 46.2 2.2 22 148-169 461-489 (1374)
17 KOG1314 DHHC-type Zn-finger pr 80.7 26 0.00055 33.0 10.9 70 119-199 70-146 (414)
18 PF10571 UPF0547: Uncharacteri 76.6 1.7 3.8E-05 24.9 1.4 22 148-169 1-22 (26)
19 PF12773 DZR: Double zinc ribb 74.3 2.7 5.9E-05 27.5 2.1 35 146-180 11-48 (50)
20 PF01363 FYVE: FYVE zinc finge 73.5 1.7 3.7E-05 30.5 1.0 26 147-172 9-36 (69)
21 KOG0509 Ankyrin repeat and DHH 67.5 2.7 5.9E-05 41.9 1.3 85 115-201 290-379 (600)
22 PF12773 DZR: Double zinc ribb 67.4 4.9 0.00011 26.2 2.2 24 145-168 27-50 (50)
23 smart00064 FYVE Protein presen 65.2 5.3 0.00011 27.8 2.1 25 147-171 10-36 (68)
24 KOG1842 FYVE finger-containing 63.9 2.1 4.6E-05 41.0 -0.2 29 143-171 176-206 (505)
25 COG1552 RPL40A Ribosomal prote 63.5 1.4 3E-05 29.2 -1.1 26 145-170 12-37 (50)
26 TIGR00155 pqiA_fam integral me 58.3 1.8E+02 0.0038 28.0 12.4 32 147-178 215-247 (403)
27 PF01020 Ribosomal_L40e: Ribos 56.8 3.4 7.4E-05 27.7 -0.1 25 146-170 16-42 (52)
28 PF07010 Endomucin: Endomucin; 56.3 22 0.00047 31.4 4.7 28 108-135 200-227 (259)
29 KOG3183 Predicted Zn-finger pr 54.5 5.3 0.00012 35.3 0.7 13 170-182 37-49 (250)
30 KOG1315 Predicted DHHC-type Zn 54.4 5.3 0.00011 36.9 0.7 47 144-201 120-166 (307)
31 KOG1729 FYVE finger containing 49.0 6.4 0.00014 36.0 0.3 28 146-173 167-197 (288)
32 PF00641 zf-RanBP: Zn-finger i 47.1 6.1 0.00013 23.0 -0.1 21 149-169 6-26 (30)
33 KOG1819 FYVE finger-containing 43.7 7.9 0.00017 37.9 0.1 22 148-169 902-925 (990)
34 COG0348 NapH Polyferredoxin [E 42.2 1.1E+02 0.0024 29.1 7.6 14 163-176 246-259 (386)
35 PF07649 C1_3: C1-like domain; 41.9 13 0.00028 21.6 0.8 21 149-169 2-23 (30)
36 cd00065 FYVE FYVE domain; Zinc 39.3 22 0.00047 23.6 1.7 23 148-170 3-27 (57)
37 PF09297 zf-NADH-PPase: NADH p 36.0 25 0.00055 20.7 1.4 23 147-169 3-29 (32)
38 KOG1398 Uncharacterized conser 35.8 15 0.00031 35.0 0.5 28 157-190 10-37 (460)
39 COG2093 DNA-directed RNA polym 33.1 21 0.00046 24.9 0.9 22 148-169 5-26 (64)
40 PF09889 DUF2116: Uncharacteri 32.5 21 0.00045 24.7 0.7 24 146-169 2-26 (59)
41 smart00661 RPOL9 RNA polymeras 31.6 33 0.00071 22.2 1.6 22 148-169 1-28 (52)
42 PRK14559 putative protein seri 31.0 29 0.00062 35.5 1.7 31 147-179 15-45 (645)
43 PF08600 Rsm1: Rsm1-like; Int 30.8 25 0.00055 26.3 1.0 13 174-186 54-66 (91)
44 cd01995 ExsB ExsB is a transcr 30.8 16 0.00034 30.0 -0.1 24 148-174 141-164 (169)
45 PF01437 PSI: Plexin repeat; 30.7 12 0.00027 24.6 -0.6 18 165-182 6-23 (51)
46 KOG1818 Membrane trafficking a 30.7 22 0.00048 36.0 0.9 24 146-169 164-189 (634)
47 PRK14559 putative protein seri 30.5 29 0.00064 35.4 1.7 23 148-170 2-24 (645)
48 PF03107 C1_2: C1 domain; Int 29.9 45 0.00098 19.4 1.8 20 149-168 2-22 (30)
49 PF02077 SURF4: SURF4 family; 28.8 4.4E+02 0.0096 23.9 9.7 52 6-66 147-198 (267)
50 PRK03681 hypA hydrogenase nick 28.0 24 0.00053 27.5 0.5 24 146-169 69-95 (114)
51 PF03503 Chlam_OMP3: Chlamydia 27.1 69 0.0015 21.1 2.4 23 148-170 24-46 (55)
52 PF02150 RNA_POL_M_15KD: RNA p 27.1 19 0.00041 22.0 -0.2 22 148-169 2-28 (35)
53 PF13842 Tnp_zf-ribbon_2: DDE_ 27.0 49 0.0011 19.7 1.6 19 150-168 3-23 (32)
54 COG2995 PqiA Uncharacterized p 27.0 1.4E+02 0.003 28.7 5.3 31 142-172 215-246 (418)
55 KOG1841 Smad anchor for recept 26.8 27 0.00058 37.6 0.7 36 150-197 560-597 (1287)
56 PRK00432 30S ribosomal protein 26.5 45 0.00097 22.1 1.5 24 146-169 19-45 (50)
57 smart00547 ZnF_RBZ Zinc finger 26.4 38 0.00082 18.7 1.0 21 149-169 4-24 (26)
58 smart00423 PSI domain found in 26.2 21 0.00046 22.8 -0.1 17 165-181 5-21 (46)
59 PF07282 OrfB_Zn_ribbon: Putat 25.5 64 0.0014 22.3 2.3 25 146-170 27-55 (69)
60 PF06336 Corona_5a: Coronaviru 24.4 1.1E+02 0.0024 20.9 3.1 21 14-34 4-25 (65)
61 KOG1409 Uncharacterized conser 22.9 19 0.00042 33.8 -1.0 26 147-172 282-320 (404)
62 PLN00186 ribosomal protein S26 22.9 34 0.00075 26.5 0.5 16 160-175 19-34 (109)
63 KOG3611 Semaphorins [Signal tr 22.8 29 0.00063 36.0 0.1 37 161-197 491-535 (737)
64 COG0603 Predicted PP-loop supe 22.5 23 0.0005 31.1 -0.6 20 156-175 187-206 (222)
65 TIGR00364 exsB protein. This p 22.4 39 0.00084 28.7 0.8 23 148-173 179-201 (201)
66 COG0805 TatC Sec-independent p 21.8 5.9E+02 0.013 22.9 9.1 23 252-274 175-197 (255)
67 PF14319 Zn_Tnp_IS91: Transpos 21.4 41 0.0009 26.1 0.7 23 147-169 42-68 (111)
68 PRK09335 30S ribosomal protein 20.9 39 0.00085 25.6 0.4 21 160-180 19-39 (95)
69 PF10497 zf-4CXXC_R1: Zinc-fin 20.7 57 0.0012 25.1 1.3 20 145-164 5-24 (105)
70 PTZ00172 40S ribosomal protein 20.4 41 0.00088 26.1 0.4 17 160-176 19-35 (108)
71 PF07754 DUF1610: Domain of un 20.1 77 0.0017 17.8 1.4 19 150-168 1-23 (24)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.8e-42 Score=309.18 Aligned_cols=198 Identities=20% Similarity=0.295 Sum_probs=147.0
Q ss_pred hcceeeecccccchhHHHHHHHHhhhhhhhhhhccch--------hhHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCC
Q 023696 64 CGWCRRLLGVCASAPAFVFFNILFIWGFYIAVVRQAV--------SSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFP 135 (278)
Q Consensus 64 ~~~~~r~~~w~~~~p~~~~~~~~~~~~~y~~v~~~~~--------~~~~~ii~~~l~~~~~~s~~~~~~~dPG~vp~~~~ 135 (278)
.++++| | .|+ +++.....|.+|+++..... .....+.++.+.++..|+|++++.+|||.+|....
