Query 023322
Match_columns 284
No_of_seqs 239 out of 1538
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 03:08:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023322.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023322hhsearch_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 1.2E-54 2.6E-59 382.1 15.5 259 8-275 13-281 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 1.2E-50 2.6E-55 351.9 11.7 258 4-280 11-283 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 2.3E-45 4.9E-50 329.6 20.7 206 65-278 79-296 (299)
4 KOG1313 DHHC-type Zn-finger pr 100.0 8.8E-42 1.9E-46 288.1 15.1 178 95-274 102-304 (309)
5 PF01529 zf-DHHC: DHHC palmito 100.0 1.8E-41 3.8E-46 281.5 11.7 163 57-219 2-173 (174)
6 COG5273 Uncharacterized protei 100.0 5.4E-40 1.2E-44 293.2 15.8 229 44-276 58-304 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 8.3E-33 1.8E-37 234.9 14.6 174 43-219 99-290 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 1.8E-32 3.9E-37 255.6 8.0 191 52-252 378-585 (600)
9 COG5273 Uncharacterized protei 95.1 0.28 6E-06 44.4 10.7 165 105-278 105-283 (309)
10 PF01529 zf-DHHC: DHHC palmito 93.9 0.69 1.5E-05 37.7 9.8 51 93-154 60-110 (174)
11 KOG1311 DHHC-type Zn-finger pr 93.7 0.27 6E-06 44.1 7.5 57 108-164 112-179 (299)
12 KOG1315 Predicted DHHC-type Zn 92.5 0.66 1.4E-05 41.8 7.9 49 234-282 248-297 (307)
13 PRK04136 rpl40e 50S ribosomal 89.5 0.25 5.4E-06 31.3 1.7 24 94-117 13-36 (48)
14 PF13240 zinc_ribbon_2: zinc-r 89.1 0.23 5E-06 26.6 1.2 21 97-117 1-21 (23)
15 PTZ00303 phosphatidylinositol 87.0 0.47 1E-05 47.3 2.6 22 96-117 461-489 (1374)
16 PF13248 zf-ribbon_3: zinc-rib 83.4 0.7 1.5E-05 25.4 1.2 22 96-117 3-24 (26)
17 KOG0509 Ankyrin repeat and DHH 80.2 0.83 1.8E-05 44.4 1.2 64 94-158 324-387 (600)
18 PRK15103 paraquat-inducible me 77.5 36 0.00078 32.2 11.3 33 94-126 220-252 (419)
19 COG1552 RPL40A Ribosomal prote 77.1 0.55 1.2E-05 29.8 -0.6 24 94-117 13-36 (50)
20 PF10571 UPF0547: Uncharacteri 76.9 1.5 3.3E-05 24.2 1.2 22 96-117 1-22 (26)
21 PF12773 DZR: Double zinc ribb 69.5 4.5 9.8E-05 25.7 2.3 34 95-128 12-48 (50)
22 PF01020 Ribosomal_L40e: Ribos 69.0 2.6 5.7E-05 27.2 1.0 25 94-118 16-42 (52)
23 PF01363 FYVE: FYVE zinc finge 65.3 2.2 4.8E-05 29.1 0.2 26 95-120 9-36 (69)
24 smart00064 FYVE Protein presen 65.2 4.9 0.00011 27.3 1.9 24 96-119 11-36 (68)
25 PF07010 Endomucin: Endomucin; 64.0 18 0.00038 31.0 5.2 30 43-72 195-224 (259)
26 PF12773 DZR: Double zinc ribb 60.9 7 0.00015 24.7 1.9 23 94-116 28-50 (50)
27 PF06906 DUF1272: Protein of u 60.7 3.7 8.1E-05 27.0 0.6 37 96-135 6-50 (57)
28 PF00641 zf-RanBP: Zn-finger i 55.6 4.1 8.8E-05 23.0 0.1 22 96-117 5-26 (30)
29 PRK02935 hypothetical protein; 54.6 30 0.00065 25.9 4.5 19 6-24 12-30 (110)
30 KOG3183 Predicted Zn-finger pr 53.0 6.4 0.00014 33.9 0.9 12 119-130 38-49 (250)
31 cd00065 FYVE FYVE domain; Zinc 51.5 11 0.00024 24.4 1.7 24 96-119 3-28 (57)
32 KOG1842 FYVE finger-containing 50.4 4.5 9.8E-05 37.9 -0.4 26 94-119 179-206 (505)
33 TIGR00155 pqiA_fam integral me 48.4 2.4E+02 0.0052 26.6 12.5 32 94-125 214-246 (403)
34 COG2093 DNA-directed RNA polym 46.2 12 0.00025 25.3 1.1 23 95-117 4-26 (64)
35 PHA02680 ORF090 IMV phosphoryl 43.6 1.2E+02 0.0027 21.9 6.6 41 176-219 43-83 (91)
36 PF07649 C1_3: C1-like domain; 43.1 7.3 0.00016 21.9 -0.2 21 97-117 2-23 (30)
37 KOG1729 FYVE finger containing 42.8 6.6 0.00014 35.1 -0.6 27 95-121 168-197 (288)
38 PF14127 DUF4294: Domain of un 40.5 26 0.00055 28.4 2.5 32 208-252 103-134 (157)
39 KOG1841 Smad anchor for recept 38.2 17 0.00036 38.2 1.4 38 96-145 558-597 (1287)
40 PF08600 Rsm1: Rsm1-like; Int 37.1 17 0.00037 26.5 0.9 12 122-133 54-65 (91)
41 TIGR02484 CitB CitB domain pro 35.9 3E+02 0.0064 25.7 8.9 15 110-128 48-62 (372)
42 PF05814 DUF843: Baculovirus p 35.7 1E+02 0.0022 22.1 4.6 27 199-226 38-64 (83)
43 PF03107 C1_2: C1 domain; Int 34.7 23 0.0005 19.9 1.1 20 97-116 2-22 (30)
44 KOG1818 Membrane trafficking a 34.5 16 0.00035 36.1 0.6 23 95-117 165-189 (634)
45 PHA02898 virion envelope prote 34.5 1.8E+02 0.0039 21.1 6.7 36 177-215 43-79 (92)
46 PLN00186 ribosomal protein S26 34.3 16 0.00036 27.4 0.5 20 108-127 19-38 (109)
47 cd01995 ExsB ExsB is a transcr 33.1 18 0.00038 29.2 0.6 28 92-122 137-164 (169)
48 PF09889 DUF2116: Uncharacteri 32.8 60 0.0013 21.7 3.0 22 96-117 4-26 (59)
49 smart00661 RPOL9 RNA polymeras 32.6 21 0.00047 22.5 0.8 8 97-104 2-9 (52)
50 PF09297 zf-NADH-PPase: NADH p 31.9 20 0.00043 20.5 0.5 22 95-116 3-28 (32)
51 PF07282 OrfB_Zn_ribbon: Putat 31.6 25 0.00054 23.8 1.1 25 94-118 27-55 (69)
52 PRK09335 30S ribosomal protein 30.5 21 0.00045 26.3 0.5 22 107-128 18-39 (95)
53 PTZ00172 40S ribosomal protein 29.9 20 0.00043 27.0 0.3 20 108-127 19-38 (108)
54 PRK00432 30S ribosomal protein 29.7 29 0.00062 22.3 1.0 23 95-117 20-45 (50)
55 smart00547 ZnF_RBZ Zinc finger 29.3 28 0.00061 18.5 0.8 21 97-117 4-24 (26)
56 PF02150 RNA_POL_M_15KD: RNA p 28.8 16 0.00036 21.5 -0.2 8 96-103 2-9 (35)
57 PRK11875 psbT photosystem II r 28.6 1.2E+02 0.0026 17.3 3.7 25 47-71 5-30 (31)
58 CHL00031 psbT photosystem II p 28.3 1.3E+02 0.0028 17.5 3.6 26 47-72 5-31 (33)
59 PF11023 DUF2614: Protein of u 28.0 1.2E+02 0.0027 23.0 4.2 18 7-24 12-29 (114)
60 PRK03681 hypA hydrogenase nick 28.0 30 0.00065 26.3 1.0 24 94-117 69-95 (114)
61 PF00751 DM: DM DNA binding do 27.9 23 0.0005 22.5 0.3 15 116-130 12-28 (47)
62 PF01437 PSI: Plexin repeat; 27.6 13 0.00027 23.8 -1.0 16 113-128 6-21 (51)
63 PF00130 C1_1: Phorbol esters/ 27.1 40 0.00088 21.3 1.4 33 94-126 10-50 (53)
64 KOG1398 Uncharacterized conser 26.6 30 0.00066 32.1 0.9 29 105-139 10-38 (460)
65 PRK15033 tricarballylate utili 26.2 2.8E+02 0.006 26.0 7.1 14 111-128 68-81 (389)
66 PRK15103 paraquat-inducible me 26.2 4.3E+02 0.0094 25.0 8.6 30 96-125 11-46 (419)
67 PRK14559 putative protein seri 25.8 39 0.00084 33.9 1.6 21 97-117 29-49 (645)
68 smart00423 PSI domain found in 25.1 31 0.00067 21.3 0.5 11 97-107 6-16 (46)
69 TIGR00155 pqiA_fam integral me 25.0 5.8E+02 0.013 24.0 9.7 31 95-125 13-49 (403)
70 KOG4399 C2HC-type Zn-finger pr 24.8 14 0.0003 32.3 -1.4 16 109-124 291-306 (325)
71 TIGR00364 exsB protein. This p 24.4 39 0.00084 28.1 1.2 23 96-121 179-201 (201)
72 KOG1819 FYVE finger-containing 24.3 30 0.00065 33.2 0.5 22 96-117 902-925 (990)
73 PRK14559 putative protein seri 24.2 44 0.00096 33.5 1.7 39 94-134 14-52 (645)
74 PF14015 DUF4231: Protein of u 23.9 2.9E+02 0.0064 20.2 9.3 21 206-226 77-97 (112)
75 KOG3611 Semaphorins [Signal tr 23.5 29 0.00064 35.3 0.3 37 109-145 491-535 (737)
76 COG0603 Predicted PP-loop supe 23.4 28 0.0006 29.9 0.1 19 104-122 187-205 (222)
77 PHA02942 putative transposase; 22.6 44 0.00096 31.2 1.3 24 94-117 324-350 (383)
78 COG4640 Predicted membrane pro 22.1 47 0.001 31.0 1.2 24 96-119 2-25 (465)
79 PF07754 DUF1610: Domain of un 21.7 62 0.0013 17.4 1.2 19 98-116 1-23 (24)
80 PRK12286 rpmF 50S ribosomal pr 21.4 55 0.0012 21.7 1.2 21 94-116 26-47 (57)
81 PF00539 Tat: Transactivating 21.4 50 0.0011 22.7 1.0 13 96-115 30-42 (68)
82 PF01283 Ribosomal_S26e: Ribos 21.2 31 0.00068 26.2 -0.0 21 108-128 19-39 (113)
83 PRK13743 conjugal transfer pro 21.2 4.1E+02 0.0089 20.8 7.1 21 138-158 38-58 (141)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-54 Score=382.07 Aligned_cols=259 Identities=36% Similarity=0.677 Sum_probs=204.8
Q ss_pred chhHHHHHHHhhhhheeeeeeeecccccccchhhHHHHHHHHHHHHHHHHHHhHHhhcCCCCCCCCCCCCCccCCCchhH
