Query 026691
Match_columns 235
No_of_seqs 94 out of 96
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 11:21:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00061 photosystem II protei 100.0 2.3E-62 4.9E-67 409.0 13.6 148 83-232 3-150 (150)
2 PLN00064 photosystem II protei 100.0 4.6E-43 1E-47 296.7 14.8 98 137-235 65-162 (166)
3 PF13326 PSII_Pbs27: Photosyst 100.0 1E-43 2.2E-48 294.4 9.2 145 71-235 1-145 (145)
4 TIGR03044 PS_II_psb27 photosys 100.0 1.9E-42 4.2E-47 285.6 14.8 103 131-235 30-132 (135)
5 TIGR02811 formate_TAT formate 93.3 0.12 2.5E-06 38.6 3.7 16 67-82 6-21 (66)
6 PF10518 TAT_signal: TAT (twin 86.2 0.73 1.6E-05 28.6 2.3 13 70-82 2-14 (26)
7 PF07240 Turandot: Stress-indu 81.5 3.3 7.2E-05 32.7 4.8 35 197-231 9-43 (85)
8 smart00040 CSF2 Granulocyte-ma 81.3 2.8 6E-05 35.0 4.5 25 191-215 68-92 (121)
9 TIGR01409 TAT_signal_seq Tat ( 81.0 1.5 3.2E-05 27.5 2.1 12 71-82 2-13 (29)
10 cd00040 CSF2 Granulocyte Macro 79.6 3.7 8E-05 34.4 4.6 25 191-215 68-92 (121)
11 PF10399 UCR_Fe-S_N: Ubiquitin 76.4 1.2 2.5E-05 30.7 0.7 29 66-95 5-33 (41)
12 PF12732 YtxH: YtxH-like prote 73.8 6 0.00013 29.0 4.0 49 129-178 22-72 (74)
13 COG1698 Uncharacterized protei 71.1 23 0.0005 28.6 6.9 86 131-232 4-89 (93)
14 PRK15102 trimethylamine N-oxid 64.2 5.2 0.00011 41.0 2.6 13 70-82 1-13 (825)
15 PRK07474 sulfur oxidation prot 60.6 6.2 0.00014 33.9 2.1 18 69-86 7-24 (154)
16 cd08054 gp6 Head-Tail Connecto 60.1 44 0.00095 24.1 6.2 76 147-222 3-85 (91)
17 PF09037 Sulphotransf: Stf0 su 57.9 8.3 0.00018 34.5 2.5 46 138-183 198-244 (245)
18 cd01018 ZntC Metal binding pro 52.5 30 0.00065 30.6 5.1 96 131-230 114-215 (266)
19 PF11674 DUF3270: Protein of u 52.1 49 0.0011 26.4 5.7 32 9-42 35-67 (90)
20 PRK10882 hydrogenase 2 protein 51.0 13 0.00028 35.1 2.7 13 70-82 1-13 (328)
21 TIGR01560 put_DNA_pack unchara 50.0 64 0.0014 24.4 5.9 59 147-209 3-62 (91)
22 TIGR02166 dmsA_ynfE anaerobic 49.5 16 0.00036 36.9 3.3 20 164-183 126-145 (797)
23 KOG3142 Prenylated rab accepto 47.0 57 0.0012 29.1 5.9 85 8-98 64-162 (187)
24 PF15519 RBM39linker: linker b 46.0 7.7 0.00017 29.3 0.3 15 118-132 59-73 (73)
25 PRK10866 outer membrane biogen 45.2 1.7E+02 0.0038 25.8 8.7 80 144-225 50-168 (243)
26 PF13551 HTH_29: Winged helix- 44.9 64 0.0014 23.7 5.1 56 161-230 16-72 (112)
27 PF02899 Phage_int_SAM_1: Phag 44.9 1E+02 0.0023 21.4 7.9 58 137-208 21-78 (84)
28 COG2822 Predicted periplasmic 44.9 72 0.0016 31.1 6.6 64 139-208 296-367 (376)
29 PF09236 AHSP: Alpha-haemoglob 40.9 35 0.00076 27.4 3.3 17 195-211 32-48 (89)
30 TIGR02659 TTQ_MADH_Lt methylam 40.5 27 0.00059 31.2 2.9 28 68-97 20-47 (186)
31 TIGR01416 Rieske_proteo ubiqui 40.1 18 0.0004 31.0 1.7 24 71-95 1-24 (174)
32 PLN00033 photosystem II stabil 40.0 21 0.00045 34.4 2.3 36 51-86 21-56 (398)
33 PF03208 PRA1: PRA1 family pro 39.9 2E+02 0.0043 23.2 8.3 18 15-32 40-57 (153)
34 PF09726 Macoilin: Transmembra 39.8 25 0.00054 36.5 2.9 13 5-17 90-102 (697)
35 PF10163 EnY2: Transcription f 39.3 1.2E+02 0.0026 23.1 5.9 50 168-230 34-83 (86)
36 PF12889 DUF3829: Protein of u 39.1 54 0.0012 28.4 4.5 48 162-209 219-274 (276)
37 PF12318 FAD-SLDH: Membrane bo 37.5 31 0.00066 29.6 2.7 8 70-77 2-9 (168)
38 PF12918 TcdB_N: TcdB toxin N- 37.3 1.1E+02 0.0024 22.7 5.3 45 143-187 4-49 (66)
39 TIGR03175 AllD ureidoglycolate 37.0 60 0.0013 31.0 4.8 81 114-216 260-347 (349)
40 PF08374 Protocadherin: Protoc 36.6 2.6 5.6E-05 38.4 -4.1 31 172-212 133-163 (221)
41 PRK15219 carbonic anhydrase; P 35.5 17 0.00037 33.0 0.9 73 68-141 7-80 (245)
42 PRK14990 anaerobic dimethyl su 34.9 31 0.00067 35.3 2.7 21 164-184 141-161 (814)
43 cd01019 ZnuA Zinc binding prot 34.8 89 0.0019 28.1 5.3 48 132-183 124-172 (286)
44 PF08611 DUF1774: Fungal prote 34.7 47 0.001 26.9 3.2 25 7-37 13-37 (97)
45 TIGR01405 polC_Gram_pos DNA po 34.5 1.5E+02 0.0033 32.9 7.9 92 133-232 539-632 (1213)
46 cd01020 TroA_b Metal binding p 33.4 1.1E+02 0.0023 27.2 5.5 47 132-182 98-145 (264)
47 PF07030 DUF1320: Protein of u 32.4 2.7E+02 0.0058 22.5 7.3 63 158-226 28-93 (130)
48 PF08479 POTRA_2: POTRA domain 31.7 1.2E+02 0.0025 21.9 4.6 34 173-211 18-51 (76)
49 PF06057 VirJ: Bacterial virul 31.7 26 0.00057 31.2 1.4 44 165-225 49-98 (192)
50 PRK09269 chorismate mutase; Pr 31.2 1.7E+02 0.0036 26.0 6.3 64 141-204 67-136 (193)
51 cd01493 APPBP1_RUB Ubiquitin a 30.0 2.8E+02 0.0061 27.2 8.2 82 133-220 222-313 (425)
52 PRK09545 znuA high-affinity zi 30.0 1.1E+02 0.0023 28.2 5.1 89 142-230 154-250 (311)
53 PF09684 Tail_P2_I: Phage tail 29.8 2.4E+02 0.0053 22.6 6.6 66 157-227 2-67 (139)
54 COG0339 Dcp Zn-dependent oligo 29.0 49 0.0011 34.8 3.0 28 196-226 514-541 (683)
55 PF05823 Gp-FAR-1: Nematode fa 28.9 1.1E+02 0.0024 25.9 4.6 58 167-230 75-135 (154)
56 cd01137 PsaA Metal binding pro 28.4 1.5E+02 0.0033 26.7 5.7 96 131-230 119-224 (287)
57 KOG2856 Adaptor protein PACSIN 28.2 51 0.0011 32.9 2.8 43 161-205 38-80 (472)
58 PRK13474 cytochrome b6-f compl 28.1 39 0.00085 29.1 1.8 14 69-82 11-24 (178)
59 PRK00035 hemH ferrochelatase; 28.1 1.7E+02 0.0037 26.7 6.1 47 172-218 20-74 (333)
60 PRK10280 dipeptidyl carboxypep 27.9 48 0.001 34.2 2.7 33 191-226 506-538 (681)
61 PF05135 Phage_connect_1: Phag 26.7 2.6E+02 0.0056 20.5 6.4 62 146-209 6-68 (101)