T Consensus 7 ~~~~~r---~---~~~-~~i~~~~~~~yy~~v~~~c~~~i~~~~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~ 79 (307)
T KOG1315|consen 7 FSKCLR---W---IPV-LIILLVIGWTYYVYVAVLCILSISLTIPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYR 79 (307)
T ss_pred chhhhc---c---hhh-eeeeeeEEEEEEEeehhhhHHHHhhhhHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccC
Confidence 345555 5 665 66667788888888765432 33456788999999999999999999999997643
Q ss_pred Cchhhh------------------cCCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchHHHHHHH
Q 023696 136 HLDKLV------------------EGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLL 197 (278)
Q Consensus 136 ~~~~~~------------------~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL 197 (278)
.+.++. ..+...++|.+|+.+||+|||||++|+|||+||||||||+|||||.+|||+|++|+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl 159 (307)
T KOG1315|consen 80 PSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFL 159 (307)
T ss_pred CCcCccccccccCcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHH
Confidence 221111 11235789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCCcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhccc
Q 023696 198 VGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVNLATSTMLFSILQLLWQAVFFMWHIYCVCFNVRTDELT 270 (278)
Q Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~i~~~~~~~~~~~ll~~hl~li~~n~TT~E~~ 270 (278)
+|..+.+.................+ ...++.......+.++.++..++.+++++++|++|+++|+||+|..
T Consensus 160 ~y~~l~~~~~lv~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~ 230 (307)
T KOG1315|consen 160 FYTNLYSIYVLVTTLIGFTKYFQGG--AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAY 230 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc--ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhh
Confidence 9999877665555444444433221 1112211222333455555566666779999999999999999999
No 2
>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=8.6e-41 Score=281.93 Aligned_cols=157 Identities=20% Similarity=0.287 Sum_probs=119.1
Q ss_pred HHHHHHHhcCCCcCCCCCCCc----------------hhhhcCCCCCCCCCCCCCCCCCCcccccccceeeccccccccc
Q 023696 117 IGLCSIMSKDPGLITNEFPHL----------------DKLVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPA 180 (278)
Q Consensus 117 ~s~~~~~~~dPG~vp~~~~~~----------------~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpW 180 (278)
++|+++..+|||++|++...+ .++.+.+...++|++|+.+||+|||||+.||+||.|+||||||
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 578999999999999881100 0011223467899999999999999999999999999999999
Q ss_pred ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023696 181 FGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVNLATSTMLFSILQLLWQAVFFMWHIYCV 260 (278)
Q Consensus 181 l~nCIG~~N~r~FilfL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~i~~~~~~~~~~~ll~~hl~li 260 (278)
+|||||++|||+|++|+++..+...+....++..+....................++.++.+++..++++.+++.|++++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999988777666555555443322222111111111124566677888889999999999999
Q ss_pred hcCcchhcccccc
Q 023696 261 CFNVRTDELTGRN 273 (278)
Q Consensus 261 ~~n~TT~E~~~~r 273 (278)
++|+||+|.+++|
T Consensus 162 ~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 162 LRNITTYERIKRK 174 (174)
T ss_pred HcCCcHHHHHHcC
Confidence 9999999999543
No 3
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.1e-37 Score=277.48 Aligned_cols=199 Identities=16% Similarity=0.118 Sum_probs=138.9
Q ss_pred eeeecccccchhHHHHHHHH-hhhh-hhh--hhhccc---hhhHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCCCchh
Q 023696 67 CRRLLGVCASAPAFVFFNIL-FIWG-FYI--AVVRQA---VSSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDK 139 (278)
Q Consensus 67 ~~r~~~w~~~~p~~~~~~~~-~~~~-~y~--~v~~~~---~~~~~~ii~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~ 139 (278)
.+|++.| +|...+.++. +++. .|. ....|. .+....+.|.+...|.+++|+.++.++||++|.++.++..
T Consensus 9 ~rr~~hw---Gpi~alsiit~i~~~~~~~n~lww~p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~ 85 (414)
T KOG1314|consen 9 FRRFLHW---GPITALSIITIITSTTGYMNSLWWFPLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENP 85 (414)
T ss_pred hhheecc---ccHHHHHHHHHHHHHHHHhhhhhhccccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Confidence 6788898 8876444322 2222 333 122232 3455788888899999999999999999999999765432
Q ss_pred hhcCCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchHHHHHHHHHHHHHHH----HHHHHHHHHh
Q 023696 140 LVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEA----SYVACSAQFV 215 (278)
Q Consensus 140 ~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~----~~~~~~~~~~ 215 (278)
. ++.-.++|..|+.+|+||||||+.|||||.+|||||||+|||||.+||.+|..||++..+++. ......++-+
T Consensus 86 ~--D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~I 163 (414)
T KOG1314|consen 86 K--DEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGI 163 (414)
T ss_pred h--hHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHH
Confidence 2 223458999999999999999999999999999999999999999999999999998877432 1111111111
Q ss_pred hhhc----CCCCCc--CCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhccc
Q 023696 216 GKSQ----NFDKSQ--SENDWVVNLATSTMLFSILQLLWQAVFFMWHIYCVCFNVRTDELT 270 (278)
Q Consensus 216 ~~~~----~~~~~~--~~~~~~~~l~i~~~i~~~~~~~~~~~ll~~hl~li~~n~TT~E~~ 270 (278)
...+ ...... ..........++.+.+++...+.++.|+..|+..|.+|+|.+|.+
T Consensus 164 y~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~w 224 (414)
T KOG1314|consen 164 YFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESW 224 (414)
T ss_pred HHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHH
Confidence 1111 111111 112222333333444555667778889999999999999999998
No 4
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=5.2e-37 Score=280.58 Aligned_cols=162 Identities=23% Similarity=0.254 Sum_probs=113.3
Q ss_pred HHHHHHHHHHHHHHh---cCCCcCCCCC--CCchh---hh-------cCCCCCCCCCCCCCCCCCCcccccccceeeccc
Q 023696 110 IEVAMIIIGLCSIMS---KDPGLITNEF--PHLDK---LV-------EGSELGVDPDNENSLSRKRVRYCKICKAHVEGF 174 (278)
Q Consensus 110 ~l~~~~~~s~~~~~~---~dPG~vp~~~--~~~~~---~~-------~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~ 174 (278)
++....+.....+.. +|||.+|++. +.+.. .. ..+.+.++|++|+..||+|||||+.||+||.||
T Consensus 61 if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rf 140 (299)
T KOG1311|consen 61 IFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRF 140 (299)
T ss_pred HHHHHHHHHHHHHHhcccCCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhccccccc
Confidence 333333444444443 4999999952 21111 00 011247899999999999999999999999999
Q ss_pred ccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC-CCCCcC--CChHHHHHHHHHHHHHHHHHHHHHH
Q 023696 175 DHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQN-FDKSQS--ENDWVVNLATSTMLFSILQLLWQAV 251 (278)
Q Consensus 175 DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~--~~~~~~~l~i~~~i~~~~~~~~~~~ 251 (278)
||||||+|||||+||||+|+.|+++..++..+.+......+..... ...... .........+...+++++....++.