Q 023322 8 SLPVSVVVLAIFYIYFTTVFIFIDRWFGLMSSPGLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHE 87 (284)
Q Consensus 8 ~lp~~~v~~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~dPG~~p~~~~~~~~~~~~~~~~ 87 (284)
++|+.++..++++.||+.++...-++.... ....+..+++.++.++..|+|++++++|||.+|..+.++.++++....+
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~-~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~ 91 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISLT-IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENG 91 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhhh-hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCcccccccc
Confidence 789999999999999988887777665543 4566778899999999999999999999999999888776655432221
Q ss_pred h----------hhcCCccccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHHHHHHHHHHHHHH
Q 023322 88 I----------KRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFVLYAVVACIYSMV 157 (284)
Q Consensus 88 ~----------~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~ 157 (284)
. ...++..|+|.+|+.+||+||||||+|+|||+||||||||+|||||.+|||+|++|++|..+.+++.++
T Consensus 92 ~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv 171 (307)
T KOG1315|consen 92 SDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLV 171 (307)
T ss_pred CcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHH
Confidence 1 223457899999999999999999999999999999999999999999999999999999999988888
Q ss_pred HHHHHHhhcccccccccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhHHhhhhhHHHHHhCCCcccCCC
Q 023322 158 LLVGSLTNDSLEDELQTGGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGGTVYKHPY 237 (284)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~~~~~~~~~npy 237 (284)
.....+......+ ..........++++.++.+.+++.+++|+.+|++||++|+||+|.++.... ..+....+.|
T Consensus 172 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~-----~~~~~~~~~~ 245 (307)
T KOG1315|consen 172 TTLIGFTKYFQGG-AGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVF-----RSGLHNKNGF 245 (307)
T ss_pred HHHHHHHHHHhcc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccc-----cccccccCCc
Confidence 8777665544221 111222334445555666777788888999999999999999999876411 2222345667
Q ss_pred ChhHHHHHHhhcCCCceeeeecCCCCCCCCeEEeeccc
Q 023322 238 DLGIFENLTSVLGPNIFSWVCPSSRHIGSGLNFRTAYH 275 (284)
Q Consensus 238 d~G~~~N~~~vfG~~~~~W~~P~~~~~~dG~~~~~~~~ 275 (284)
++ ..|++|+||+++..|++|.....+||.+++.+.+
T Consensus 246 ~~--~~n~~~vfg~~~~~wl~P~~~s~~~~~~~~~~~~ 281 (307)
T KOG1315|consen 246 NL--YVNFREVFGSNLLYWLLPIDSSWGDGVSFPLRGD 281 (307)
T ss_pred ce--eecHHHHhCCCceEEeccccCccccCcccccccc
Confidence 66 8899999999999999998777777777766544
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-50 Score=351.85 Aligned_cols=258 Identities=32% Similarity=0.515 Sum_probs=184.0
Q ss_pred CcccchhHHHHHHHhhhhheeeeeeeecccccccchhhHHHHHHHHHHHHHHHHHHhHHhhcCCCCCCCCCCCCCccCCC
Q 023322 4 GFTFSLPVSVVVLAIFYIYFTTVFIFIDRWFGLMSSPGLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQN 83 (284)
Q Consensus 4 ~~~~~lp~~~v~~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~dPG~~p~~~~~~~~~~~~ 83 (284)
|.+.+-|+..+.++......+ .+.-...|....+..++.+.+.|.+...+++++|+.+++++||++|..|.|+...++
T Consensus 11 r~~hwGpi~alsiit~i~~~~-~~~n~lww~p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~- 88 (414)
T KOG1314|consen 11 RFLHWGPITALSIITIITSTT-GYMNSLWWFPLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDE- 88 (414)
T ss_pred heeccccHHHHHHHHHHHHHH-HHhhhhhhccccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhH-
Confidence 334444776664433322221 122122344456667888889999999999999999999999999999998765542
Q ss_pred chhHhhhcCCccccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023322 84 PMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSL 163 (284)
Q Consensus 84 ~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~ 163 (284)
...+||.+|+.+|+||||||+.|||||.+|||||||+|||||..||.+|+.||++..++|+-+.++....+
T Consensus 89 ---------~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~ 159 (414)
T KOG1314|consen 89 ---------MFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQ 159 (414)
T ss_pred ---------HHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHH
Confidence 13589999999999999999999999999999999999999999999999999999998765554433322
Q ss_pred hhcccc-------cccccCCchhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhHHhhhhhHHHH----Hh
Q 023322 164 TNDSLE-------DELQTGGSFRTA----YVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLA----EK 228 (284)
Q Consensus 164 ~~~~~~-------~~~~~~~~~~~~----~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~----~~ 228 (284)
+..+.. ........+... .++..-+++++.++++.|++.|+..|++|+|.+|.+..+++.... ..
T Consensus 160 ~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d 239 (414)
T KOG1314|consen 160 YRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFND 239 (414)
T ss_pred HHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccC
Confidence 221110 001111111111 122222335567788899999999999999999998744332222 22
Q ss_pred CCCcccCCCChhHHHHHHhhcCCCceeeeecCCCCCCCCeEEeeccccccCC
Q 023322 229 GGTVYKHPYDLGIFENLTSVLGPNIFSWVCPSSRHIGSGLNFRTAYHNAVGA 280 (284)
Q Consensus 229 ~~~~~~npyd~G~~~N~~~vfG~~~~~W~~P~~~~~~dG~~~~~~~~~~~~~ 280 (284)
...++..|||+||+.|+++||-.+. .+.|||++||..++....+
T Consensus 240 ~~~~f~ypydlgWr~n~r~vf~~~~--------~~~gdg~~wPv~~gc~qyt 283 (414)
T KOG1314|consen 240 DEGEFTYPYDLGWRINLREVFFQNK--------KEEGDGIEWPVVEGCVQYT 283 (414)
T ss_pred CCCceeeeccccccccHHHHhhhcc--------ccCCCCccccccCcccccc
Confidence 2245789999999999999996542 4689999999998887654
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=2.3e-45 Score=329.64 Aligned_cols=206 Identities=32% Similarity=0.603 Sum_probs=149.2
Q ss_pred cCCCCCCCCCCCCCccC-C---CchhHhhhcCCccccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHH
Q 023322 65 RDPGRVPADYMPDVEDD-Q---NPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKV 140 (284)
Q Consensus 65 ~dPG~~p~~~~~~~~~~-~---~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~ 140 (284)
+|||.+|++..+..+.. + .+..+.++...+.+||.+|+.+||||||||++||+||+||||||||+|||||++|||+
T Consensus 79 sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~ 158 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRY 158 (299)
T ss_pred CCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHH
Confidence 49999998532222211 1 1112223334568999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcccccccc----cCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhH
Q 023322 141 FFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQ----TGGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEY 216 (284)
Q Consensus 141 Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~ 216 (284)
|+.|+++..+++++.++.....+.....+.... .........++++++.+.....++.|+.+|++++.+|+||+|+
T Consensus 159 F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~ 238 (299)
T KOG1311|consen 159 FVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYES 238 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhh
Confidence 999999999999998888776654422211111 1111222333444444556666778999999999999999998
Q ss_pred HhhhhhHHHHHhCCCcccCCCChhHHHHHHhhcCCC-ceeeeecCC---CCCCCCeEEeecccccc
Q 023322 217 HEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN-IFSWVCPSS---RHIGSGLNFRTAYHNAV 278 (284)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~npyd~G~~~N~~~vfG~~-~~~W~~P~~---~~~~dG~~~~~~~~~~~ 278 (284)
.++.+ .+...+|||.|.++|++++||.+ ...|+.|.. +.+.||..++.....+.