62 PF04740 LXG: LXG domain of WX 25.9 3.2E+02 0.007 22.8 6.9 66 167-233 44-113 (204)
63 PRK00448 polC DNA polymerase I 25.6 2.3E+02 0.005 32.3 7.5 92 133-232 764-857 (1437)
64 PF01297 TroA: Periplasmic sol 25.2 48 0.0011 28.7 1.9 96 131-230 94-197 (256)
65 TIGR00831 a_cpa1 Na+/H+ antipo 25.2 6.8E+02 0.015 24.8 12.0 29 202-234 494-522 (525)
66 cd01145 TroA_c Periplasmic bin 25.1 68 0.0015 27.2 2.8 47 132-182 111-158 (203)
67 TIGR01480 copper_res_A copper- 25.1 52 0.0011 33.4 2.4 12 69-80 5-16 (587)
68 PF04011 LemA: LemA family; I 24.6 1.3E+02 0.0028 25.4 4.3 65 140-204 65-131 (186)
69 PF05478 Prominin: Prominin; 24.1 3.7E+02 0.008 28.2 8.2 28 54-81 118-147 (806)
70 PF01109 GM_CSF: Granulocyte-m 23.9 43 0.00093 28.3 1.3 37 173-219 58-94 (122)
71 PRK14993 tetrathionate reducta 23.5 60 0.0013 29.2 2.2 12 70-81 3-14 (244)
72 PRK03620 5-dehydro-4-deoxygluc 23.2 1.6E+02 0.0035 26.8 4.9 42 193-235 258-301 (303)
73 PRK14996 TetR family transcrip 22.6 4.2E+02 0.0091 21.4 10.0 68 165-234 120-191 (192)
74 PF13333 rve_2: Integrase core 22.4 1.1E+02 0.0023 20.9 2.9 24 165-189 18-41 (52)
75 PRK15488 thiosulfate reductase 22.4 69 0.0015 32.5 2.6 62 121-184 70-140 (759)
76 PF05105 Phage_holin_4: Holin 22.4 1E+02 0.0022 24.3 3.1 25 200-226 89-113 (118)
77 PF06761 IcmF-related: Intrace 22.1 5.3E+02 0.012 23.3 8.0 79 126-204 191-293 (312)
78 PF10428 SOG2: RAM signalling 21.9 2E+02 0.0044 28.3 5.6 52 174-225 364-424 (445)
79 smart00167 VPS9 Domain present 21.6 1.1E+02 0.0024 24.7 3.2 34 173-206 67-102 (117)
80 cd01017 AdcA Metal binding pro 21.5 80 0.0017 28.1 2.6 48 132-183 116-164 (282)
81 TIGR03149 cyt_nit_nrfC cytochr 21.4 55 0.0012 28.8 1.5 13 70-82 2-14 (225)
82 cd03568 VHS_STAM VHS domain fa 21.2 3.9E+02 0.0085 22.2 6.5 57 143-210 79-135 (144)
83 PF09373 PMBR: Pseudomurein-bi 21.1 1.5E+02 0.0033 18.9 3.2 24 188-211 2-25 (33)
84 PF14461 Prok-E2_B: Prokaryoti 21.0 1.8E+02 0.0038 23.5 4.3 37 143-187 94-130 (133)
85 smart00288 VHS Domain present 20.9 4.2E+02 0.0092 21.3 6.5 38 142-183 78-115 (133)
86 PF12994 DUF3878: Domain of un 20.7 2.7E+02 0.0059 26.8 6.0 85 138-235 164-257 (299)
87 PF08463 EcoEI_R_C: EcoEI R pr 20.5 1.3E+02 0.0027 24.6 3.4 63 137-213 60-123 (164)
88 PLN02382 probable sucrose-phos 20.5 77 0.0017 30.5 2.4 39 110-154 304-344 (413)
89 PRK10911 oligopeptidase A; Pro 20.4 1.1E+02 0.0025 31.4 3.7 29 195-226 510-538 (680)
90 TIGR02949 anti_SigH_actin anti 20.2 2.7E+02 0.0059 21.0 4.9 19 213-231 62-80 (84)
No 1
>PLN00061 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=2.3e-62 Score=409.04 Aligned_cols=148 Identities=78% Similarity=1.098 Sum_probs=143.2
Q ss_pred HHHHHHhhccCCCchhhhccccCCCCccccccccchhcccCCCCcccCCCCCchHHHHHHHHHHHHHHHHhcCCCCCchH
Q 026691 83 LVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN 162 (235)
Q Consensus 83 ~~~~~~~~~~~~P~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~tkSg~~LPkdY~kdT~~VV~tLReaLelDp~D~~~ 162 (235)
++++++++|...|++++|++|+ +.+++|||||||||+|||||+||||+.||++|++||++||++||++|+++|+|+++
T Consensus 3 ~~~~~~~~~~~~~~~~~a~~e~--~~~~~~~~~~~~~~~fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~ 80 (150)
T PLN00061 3 FAASLTLNGQMTPLQARAEEEA--KVEEGEGVVGAIKSLFDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAK 80 (150)
T ss_pred HHHHHHHhcCCCCCcchHHHHh--cccccccHHHHHHHhcCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHH
Confidence 3578899999999999999997 57778899999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHHHH
Q 026691 163 FRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAE 232 (235)
Q Consensus 163 ~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~AE 232 (235)
+++++++||++|||||++|||+++|+|++||+||+||||+|||||++|||+||||||+|+||++||++||
T Consensus 81 ~~~aa~~Ake~IndYisryR~~~~V~gl~SfttMqtALnsLAghYssyGpnrPLPe~lK~Rll~EL~~AE 150 (150)
T PLN00061 81 FRRTADAAKESIREYLGNWRGQKTVAEEESYVELEKAIRSLASFYSKAGPSAPLPEDVKSEILDDLNKAE 150 (150)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCccccccchHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PLN00064 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=4.6e-43 Score=296.69 Aligned_cols=98 Identities=27% Similarity=0.555 Sum_probs=96.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCC
Q 026691 137 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL 216 (235)
Q Consensus 137 dY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPL 216 (235)
+|.+||.+||++||++|+| |+|++++.++++++|++||||||||||+++|+|++||+|||||||+|||||+||||+|||
T Consensus 65 ~Y~~DT~aVi~~lr~tI~L-~~ddp~~a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SFttMyTALNaLAGHY~SfgpnrPl 143 (166)
T PLN00064 65 EYVKETKDVIGKVRSTINM-DKTDPNVADAVAELRETSNSWVAKYRREKALLGRPSFRDMYSALNAVSGHYISFGPTAPI 143 (166)
T ss_pred ChHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcccHHHHHHHHHHHHHHhhccCCCCCC
Confidence 4999999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHHhcC
Q 026691 217 PGEVKSEILNDLDTAEKFL 235 (235)
Q Consensus 217 PeklK~RLLqEL~~AEkaL 235 (235)
|+|+|+||+|||++||++|
T Consensus 144 PeKlK~RL~qE~~~AEkal 162 (166)
T PLN00064 144 PAKRKARILEEMDTAEKAL 162 (166)
T ss_pred cHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999986
No 3