T Consensus 141 DHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 220 (299)
T KOG1311|consen 141 DHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSA 220 (299)
T ss_pred CCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999997777655544443333322111 111111 2222333445556778888889999
Q ss_pred HHHHHHHHHhcCcchhcccc
Q 023696 252 FFMWHIYCVCFNVRTDELTG 271 (278)
Q Consensus 252 ll~~hl~li~~n~TT~E~~~ 271 (278)
++.+|++++.+|+||+|+++
T Consensus 221 l~~fh~~li~~~~Tt~e~~~ 240 (299)
T KOG1311|consen 221 LLCFHIYLIKSGSTTYESIK 240 (299)
T ss_pred HHHhheeeEecCcchhhhhh
Confidence 99999999999999999984
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=1.5e-35 Score=270.80 Aligned_cols=183 Identities=19% Similarity=0.308 Sum_probs=133.0
Q ss_pred HhhhhhhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCCCc------hh--hhcCCCCCCCCCCCCCCC
Q 023696 86 LFIWGFYIAVVRQAVSSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHL------DK--LVEGSELGVDPDNENSLS 157 (278)
Q Consensus 86 ~~~~~~y~~v~~~~~~~~~~ii~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~------~~--~~~~~~~~~~C~~C~~~k 157 (278)
...|.....+..........+.+.+.......++++...+|||+.+++.... ++ +......+++|.+|+.+|
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~K 119 (309)
T COG5273 40 IVVYTLLVIVKSLSLVVLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYK 119 (309)
T ss_pred HHHHhhhheeeeccchhhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceecccccccc
Confidence 4555554444444455666777888888999999999999999998653211 11 122335689999999999
Q ss_pred CCCcccccccceeecccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCcCCChHHHHHHHH
Q 023696 158 RKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVVNLATS 237 (278)
Q Consensus 158 P~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~ 237 (278)
|+|||||+.|||||+||||||||+|||||.+|||+|+.|+++........+.....+......... ..+.+...++..
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~li~~ 197 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRH--DTSLAICFLIFG 197 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccC--ChHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999987666555544444443322211 112221112222
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcchhccc
Q 023696 238 TMLFSILQLLWQAVFFMWHIYCVCFNVRTDELT 270 (278)
Q Consensus 238 ~~i~~~~~~~~~~~ll~~hl~li~~n~TT~E~~ 270 (278)
....+...+..+..++.++.+++..|+|+.|..
T Consensus 198 ~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~ 230 (309)
T COG5273 198 CSLLGVVFFIITTLLLLFLIYLILNNLTTIEFI 230 (309)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 234555556777888999999999999999998
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=3.1e-33 Score=243.66 Aligned_cols=149 Identities=18% Similarity=0.204 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHHHhcCCCcCCCCCCCchhhhcCCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccch
Q 023696 111 EVAMIIIGLCSIMSKDPGLITNEFPHLDKLVEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNY 190 (278)
Q Consensus 111 l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~ 190 (278)
++...++.|+++....| ... +..+...+|.+|+.+||||+|||+.|||||+||||||||+|||||.+||
T Consensus 77 ~l~nvi~hy~ka~t~pP----vgn-------~~~~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH 145 (309)
T KOG1313|consen 77 LLSNVIFHYYKARTKPP----VGN-------PGLENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNH 145 (309)
T ss_pred HHHHHHHhheeecccCC----cCC-------CCCccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccc
Confidence 44556667788776665 111 1112347999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC--------CcCCCh----------HHHHHHHHHHHHHHHHHHHHHHH
Q 023696 191 FLFIVLLVGFLATEASYVACSAQFVGKSQNFDK--------SQSEND----------WVVNLATSTMLFSILQLLWQAVF 252 (278)
Q Consensus 191 r~FilfL~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~----------~~~~l~i~~~i~~~~~~~~~~~l 252 (278)
|||++|++|+.+++.+..+...+.+.+.....+ .....| +.-.-+......+....+.++.+
T Consensus 146 ryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l 225 (309)
T KOG1313|consen 146 RYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEITAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLL 225 (309)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhcccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999888776655555543322110 000111 00001222444566677788999
Q ss_pred HHHHHHHHhcCcchhccc
Q 023696 253 FMWHIYCVCFNVRTDELT 270 (278)
Q Consensus 253 l~~hl~li~~n~TT~E~~ 270 (278)
..+|.++|.+|.|++|..
T Consensus 226 ~~W~~vlI~~G~tsi~~~ 243 (309)
T KOG1313|consen 226 TAWHAVLISRGETSIEQL 243 (309)
T ss_pred HHHhheeeehhhhhHHHH
Confidence 999999999999999988
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.97 E-value=1.5e-30 Score=227.99 Aligned_cols=103 Identities=26% Similarity=0.333 Sum_probs=81.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCCCchhh-hcCC----CCCCCCCCCCCCCCCCcccccccceeecccc
Q 023696 101 SSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDKL-VEGS----ELGVDPDNENSLSRKRVRYCKICKAHVEGFD 175 (278)
Q Consensus 101 ~~~~~ii~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~-~~~~----~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~D 175 (278)
+...-+....+.+.-..++..++.+|||.+.++.+..... -+-| .+.+.|+||+.+||.||||||.|||||.|||
T Consensus 97 sl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if~k~~kCSTCki~KPARSKHCsiCNrCV~rfD 176 (341)
T KOG1312|consen 97 SLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIFPKNVKCSTCKIRKPARSKHCSICNRCVHRFD 176 (341)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceeecCCCccccccCCCccccccchHHHHHHHHhc
Confidence 3334444445556667788899999999999875543211 1112 2448899999999999999999999999999
Q ss_pred cccccccccccccchHHHHHHHHHHHHH
Q 023696 176 HHCPAFGNCIGQNNYFLFIVLLVGFLAT 203 (278)
Q Consensus 176 HHCpWl~nCIG~~N~r~FilfL~~~~~~ 203 (278)
|||.|+|||||++|.|||++|+++...+
T Consensus 177 HHCiWiNNCIG~~N~ryF~lFLL~~i~l 204 (341)
T KOG1312|consen 177 HHCIWINNCIGAWNIRYFLLFLLTLISL 204 (341)
T ss_pred cceEeeecccccchHHHHHHHHHHHHHH
Confidence 9999999999999999999999988543
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.96 E-value=4e-29 Score=239.34 Aligned_cols=191 Identities=23% Similarity=0.355 Sum_probs=126.4
Q ss_pred HHHHHhhhhhhhhhhc--cchhhHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCCCchhh------hcCCCCC-CCCCC
Q 023696 82 FFNILFIWGFYIAVVR--QAVSSLIGGLFNIEVAMIIIGLCSIMSKDPGLITNEFPHLDKL------VEGSELG-VDPDN 152 (278)
Q Consensus 82 ~~~~~~~~~~y~~v~~--~~~~~~~~ii~~~l~~~~~~s~~~~~~~dPG~vp~~~~~~~~~------~~~~~~~-~~C~~ 152 (278)
...+...|.++.+... +...+.....+.+..+..++++.+...+|||++|...+...+. ..+...+ ++|.+
T Consensus 346 ~~~~~~fw~~~~w~~~i~~~~~~~~~~~~i~~~l~~~~~f~~~~rsDPg~i~~~~~~~~~tIs~l~d~gkf~~en~FC~~ 425 (600)
T KOG0509|consen 346 FFLSTLFWFYYFWFSKITPYTLFDFHYCFIISVLAYFITFGLFLRSDPGFIPTSTEVGRETISQLIDFGKFDLENRFCLT 425 (600)
T ss_pred HHHHHHHHHHHhhheeccchhhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCchhhHHHHHHHhhccccccccccceee
Confidence 3456666766665541 1233334455555566667777888889999999886544221 1112234 69999
Q ss_pred CCCCCCCCcccccccceeecccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCcCCChHHH
Q 023696 153 ENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFDKSQSENDWVV 232 (278)
Q Consensus 153 C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (278)
|.++||.|||||+.|||||.||||||||++||||.+|||+|+.|++.....+.++++....++....+.. ..+..