T Consensus 239 ~~~~~--------~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~~~~p~~~~~~~~~~~~~~ 296 (299)
T KOG1311|consen 239 IKSLD--------FVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARSGPLPHDGEGGPPTPHVSI 296 (299)
T ss_pred hhccc--------cccccCCCchhHHHHHHHHhCCCCCcccccccccCCCCCCCCCCCCccccccc
Confidence 87511 11114899999999999999985 578999976 35678877776655444
No 4
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=8.8e-42 Score=288.09 Aligned_cols=178 Identities=30% Similarity=0.544 Sum_probs=133.4
Q ss_pred cccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccc-
Q 023322 95 LRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQ- 173 (284)
Q Consensus 95 ~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 173 (284)
..+|.+|..+||||+||||.|||||+||||||||+|||||..|||||++|++|+.+++.|..++..+.........+..
T Consensus 102 ~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~t 181 (309)
T KOG1313|consen 102 DSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEIT 181 (309)
T ss_pred ccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhcc
Confidence 3899999999999999999999999999999999999999999999999999999999998887665444332211110
Q ss_pred --------cCCchh----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhHHhhhhhHHHHHhCCCcccC
Q 023322 174 --------TGGSFR----------TAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGGTVYKH 235 (284)
Q Consensus 174 --------~~~~~~----------~~~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~~~~~~~~~n 235 (284)
...+.. ...+-+.+++..+.++++.+..+|.++|.+|.|++|++.....++..... ...|
T Consensus 182 ay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~--~R~~ 259 (309)
T KOG1313|consen 182 AYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAH--LRSN 259 (309)
T ss_pred cccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHh--ccCC
Confidence 000111 11122333445567788999999999999999999998765443222222 2379
Q ss_pred CCChhHHHHHHhhcCC--Cceee---eecCC-CCCCCCeEEeecc
Q 023322 236 PYDLGIFENLTSVLGP--NIFSW---VCPSS-RHIGSGLNFRTAY 274 (284)
Q Consensus 236 pyd~G~~~N~~~vfG~--~~~~W---~~P~~-~~~~dG~~~~~~~ 274 (284)
|++.|.++||+.++|- .+-.| ++|.. ++.+.|..+++++
T Consensus 260 ~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p~~~~~~~~~~d 304 (309)
T KOG1313|consen 260 PTNFGGKANWRNFLGLFRGRHFWKTVLLPTIRKPVKYGDSKEKSD 304 (309)
T ss_pred CcccchHHHHHHhhccccCCceeEEEeccccccccccCCcccccc
Confidence 9999999999999984 33244 78976 6788888888543
No 5
>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=1.8e-41 Score=281.46 Aligned_cols=163 Identities=34% Similarity=0.686 Sum_probs=119.8
Q ss_pred HHHhHHhhcCCCCCCCCCCCCCc-cCC-------CchhHhhhcCCccccccccCcccCCCCCCCcccCccccCCcccCcc
Q 023322 57 FSYTVAILRDPGRVPADYMPDVE-DDQ-------NPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 57 ~~~~~~~~~dPG~~p~~~~~~~~-~~~-------~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w 128 (284)
++|++++++|||++|+....+.+ .++ .......+..++.++|.+|+..||+|||||+.||+||+||||||+|
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 57889999999999986111111 000 0111122334578999999999999999999999999999999999
Q ss_pred cccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccCCchhHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023322 129 ISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQTGGSFRTA-YVISGLLLVPLSVALSVLLGWHIYLI 207 (284)
Q Consensus 129 i~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~~~~~~~~~~~~~l~~~h~~li 207 (284)
+|||||++|||+|++|+++..+++++.....+..+.................. .+++.++.+.++++++.++++|++++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998888777666553332221111111111 13333344556677889999999999
Q ss_pred hhCcchhhHHhh
Q 023322 208 FHNKTTIEYHEG 219 (284)
Q Consensus 208 ~~n~Tt~E~~~~ 219 (284)
++|+||+|.+++
T Consensus 162 ~~n~Tt~E~~~~ 173 (174)
T PF01529_consen 162 LRNITTYERIKR 173 (174)
T ss_pred HcCCcHHHHHHc
Confidence 999999999875
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=5.4e-40 Score=293.16 Aligned_cols=229 Identities=31% Similarity=0.572 Sum_probs=159.4
Q ss_pred HHHHHHHHHHHHHHHHhHHhhcCCCCCCCCCCCCCccCCCchhHhhhcCCccccccccCcccCCCCCCCcccCccccCCc
Q 023322 44 NAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRMD 123 (284)
Q Consensus 44 ~~~~~~~l~~~~~~~~~~~~~~dPG~~p~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~D 123 (284)
..+.+.+...++..+|+..+++|||..+++.....-++..+..-..++.+..++|.+|+.+||+|||||+.|||||+|||
T Consensus 58 ~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~D 137 (309)
T COG5273 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFD 137 (309)
T ss_pred hhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccC
Confidence 34455556667889999999999999985432211111111111233456789999999999999999999999999999
Q ss_pred ccCcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccCCchhH-HHHHH--HHHHHHHHHHHHHHH
Q 023322 124 HHCIWISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQTGGSFRT-AYVIS--GLLLVPLSVALSVLL 200 (284)
Q Consensus 124 HHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~--~~~~~~~~~~~~~l~ 200 (284)
|||||+|||||.+|||+|++|++++....+..+......+...... ....... ..++. ....+.+++.+..++
T Consensus 138 HHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~li~~~~~~~~~~f~~~~~~~ 213 (309)
T COG5273 138 HHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSI----RHDTSLAICFLIFGCSLLGVVFFIITTLLL 213 (309)
T ss_pred ccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc----cCChHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 9999999999999999999999999877776666655444332111 1111111 22222 233344566778889
Q ss_pred HHHHHHHhhCcchhhHHhhhhhHHHHH------hC---------CCcccCCCChhHHHHHHhhcCCCceeeeecCCCCCC
Q 023322 201 GWHIYLIFHNKTTIEYHEGVRALWLAE------KG---------GTVYKHPYDLGIFENLTSVLGPNIFSWVCPSSRHIG 265 (284)
Q Consensus 201 ~~h~~li~~n~Tt~E~~~~~~~~~~~~------~~---------~~~~~npyd~G~~~N~~~vfG~~~~~W~~P~~~~~~ 265 (284)
.++.+++..|+|++|..+..|.....+ .. ..+...|++.|.-+|++.++|.+...|..|......
T Consensus 214 ~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~ 293 (309)
T COG5273 214 LFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLSTIKGSNALYWLTPLHTNYC 293 (309)
T ss_pred HHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccceeecCCCceeeccccccCCC
Confidence 999999999999999987655432211 01 112346889999999999999999999999653335
Q ss_pred CCeEEeecccc
Q 023322 266 SGLNFRTAYHN 276 (284)
Q Consensus 266 dG~~~~~~~~~ 276 (284)
.+..|+.+.+.