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=100.00 E-value=1e-43 Score=294.38 Aligned_cols=145 Identities=41% Similarity=0.562 Sum_probs=93.0
Q ss_pred hhHHHHHhhhhhHHHHHHhhccCCCchhhhccccCCCCccccccccchhcccCCCCcccCCCCCchHHHHHHHHHHHHHH
Q 026691 71 SRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLR 150 (235)
Q Consensus 71 ~RR~~L~~~~~~~~~~~~~~~~~~P~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~tkSg~~LPkdY~kdT~~VV~tLR 150 (235)
+||++|...+..++++ ++.+..+++.+++..+.. + ++|. |||+ .|+++|++||++||++||
T Consensus 1 ~rr~~l~~~~~~~~al-~l~~~~~~l~~~~l~~c~-------~----~~s~-~~~~------~l~~~Y~~dt~~vv~~lr 61 (145)
T PF13326_consen 1 SRRRLLLAASSALLAL-TLSARGAALAVIALTACR-------A----AKSG-DPNA------GLTGDYVKDTRAVVKTLR 61 (145)
T ss_dssp ---------------------------------S------------------S--S------S--S-CHHHHHHHHHHHH
T ss_pred CcchhhhHHHHHHHHH-HHhhhhHHHHhhcchhhh-------h----cccC-Cccc------cccchHHHHHHHHHHHHH
Confidence 6899998887775443 444444555444422211 0 4444 6655 455679999999999999
Q ss_pred HHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 151 ESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 151 eaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
++|++ |+|++++++++++||++|||||++|||+++|+|++||++||+|||+|||||++|||++|||+|+|+||++||++
T Consensus 62 ~~l~l-~~d~~~~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf~~m~tAln~LaghY~s~g~raPlP~k~k~rll~el~~ 140 (145)
T PF13326_consen 62 EALEL-DKDDPNRAEAAAEARELINDYVSRYRRGPSVSGLPSFTTMYTALNALAGHYSSYGNRAPLPEKLKERLLKELDQ 140 (145)
T ss_dssp HHHCS--TT-TTHHHHHHHHHHHHHHHHCCCCCCHHCCTSHHHHHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHH
T ss_pred HHHcC-CCCCccHHHHHHHHHHHHHHHHHHhCCCCCcCCcchHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Confidence 99998 78999999999999999999999999999999999999999999999999999998889999999999999999
Q ss_pred HHhcC
Q 026691 231 AEKFL 235 (235)
Q Consensus 231 AEkaL 235 (235)
||++|
T Consensus 141 Ae~aL 145 (145)
T PF13326_consen 141 AEKAL 145 (145)
T ss_dssp HHHHH
T ss_pred HHhcC
Confidence 99986
No 4
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=100.00 E-value=1.9e-42 Score=285.63 Aligned_cols=103 Identities=31% Similarity=0.522 Sum_probs=99.9
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhc
Q 026691 131 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 210 (235)
Q Consensus 131 g~~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSf 210 (235)
.+.|+++|.+||++||++||++|++ |+|++++++++++||++|||||+||||+++|+|++||+|||||||+|||||++|
T Consensus 30 ~~~Ltg~Y~~DT~~Vi~tlr~~i~l-pkd~p~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~sy 108 (135)
T TIGR03044 30 KTRLTGDYVEDTLAVIQTLREAIDL-PDDDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKSY 108 (135)
T ss_pred cccccchHHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhccC
Confidence 3578999999999999999999999 999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHHhcC
Q 026691 211 GPSAPLPGEVKSEILNDLDTAEKFL 235 (235)
Q Consensus 211 Gp~rPLPeklK~RLLqEL~~AEkaL 235 (235)
| +||||||+|+||+|||++||++|
T Consensus 109 ~-~rPlPeklk~Rl~~El~~AE~al 132 (135)
T TIGR03044 109 A-NRPLPEKLKERLEKELKKAEKAL 132 (135)
T ss_pred C-CCCCCHHHHHHHHHHHHHHHHHH
Confidence 5 99999999999999999999986
No 5
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=93.34 E-value=0.12 Score=38.58 Aligned_cols=16 Identities=25% Similarity=0.360 Sum_probs=12.1
Q ss_pred chhhhhHHHHHhhhhh
Q 026691 67 EAASSRRHVISCSSTA 82 (235)
Q Consensus 67 ~~~~~RR~~L~~~~~~ 82 (235)
....+||+||.+.+++
T Consensus 6 ~~~~sRR~Flk~lg~~ 21 (66)
T TIGR02811 6 KADPSRRDLLKGLGVG 21 (66)
T ss_pred cCCccHHHHHHHHHHH
Confidence 3356899999987764
No 6
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=86.21 E-value=0.73 Score=28.61 Aligned_cols=13 Identities=31% Similarity=0.417 Sum_probs=11.0
Q ss_pred hhhHHHHHhhhhh
Q 026691 70 SSRRHVISCSSTA 82 (235)
Q Consensus 70 ~~RR~~L~~~~~~ 82 (235)
.+||+||.++++.
T Consensus 2 ~sRR~fLk~~~a~ 14 (26)
T PF10518_consen 2 LSRRQFLKGGAAA 14 (26)
T ss_pred CcHHHHHHHHHHH
Confidence 4899999999765
No 7
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=81.54 E-value=3.3 Score=32.68 Aligned_cols=35 Identities=26% Similarity=0.386 Sum_probs=29.9
Q ss_pred HHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHHH
Q 026691 197 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTA 231 (235)
Q Consensus 197 ~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~A 231 (235)
..=+.+|.+||..|.|.-||++..|+++...+++=
T Consensus 9 ~rni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~y 43 (85)
T PF07240_consen 9 IRNIQELIAFYEKYSPRLPLTPQDRQRIDRFIRRY 43 (85)
T ss_pred HhhHHHHHHHHHHcCccCCCCHHHHHHHHHHHHHH
Confidence 34467899999999999999999999998887653
No 8
>smart00040 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic activity of white blood cells.
Probab=81.31 E-value=2.8 Score=35.00 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHhhHhhcCCCCC
Q 026691 191 ESYVELEKAIRSLASFYSKAGPSAP 215 (235)
Q Consensus 191 ~SFttM~TALNsLAGHYsSfGp~rP 215 (235)
-|++.+..+|+-+|.||..+-|..|
T Consensus 68 Gslt~Lkg~LtmmA~hYkq~CppTp 92 (121)
T smart00040 68 GSLTKLKGPLTMMASHYKQHCPPTP 92 (121)
T ss_pred ccHHHhhcHHHHHHHHHHhcCCCCC
Confidence 4899999999999999999977655
No 9
>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.