T Consensus 426 clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~-----~~~~~ 500 (600)
T KOG0509|consen 426 CLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENAS-----TIYVG 500 (600)
T ss_pred eeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhH-----HHHHH
Confidence 9999999999999999999999999999999999999999999999998888787776666664322110 11111
Q ss_pred HHHHHHHHHHH-------------HHHHHHHHH-HHHHHHHHhcCcchhccc-cccCCCCC
Q 023696 233 NLATSTMLFSI-------------LQLLWQAVF-FMWHIYCVCFNVRTDELT-GRNIPSFK 278 (278)
Q Consensus 233 ~l~i~~~i~~~-------------~~~~~~~~l-l~~hl~li~~n~TT~E~~-~~r~~~~~ 278 (278)
. .+.+..+.. +.-.+.... -..|-..++.+.||+|.+ .+|+++++
T Consensus 501 ~-l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~ 560 (600)
T KOG0509|consen 501 F-LIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLG 560 (600)
T ss_pred H-HHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccc
Confidence 1 111111110 001111222 233445688899999999 88888864
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=94.10 E-value=0.15 Score=46.63 Aligned_cols=42 Identities=17% Similarity=0.411 Sum_probs=33.7
Q ss_pred Ccccccccceeecccccccccccccccccc-----------hHHHHHHHHHHH
Q 023696 160 RVRYCKICKAHVEGFDHHCPAFGNCIGQNN-----------YFLFIVLLVGFL 201 (278)
Q Consensus 160 Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N-----------~r~FilfL~~~~ 201 (278)
+.|+|..|+..+.++-|||+.-|+||-+.= +|.+-.|+.+..
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHH
Confidence 378899999999999999999999998774 467777875544
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=93.13 E-value=1.5 Score=36.28 Aligned_cols=51 Identities=12% Similarity=0.058 Sum_probs=37.9
Q ss_pred CCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchHHHHHHHHHHHHHHH
Q 023696 144 SELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEA 205 (278)
Q Consensus 144 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~ 205 (278)
..+.++|+.|+.-...+-|||.--|.||.+..| +.+=.|+.+.....+...
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~-----------~~F~~fl~~~~~~~~~~~ 109 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH-----------RYFLLFLLYLCLYCLYFF 109 (174)
T ss_pred CCcceeccccccccccccccchhhccccccccH-----------HHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999999999998766 345567666654444333
No 11
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=89.38 E-value=2.9 Score=38.64 Aligned_cols=117 Identities=11% Similarity=-0.078 Sum_probs=70.2
Q ss_pred CCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023696 143 GSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFLATEASYVACSAQFVGKSQNFD 222 (278)
Q Consensus 143 ~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (278)
+.++.++|+.|+.=-...-|||.-=|+||.+..| |=.-.|+.++....+...+..............+.
T Consensus 119 KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~-----------r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 187 (309)
T COG5273 119 KPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNY-----------RFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDT 187 (309)
T ss_pred cCCCCccchhhcchhhccCccCcccccccCcchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCh
Confidence 3456789999999999999999999999998654 55667887775554433332222222222111111
Q ss_pred CCc------CCChHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhccc
Q 023696 223 KSQ------SENDWVV-NLATSTMLFSILQLLWQAVFFMWHIYCVCFNVRTDELT 270 (278)
Q Consensus 223 ~~~------~~~~~~~-~l~i~~~i~~~~~~~~~~~ll~~hl~li~~n~TT~E~~ 270 (278)
... ....... .+.+....+......+.......+.+...++.++-|..
T Consensus 188 ~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~ 242 (309)
T COG5273 188 SLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFF 242 (309)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceeccccc
Confidence 111 1111111 12233333344445566667788889999999999887
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.32 E-value=0.22 Score=27.67 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCcccccccce
Q 023696 149 DPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
+|+.|...-++.++.|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999985
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=88.07 E-value=0.24 Score=32.57 Aligned_cols=26 Identities=15% Similarity=-0.014 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCCCCCcccccccce
Q 023696 144 SELGVDPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 144 ~~~~~~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
.....+|..|..+-|+|+..|+.||.
T Consensus 11 ~~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 11 VFNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hhcccchhcccCCCCccccccccCCC
Confidence 34568999999999999999999886
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.60 E-value=0.35 Score=27.61 Aligned_cols=23 Identities=17% Similarity=0.260 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCCCCcccccccce
Q 023696 147 GVDPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
..+|+.|...-++.++.|+.||.
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 36899999988999999999985
No 15
>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=85.19 E-value=0.41 Score=32.59 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=29.5
Q ss_pred CCCCCCCCCCCCCc-------ccccccceeeccc-ccccccccccccc
Q 023696 148 VDPDNENSLSRKRV-------RYCKICKAHVEGF-DHHCPAFGNCIGQ 187 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs-------~HC~~C~~CV~r~-DHHCpWl~nCIG~ 187 (278)
.-|+.|+..-|+-| +-|..|..|+... +++|| ||=|.
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 45788877766654 6688999999998 99999 88775
No 16
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=81.10 E-value=1 Score=46.17 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=17.7
Q ss_pred CCCCCCCCCCC-------CCcccccccce
Q 023696 148 VDPDNENSLSR-------KRVRYCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~kP-------~Rs~HC~~C~~ 169 (278)
+.|..|+..-. .|-||||.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 56999987664 39999999876
No 17
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=80.72 E-value=26 Score=33.00 Aligned_cols=70 Identities=11% Similarity=-0.035 Sum_probs=49.7
Q ss_pred HHHHHhcCCCcCCCCCCCchhh-------hcCCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchH
Q 023696 119 LCSIMSKDPGLITNEFPHLDKL-------VEGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYF 191 (278)
Q Consensus 119 ~~~~~~~dPG~vp~~~~~~~~~-------~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r 191 (278)
+.---+..||+-|++..+.... +.+.+..+.|.+|+.-.-.--|||+--|.||--..| .-.-
T Consensus 70 ~~gPG~vp~~wkPe~~~D~~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh-----------~~F~ 138 (414)
T KOG1314|consen 70 FTGPGFVPLGWKPENPKDEMFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANH-----------AYFL 138 (414)
T ss_pred hcCCCCCCCCCCCCCChhHHHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhccccccc-----------HHHH
Confidence 3444567899999876653221 223456789999998777788999999999986655 3356
Q ss_pred HHHHHHHH
Q 023696 192 LFIVLLVG 199 (278)
Q Consensus 192 ~FilfL~~ 199 (278)
+|++|...