T Consensus 294 ~~~~~~~~~~~ 304 (309)
T COG5273 294 NSYDFSLRSDT 304 (309)
T ss_pred CccCcccchhh
Confidence 56666655443
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=8.3e-33 Score=234.90 Aligned_cols=174 Identities=26% Similarity=0.409 Sum_probs=108.9
Q ss_pred HHHHHHHHHHHHHHHHHhHHhhcCCCCCCCCCCCCCccCCCchhHhhhcCCccccccccCcccCCCCCCCcccCccccCC
Q 023322 43 MNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (284)
Q Consensus 43 ~~~~~~~~l~~~~~~~~~~~~~~dPG~~p~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~ 122 (284)
.+.+.-..+.++-.+++..++.+|||.+.+......-+..+.+..+- .....|+||+..||+||||||.|||||.||
T Consensus 99 ~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if---~k~~kCSTCki~KPARSKHCsiCNrCV~rf 175 (341)
T KOG1312|consen 99 HYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIF---PKNVKCSTCKIRKPARSKHCSICNRCVHRF 175 (341)
T ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceee---cCCCccccccCCCccccccchHHHHHHHHh
Confidence 33333334445557778899999999997642211111100011111 122789999999999999999999999999
Q ss_pred cccCcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccc--------c--CCchh-HHHHHHHHHH--
Q 023322 123 DHHCIWISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQ--------T--GGSFR-TAYVISGLLL-- 189 (284)
Q Consensus 123 DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~--~~~~~-~~~~i~~~~~-- 189 (284)
||||.|+|||||++|.|||++|+++...++.++.+-..........+.... . .+... .-.++.++.-
T Consensus 176 DHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlgfi~ln~~sdl~q~v~ilt~~~g~~ks~~~L~~yl~la~~~~v 255 (341)
T KOG1312|consen 176 DHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLGFIVLNVMSDLYQEVYILTLGHGHVKSTVFLIQYLFLAFPRIV 255 (341)
T ss_pred ccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHHheehhhccccchheeeeeeeecchhhHHHHHHHHHHHhccce
Confidence 999999999999999999999999997777776655443322222211111 0 00000 0011111100
Q ss_pred -----HHHHHHHHHHHHHHHHHHhhCcchhhHHhh
Q 023322 190 -----VPLSVALSVLLGWHIYLIFHNKTTIEYHEG 219 (284)
Q Consensus 190 -----~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~ 219 (284)
....-+++.-..+-.++..+|+||.|...+
T Consensus 256 ~~l~~~~~~~~~~~Y~~f~~y~~~t~~~~~~W~~~ 290 (341)
T KOG1312|consen 256 FMLGFVVVLSFLGGYLLFVLYLAATNQTTNEWYRG 290 (341)
T ss_pred eeeehhhhhhHhHHHHHHHHHHHhccCCchhhhcc
Confidence 111223455666778889999999998776
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.97 E-value=1.8e-32 Score=255.61 Aligned_cols=191 Identities=25% Similarity=0.426 Sum_probs=128.1
Q ss_pred HHHHHHHHhHHhhcCCCCCCCCCCCCCccCCCchhHhhhc--CCcc-ccccccCcccCCCCCCCcccCccccCCcccCcc
Q 023322 52 ALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRK--GGDL-RYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 52 ~~~~~~~~~~~~~~dPG~~p~~~~~~~~~~~~~~~~~~~~--~~~~-~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w 128 (284)
.+..++++.++..+|||++|.+.... +....+..+. -+.. ++|.+|.+.||.|||||++|||||.||||||||
T Consensus 378 ~l~~~~~f~~~~rsDPg~i~~~~~~~----~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPw 453 (600)
T KOG0509|consen 378 VLAYFITFGLFLRSDPGFIPTSTEVG----RETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPW 453 (600)
T ss_pred HHHHHHHHHHHhccCCCCCCCchhhH----HHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCc
Confidence 34456667777789999999753222 1111111111 1223 799999999999999999999999999999999
Q ss_pred cccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccCCchhHHHHHHHHHHHH--HH------------H
Q 023322 129 ISNCVGHANYKVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQTGGSFRTAYVISGLLLVP--LS------------V 194 (284)
Q Consensus 129 i~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~--~~------------~ 194 (284)
++||||.+|||+|+.|++.+...+.+.+.....++... .+. .......+..+..+..+ +. -
T Consensus 454 i~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~-~~~----~~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~ 528 (600)
T KOG0509|consen 454 IGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNL-ENA----STIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTW 528 (600)
T ss_pred cccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhc-chh----HHHHHHHHHHHHHHhCCccceeeeeecccccccc
Confidence 99999999999999999998888777776665554321 110 01111111111111110 00 0
Q ss_pred HHHHHHHHHHHHHhhCcchhhHHhhhhhHHHHHhCCCcccCCCChhHHHHHHhhcCCC
Q 023322 195 ALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN 252 (284)
Q Consensus 195 ~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~~~~~~~~~npyd~G~~~N~~~vfG~~ 252 (284)
..+..-..|...++.+.||+|+++..|++....+.+. .++|++.|+.+|+.+++=.+
T Consensus 529 ~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~-~~~~~s~g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 529 GSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGP-TRSPFSPGPIRNLVDFFLCS 585 (600)
T ss_pred ccccccccccceeeecccHHHHHHHHHhhccccccCc-CCCCCCchhhhcchheeecc
Confidence 0111222344568999999999999988777666553 67899999999999988543
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=95.08 E-value=0.28 Score=44.41 Aligned_cols=165 Identities=16% Similarity=0.197 Sum_probs=88.6
Q ss_pred cCCCCCCCcccCccccCCcccCcccccccCCcch-----------HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccc
Q 023322 105 KPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANY-----------KVFFIFVLYAVVACIYSMVLLVGSLTNDSLEDELQ 173 (284)
Q Consensus 105 kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~-----------~~Fi~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (284)
+-.+.+-|++|+.-....-|||.--|.||-..-| +-.=.|..++......+..+......... ..
T Consensus 105 ~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~----~~ 180 (309)
T COG5273 105 KFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIA----GI 180 (309)
T ss_pred ccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH----hh
Confidence 4456778999999999999999999999988755 45557777766666666655554443311 11
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhHHhhhhhHHHHHhCC-CcccCCCChhHHHH--HHhhcC
Q 023322 174 TGGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGG-TVYKHPYDLGIFEN--LTSVLG 250 (284)
Q Consensus 174 ~~~~~~~~~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~~~~~-~~~~npyd~G~~~N--~~~vfG 250 (284)
.............++..........+......++..+....+...-.+.... .+++ .....++.++. | +...+.
T Consensus 181 ~~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~d 257 (309)
T COG5273 181 FSIRHDTSLAICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQI-SRGGSTLEFFPLCRES--NLPFTNIFD 257 (309)
T ss_pred ccccCChHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHh-ccceecccccchhccC--CcCceeccC
Confidence 1222223333233333222333444555566666666666665544322211 1111 11223444433 3 122222
Q ss_pred CCceeeeecCCCCCCCCeEEeecccccc
Q 023322 251 PNIFSWVCPSSRHIGSGLNFRTAYHNAV 278 (284)
Q Consensus 251 ~~~~~W~~P~~~~~~dG~~~~~~~~~~~ 278 (284)
..+ |.+|...+.++++++.+..+...
T Consensus 258 ~~~--~~~~~~~~~~~~~~~i~~~~~~~ 283 (309)
T COG5273 258 SSE--GALPLDLGIGQNLSTIKGSNALY 283 (309)
T ss_pred CCc--cccccccCccccceeecCCCcee
Confidence 222 66776666677777766554433
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=93.91 E-value=0.69 Score=37.70 Aligned_cols=51 Identities=18% Similarity=0.439 Sum_probs=37.2
Q ss_pred CccccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHHHHHHHHHHH
Q 023322 93 GDLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFVLYAVVACIY 154 (284)
Q Consensus 93 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~ 154 (284)
...++|..|+.-...+-|||..-|.||.+.-|. .+-.|+++.....+..++
T Consensus 60 ~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~~-----------~F~~fl~~~~~~~~~~~~ 110 (174)
T PF01529_consen 60 PRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNHR-----------YFLLFLLYLCLYCLYFFI 110 (174)
T ss_pred CcceeccccccccccccccchhhccccccccHH-----------HHHHHHHHHHHHHHHHHH
Confidence 356889999999999999999999999887663 445676666554444443
No 11
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=93.67 E-value=0.27 Score=44.11 Aligned_cols=57 Identities=19% Similarity=0.303 Sum_probs=43.6
Q ss_pred CCCCCcccCccccCCcccCcccccccCCcc-----------hHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023322 108 RAHHCRVCKRCVLRMDHHCIWISNCVGHAN-----------YKVFFIFVLYAVVACIYSMVLLVGSLT 164 (284)
Q Consensus 108 Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N-----------~~~Fi~fl~~~~~~~~~~~~~~~~~~~ 164 (284)
+.|+|..|+..+..+-|||+.=|+||-..- +|-+-.|+.+++...+..+........
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~ 179 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFY 179 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 389999999999999999999999999985 578889997766444444444333333
No 12
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=92.46 E-value=0.66 Score=41.79 Aligned_cols=49 Identities=31% Similarity=0.193 Sum_probs=33.2
Q ss_pred cCCCChhHHHHHHhhcCCCceeeeecCC-CCCCCCeEEeeccccccCCCC
Q 023322 234 KHPYDLGIFENLTSVLGPNIFSWVCPSS-RHIGSGLNFRTAYHNAVGASM 282 (284)
Q Consensus 234 ~npyd~G~~~N~~~vfG~~~~~W~~P~~-~~~~dG~~~~~~~~~~~~~~~ 282 (284)
..+|+.+.-.|+...++|....|.-+.. +-.+||.++....+.+..+++
T Consensus 248 ~~n~~~vfg~~~~~wl~P~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (307)
T KOG1315|consen 248 YVNFREVFGSNLLYWLLPIDSSWGDGVSFPLRGDGLDFRTASDSKPDNSS 297 (307)
T ss_pred eecHHHHhCCCceEEeccccCccccCccccccccCCccccccccCcccCc
Confidence 3467777778888888877666766654 456788877776655555443
No 13
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=89.49 E-value=0.25 Score=31.30 Aligned_cols=24 Identities=33% Similarity=0.819 Sum_probs=21.9
Q ss_pred ccccccccCcccCCCCCCCcccCc
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
....|..|...-|+|+..|+.|+.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 568999999999999999998875
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.14 E-value=0.23 Score=26.58 Aligned_cols=21 Identities=29% Similarity=0.733 Sum_probs=18.5
Q ss_pred cccccCcccCCCCCCCcccCc
Q 023322 97 YCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 97 ~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
+|..|...-++.++.|+.|+.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999875
No 15
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=86.95 E-value=0.47 Score=47.27 Aligned_cols=22 Identities=41% Similarity=0.848 Sum_probs=18.5
Q ss_pred ccccccCcccC-------CCCCCCcccCc
Q 023322 96 RYCQKCSHYKP-------PRAHHCRVCKR 117 (284)
Q Consensus 96 ~~C~~C~~~kP-------~Rs~HC~~C~~ 117 (284)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 67999998764 39999999987
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.38 E-value=0.7 Score=25.40 Aligned_cols=22 Identities=27% Similarity=0.750 Sum_probs=19.1
Q ss_pred ccccccCcccCCCCCCCcccCc
Q 023322 96 RYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
++|..|...-++.++.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6899999988899999998875
No 17
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=80.20 E-value=0.83 Score=44.41 Aligned_cols=64 Identities=11% Similarity=-0.054 Sum_probs=52.6
Q ss_pred ccccccccCcccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHHHHHHHHHHHHHHH
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFVLYAVVACIYSMVL 158 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl~~~~~~~~~~~~~ 158 (284)
....|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-..+-...+...+..++....