Probab=80.98 E-value=1.5 Score=27.53 Aligned_cols=12 Identities=33% Similarity=0.506 Sum_probs=10.2
Q ss_pred hhHHHHHhhhhh
Q 026691 71 SRRHVISCSSTA 82 (235)
Q Consensus 71 ~RR~~L~~~~~~ 82 (235)
+||+||..++.+
T Consensus 2 sRR~Flk~~~~~ 13 (29)
T TIGR01409 2 SRRDFLKGAAAA 13 (29)
T ss_pred chhhhHHHHHHH
Confidence 799999999654
No 10
>cd00040 CSF2 Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) is a member of the large family of polypeptide growth factors called cytokines. It stimulates a wide variety of hematopoietic and nonhematopoietic cell types via binding to members of the cytokine receptor family, mainly the GM-CSF receptor.
Probab=79.56 E-value=3.7 Score=34.37 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHhhHhhcCCCCC
Q 026691 191 ESYVELEKAIRSLASFYSKAGPSAP 215 (235)
Q Consensus 191 ~SFttM~TALNsLAGHYsSfGp~rP 215 (235)
-|++.+..+|+-+|.||..+-|..|
T Consensus 68 GsltkLkg~LtmmAshYkqhCppTp 92 (121)
T cd00040 68 GSLTKLKGPLTMMASHYKQHCPPTP 92 (121)
T ss_pred ccHHHhccHHHHHHHHHHhcCCCCC
Confidence 4899999999999999999877655
No 11
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=76.41 E-value=1.2 Score=30.71 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=14.2
Q ss_pred cchhhhhHHHHHhhhhhHHHHHHhhccCCC
Q 026691 66 VEAASSRRHVISCSSTALVAILTFNCGLAP 95 (235)
Q Consensus 66 ~~~~~~RR~~L~~~~~~~~~~~~~~~~~~P 95 (235)
.....+||+||..+.++ ++++-..+..+|
T Consensus 5 ~~~~~~RRdFL~~at~~-~gavG~~~~a~P 33 (41)
T PF10399_consen 5 EPVDPTRRDFLTIATSA-VGAVGAAAAAWP 33 (41)
T ss_dssp -----HHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred CCCCchHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 45578999999555433 344444444445
No 12
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=73.76 E-value=6 Score=29.01 Aligned_cols=49 Identities=27% Similarity=0.333 Sum_probs=22.1
Q ss_pred cCCCCCchHHHHHHHHHHHHHHHHhcCCCCC--chHHHHhHHHHHHHHHHHH
Q 026691 129 KSGKVLPKAYLKSARELVKTLRESLKEDPKD--IANFRRNADSAKESIRDYL 178 (235)
Q Consensus 129 kSg~~LPkdY~kdT~~VV~tLReaLelDp~D--~~~~~~aa~~AKe~InDyV 178 (235)
+||+.+=++-.+.+.++.+.+.+..+. -.+ .+...+..+.+++.+++++
T Consensus 22 ~sG~e~R~~l~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~~~~~e~~~e~~ 72 (74)
T PF12732_consen 22 KSGKETREKLKDKAEDLKDKAKDLYEE-AKEKVKEKAEETADEAKEKAKELK 72 (74)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345544444444444444444443332 111 1233445556666666654
No 13
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.12 E-value=23 Score=28.63 Aligned_cols=86 Identities=27% Similarity=0.371 Sum_probs=62.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhc
Q 026691 131 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 210 (235)
Q Consensus 131 g~~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSf 210 (235)
|..++.++.+.-.+++..|++.+. |..=+.+.|+++++|++..++ .|++.+..-.+||.-|=.- |+
T Consensus 4 ~~~~~~d~~e~i~q~~~lL~~Ii~-DttVPRNIRraA~~a~e~L~~-----------e~e~p~vRaAtaIsiLeei--sn 69 (93)
T COG1698 4 GQGLMNDSEEKINQVMQLLDEIIQ-DTTVPRNIRRAAEEAKEALNN-----------EGESPAVRAATAISILEEI--SN 69 (93)
T ss_pred hhcchhhhHHHHHHHHHHHHHHHc-cccccHHHHHHHHHHHHHHhC-----------CCCCchhHHHHHHHHHHHH--hc
Confidence 456778888888999999999554 666678899999999998764 3677777777888777664 44
Q ss_pred CCCCCCChhHHHHHHHHHHHHH
Q 026691 211 GPSAPLPGEVKSEILNDLDTAE 232 (235)
Q Consensus 211 Gp~rPLPeklK~RLLqEL~~AE 232 (235)
-||-| --.|..|.+=+.+-|
T Consensus 70 DPNmP--~h~RT~iw~vis~LE 89 (93)
T COG1698 70 DPNMP--LHARTLIWNVISQLE 89 (93)
T ss_pred CCCCc--hHHHHHHHHHHHHHH
Confidence 57755 456776666554443
No 14
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=64.20 E-value=5.2 Score=41.03 Aligned_cols=13 Identities=23% Similarity=0.266 Sum_probs=10.4
Q ss_pred hhhHHHHHhhhhh
Q 026691 70 SSRRHVISCSSTA 82 (235)
Q Consensus 70 ~~RR~~L~~~~~~ 82 (235)
.|||.||.+++++
T Consensus 1 ~sRR~flk~~~~~ 13 (825)
T PRK15102 1 ASRRRFLKGLGGL 13 (825)
T ss_pred CCHHHHHHHHHHH
Confidence 3799999987765
No 15
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=60.58 E-value=6.2 Score=33.88 Aligned_cols=18 Identities=39% Similarity=0.434 Sum_probs=13.4
Q ss_pred hhhhHHHHHhhhhhHHHH
Q 026691 69 ASSRRHVISCSSTALVAI 86 (235)
Q Consensus 69 ~~~RR~~L~~~~~~~~~~ 86 (235)
..+||+||+..+++++++
T Consensus 7 ~~~rr~~l~~~~~~~~~~ 24 (154)
T PRK07474 7 ALSRRQALALGGGALAAA 24 (154)
T ss_pred CcCHHHHHHHHHHHHHHH
Confidence 479999999987664333
No 16
>cd08054 gp6 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins. The bacteriophage HK97 gp6 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp7 ring (attached to the tail). It is a component of the mature phage and the absence of HK97 gp6 results in defective head-tail joining and the absence of mature phage particles. Although the crystal structure of HK97 gp6 shows an unexpected 13-mer ring, the biological form present in the mature phage is believed to be a dodecamer.
Probab=60.06 E-value=44 Score=24.13 Aligned_cols=76 Identities=24% Similarity=0.225 Sum_probs=49.4
Q ss_pred HHHHHHhcCCCC-CchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhc-C-----CCCCCChh
Q 026691 147 KTLRESLKEDPK-DIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA-G-----PSAPLPGE 219 (235)
Q Consensus 147 ~tLReaLelDp~-D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSf-G-----p~rPLPek 219 (235)
+.+++.|..|.. |++......+.|++.|..|+.+--......+..--..+..|+..+++|+=.+ + ...++|.-
T Consensus 3 ~~~K~~Lrid~d~dD~~i~~li~aA~~~i~~~~g~~~~~~~~~~~~~~~~~~~Ail~l~~~~Y~nR~~~~~~~~~~~~~~ 82 (91)
T cd08054 3 EEAKAHLRIDHDDDDALIELLIDAAEEYIENYTGRDLDEQTADAEEVPALIKLAVLLLVAHLYENREAVTDVTASELPFG 82 (91)
T ss_pred HHHHhHcCCCCCCCHHHHHHHHHHHHHHHHHHhCCchhhcCCccccCCHHHHHHHHHHHHHHHhCccchhhcccccCCHH
Confidence 456677776543 3556677778888888888776654333346666778889999998886443 1 13566655
Q ss_pred HHH
Q 026691 220 VKS 222 (235)
Q Consensus 220 lK~ 222 (235)
++.