T Consensus 139 ~FLlf~iv 146 (414)
T KOG1314|consen 139 RFLLFSIV 146 (414)
T ss_pred HHHHHHHH
Confidence 77777764
No 18
>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=76.62 E-value=1.7 Score=24.86 Aligned_cols=22 Identities=9% Similarity=0.229 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCCcccccccce
Q 023696 148 VDPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
+.|+.|...-|.-++-|+.||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4689999999999999998874
No 19
>PF12773 DZR: Double zinc ribbon
Probab=74.33 E-value=2.7 Score=27.46 Aligned_cols=35 Identities=14% Similarity=0.152 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCCC---CCcccccccceeeccccccccc
Q 023696 146 LGVDPDNENSLSR---KRVRYCKICKAHVEGFDHHCPA 180 (278)
Q Consensus 146 ~~~~C~~C~~~kP---~Rs~HC~~C~~CV~r~DHHCpW 180 (278)
..++|..|...-+ .....|+.|++=+...+.+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 3467777766555 3356677777766666666653
No 20
>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=73.48 E-value=1.7 Score=30.47 Aligned_cols=26 Identities=15% Similarity=0.083 Sum_probs=12.8
Q ss_pred CCCCCCCCCC--CCCCcccccccceeec
Q 023696 147 GVDPDNENSL--SRKRVRYCKICKAHVE 172 (278)
Q Consensus 147 ~~~C~~C~~~--kP~Rs~HC~~C~~CV~ 172 (278)
...|..|+.. --.|-|||+.||+-|=
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 4668888642 3478999999998653
No 21
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=67.50 E-value=2.7 Score=41.88 Aligned_cols=85 Identities=15% Similarity=-0.099 Sum_probs=59.3
Q ss_pred HHHHHHHHHhcCCCcCCCCCCCchhhh----cCCCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccch
Q 023696 115 IIIGLCSIMSKDPGLITNEFPHLDKLV----EGSELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNY 190 (278)
Q Consensus 115 ~~~s~~~~~~~dPG~vp~~~~~~~~~~----~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~ 190 (278)
.....+.++..+||++-.... .-..+ ..-.....|.+|....+.+..++..+..+...+++||+|.. +|+.+|-
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 344455566677877765432 11111 11123467888999999999999999999999999999999 9999998
Q ss_pred HHHH-HHHHHHH
Q 023696 191 FLFI-VLLVGFL 201 (278)
Q Consensus 191 r~Fi-lfL~~~~ 201 (278)
..+- .++++.+
T Consensus 368 ~~~~~~~i~~~l 379 (600)
T KOG0509|consen 368 FDFHYCFIISVL 379 (600)
T ss_pred hhhHHHHHHHHH
Confidence 7544 4444433
No 22
>PF12773 DZR: Double zinc ribbon
Probab=67.36 E-value=4.9 Score=26.19 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCCCCCcccccccc
Q 023696 145 ELGVDPDNENSLSRKRVRYCKICK 168 (278)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~C~ 168 (278)
....+|+.|....++.+++|..||
T Consensus 27 ~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 27 QSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCCcCCcCCCcCCcCccCccc
Confidence 445789999999999999999986
No 23
>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 KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=63.87 E-value=2.1 Score=41.05 Aligned_cols=29 Identities=10% Similarity=0.116 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCCC--CCCCcccccccceee
Q 023696 143 GSELGVDPDNENSL--SRKRVRYCKICKAHV 171 (278)
Q Consensus 143 ~~~~~~~C~~C~~~--kP~Rs~HC~~C~~CV 171 (278)
++....+|+.|... --.|-|||+.||+-+
T Consensus 176 DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 176 DDSSVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred CCCcccccccccchhhhHHHhhhhhhcchHH
Confidence 44567899999754 356899999999843
No 25
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=63.49 E-value=1.4 Score=29.17 Aligned_cols=26 Identities=12% Similarity=0.011 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCCCCccccccccee
Q 023696 145 ELGVDPDNENSLSRKRVRYCKICKAH 170 (278)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC~~C~~C 170 (278)
.+.++|..|+..-|+|+.-|+.|+.=
T Consensus 12 ~~kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 12 FNKKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred hhHHHHHHhcCCCCcchhHHhhccCC
Confidence 45578999999999999999988753
No 26
>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=58.33 E-value=1.8e+02 Score=27.97 Aligned_cols=32 Identities=6% Similarity=0.020 Sum_probs=23.0
Q ss_pred CCCCCCCCC-CCCCCcccccccceeeccccccc
Q 023696 147 GVDPDNENS-LSRKRVRYCKICKAHVEGFDHHC 178 (278)
Q Consensus 147 ~~~C~~C~~-~kP~Rs~HC~~C~~CV~r~DHHC 178 (278)
..-|+.|+. .+|....||+.||.-..|.+++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 455999997 45566678888888776666553
No 27
>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=56.81 E-value=3.4 Score=27.70 Aligned_cols=25 Identities=12% Similarity=0.078 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCCCCCcccccc--ccee
Q 023696 146 LGVDPDNENSLSRKRVRYCKI--CKAH 170 (278)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 170 (278)
+...|..|..+-|+|+..|+. ||.+
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 28
>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=56.34 E-value=22 Score=31.38 Aligned_cols=28 Identities=18% Similarity=0.120 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcCCCCCC
Q 023696 108 FNIEVAMIIIGLCSIMSKDPGLITNEFP 135 (278)
Q Consensus 108 ~~~l~~~~~~s~~~~~~~dPG~vp~~~~ 135 (278)
..++.+.++-.|..+..+|||...+..+
T Consensus 200 itl~vf~LvgLyr~C~k~dPg~p~~g~~ 227 (259)
T PF07010_consen 200 ITLSVFTLVGLYRMCWKTDPGTPENGPD 227 (259)
T ss_pred HHHHHHHHHHHHHHhhcCCCCCcccCCC
Confidence 3444555666777788999997665543
No 29
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=54.49 E-value=5.3 Score=35.31 Aligned_cols=13 Identities=38% Similarity=0.460 Sum_probs=9.6
Q ss_pred eeccccccccccc
Q 023696 170 HVEGFDHHCPAFG 182 (278)
Q Consensus 170 CV~r~DHHCpWl~ 182 (278)
=..+.+|||||..
T Consensus 37 Hrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 37 HRSYESHHCPKGL 49 (250)
T ss_pred cchHhhcCCCccc
Confidence 3667788888875
No 30
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=54.36 E-value=5.3 Score=36.91 Aligned_cols=47 Identities=13% Similarity=0.024 Sum_probs=34.1
Q ss_pred CCCCCCCCCCCCCCCCCcccccccceeecccccccccccccccccchHHHHHHHHHHH
Q 023696 144 SELGVDPDNENSLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLLVGFL 201 (278)
Q Consensus 144 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL~~~~ 201 (278)
.++.+.|+.|+.=--..-|||+-=|+||.-.++ +=.-.|+.+.....
T Consensus 120 PdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~Ny-----------KfF~lfl~y~~l~~ 166 (307)
T KOG1315|consen 120 PDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNY-----------KFFLLFLFYTNLYS 166 (307)
T ss_pred CCccccchhhhhhhhccccCCcceeceecccch-----------HHHHHHHHHHHHHH
Confidence 356678999988778889999999999986554 44455555554333
No 31
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=49.01 E-value=6.4 Score=36.02 Aligned_cols=28 Identities=14% Similarity=0.095 Sum_probs=19.6
Q ss_pred CCCCCCCCCCC-C--CCCcccccccceeecc
Q 023696 146 LGVDPDNENSL-S--RKRVRYCKICKAHVEG 173 (278)
Q Consensus 146 ~~~~C~~C~~~-k--P~Rs~HC~~C~~CV~r 173 (278)
....|..|... . -.|-|||+.||+-|-.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 34678888762 2 4588999999886654
No 32
>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=47.13 E-value=6.1 Score=23.03 Aligned_cols=21 Identities=14% Similarity=0.192 Sum_probs=14.1
Q ss_pred CCCCCCCCCCCCcccccccce
Q 023696 149 DPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
.|+.|...-++++.+|..|+.