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i~~~l~~~~~f~~ 387 (600)
T KOG0509|consen 324 LTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFIISVLAYFITFGL 387 (600)
T ss_pred hheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999999 999999877765555444444444444
No 18
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=77.53 E-value=36 Score=32.23 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=25.2
Q ss_pred ccccccccCcccCCCCCCCcccCccccCCcccC
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHC 126 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC 126 (284)
+..-|+.|+...|....||..|+.-..+..++.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~~s 252 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRRNS 252 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCCCC
Confidence 356799999988877778988888776655553
No 19
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=77.12 E-value=0.55 Score=29.83 Aligned_cols=24 Identities=38% Similarity=0.989 Sum_probs=21.4
Q ss_pred ccccccccCcccCCCCCCCcccCc
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
..+.|..|...-|+|+--|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 458999999999999999998864
No 20
>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=76.90 E-value=1.5 Score=24.15 Aligned_cols=22 Identities=27% Similarity=0.712 Sum_probs=18.7
Q ss_pred ccccccCcccCCCCCCCcccCc
Q 023322 96 RYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
+.|+.|....|.-++-|..||.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4689999999999999988874
No 21
>PF12773 DZR: Double zinc ribbon
Probab=69.45 E-value=4.5 Score=25.65 Aligned_cols=34 Identities=18% Similarity=0.425 Sum_probs=21.4
Q ss_pred cccccccCcccC---CCCCCCcccCccccCCcccCcc
Q 023322 95 LRYCQKCSHYKP---PRAHHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 95 ~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHHC~w 128 (284)
.++|..|...-+ .....|..|+.=+...+.+|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCc
Confidence 467777776554 3355677777766666666653
No 22
>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=69.01 E-value=2.6 Score=27.20 Aligned_cols=25 Identities=44% Similarity=0.934 Sum_probs=17.2
Q ss_pred ccccccccCcccCCCCCCCcc--cCcc
Q 023322 94 DLRYCQKCSHYKPPRAHHCRV--CKRC 118 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~--C~~C 118 (284)
+...|.+|...-|+|+..|+. ||.+
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 568999999999999999998 8764
No 23
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=65.32 E-value=2.2 Score=29.11 Aligned_cols=26 Identities=38% Similarity=0.722 Sum_probs=13.1
Q ss_pred cccccccCcc--cCCCCCCCcccCcccc
Q 023322 95 LRYCQKCSHY--KPPRAHHCRVCKRCVL 120 (284)
Q Consensus 95 ~~~C~~C~~~--kP~Rs~HC~~C~~CV~ 120 (284)
...|..|... --.|-|||+.||+.|=
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 4678888753 3478999999998553
No 24
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=63.98 E-value=18 Score=31.03 Aligned_cols=30 Identities=27% Similarity=0.307 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHhHHhhcCCCCCCC
Q 023322 43 MNAIVFTAVALMCVFSYTVAILRDPGRVPA 72 (284)
Q Consensus 43 ~~~~~~~~l~~~~~~~~~~~~~~dPG~~p~ 72 (284)
+.+++..++.+.++..|.+|..+|||..-.
T Consensus 195 IaliVitl~vf~LvgLyr~C~k~dPg~p~~ 224 (259)
T PF07010_consen 195 IALIVITLSVFTLVGLYRMCWKTDPGTPEN 224 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCccc
Confidence 445566666777788888999999996543
No 26
>PF12773 DZR: Double zinc ribbon
Probab=60.88 E-value=7 Score=24.74 Aligned_cols=23 Identities=30% Similarity=0.853 Sum_probs=20.9
Q ss_pred ccccccccCcccCCCCCCCcccC
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCK 116 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~ 116 (284)
...+|..|....++.++.|..|+
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 45899999999999999999986
No 27
>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=60.74 E-value=3.7 Score=26.99 Aligned_cols=37 Identities=32% Similarity=0.846 Sum_probs=28.1
Q ss_pred ccccccCcccCCCC-------CCCcccCccccCC-cccCcccccccCC
Q 023322 96 RYCQKCSHYKPPRA-------HHCRVCKRCVLRM-DHHCIWISNCVGH 135 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs-------~HC~~C~~CV~~~-DHHC~wi~nCIG~ 135 (284)
.-|..|+.--|+-| +-|..|..|+..+ +++|| ||=|.
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 34677776666554 6789999999999 99999 66664
No 28
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=55.56 E-value=4.1 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.729 Sum_probs=15.2
Q ss_pred ccccccCcccCCCCCCCcccCc
Q 023322 96 RYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
=.|..|...-++++.+|..|+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--
T ss_pred ccCCCCcCCchHHhhhhhCcCC
Confidence 4588888888888888888763
No 29
>PRK02935 hypothetical protein; Provisional
Probab=54.61 E-value=30 Score=25.94 Aligned_cols=19 Identities=16% Similarity=0.434 Sum_probs=9.0
Q ss_pred ccchhHHHHHHHhhhhhee
Q 023322 6 TFSLPVSVVVLAIFYIYFT 24 (284)
Q Consensus 6 ~~~lp~~~v~~li~~~~~~ 24 (284)
.+.+.+..+++-+...|..
T Consensus 12 iRt~aL~lvfiG~~vMy~G 30 (110)
T PRK02935 12 IRTFALSLVFIGFIVMYLG 30 (110)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444455444444544
No 30
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=53.00 E-value=6.4 Score=33.88 Aligned_cols=12 Identities=25% Similarity=0.097 Sum_probs=9.8
Q ss_pred ccCCcccCcccc
Q 023322 119 VLRMDHHCIWIS 130 (284)
Q Consensus 119 V~~~DHHC~wi~ 130 (284)
..+.+|||||..
T Consensus 38 rsye~H~Cp~~~ 49 (250)
T KOG3183|consen 38 RSYESHHCPKGL 49 (250)
T ss_pred chHhhcCCCccc
Confidence 567899999975
No 31
>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=51.51 E-value=11 Score=24.42 Aligned_cols=24 Identities=38% Similarity=0.822 Sum_probs=16.0
Q ss_pred ccccccCc--ccCCCCCCCcccCccc
Q 023322 96 RYCQKCSH--YKPPRAHHCRVCKRCV 119 (284)
Q Consensus 96 ~~C~~C~~--~kP~Rs~HC~~C~~CV 119 (284)
+.|..|+. -.-.|.|||+.|++-+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCc
Confidence 44666654 2456789999998743
No 32
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=50.43 E-value=4.5 Score=37.93 Aligned_cols=26 Identities=35% Similarity=1.040 Sum_probs=20.7
Q ss_pred ccccccccCcc--cCCCCCCCcccCccc
Q 023322 94 DLRYCQKCSHY--KPPRAHHCRVCKRCV 119 (284)
Q Consensus 94 ~~~~C~~C~~~--kP~Rs~HC~~C~~CV 119 (284)
...+|+.|... ---|-|||+.||+-+
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHH
Confidence 56899999864 456899999999843
No 33
>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=48.43 E-value=2.4e+02 Score=26.56 Aligned_cols=32 Identities=22% Similarity=0.517 Sum_probs=22.7
Q ss_pred ccccccccCc-ccCCCCCCCcccCccccCCccc
Q 023322 94 DLRYCQKCSH-YKPPRAHHCRVCKRCVLRMDHH 125 (284)
Q Consensus 94 ~~~~C~~C~~-~kP~Rs~HC~~C~~CV~~~DHH 125 (284)
...-|+.|+. .+|....||..|+.-..+..++
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~ 246 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVRRRN 246 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCCCCC
Confidence 3466999998 4555566788888877665555
No 34
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=46.16 E-value=12 Score=25.27 Aligned_cols=23 Identities=26% Similarity=0.777 Sum_probs=20.6
Q ss_pred cccccccCcccCCCCCCCcccCc
Q 023322 95 LRYCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 95 ~~~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
.+-|..|+...|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 36799999999999999999986
No 35
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=43.61 E-value=1.2e+02 Score=21.87 Aligned_cols=41 Identities=17% Similarity=0.101 Sum_probs=24.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhHHhh
Q 023322 176 GSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEG 219 (284)
Q Consensus 176 ~~~~~~~~i~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~ 219 (284)
..++.+.+++.++. .+.+.+++++-.|--+++.++.|+++.