T Consensus 83 v~~ 85 (91)
T cd08054 83 VES 85 (91)
T ss_pred HHH
Confidence 544
No 17
>PF09037 Sulphotransf: Stf0 sulphotransferase; InterPro: IPR024628 Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices []. ; PDB: 1TEX_B.
Probab=57.92 E-value=8.3 Score=34.51 Aligned_cols=46 Identities=15% Similarity=0.203 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCchH-HHHhHHHHHHHHHHHHHhhhC
Q 026691 138 YLKSARELVKTLRESLKEDPKDIAN-FRRNADSAKESIRDYLSNWRG 183 (235)
Q Consensus 138 Y~kdT~~VV~tLReaLelDp~D~~~-~~~aa~~AKe~InDyVSrYRr 183 (235)
..+|-.++++.+-+.|..|+...+. .......+-+...||+.|||.
T Consensus 198 L~~dp~~~~~~Vl~fLgv~~~~~~~~~~~~~kqsd~~s~eW~~ry~~ 244 (245)
T PF09037_consen 198 LLADPQKTVARVLDFLGVDPPLAPIVKPPLKKQSDERSEEWVERYRA 244 (245)
T ss_dssp HHHHHHHHHHHHHHHTTS-GGGS----------------HHHHHHHH
T ss_pred HHhCHHHHHHHHHHHhCCCCcccccCCCCceecCCCChHHHHHHHhc
Confidence 3445566788888888886655432 234444555678899999985
No 18
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=52.55 E-value=30 Score=30.59 Aligned_cols=96 Identities=14% Similarity=0.145 Sum_probs=52.5
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcC-CCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhh
Q 026691 131 GKVLPKAYLKSARELVKTLRESLKE-DPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 209 (235)
Q Consensus 131 g~~LPkdY~kdT~~VV~tLReaLel-Dp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsS 209 (235)
-|-=|..+ ..++++|.+.|.. ||.+.+.+++..+...+.+.+.-+.|+..-.-.....|-+.-.|.+=|+.-|.=
T Consensus 114 ~Wldp~~~----~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~ygl 189 (266)
T cd01018 114 IWLSPANA----KIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMVYHPAWGYFARDYGL 189 (266)
T ss_pred cCcCHHHH----HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEECchhHHHHHHcCC
Confidence 45566666 5556666666654 898888888888888887777776666321111111222222233333333321
Q ss_pred c-----CCCCCCChhHHHHHHHHHHH
Q 026691 210 A-----GPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 210 f-----Gp~rPLPeklK~RLLqEL~~ 230 (235)
. +|....+.+.-.++.+.+++
T Consensus 190 ~~~~~~~~~~eps~~~l~~l~~~ik~ 215 (266)
T cd01018 190 TQIPIEEEGKEPSPADLKRLIDLAKE 215 (266)
T ss_pred EEEecCCCCCCCCHHHHHHHHHHHHH
Confidence 1 24455556666666666654
No 19
>PF11674 DUF3270: Protein of unknown function (DUF3270); InterPro: IPR021688 This family of proteins with unknown function appears to be restricted to Streptococcus.
Probab=52.11 E-value=49 Score=26.36 Aligned_cols=32 Identities=50% Similarity=0.813 Sum_probs=21.0
Q ss_pred HHHHHHHHHhHHHHHHHhhhHHHHHHHHHH-HHHH
Q 026691 9 NLVHLLFFQNYIIAFFVSASLCTSFLMLSF-INLF 42 (235)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 42 (235)
+|--|+||-| ||+|.....-.||+.|+. +|-+
T Consensus 35 kL~ELlFF~n--IA~FcI~tvlfsFvfLs~kl~t~ 67 (90)
T PF11674_consen 35 KLKELLFFAN--IAFFCIFTVLFSFVFLSLKLNTF 67 (90)
T ss_pred hHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhHH
Confidence 4667888887 677666566666766665 4443
No 20
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=51.04 E-value=13 Score=35.14 Aligned_cols=13 Identities=23% Similarity=0.463 Sum_probs=10.0
Q ss_pred hhhHHHHHhhhhh
Q 026691 70 SSRRHVISCSSTA 82 (235)
Q Consensus 70 ~~RR~~L~~~~~~ 82 (235)
++||+||.+++++
T Consensus 1 ~~RR~fl~~~~~~ 13 (328)
T PRK10882 1 MNRRNFLKAASAG 13 (328)
T ss_pred CCHHHHHHHHHHH
Confidence 3699999987553
No 21
>TIGR01560 put_DNA_pack uncharacterized phage protein (possible DNA packaging). This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model.
Probab=49.98 E-value=64 Score=24.36 Aligned_cols=59 Identities=17% Similarity=0.130 Sum_probs=40.1
Q ss_pred HHHHHHhcCCCC-CchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhh
Q 026691 147 KTLRESLKEDPK-DIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 209 (235)
Q Consensus 147 ~tLReaLelDp~-D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsS 209 (235)
+.++..|..|.. |++-.....+.|++.|..++.+.-.. +......+..|+..|++|+=.
T Consensus 3 ~~vK~~LrId~d~dD~li~~~i~aA~~~i~~~ig~~~~~----~~~~~~~~~~Avl~lv~~~Ye 62 (91)
T TIGR01560 3 DEVKLSLRIDHDDDDELIKLMIAAAQDYIQSAIGTGVKD----SFDSKPLFKLACIKLVAHYYE 62 (91)
T ss_pred HHHHhHhcCCCCccHHHHHHHHHHHHHHHHHHhCCCccc----ccccCHHHHHHHHHHHHHHHH
Confidence 456666666543 45555677888888888888765332 333445678899999999754
No 22
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=49.53 E-value=16 Score=36.94 Aligned_cols=20 Identities=5% Similarity=0.348 Sum_probs=13.2
Q ss_pred HHhHHHHHHHHHHHHHhhhC
Q 026691 164 RRNADSAKESIRDYLSNWRG 183 (235)
Q Consensus 164 ~~aa~~AKe~InDyVSrYRr 183 (235)
.++.+..-+.+++...+|-+
T Consensus 126 deAl~~ia~kl~~i~~~~G~ 145 (797)
T TIGR02166 126 DEATDTIADNLKRIIEKYGN 145 (797)
T ss_pred HHHHHHHHHHHHHHHHHhCc
Confidence 45666667777777777643
No 23
>KOG3142 consensus Prenylated rab acceptor 1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.00 E-value=57 Score=29.07 Aligned_cols=85 Identities=24% Similarity=0.134 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhHHHHHHHhhhHHHHHHHHHHHHHHHHHhhhhhhhcccccccccCCCCcchhhhhHHHH-----------
Q 026691 8 FNLVHLLFFQNYIIAFFVSASLCTSFLMLSFINLFCFFTASLWKADKLHSRTHVVLPPVEAASSRRHVI----------- 76 (235)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~p~~~~~~~RR~~L----------- 76 (235)
.|+.| |.-||++.+.+...+|--.=-++.|-+.|++.+- +.-+++. -.|.+..-. +-+.|+.|
T Consensus 64 ~Nl~y--F~~NY~~iv~~~~~~sLi~~P~~Livl~~lv~~w-~~LY~~r-d~pLvlfgr--~i~d~~~l~~L~~~ti~~l 137 (187)
T KOG3142|consen 64 RNLSY--FRVNYVIIVAILLFLSLITHPLSLIVLLALVAAW-LFLYFLR-DEPLVLFGR--QISDREVLIGLVLITIPVL 137 (187)
T ss_pred HHHHH--HHHhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-Hheeeec-CCCeEEeeE--EecCcchhhhHHHHHHHHH
Confidence 46554 6679988777666555433334445455554433 3334444 334333332 23445443
Q ss_pred --HhhhhhHHHHHHhhccCC-Cchh
Q 026691 77 --SCSSTALVAILTFNCGLA-PLPV 98 (235)
Q Consensus 77 --~~~~~~~~~~~~~~~~~~-P~~~ 98 (235)
..++..++.++..++.++ -|++
T Consensus 138 flt~~~~~l~~~l~~g~~vv~~Haa 162 (187)
T KOG3142|consen 138 FLTSAGSNLLWALGAGLVVVLIHAA 162 (187)
T ss_pred HHhhHHHHHHHHHHHhHHHHHhHHH
Confidence 334444455555555444 3555
No 24
>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A.