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--
T ss_pred cCCCCcCCchHHhhhhhCcCC
Confidence 477888777888888888764
No 33
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=43.74 E-value=7.9 Score=37.91 Aligned_cols=22 Identities=14% Similarity=0.104 Sum_probs=15.1
Q ss_pred CCCCCCCCCC--CCCcccccccce
Q 023696 148 VDPDNENSLS--RKRVRYCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~k--P~Rs~HC~~C~~ 169 (278)
..|..|+.+- -.|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 4466666542 347899999886
No 34
>COG0348 NapH Polyferredoxin [Energy production and conversion]
Probab=42.22 E-value=1.1e+02 Score=29.08 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=10.9
Q ss_pred cccccceeeccccc
Q 023696 163 YCKICKAHVEGFDH 176 (278)
Q Consensus 163 HC~~C~~CV~r~DH 176 (278)
-|-.|++|+.--||
T Consensus 246 ~CI~C~~CidaCd~ 259 (386)
T COG0348 246 ECIGCGRCIDACDD 259 (386)
T ss_pred ccccHhhHhhhCCH
Confidence 48888888887665
No 35
>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=41.91 E-value=13 Score=21.62 Aligned_cols=21 Identities=14% Similarity=0.105 Sum_probs=9.2
Q ss_pred CCCCCCCCCCC-Ccccccccce
Q 023696 149 DPDNENSLSRK-RVRYCKICKA 169 (278)
Q Consensus 149 ~C~~C~~~kP~-Rs~HC~~C~~ 169 (278)
.|..|+..... ...+|+.||-
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 47788877766 7888999875
No 36
>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=39.31 E-value=22 Score=23.56 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=15.2
Q ss_pred CCCCCCCC--CCCCCccccccccee
Q 023696 148 VDPDNENS--LSRKRVRYCKICKAH 170 (278)
Q Consensus 148 ~~C~~C~~--~kP~Rs~HC~~C~~C 170 (278)
+.|..|+. -.-.|.|||+.|++-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCCccccccCcCcCC
Confidence 34666653 235678999988874
No 37
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=36.04 E-value=25 Score=20.71 Aligned_cols=23 Identities=13% Similarity=0.060 Sum_probs=12.3
Q ss_pred CCCCCCCCCC----CCCCcccccccce
Q 023696 147 GVDPDNENSL----SRKRVRYCKICKA 169 (278)
Q Consensus 147 ~~~C~~C~~~----kP~Rs~HC~~C~~ 169 (278)
.+||..|... .-.+++.|+.|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 4788888653 3346777777765
No 38
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.77 E-value=15 Score=35.02 Aligned_cols=28 Identities=32% Similarity=0.482 Sum_probs=21.0
Q ss_pred CCCCcccccccceeecccccccccccccccccch
Q 023696 157 SRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNY 190 (278)
Q Consensus 157 kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~ 190 (278)
+-.|-.||..|+. .|| +|..||||.--+
T Consensus 10 sl~~p~l~~tC~e----~~h--~w~~~c~ga~~~ 37 (460)
T KOG1398|consen 10 SLARPSLAETCDE----ADH--SWVANCIGALCQ 37 (460)
T ss_pred hhcCchHhhhhhh----ccC--CcccchhHHHHH
Confidence 4556678888875 788 689999998443
No 39
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.08 E-value=21 Score=24.89 Aligned_cols=22 Identities=18% Similarity=0.418 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCCCcccccccce
Q 023696 148 VDPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
+-|..|+...|+.+.-|+.|+.
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred HHHhhccccCCCCCccCCCCCC
Confidence 4588899999999999999986
No 40
>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=32.51 E-value=21 Score=24.70 Aligned_cols=24 Identities=8% Similarity=0.103 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCCCCccccc-ccce
Q 023696 146 LGVDPDNENSLSRKRVRYCK-ICKA 169 (278)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~HC~-~C~~ 169 (278)
+.+.|..|...-|+.-..|+ .|+.
T Consensus 2 ~HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCCcCCcCCCcCCcchhhhCHHHHH
Confidence 34779999988888888885 6665
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.60 E-value=33 Score=22.24 Aligned_cols=22 Identities=9% Similarity=0.055 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCC------cccccccce
Q 023696 148 VDPDNENSLSRKR------VRYCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~kP~R------s~HC~~C~~ 169 (278)
++|+.|+....++ ...|+.||.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCC
Confidence 3677775533222 344777763
No 42
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.95 E-value=29 Score=35.48 Aligned_cols=31 Identities=19% Similarity=0.293 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCCCCcccccccceeecccccccc
Q 023696 147 GVDPDNENSLSRKRVRYCKICKAHVEGFDHHCP 179 (278)
Q Consensus 147 ~~~C~~C~~~kP~Rs~HC~~C~~CV~r~DHHCp 179 (278)
.+||..|...-+ .+.|..||.=+..-..+|+
T Consensus 15 akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~ 45 (645)
T PRK14559 15 NRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCP 45 (645)
T ss_pred CccccccCCCCC--CCcCCCCCCCCCccccccc
Confidence 345555544322 2345555555555555554
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=30.79 E-value=25 Score=26.27 Aligned_cols=13 Identities=15% Similarity=0.294 Sum_probs=9.4
Q ss_pred ccccccccccccc
Q 023696 174 FDHHCPAFGNCIG 186 (278)
Q Consensus 174 ~DHHCpWl~nCIG 186 (278)
+-.||||++.-..
T Consensus 54 Hr~~CPwv~~~~q 66 (91)
T PF08600_consen 54 HREYCPWVNPSTQ 66 (91)
T ss_pred ccccCCccCCccc
Confidence 3468999987653
No 44
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=30.78 E-value=16 Score=30.04 Aligned_cols=24 Identities=8% Similarity=-0.083 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCcccccccceeeccc
Q 023696 148 VDPDNENSLSRKRVRYCKICKAHVEGF 174 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~CV~r~ 174 (278)
....+|... +.+||..|..|+.|+
T Consensus 141 ~~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 141 ELTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred hheeeccCC---CCCCCCCCHHHHHHH
Confidence 345566554 338999999999874
No 45
>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=30.71 E-value=12 Score=24.56 Aligned_cols=18 Identities=17% Similarity=0.302 Sum_probs=12.4
Q ss_pred cccceeeccccccccccc
Q 023696 165 KICKAHVEGFDHHCPAFG 182 (278)
Q Consensus 165 ~~C~~CV~r~DHHCpWl~ 182 (278)
..|+.|+.-.|-+|.|-.
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 567777777777777743
No 46
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.70 E-value=22 Score=35.97 Aligned_cols=24 Identities=13% Similarity=0.087 Sum_probs=17.9
Q ss_pred CCCCCCCCCCC--CCCCcccccccce
Q 023696 146 LGVDPDNENSL--SRKRVRYCKICKA 169 (278)
Q Consensus 146 ~~~~C~~C~~~--kP~Rs~HC~~C~~ 169 (278)
....|..|... --.|.|||+.||+
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccccceeeeeeeeccccccccccch
Confidence 44678888642 2349999999998
No 47
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.47 E-value=29 Score=35.41 Aligned_cols=23 Identities=13% Similarity=0.254 Sum_probs=17.6
Q ss_pred CCCCCCCCCCCCCccccccccee
Q 023696 148 VDPDNENSLSRKRVRYCKICKAH 170 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~C 170 (278)
..|+.|+..-|+.++.|..||.=
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCC
Confidence 36888888888888888877763
No 48
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.92 E-value=45 Score=19.36 Aligned_cols=20 Identities=15% Similarity=-0.056 Sum_probs=14.4
Q ss_pred CCCCCCCCCCCC-cccccccc
Q 023696 149 DPDNENSLSRKR-VRYCKICK 168 (278)
Q Consensus 149 ~C~~C~~~kP~R-s~HC~~C~ 168 (278)
.|..|+...... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477777666666 78888777
No 49
>PF02077 SURF4: SURF4 family; InterPro: IPR002995 The surfeit locus gene SURF4 (or surf-4) encodes a conserved integral eukaryotic membrane protein of about 270 to 300 amino-acid residues that seems to be located in the endoplasmic reticulum [].; GO: 0016021 integral to membrane
Probab=28.81 E-value=4.4e+02 Score=23.86 Aligned_cols=52 Identities=19% Similarity=0.267 Sum_probs=28.4
Q ss_pred hhhhhccchhhhhHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHhhhcc
Q 023696 6 EQRKLSASLPLICRCIISCILVLLTQLTLSLVPRFFAASPFIVQFALSGLVLLLVQTLCGW 66 (278)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (278)
|++|....+-+.||.+...+.+-+..... +.+-+...+.|..+......++.