T Consensus 43 ~~wRalSii~FIlG---~vl~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 43 YVWRALSVTCFIVG---AVLLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred hhHHHHHHHHHHHH---HHHHHHHHHHHHhcccCCCceeecccC
Confidence 34455444444432 233444777777878888888887765
No 36
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=43.07 E-value=7.3 Score=21.94 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=8.3
Q ss_pred cccccCcccCC-CCCCCcccCc
Q 023322 97 YCQKCSHYKPP-RAHHCRVCKR 117 (284)
Q Consensus 97 ~C~~C~~~kP~-Rs~HC~~C~~ 117 (284)
.|..|+..... ...+|+.|+-
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 47777766665 6778888764
No 37
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=42.77 E-value=6.6 Score=35.11 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=16.8
Q ss_pred cccccccCc---ccCCCCCCCcccCccccC
Q 023322 95 LRYCQKCSH---YKPPRAHHCRVCKRCVLR 121 (284)
Q Consensus 95 ~~~C~~C~~---~kP~Rs~HC~~C~~CV~~ 121 (284)
...|..|.. ---.|-|||+.||+-|-.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 356666665 233577888888875543
No 38
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=40.54 E-value=26 Score=28.40 Aligned_cols=32 Identities=9% Similarity=0.127 Sum_probs=26.9
Q ss_pred hhCcchhhHHhhhhhHHHHHhCCCcccCCCChhHHHHHHhhcCCC
Q 023322 208 FHNKTTIEYHEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN 252 (284)
Q Consensus 208 ~~n~Tt~E~~~~~~~~~~~~~~~~~~~npyd~G~~~N~~~vfG~~ 252 (284)
-+|.|++|-.+. +.+++.-||++....+||-+
T Consensus 103 etg~TsyelIK~-------------~rgg~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 103 ETGSTSYELIKE-------------LRGGWRAFWYQTFAWLFGIS 134 (157)
T ss_pred hcCCcHHHHHHH-------------hhCChhHHHHHHHHHHhCcc
Confidence 569999998875 45678889999999999965
No 39
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=38.25 E-value=17 Score=38.23 Aligned_cols=38 Identities=29% Similarity=0.622 Sum_probs=25.1
Q ss_pred ccccccC--cccCCCCCCCcccCccccCCcccCcccccccCCcchHHHHHHH
Q 023322 96 RYCQKCS--HYKPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYKVFFIFV 145 (284)
Q Consensus 96 ~~C~~C~--~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~~Fi~fl 145 (284)
.-|-.|. ..--.|-|||+.||+-- |-.--|.|.++-|+
T Consensus 558 pncm~clqkft~ikrrhhcRacgkVl------------cgvccnek~~leyl 597 (1287)
T KOG1841|consen 558 PNCMDCLQKFTPIKRRHHCRACGKVL------------CGVCCNEKSALEYL 597 (1287)
T ss_pred chHHHHHhhcccccccccchhcccee------------ehhhcchhhhhhhc
Confidence 4455555 45667999999999831 22334667777776
No 40
>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=37.11 E-value=17 Score=26.50 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=8.7
Q ss_pred CcccCccccccc
Q 023322 122 MDHHCIWISNCV 133 (284)
Q Consensus 122 ~DHHC~wi~nCI 133 (284)
+-.||||++.-.
T Consensus 54 Hr~~CPwv~~~~ 65 (91)
T PF08600_consen 54 HREYCPWVNPST 65 (91)
T ss_pred ccccCCccCCcc
Confidence 336899998654
No 41
>TIGR02484 CitB CitB domain protein. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the C-terminal domain of the R. capsulatus CobZ, which, in most other species exists as a separate gene adjacent to CobZ.
Probab=35.89 E-value=3e+02 Score=25.69 Aligned_cols=15 Identities=40% Similarity=1.165 Sum_probs=13.1
Q ss_pred CCCcccCccccCCcccCcc
Q 023322 110 HHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 110 ~HC~~C~~CV~~~DHHC~w 128 (284)
..|..|++| +|+||.
T Consensus 48 ~lChnC~~C----~~~CPy 62 (372)
T TIGR02484 48 HLCHDCQSC----WHDCQY 62 (372)
T ss_pred HHCcCcccc----cccCcC
Confidence 789999999 679997
No 42
>PF05814 DUF843: Baculovirus protein of unknown function (DUF843); InterPro: IPR008561 This family consists of several unidentified baculovirus proteins of around 85 residues long with no known function.
Probab=35.74 E-value=1e+02 Score=22.07 Aligned_cols=27 Identities=15% Similarity=0.176 Sum_probs=15.5
Q ss_pred HHHHHHHHHhhCcchhhHHhhhhhHHHH
Q 023322 199 LLGWHIYLIFHNKTTIEYHEGVRALWLA 226 (284)
Q Consensus 199 l~~~h~~li~~n~Tt~E~~~~~~~~~~~ 226 (284)
++..|+|.+ +.+++.+.......+..+
T Consensus 38 ~~~L~~yy~-kteS~~~dL~t~k~K~~K 64 (83)
T PF05814_consen 38 FCVLQVYYI-KTESTPQDLQTEKAKSIK 64 (83)
T ss_pred HHHHHHHHc-CCCCcHHHHhhhhhhhHH
Confidence 445577766 667776665544443333
No 43
>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=34.66 E-value=23 Score=19.91 Aligned_cols=20 Identities=25% Similarity=0.610 Sum_probs=13.0
Q ss_pred cccccCcccCCC-CCCCcccC
Q 023322 97 YCQKCSHYKPPR-AHHCRVCK 116 (284)
Q Consensus 97 ~C~~C~~~kP~R-s~HC~~C~ 116 (284)
.|..|+...... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 466666665555 67777666
No 44
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.51 E-value=16 Score=36.08 Aligned_cols=23 Identities=35% Similarity=0.793 Sum_probs=18.1
Q ss_pred cccccccCcc--cCCCCCCCcccCc
Q 023322 95 LRYCQKCSHY--KPPRAHHCRVCKR 117 (284)
Q Consensus 95 ~~~C~~C~~~--kP~Rs~HC~~C~~ 117 (284)
..-|.+|... ---|.|||+.||+
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred ccccceeeeeeeeccccccccccch
Confidence 3679999863 3349999999998
No 45
>PHA02898 virion envelope protein; Provisional
Probab=34.46 E-value=1.8e+02 Score=21.09 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=19.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhCcchhh
Q 023322 177 SFRTAYVISGLLLVPLSVALSVLLGWHIYL-IFHNKTTIE 215 (284)
Q Consensus 177 ~~~~~~~i~~~~~~~~~~~~~~l~~~h~~l-i~~n~Tt~E 215 (284)
.++.+.+++.++ ..+.+.+++++-.|. -+++.++.|
T Consensus 43 ~wRalSii~FIl---givl~lG~~ifs~y~r~C~~~~~~e 79 (92)
T PHA02898 43 ALRSISIISFIL---AIILILGIIFFKGYNMFCGGNTTDE 79 (92)
T ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHhhhcCCCcccc
Confidence 344444444333 333445566677776 566766665
No 46
>PLN00186 ribosomal protein S26; Provisional
Probab=34.27 E-value=16 Score=27.43 Aligned_cols=20 Identities=20% Similarity=0.456 Sum_probs=15.0
Q ss_pred CCCCCcccCccccCCcccCc
Q 023322 108 RAHHCRVCKRCVLRMDHHCI 127 (284)
Q Consensus 108 Rs~HC~~C~~CV~~~DHHC~ 127 (284)
+.-||..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (109)
T PLN00186 19 KRIRCSNCGKCVPKDKAIKR 38 (109)
T ss_pred cceeeCCCcccccccceEEE
Confidence 46689999999997554443
No 47
>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=33.08 E-value=18 Score=29.17 Aligned_cols=28 Identities=32% Similarity=0.682 Sum_probs=19.0
Q ss_pred CCccccccccCcccCCCCCCCcccCccccCC
Q 023322 92 GGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (284)
Q Consensus 92 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~ 122 (284)
+.....-.+|... +.+||..|..|+.|.
T Consensus 137 g~~~~~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 137 GVPLELTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred CCChhheeeccCC---CCCCCCCCHHHHHHH
Confidence 3344456666644 338999999998864
No 48
>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=32.85 E-value=60 Score=21.68 Aligned_cols=22 Identities=27% Similarity=0.851 Sum_probs=14.4
Q ss_pred ccccccCcccCCCCCCCc-ccCc
Q 023322 96 RYCQKCSHYKPPRAHHCR-VCKR 117 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~-~C~~ 117 (284)
+.|..|...-|+--..|| .|+.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 567777777666666664 5554
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.57 E-value=21 Score=22.53 Aligned_cols=8 Identities=38% Similarity=1.352 Sum_probs=4.3
Q ss_pred cccccCcc
Q 023322 97 YCQKCSHY 104 (284)
Q Consensus 97 ~C~~C~~~ 104 (284)
+|+.|...