Probab=46.03 E-value=7.7 Score=29.29 Aligned_cols=15 Identities=40% Similarity=0.760 Sum_probs=12.3
Q ss_pred hhcccCCCCcccCCC
Q 026691 118 IKSLFDPNEKTKSGK 132 (235)
Q Consensus 118 ~~~~fdp~~~tkSg~ 132 (235)
||..|||.++|..+|
T Consensus 59 LkNMFDP~~Ete~~W 73 (73)
T PF15519_consen 59 LKNMFDPAEETEPDW 73 (73)
T ss_dssp EESSS-TTCGGSTTH
T ss_pred eecCCCcccccCCCC
Confidence 678999999998876
No 25
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=45.22 E-value=1.7e+02 Score=25.81 Aligned_cols=80 Identities=10% Similarity=0.163 Sum_probs=54.0
Q ss_pred HHHHHHHHHhcCCCCCchHHHHh-------------HHHHHHHHHHHHHhhhCCCCCC------Cch----------hH-
Q 026691 144 ELVKTLRESLKEDPKDIANFRRN-------------ADSAKESIRDYLSNWRGQKTVA------GEE----------SY- 193 (235)
Q Consensus 144 ~VV~tLReaLelDp~D~~~~~~a-------------a~~AKe~InDyVSrYRr~~~V~------G~~----------SF- 193 (235)
+.++.+++.++..|... -...+ -+.|....++|+..|-+++.+. |.. .|
T Consensus 50 ~Ai~~f~~l~~~yP~s~-~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~ 128 (243)
T PRK10866 50 QAITQLEALDNRYPFGP-YSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFF 128 (243)
T ss_pred HHHHHHHHHHHhCCCCh-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhcc
Confidence 44555666666656442 22222 3677888888888888887775 211 11
Q ss_pred ---------HHHHHHHHHHHhhHhhcCCCCCCChhHHHHHH
Q 026691 194 ---------VELEKAIRSLASFYSKAGPSAPLPGEVKSEIL 225 (235)
Q Consensus 194 ---------ttM~TALNsLAGHYsSfGp~rPLPeklK~RLL 225 (235)
+..+.|++++..+=..| |+.+--++.++||.
T Consensus 129 ~~~~~~rD~~~~~~A~~~~~~li~~y-P~S~ya~~A~~rl~ 168 (243)
T PRK10866 129 GVDRSDRDPQHARAAFRDFSKLVRGY-PNSQYTTDATKRLV 168 (243)
T ss_pred CCCccccCHHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHH
Confidence 33568999999999997 99999888888764
No 26
>PF13551 HTH_29: Winged helix-turn helix
Probab=44.95 E-value=64 Score=23.71 Aligned_cols=56 Identities=18% Similarity=0.300 Sum_probs=32.9
Q ss_pred hHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHh-hHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 161 ANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLAS-FYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 161 ~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAG-HYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
.+..+...-.+..|..|+.+|+..+ +..|-. .+..-.|..+|+++.++.|.+.+.+
T Consensus 16 ~~ia~~lg~s~~Tv~r~~~~~~~~G--------------~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 16 AEIARRLGISRRTVYRWLKRYREGG--------------IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHccc--------------HHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 3444445556788999999998764 111222 2322122334788888877766654
No 27
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=44.94 E-value=1e+02 Score=21.40 Aligned_cols=58 Identities=21% Similarity=0.409 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHh
Q 026691 137 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYS 208 (235)
Q Consensus 137 dY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYs 208 (235)
.|..+-....+-+.+ . ...+... --.+.|.+|+......+ -|-+|+...+++|-.||.
T Consensus 21 ~Y~~~l~~f~~~~~~--~-~~~~~~~------i~~~~v~~f~~~~~~~~-----~s~~T~~~~~~alr~f~~ 78 (84)
T PF02899_consen 21 SYRRDLRRFIRWLEE--H-GIIDWED------ITEEDVRDFLEYLAKEG-----LSPSTINRRLSALRAFFR 78 (84)
T ss_dssp HHHHHHHHHHHHHHH--T-TS-CGGG--------HHHHHHHHHHHHCTT-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhh--h-hhhhhhh------hhhHHHHHHHHHHHccC-----CCHHHHHHHHHHHHHHHH
Confidence 365555555555555 1 1222222 34567889999987754 788999999999999985
No 28
>COG2822 Predicted periplasmic lipoprotein involved in iron transport [Inorganic ion transport and metabolism]
Probab=44.87 E-value=72 Score=31.15 Aligned_cols=64 Identities=25% Similarity=0.440 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHH--------HHHHHHHHhhHh
Q 026691 139 LKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVEL--------EKAIRSLASFYS 208 (235)
Q Consensus 139 ~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM--------~TALNsLAGHYs 208 (235)
++-+..|++.+|-.|+- +|. ...+-.+..=..+++-+++||... |-.||..+ ...||+||+--+
T Consensus 296 VeGsqki~dl~rp~Lek--~dk-~L~~kid~nF~kv~~~LakYkt~d---g~esydklt~~dr~al~~~itaLaE~la 367 (376)
T COG2822 296 VEGSQKIVDLFRPALEK--KDK-DLLDKIDANFKKVNTILAKYRTKD---GFESYDKLTKADRKALKDPITALAEDLA 367 (376)
T ss_pred chhHHHHHHHHHHHHhh--ccH-HHHHHHHHHHHHHHHHHHHhccCC---cceeHHHhhHHHHHHHhhHHHHHHHHHH
Confidence 55678999999999985 333 445557778889999999999865 88888765 455666665443
No 29
>PF09236 AHSP: Alpha-haemoglobin stabilising protein; InterPro: IPR015317 Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle []. ; GO: 0030492 hemoglobin binding, 0006457 protein folding, 0020027 hemoglobin metabolic process, 0030097 hemopoiesis, 0050821 protein stabilization; PDB: 1Y01_A 1XZY_A 3OVU_A 1W0A_A 3IA3_C 1Z8U_A 1W0B_A 1W09_A.