T Consensus 147 ~~~~~~~yl~LaGRill~~mFi~~~~~~~---------s~~~ii~~~~g~~l~i~v~vGyk 198 (267)
T PF02077_consen 147 EKNKPKSYLQLAGRILLVLMFITLLHFEW---------SFLRIILSIVGLALCILVVVGYK 198 (267)
T ss_pred cCCCcchHHHHHhHHHHHHHHHHHHHHhc---------cHHHHHHHHHHHHHHHHHHHhHh
Confidence 33455556667888888777766644331 22223344556655555555553
No 50
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.01 E-value=24 Score=27.52 Aligned_cols=24 Identities=8% Similarity=0.094 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCCCCCccc---ccccce
Q 023696 146 LGVDPDNENSLSRKRVRY---CKICKA 169 (278)
Q Consensus 146 ~~~~C~~C~~~kP~Rs~H---C~~C~~ 169 (278)
..-+|..|+..-|...++ |+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 346799998877665444 888874
No 51
>PF03503 Chlam_OMP3: Chlamydia cysteine-rich outer membrane protein 3; InterPro: IPR003517 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP2 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP3 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=27.10 E-value=69 Score=21.14 Aligned_cols=23 Identities=9% Similarity=0.060 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCCccccccccee
Q 023696 148 VDPDNENSLSRKRVRYCKICKAH 170 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~C 170 (278)
.-|..|+..|-+++--|..||.-
T Consensus 24 ~sc~pc~~~kkd~~~g~n~cg~y 46 (55)
T PF03503_consen 24 KSCNPCEVNKKDVSCGCNPCGSY 46 (55)
T ss_pred CcccccccccccccCCccccccc
Confidence 44555555555555555555543
No 52
>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=27.08 E-value=19 Score=22.00 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=10.5
Q ss_pred CCCCCCCCC---CCCCcc--cccccce
Q 023696 148 VDPDNENSL---SRKRVR--YCKICKA 169 (278)
Q Consensus 148 ~~C~~C~~~---kP~Rs~--HC~~C~~ 169 (278)
++|++|+.. +..+.. .|+.|+.
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 578888642 222222 4666665
No 53
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.00 E-value=49 Score=19.71 Aligned_cols=19 Identities=16% Similarity=0.366 Sum_probs=10.6
Q ss_pred CCCCCCCCCCC-c-ccccccc
Q 023696 150 PDNENSLSRKR-V-RYCKICK 168 (278)
Q Consensus 150 C~~C~~~kP~R-s-~HC~~C~ 168 (278)
|..|...+..+ | .-|+.|+
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~ 23 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCD 23 (32)
T ss_pred CeECCcCCccceeEEEccCCC
Confidence 55565554444 3 3477776
No 54
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.99 E-value=1.4e+02 Score=28.72 Aligned_cols=31 Identities=10% Similarity=-0.047 Sum_probs=20.5
Q ss_pred cCCCCCCCCCCCCCCCCCC-cccccccceeec
Q 023696 142 EGSELGVDPDNENSLSRKR-VRYCKICKAHVE 172 (278)
Q Consensus 142 ~~~~~~~~C~~C~~~kP~R-s~HC~~C~~CV~ 172 (278)
..++..+.|+.|+...|.+ --+|..|+.=-.
T Consensus 215 ~~~~~~~~C~~C~~~~~~~~~~~CpRC~~~Ly 246 (418)
T COG2995 215 GAREGLRSCLCCHYILPHDAEPRCPRCGSKLY 246 (418)
T ss_pred CCcccceecccccccCCHhhCCCCCCCCChhh
Confidence 3445678899999888874 445666655333
No 55
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=26.77 E-value=27 Score=37.58 Aligned_cols=36 Identities=22% Similarity=0.216 Sum_probs=22.4
Q ss_pred CCCCC--CCCCCCcccccccceeecccccccccccccccccchHHHHHHH
Q 023696 150 PDNEN--SLSRKRVRYCKICKAHVEGFDHHCPAFGNCIGQNNYFLFIVLL 197 (278)
Q Consensus 150 C~~C~--~~kP~Rs~HC~~C~~CV~r~DHHCpWl~nCIG~~N~r~FilfL 197 (278)
|..|. -.--.|-||||.||+-- -+.| -|.|.++-|+
T Consensus 560 cm~clqkft~ikrrhhcRacgkVl---------cgvc---cnek~~leyl 597 (1287)
T KOG1841|consen 560 CMDCLQKFTPIKRRHHCRACGKVL---------CGVC---CNEKSALEYL 597 (1287)
T ss_pred HHHHHhhcccccccccchhcccee---------ehhh---cchhhhhhhc
Confidence 44443 34456899999999831 1233 4667777666
No 56
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.49 E-value=45 Score=22.11 Aligned_cols=24 Identities=13% Similarity=-0.029 Sum_probs=14.8
Q ss_pred CCCCCCCCCC-CC--CCCcccccccce
Q 023696 146 LGVDPDNENS-LS--RKRVRYCKICKA 169 (278)
Q Consensus 146 ~~~~C~~C~~-~k--P~Rs~HC~~C~~ 169 (278)
..++|+.|.. .. -....+|+.|+.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCC
Confidence 3568999976 22 223567777764
No 57
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=26.37 E-value=38 Score=18.67 Aligned_cols=21 Identities=19% Similarity=0.165 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCCcccccccce
Q 023696 149 DPDNENSLSRKRVRYCKICKA 169 (278)
Q Consensus 149 ~C~~C~~~kP~Rs~HC~~C~~ 169 (278)
.|..|...-.+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 588888887788888887764
No 58
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=26.21 E-value=21 Score=22.78 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=10.4
Q ss_pred cccceeecccccccccc
Q 023696 165 KICKAHVEGFDHHCPAF 181 (278)
Q Consensus 165 ~~C~~CV~r~DHHCpWl 181 (278)
+.|..|+...|-||.|-
T Consensus 5 ~sC~~C~~~~~~~C~Wc 21 (46)
T smart00423 5 TSCSECLLARDPYCAWC 21 (46)
T ss_pred CcHHHHHcCCCCCCCcc
Confidence 45666666666666664
No 59
>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=25.54 E-value=64 Score=22.28 Aligned_cols=25 Identities=16% Similarity=0.098 Sum_probs=18.6
Q ss_pred CCCCCCCCCCC----CCCCccccccccee
Q 023696 146 LGVDPDNENSL----SRKRVRYCKICKAH 170 (278)
Q Consensus 146 ~~~~C~~C~~~----kP~Rs~HC~~C~~C 170 (278)
..+.|+.|... ...|.++|+.||.-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45779999654 35578889998875
No 60
>PF06336 Corona_5a: Coronavirus 5a protein; InterPro: IPR009404 This family consists of several Coronavirus 5a proteins. The function of this family is unknown [].