T Consensus 2 FCp~Cg~~ 9 (52)
T smart00661 2 FCPKCGNM 9 (52)
T ss_pred CCCCCCCc
Confidence 55566543
No 50
>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=31.89 E-value=20 Score=20.47 Aligned_cols=22 Identities=27% Similarity=0.717 Sum_probs=10.0
Q ss_pred cccccccCcc----cCCCCCCCcccC
Q 023322 95 LRYCQKCSHY----KPPRAHHCRVCK 116 (284)
Q Consensus 95 ~~~C~~C~~~----kP~Rs~HC~~C~ 116 (284)
.+||..|... .-.++..|..|+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 3788888753 223455555554
No 51
>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=31.65 E-value=25 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=18.6
Q ss_pred ccccccccCccc----CCCCCCCcccCcc
Q 023322 94 DLRYCQKCSHYK----PPRAHHCRVCKRC 118 (284)
Q Consensus 94 ~~~~C~~C~~~k----P~Rs~HC~~C~~C 118 (284)
..+.|+.|.... ..|.++|..|+.-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 458899998754 4577888888865
No 52
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=30.48 E-value=21 Score=26.26 Aligned_cols=22 Identities=27% Similarity=0.421 Sum_probs=16.8
Q ss_pred CCCCCCcccCccccCCcccCcc
Q 023322 107 PRAHHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 107 ~Rs~HC~~C~~CV~~~DHHC~w 128 (284)
.+.-+|..|++||.+.---+.+
T Consensus 18 v~~V~C~nCgr~vPKDKAIkrf 39 (95)
T PRK09335 18 VGYVQCDNCGRRVPRDKAVCVT 39 (95)
T ss_pred CccEEeCCCCCcCcCCceEEEE
Confidence 3466899999999987666654
No 53
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=29.94 E-value=20 Score=26.98 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=15.1
Q ss_pred CCCCCcccCccccCCcccCc
Q 023322 108 RAHHCRVCKRCVLRMDHHCI 127 (284)
Q Consensus 108 Rs~HC~~C~~CV~~~DHHC~ 127 (284)
+.-||..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKAIKR 38 (108)
T ss_pred ccEEeCCccccccccceEEE
Confidence 45689999999997555444
No 54
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=29.67 E-value=29 Score=22.31 Aligned_cols=23 Identities=22% Similarity=0.798 Sum_probs=14.4
Q ss_pred cccccccCc-c--cCCCCCCCcccCc
Q 023322 95 LRYCQKCSH-Y--KPPRAHHCRVCKR 117 (284)
Q Consensus 95 ~~~C~~C~~-~--kP~Rs~HC~~C~~ 117 (284)
.++|+.|.. . .-....+|..|+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCC
Confidence 479999976 2 2223556777763
No 55
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=29.25 E-value=28 Score=18.53 Aligned_cols=21 Identities=19% Similarity=0.575 Sum_probs=15.8
Q ss_pred cccccCcccCCCCCCCcccCc
Q 023322 97 YCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 97 ~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
.|..|...-.+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477888777777778877764
No 56
>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=28.79 E-value=16 Score=21.49 Aligned_cols=8 Identities=38% Similarity=1.472 Sum_probs=4.6
Q ss_pred ccccccCc
Q 023322 96 RYCQKCSH 103 (284)
Q Consensus 96 ~~C~~C~~ 103 (284)
++|++|..
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 56777764
No 57
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=28.57 E-value=1.2e+02 Score=17.32 Aligned_cols=25 Identities=12% Similarity=0.384 Sum_probs=12.9
Q ss_pred HHHHHHHHHH-HHHhHHhhcCCCCCC
Q 023322 47 VFTAVALMCV-FSYTVAILRDPGRVP 71 (284)
Q Consensus 47 ~~~~l~~~~~-~~~~~~~~~dPG~~p 71 (284)
.|+++....+ ..++...++||-.++
T Consensus 5 ~Ytfll~~tlgiiFFAIfFRepPri~ 30 (31)
T PRK11875 5 AYILILTLALVTLFFAIAFRDPPKID 30 (31)
T ss_pred HHHHHHHHHHHHHHHhhhccCCCCCC
Confidence 3444444333 334555679986554
No 58
>CHL00031 psbT photosystem II protein T
Probab=28.25 E-value=1.3e+02 Score=17.51 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=14.1
Q ss_pred HHHHHHHHHH-HHHhHHhhcCCCCCCC
Q 023322 47 VFTAVALMCV-FSYTVAILRDPGRVPA 72 (284)
Q Consensus 47 ~~~~l~~~~~-~~~~~~~~~dPG~~p~ 72 (284)
.|+++.+..+ ..++...++||-.+++
T Consensus 5 vYtfll~~tlgilFFAI~FRePPri~k 31 (33)
T CHL00031 5 VYTFLLVSTLGIIFFAIFFREPPKVPT 31 (33)
T ss_pred HHHHHHHHHHHHHHHhheecCCCCCCC
Confidence 3444444443 3345556899966654
No 59
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=28.02 E-value=1.2e+02 Score=23.03 Aligned_cols=18 Identities=11% Similarity=0.473 Sum_probs=8.1
Q ss_pred cchhHHHHHHHhhhhhee
Q 023322 7 FSLPVSVVVLAIFYIYFT 24 (284)
Q Consensus 7 ~~lp~~~v~~li~~~~~~ 24 (284)
+.+.+..+++.+...|..
T Consensus 12 R~~al~lif~g~~vmy~g 29 (114)
T PF11023_consen 12 RTFALSLIFIGMIVMYIG 29 (114)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 344444444444444443
No 60
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.00 E-value=30 Score=26.33 Aligned_cols=24 Identities=21% Similarity=0.685 Sum_probs=17.7
Q ss_pred ccccccccCcccCCCCCC---CcccCc
Q 023322 94 DLRYCQKCSHYKPPRAHH---CRVCKR 117 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~H---C~~C~~ 117 (284)
..-+|..|...-|...++ |..|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 347899999887775444 888874
No 61
>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=27.93 E-value=23 Score=22.49 Aligned_cols=15 Identities=20% Similarity=0.175 Sum_probs=6.0
Q ss_pred CccccCCcc--cCcccc
Q 023322 116 KRCVLRMDH--HCIWIS 130 (284)
Q Consensus 116 ~~CV~~~DH--HC~wi~ 130 (284)
|.-+..-+| .|||-+
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 345555666 688754
No 62
>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=27.63 E-value=13 Score=23.80 Aligned_cols=16 Identities=31% Similarity=0.877 Sum_probs=10.4
Q ss_pred cccCccccCCcccCcc
Q 023322 113 RVCKRCVLRMDHHCIW 128 (284)
Q Consensus 113 ~~C~~CV~~~DHHC~w 128 (284)
..|..|+...|-+|.|
T Consensus 6 ~sC~~Cl~~~dp~CgW 21 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGW 21 (51)
T ss_dssp SSHHHHHHSTCTTEEE
T ss_pred CcHHHHHcCCCcCccc
Confidence 4566666666666666
No 63
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=27.13 E-value=40 Score=21.30 Aligned_cols=33 Identities=21% Similarity=0.728 Sum_probs=21.8
Q ss_pred ccccccccCccc---CCCCCCCcccCc-----cccCCcccC
Q 023322 94 DLRYCQKCSHYK---PPRAHHCRVCKR-----CVLRMDHHC 126 (284)
Q Consensus 94 ~~~~C~~C~~~k---P~Rs~HC~~C~~-----CV~~~DHHC 126 (284)
.+.+|..|+..- -..+.+|+.|+. |..+.+.-|
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 458899999876 566788998874 555554444
No 64
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.65 E-value=30 Score=32.12 Aligned_cols=29 Identities=28% Similarity=0.696 Sum_probs=19.9
Q ss_pred cCCCCCCCcccCccccCCcccCcccccccCCcchH
Q 023322 105 KPPRAHHCRVCKRCVLRMDHHCIWISNCVGHANYK 139 (284)
Q Consensus 105 kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG~~N~~ 139 (284)
+-.|..||..|+. +|| +|+.||||.-=.-
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 3445667777764 677 6999999974433
No 65
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=26.24 E-value=2.8e+02 Score=26.04 Aligned_cols=14 Identities=36% Similarity=1.051 Sum_probs=12.1
Q ss_pred CCcccCccccCCcccCcc
Q 023322 111 HCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 111 HC~~C~~CV~~~DHHC~w 128 (284)
.|..|+.| +|+||-
T Consensus 68 ~C~~Cg~C----~~~CP~ 81 (389)
T PRK15033 68 LCHNCGAC----LHACQY 81 (389)
T ss_pred hCcCcccc----cccCcC
Confidence 89999999 469997
No 66
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=26.20 E-value=4.3e+02 Score=25.00 Aligned_cols=30 Identities=17% Similarity=0.397 Sum_probs=18.3
Q ss_pred ccccccCccc--C----CCCCCCcccCccccCCccc
Q 023322 96 RYCQKCSHYK--P----PRAHHCRVCKRCVLRMDHH 125 (284)
Q Consensus 96 ~~C~~C~~~k--P----~Rs~HC~~C~~CV~~~DHH 125 (284)
.-|+.|+..- | ...-+|..|+.-..+.+++
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~ 46 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTVRWDE 46 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcCCCCC
Confidence 5699999642 2 2344577777766555544
No 67
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.79 E-value=39 Score=33.89 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=9.9
Q ss_pred cccccCcccCCCCCCCcccCc
Q 023322 97 YCQKCSHYKPPRAHHCRVCKR 117 (284)
Q Consensus 97 ~C~~C~~~kP~Rs~HC~~C~~ 117 (284)
.|..|...-|+.+++|..||.