Probab=40.90 E-value=35 Score=27.38 Aligned_cols=17 Identities=12% Similarity=0.255 Sum_probs=7.5
Q ss_pred HHHHHHHHHHhhHhhcC
Q 026691 195 ELEKAIRSLASFYSKAG 211 (235)
Q Consensus 195 tM~TALNsLAGHYsSfG 211 (235)
.|.|.+|-.-.||.+|+
T Consensus 32 ~MvtvV~DwvnfYINYy 48 (89)
T PF09236_consen 32 AMVTVVNDWVNFYINYY 48 (89)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444443
No 30
>TIGR02659 TTQ_MADH_Lt methylamine dehydrogenase light chain. This family consists of the light chain of methylamine dehydrogenase light chain, a periplasmic enzyme. This subunit contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from Trp-114 and Trp-165 of the precursor, numbered according to the sequence from Paracoccus denitrificans. The enzyme forms a complex with the type I blue copper protein amicyanin and cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome.
Probab=40.50 E-value=27 Score=31.24 Aligned_cols=28 Identities=32% Similarity=0.309 Sum_probs=19.6
Q ss_pred hhhhhHHHHHhhhhhHHHHHHhhccCCCch
Q 026691 68 AASSRRHVISCSSTALVAILTFNCGLAPLP 97 (235)
Q Consensus 68 ~~~~RR~~L~~~~~~~~~~~~~~~~~~P~~ 97 (235)
...+||.||+..+++|+.+. ...++|.+
T Consensus 20 ~~tsRRs~l~~lG~~l~g~a--~~PlLPv~ 47 (186)
T TIGR02659 20 GKTSRRGFIGRLGTALAGSA--LVPLLPVD 47 (186)
T ss_pred hccchHHHHHHHHHHHhhhh--hccccccc
Confidence 46789999999988766554 23455543
No 31
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=40.06 E-value=18 Score=30.96 Aligned_cols=24 Identities=17% Similarity=0.332 Sum_probs=13.8
Q ss_pred hhHHHHHhhhhhHHHHHHhhccCCC
Q 026691 71 SRRHVISCSSTALVAILTFNCGLAP 95 (235)
Q Consensus 71 ~RR~~L~~~~~~~~~~~~~~~~~~P 95 (235)
+||+||..+++++ ..+.....++|
T Consensus 1 ~RR~fl~~~~~~~-~~~~~~~~~~p 24 (174)
T TIGR01416 1 TRRDFLYAATGAV-GAVGAAAAAVP 24 (174)
T ss_pred ChHHHHHHHHHHH-HHHHHHHHHHH
Confidence 6999998776542 33333333344
No 32
>PLN00033 photosystem II stability/assembly factor; Provisional
Probab=40.04 E-value=21 Score=34.39 Aligned_cols=36 Identities=17% Similarity=0.167 Sum_probs=27.2
Q ss_pred hhcccccccccCCCCcchhhhhHHHHHhhhhhHHHH
Q 026691 51 KADKLHSRTHVVLPPVEAASSRRHVISCSSTALVAI 86 (235)
Q Consensus 51 ~~~k~~~~~~~~~p~~~~~~~RR~~L~~~~~~~~~~ 86 (235)
...+..++++...+.+.....||+|+...++..++.
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (398)
T PLN00033 21 STVSKTVSSNVNELSSNSSENRRSFLRQTATAAAAL 56 (398)
T ss_pred ccccceeecCCccccccccchhhhHHHhhhHhhhhh
Confidence 344567778888888888999999998887654333
No 33
>PF03208 PRA1: PRA1 family protein; InterPro: IPR004895 This family includes yeast hypothetical proteins and the uncharacterised rat prenylated rab acceptor protein PRA1.
Probab=39.91 E-value=2e+02 Score=23.18 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=11.9
Q ss_pred HHHhHHHHHHHhhhHHHH
Q 026691 15 FFQNYIIAFFVSASLCTS 32 (235)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~ 32 (235)
|-.||++.+.+...+|.-
T Consensus 40 F~~NY~~i~~~~~~~~ll 57 (153)
T PF03208_consen 40 FQTNYLLIFLLLFLIFLL 57 (153)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 567998877666555443
No 34
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=39.76 E-value=25 Score=36.54 Aligned_cols=13 Identities=62% Similarity=1.201 Sum_probs=11.8
Q ss_pred chHHHHHHHHHHH
Q 026691 5 CYFFNLVHLLFFQ 17 (235)
Q Consensus 5 ~~~~~~~~~~~~~ 17 (235)
||||-.||+|||-
T Consensus 90 ~~~~~p~~~~~~~ 102 (697)
T PF09726_consen 90 CLFFIPVHWLFFA 102 (697)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999985
No 35
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=39.26 E-value=1.2e+02 Score=23.10 Aligned_cols=50 Identities=28% Similarity=0.482 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 168 DSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 168 ~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
+..|+.+++.+.+ ++.. ..+|.++...+---| ..-+|+.+|+.+++.+.+
T Consensus 34 d~vr~~~re~i~~-~g~~----~~~~~~l~~~i~P~A--------r~~VP~~vk~ell~~Ir~ 83 (86)
T PF10163_consen 34 DEVRQLCREIIRE-RGID----NLTFEDLLEEITPKA--------RAMVPDEVKKELLQRIRA 83 (86)
T ss_dssp HHHHHHHHHHHHH-H-TT----TSBHHHHHHHHHHHH--------HHCS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh-hCCC----CCCHHHHHHHHHHHH--------HHHCCHHHHHHHHHHHHH
Confidence 3555555555555 4443 447777766665433 667999999999998765
No 36
>PF12889 DUF3829: Protein of unknown function (DUF3829); InterPro: IPR024291 This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL_GvpF family of proteins (PF06386 from PFAM).; PDB: 3RH3_B 3IEE_A.
Probab=39.11 E-value=54 Score=28.40 Aligned_cols=48 Identities=29% Similarity=0.324 Sum_probs=31.1
Q ss_pred HHHHhHHHHHHHHHHHHHhhhC--------CCCCCCchhHHHHHHHHHHHHhhHhh
Q 026691 162 NFRRNADSAKESIRDYLSNWRG--------QKTVAGEESYVELEKAIRSLASFYSK 209 (235)
Q Consensus 162 ~~~~aa~~AKe~InDyVSrYRr--------~~~V~G~~SFttM~TALNsLAGHYsS 209 (235)
.+....+.-+..+++||.+.|. ...-....|+..|....|.|.+-|++
T Consensus 219 ~~~~~~~~~~~~~~~~i~~vr~~~~~~~~~~~~~~~~~~~~~l~~~yn~lI~~yN~ 274 (276)
T PF12889_consen 219 SFMSSADSFKSSAKSFIRRVRDLQQSESNWMSGEPTEGSPEKLLKSYNDLISDYNR 274 (276)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH-------------HCTTSS--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcchhhhhhcccCCCCCHHHHHHHHHHHHHHhcc
Confidence 4556677778888888888887 33334466777888888888888776
No 37
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=37.47 E-value=31 Score=29.55 Aligned_cols=8 Identities=38% Similarity=0.659 Sum_probs=6.5
Q ss_pred hhhHHHHH
Q 026691 70 SSRRHVIS 77 (235)
Q Consensus 70 ~~RR~~L~ 77 (235)
.+||+||+
T Consensus 2 ~sRR~~L~ 9 (168)
T PF12318_consen 2 LSRRRLLA 9 (168)
T ss_pred CcHHHHHH
Confidence 48999993
No 38
>PF12918 TcdB_N: TcdB toxin N-terminal helical domain; InterPro: IPR024772 Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 []. This entry represents a short helical bundle domain found associated with the catalytic domain of TcdA and TcdB []. It is also found in some other toxins. The function of this domain is unknown, but it may be involved in substrate recognition.; PDB: 2VKH_C 2VL8_A 2VKD_A 2BVL_A 2BVM_A 3SS1_A 3SRZ_A 2VK9_A.