Probab=24.43 E-value=1.1e+02 Score=20.90 Aligned_cols=21 Identities=48% Similarity=0.678 Sum_probs=15.4
Q ss_pred hhhhhHHHHHHHH-HHHHHHHH
Q 023696 14 LPLICRCIISCIL-VLLTQLTL 34 (278)
Q Consensus 14 ~~~~~~~~~~~~~-~~~~~~~~ 34 (278)
|..++|+.+||+= +|++|+-+
T Consensus 4 ltsfgra~iscyksllltqlrv 25 (65)
T PF06336_consen 4 LTSFGRAFISCYKSLLLTQLRV 25 (65)
T ss_pred HHHHhHHHHHHHHHHHHHHHHH
Confidence 5678999999995 45666544
No 61
>KOG1409 consensus Uncharacterized conserved protein, contains WD40 repeats and FYVE domains [Function unknown]
Probab=22.95 E-value=19 Score=33.76 Aligned_cols=26 Identities=19% Similarity=0.174 Sum_probs=19.7
Q ss_pred CCCCCCCCCC-------------CCCCcccccccceeec
Q 023696 147 GVDPDNENSL-------------SRKRVRYCKICKAHVE 172 (278)
Q Consensus 147 ~~~C~~C~~~-------------kP~Rs~HC~~C~~CV~ 172 (278)
..-|..|+++ -+.|-|||+.|++-|-
T Consensus 282 s~~cQ~c~qpffwn~~~m~~~k~~glr~h~crkcg~avc 320 (404)
T KOG1409|consen 282 SDSCQKCNQPFFWNFRQMWDRKQLGLRQHHCRKCGKAVC 320 (404)
T ss_pred cchhhhhCchHHHHHHHHHhhhhhhhhhhhhhhhhhhcC
Confidence 4558888763 5889999999887554
No 62
>PLN00186 ribosomal protein S26; Provisional
Probab=22.89 E-value=34 Score=26.54 Aligned_cols=16 Identities=19% Similarity=0.247 Sum_probs=12.8
Q ss_pred Ccccccccceeecccc
Q 023696 160 RVRYCKICKAHVEGFD 175 (278)
Q Consensus 160 Rs~HC~~C~~CV~r~D 175 (278)
+.-||..|++||.+=-
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (109)
T PLN00186 19 KRIRCSNCGKCVPKDK 34 (109)
T ss_pred cceeeCCCcccccccc
Confidence 4568999999999733
No 63
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=22.81 E-value=29 Score=36.02 Aligned_cols=37 Identities=22% Similarity=0.301 Sum_probs=27.9
Q ss_pred ccccc---ccceeeccccccccccc---ccc--cccchHHHHHHH
Q 023696 161 VRYCK---ICKAHVEGFDHHCPAFG---NCI--GQNNYFLFIVLL 197 (278)
Q Consensus 161 s~HC~---~C~~CV~r~DHHCpWl~---nCI--G~~N~r~FilfL 197 (278)
-|+|. .|..|++..|-||.|-+ .|+ +..|.|.+..=+
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~ 535 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDV 535 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhh
Confidence 46787 89998888999999998 787 344566665443
No 64
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=22.49 E-value=23 Score=31.14 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=15.3
Q ss_pred CCCCCcccccccceeecccc
Q 023696 156 LSRKRVRYCKICKAHVEGFD 175 (278)
Q Consensus 156 ~kP~Rs~HC~~C~~CV~r~D 175 (278)
+++.+-.||..|+.|+.|.+
T Consensus 187 Y~g~~~~~CG~C~sC~~R~~ 206 (222)
T COG0603 187 YNGGEGDHCGECESCVLRER 206 (222)
T ss_pred eCCCCCCCCCCCHHHHHHHH
Confidence 45555559999999999854
No 65
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=22.44 E-value=39 Score=28.67 Aligned_cols=23 Identities=9% Similarity=-0.068 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCCcccccccceeecc
Q 023696 148 VDPDNENSLSRKRVRYCKICKAHVEG 173 (278)
Q Consensus 148 ~~C~~C~~~kP~Rs~HC~~C~~CV~r 173 (278)
..-.+|.... .+||..|..|+.|
T Consensus 179 ~~t~sC~~~~---~~~CG~C~~C~~r 201 (201)
T TIGR00364 179 KLTYSCYAGG---GEGCGKCPSCMLR 201 (201)
T ss_pred hhCCcCCCcC---CCCCCCChhhhcc
Confidence 3445565542 4599999999875
No 66
>COG0805 TatC Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]
Probab=21.81 E-value=5.9e+02 Score=22.88 Aligned_cols=23 Identities=9% Similarity=0.013 Sum_probs=15.9
Q ss_pred HHHHHHHHHhcCcchhccccccC
Q 023696 252 FFMWHIYCVCFNVRTDELTGRNI 274 (278)
Q Consensus 252 ll~~hl~li~~n~TT~E~~~~r~ 274 (278)
+=+....+...|.+|.|.++++.
T Consensus 175 lPvv~~~L~~~Giv~~~~L~~~r 197 (255)
T COG0805 175 LPVVIVLLTRLGIVTPETLKKKR 197 (255)
T ss_pred HHHHHHHHHHcCCccHHHHHHcC
Confidence 33444567778999999994433
No 67
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.40 E-value=41 Score=26.11 Aligned_cols=23 Identities=17% Similarity=0.268 Sum_probs=14.2
Q ss_pred CCCCCCCCCCC----CCCcccccccce
Q 023696 147 GVDPDNENSLS----RKRVRYCKICKA 169 (278)
Q Consensus 147 ~~~C~~C~~~k----P~Rs~HC~~C~~ 169 (278)
.-.|+.|...+ .=|++||+.|+.
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred eeecCCCCceEEecCcccCcCCCCCCC
Confidence 45688887654 225566776664
No 68
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=20.95 E-value=39 Score=25.63 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=15.7
Q ss_pred Ccccccccceeeccccccccc
Q 023696 160 RVRYCKICKAHVEGFDHHCPA 180 (278)
Q Consensus 160 Rs~HC~~C~~CV~r~DHHCpW 180 (278)
+.-+|..|++||.+----+.+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEE
Confidence 456899999999985555543
No 69
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=20.69 E-value=57 Score=25.14 Aligned_cols=20 Identities=10% Similarity=-0.016 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCCCCcccc
Q 023696 145 ELGVDPDNENSLSRKRVRYC 164 (278)
Q Consensus 145 ~~~~~C~~C~~~kP~Rs~HC 164 (278)
..+..|+.|++.+++....|
T Consensus 5 ~~g~~CHqCrqKt~~~~~~C 24 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDFKTIC 24 (105)
T ss_pred CCCCCchhhcCCCCCCceEc
Confidence 45678999999888777777
No 70
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=20.39 E-value=41 Score=26.13 Aligned_cols=17 Identities=18% Similarity=0.225 Sum_probs=13.2
Q ss_pred Ccccccccceeeccccc
Q 023696 160 RVRYCKICKAHVEGFDH 176 (278)
Q Consensus 160 Rs~HC~~C~~CV~r~DH 176 (278)
+.-||..|++||.+=--
T Consensus 19 ~~V~C~nCgr~vPKDKA 35 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKA 35 (108)
T ss_pred ccEEeCCccccccccce
Confidence 45689999999998433
No 71
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.07 E-value=77 Score=17.78 Aligned_cols=19 Identities=16% Similarity=0.084 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCc----ccccccc
Q 023696 150 PDNENSLSRKRV----RYCKICK 168 (278)
Q Consensus 150 C~~C~~~kP~Rs----~HC~~C~ 168 (278)
|.+|+..-.+|- ..|+.||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 556655544442 4466665
Done!