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred cCCCCCCCCCcccccccccCC
Confidence 344444444444444444443
No 68
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=25.06 E-value=31 Score=21.33 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=5.3
Q ss_pred cccccCcccCC
Q 023322 97 YCQKCSHYKPP 107 (284)
Q Consensus 97 ~C~~C~~~kP~ 107 (284)
-|..|...+++
T Consensus 6 sC~~C~~~~~~ 16 (46)
T smart00423 6 SCSECLLARDP 16 (46)
T ss_pred cHHHHHcCCCC
Confidence 34555544444
No 69
>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=24.98 E-value=5.8e+02 Score=23.98 Aligned_cols=31 Identities=16% Similarity=0.327 Sum_probs=19.0
Q ss_pred cccccccCcc--cCC-C---CCCCcccCccccCCccc
Q 023322 95 LRYCQKCSHY--KPP-R---AHHCRVCKRCVLRMDHH 125 (284)
Q Consensus 95 ~~~C~~C~~~--kP~-R---s~HC~~C~~CV~~~DHH 125 (284)
..-|+.|+.. +|+ + .-+|..||.-..+.+++
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~ 49 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLTVGWDW 49 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCcCCCCC
Confidence 4569999953 222 2 33477777766665554
No 70
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.84 E-value=14 Score=32.27 Aligned_cols=16 Identities=13% Similarity=0.164 Sum_probs=9.3
Q ss_pred CCCCcccCccccCCcc
Q 023322 109 AHHCRVCKRCVLRMDH 124 (284)
Q Consensus 109 s~HC~~C~~CV~~~DH 124 (284)
+-||..|++|+.+|.|
T Consensus 291 ~N~~~~~~~~~q~~~H 306 (325)
T KOG4399|consen 291 SNKMKMETTKGQSMNH 306 (325)
T ss_pred cchhhhhhhhhhhhHH
Confidence 4455666666665554
No 71
>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=24.41 E-value=39 Score=28.14 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=15.2
Q ss_pred ccccccCcccCCCCCCCcccCccccC
Q 023322 96 RYCQKCSHYKPPRAHHCRVCKRCVLR 121 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C~~CV~~ 121 (284)
..=..|... ..+||..|..|+.|
T Consensus 179 ~~t~sC~~~---~~~~CG~C~~C~~r 201 (201)
T TIGR00364 179 KLTYSCYAG---GGEGCGKCPSCMLR 201 (201)
T ss_pred hhCCcCCCc---CCCCCCCChhhhcc
Confidence 334445543 24699999999875
No 72
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=24.34 E-value=30 Score=33.17 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=14.9
Q ss_pred ccccccCcc--cCCCCCCCcccCc
Q 023322 96 RYCQKCSHY--KPPRAHHCRVCKR 117 (284)
Q Consensus 96 ~~C~~C~~~--kP~Rs~HC~~C~~ 117 (284)
..|-.|+.. .--|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 457777643 2247899998886
No 73
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.16 E-value=44 Score=33.50 Aligned_cols=39 Identities=28% Similarity=0.522 Sum_probs=26.1
Q ss_pred ccccccccCcccCCCCCCCcccCccccCCcccCcccccccC
Q 023322 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRMDHHCIWISNCVG 134 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~wi~nCIG 134 (284)
..+||..|...-+ .+.|..|+.=+..-..+|+==|.=.|
T Consensus 14 ~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 14 NNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCccccccCCCCC--CCcCCCCCCCCCcccccccccCCccc
Confidence 4578888876433 35788888878777778875443333
No 74
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=23.90 E-value=2.9e+02 Score=20.15 Aligned_cols=21 Identities=24% Similarity=0.207 Sum_probs=16.2
Q ss_pred HHhhCcchhhHHhhhhhHHHH
Q 023322 206 LIFHNKTTIEYHEGVRALWLA 226 (284)
Q Consensus 206 li~~n~Tt~E~~~~~~~~~~~ 226 (284)
.-.++++|-|.++..+..+..
T Consensus 77 ~W~~~r~tae~lk~e~~~~~~ 97 (112)
T PF14015_consen 77 RWIRYRATAESLKREKWLYLA 97 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 357789999999987776554
No 75
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=23.46 E-value=29 Score=35.27 Aligned_cols=37 Identities=27% Similarity=0.570 Sum_probs=27.0
Q ss_pred CCCCc---ccCccccCCcccCcccc---cccCC--cchHHHHHHH
Q 023322 109 AHHCR---VCKRCVLRMDHHCIWIS---NCVGH--ANYKVFFIFV 145 (284)
Q Consensus 109 s~HC~---~C~~CV~~~DHHC~wi~---nCIG~--~N~~~Fi~fl 145 (284)
-|+|+ .|-.|++..|-||-|-+ .|+-. .|.|.+.+=+
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 56787 89888888999999976 78643 3556555443
No 76
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=23.37 E-value=28 Score=29.91 Aligned_cols=19 Identities=42% Similarity=0.971 Sum_probs=15.4
Q ss_pred ccCCCCCCCcccCccccCC
Q 023322 104 YKPPRAHHCRVCKRCVLRM 122 (284)
Q Consensus 104 ~kP~Rs~HC~~C~~CV~~~ 122 (284)
+++.+..||..|.-|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 4666666999999999874
No 77
>PHA02942 putative transposase; Provisional
Probab=22.60 E-value=44 Score=31.18 Aligned_cols=24 Identities=33% Similarity=0.663 Sum_probs=17.5
Q ss_pred ccccccccCcccCC---CCCCCcccCc
Q 023322 94 DLRYCQKCSHYKPP---RAHHCRVCKR 117 (284)
Q Consensus 94 ~~~~C~~C~~~kP~---Rs~HC~~C~~ 117 (284)
..+.|+.|....++ |.+.|..||.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCC
Confidence 45789999876543 7778887776
No 78
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.13 E-value=47 Score=30.99 Aligned_cols=24 Identities=25% Similarity=0.722 Sum_probs=20.8
Q ss_pred ccccccCcccCCCCCCCcccCccc
Q 023322 96 RYCQKCSHYKPPRAHHCRVCKRCV 119 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C~~CV 119 (284)
++|..|...+-+-+..|..||.=+
T Consensus 2 ~fC~kcG~qk~Ed~~qC~qCG~~~ 25 (465)
T COG4640 2 KFCPKCGSQKAEDDVQCTQCGHKF 25 (465)
T ss_pred CcccccccccccccccccccCCcC
Confidence 789999999999999999988743
No 79
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=21.72 E-value=62 Score=17.44 Aligned_cols=19 Identities=32% Similarity=0.861 Sum_probs=9.1
Q ss_pred ccccCcccCCCC----CCCcccC
Q 023322 98 CQKCSHYKPPRA----HHCRVCK 116 (284)
Q Consensus 98 C~~C~~~kP~Rs----~HC~~C~ 116 (284)
|.+|...-.+|- ..|..|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 445554444442 3455554
No 80
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.39 E-value=55 Score=21.66 Aligned_cols=21 Identities=38% Similarity=0.885 Sum_probs=14.8
Q ss_pred ccccccccCcccCCCCCC-CcccC
Q 023322 94 DLRYCQKCSHYKPPRAHH-CRVCK 116 (284)
Q Consensus 94 ~~~~C~~C~~~kP~Rs~H-C~~C~ 116 (284)
....|..|...+.+ || |..||
T Consensus 26 ~l~~C~~CG~~~~~--H~vC~~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKLP--HRVCPSCG 47 (57)
T ss_pred cceECCCCCCccCC--eEECCCCC
Confidence 45679999976644 55 77776
No 81
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=21.38 E-value=50 Score=22.71 Aligned_cols=13 Identities=54% Similarity=1.635 Sum_probs=8.2
Q ss_pred ccccccCcccCCCCCCCccc
Q 023322 96 RYCQKCSHYKPPRAHHCRVC 115 (284)
Q Consensus 96 ~~C~~C~~~kP~Rs~HC~~C 115 (284)
-||.+| +.||-.|
T Consensus 30 CyCK~C-------cyHCqlC 42 (68)
T PF00539_consen 30 CYCKKC-------CYHCQLC 42 (68)
T ss_dssp SSSTTS-------TSSSSCC
T ss_pred cccCcc-------eeeceee
Confidence 466666 6677665
No 82
>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=21.20 E-value=31 Score=26.24 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=13.8
Q ss_pred CCCCCcccCccccCCcccCcc
Q 023322 108 RAHHCRVCKRCVLRMDHHCIW 128 (284)
Q Consensus 108 Rs~HC~~C~~CV~~~DHHC~w 128 (284)
+.-||..|++||.+----..+
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf 39 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKRF 39 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEEE
T ss_pred cCEeeCcccccCcCCceEEEE
Confidence 456899999999986665554
No 83
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=21.15 E-value=4.1e+02 Score=20.78 Aligned_cols=21 Identities=10% Similarity=0.349 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 023322 138 YKVFFIFVLYAVVACIYSMVL 158 (284)
Q Consensus 138 ~~~Fi~fl~~~~~~~~~~~~~ 158 (284)
-+||-+|+++++.+.+.-.++
T Consensus 38 ~~Y~~LfiVFl~AG~vLw~vM 58 (141)
T PRK13743 38 DIYFDLFIVFLTAGIVLWVIM 58 (141)
T ss_pred HHHHHHHHHHHHhhHHHHHHH
Confidence 478999998888776654444
Done!