Probab=37.35 E-value=1.1e+02 Score=22.70 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=35.4
Q ss_pred HHHHHHHHHHh-cCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCC
Q 026691 143 RELVKTLRESL-KEDPKDIANFRRNADSAKESIRDYLSNWRGQKTV 187 (235)
Q Consensus 143 ~~VV~tLReaL-elDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V 187 (235)
-.+++.|-+-| .+++.-.+........++++|+.|...|-.++..
T Consensus 4 dl~~~ni~~~l~~l~~~~~~~~~~~l~~lk~~I~~Y~~l~~~~kns 49 (66)
T PF12918_consen 4 DLTIDNIEEKLFKLTEEQSPKCYELLKKLKKAIDNYNNLYENEKNS 49 (66)
T ss_dssp HHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHHTTT-TTH
T ss_pred HhHHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHhhhccCc
Confidence 45778888888 7776777788888999999999999998765544
No 39
>TIGR03175 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis.
Probab=37.05 E-value=60 Score=31.00 Aligned_cols=81 Identities=15% Similarity=0.247 Sum_probs=51.3
Q ss_pred cccchhcccCCCCcccCCCCCchHHHHHHHHHHHHHHHHhcCC-------CCCchHHHHhHHHHHHHHHHHHHhhhCCCC
Q 026691 114 VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKED-------PKDIANFRRNADSAKESIRDYLSNWRGQKT 186 (235)
Q Consensus 114 ~~~~~~~~fdp~~~tkSg~~LPkdY~kdT~~VV~tLReaLelD-------p~D~~~~~~aa~~AKe~InDyVSrYRr~~~ 186 (235)
-+|.+--..||+--.. ..+|.+...++++.||++--.+ |.|.+.. . .+ + ..
T Consensus 260 ~~G~~~iaIDP~~F~~-----~~~f~~~~~~~~~~~r~~~~a~g~~~V~~PGe~e~~-~---~~---------~----~~ 317 (349)
T TIGR03175 260 NLGQLHLVINPAFFTD-----CELFKKHISQMMQELNSVPPAEGFKQVYYPGEDGDL-K---QK---------K----AD 317 (349)
T ss_pred CcceEEEEEChHHcCC-----HHHHHHHHHHHHHHHhcCCCCCCCCceECCCcHHHH-H---HH---------H----HH
Confidence 3566777888864421 3579999999999999883322 3443221 1 10 0 12
Q ss_pred CCCchhHHHHHHHHHHHHhhHhhcCCCCCC
Q 026691 187 VAGEESYVELEKAIRSLASFYSKAGPSAPL 216 (235)
Q Consensus 187 V~G~~SFttM~TALNsLAGHYsSfGp~rPL 216 (235)
..|-+==..+...|++++-||+||-.+-|.
T Consensus 318 ~~GI~l~~~~~~~L~~la~~~~~~~~~~~~ 347 (349)
T TIGR03175 318 MEGIEIVDDIYQYLVSDAVHYKSYEGKNPF 347 (349)
T ss_pred ccCCccCHHHHHHHHHHHHHHHhccCCCcC
Confidence 234444556777889999999999766665
No 40
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=36.62 E-value=2.6 Score=38.42 Aligned_cols=31 Identities=23% Similarity=0.298 Sum_probs=22.7
Q ss_pred HHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCC
Q 026691 172 ESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGP 212 (235)
Q Consensus 172 e~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp 212 (235)
+..++=+++|.+-.--.|.+. ||.||+|.+|
T Consensus 133 ~~~~~~~~~~~pt~~~P~sPD----------LarHYkS~SP 163 (221)
T PF08374_consen 133 ELEEDSMGKYLPTTFKPDSPD----------LARHYKSASP 163 (221)
T ss_pred ccCCCCcccccCCCCCCCCcc----------hhhhcccCCC
Confidence 667778888876655556554 9999999653
No 41
>PRK15219 carbonic anhydrase; Provisional
Probab=35.47 E-value=17 Score=33.02 Aligned_cols=73 Identities=22% Similarity=0.177 Sum_probs=39.1
Q ss_pred hhhhhHHHHHhhhhhHHHHHHhhc-cCCCchhhhccccCCCCccccccccchhcccCCCCcccCCCCCchHHHHH
Q 026691 68 AASSRRHVISCSSTALVAILTFNC-GLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKS 141 (235)
Q Consensus 68 ~~~~RR~~L~~~~~~~~~~~~~~~-~~~P~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~tkSg~~LPkdY~kd 141 (235)
...+||++|..+++.+.+++.... ...|....+..-...+. +.-.--.+++.|.|=|.+...|...+.+|...
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~p~~al~~L~~GN~rF~~~~~~~~~~~~~ 80 (245)
T PRK15219 7 NQPSRRAVLKAALAMTAASVIGLAGLGVPQISYAASLTKEER-DKMTPDQIIESLKQGNKRFRSGKPAQHDYLAQ 80 (245)
T ss_pred cchHHHHHHHHHHHHHHHhhhhccccccchhhhhhccccccc-CCCCHHHHHHHHHHHHHHHHhcCcCCchhhHH
Confidence 356899999877654333322111 12333322221111000 11122346899999999999998777777654
No 42
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=34.91 E-value=31 Score=35.33 Aligned_cols=21 Identities=5% Similarity=0.216 Sum_probs=15.8
Q ss_pred HHhHHHHHHHHHHHHHhhhCC
Q 026691 164 RRNADSAKESIRDYLSNWRGQ 184 (235)
Q Consensus 164 ~~aa~~AKe~InDyVSrYRr~ 184 (235)
.+|.+...+.|++.+.+|.++
T Consensus 141 dEAl~~Ia~kl~~i~~~~G~~ 161 (814)
T PRK14990 141 EEAYDIIATNMQRLIKEYGNE 161 (814)
T ss_pred HHHHHHHHHHHHHHHHhhCcc
Confidence 567777788888888888654
No 43
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=34.77 E-value=89 Score=28.11 Aligned_cols=48 Identities=17% Similarity=0.307 Sum_probs=33.0
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc-CCCCCchHHHHhHHHHHHHHHHHHHhhhC
Q 026691 132 KVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRG 183 (235)
Q Consensus 132 ~~LPkdY~kdT~~VV~tLReaLe-lDp~D~~~~~~aa~~AKe~InDyVSrYRr 183 (235)
|-=|..+ ..++++|.+.|. +||.+.+..++..+...+.+++.-++|+.
T Consensus 124 Wldp~n~----~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~ 172 (286)
T cd01019 124 WLSPENA----AEVAQAVAEKLSALDPDNAATYAANLEAFNARLAELDATIKE 172 (286)
T ss_pred CCCHHHH----HHHHHHHHHHHHHHCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666 555566666554 48888878887777777777776666663
No 44
>PF08611 DUF1774: Fungal protein of unknown function (DUF1774); InterPro: IPR013920 This is a fungal protein of unknown function.
Probab=34.74 E-value=47 Score=26.91 Aligned_cols=25 Identities=28% Similarity=0.547 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhHHHHHHHHH
Q 026691 7 FFNLVHLLFFQNYIIAFFVSASLCTSFLMLS 37 (235)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (235)
.+..+|++.|+.|.++|- .|+||+|
T Consensus 13 ~~g~~~i~~~~D~~~Gfs------lS~L~~s 37 (97)
T PF08611_consen 13 VYGGFFILAFKDYAMGFS------LSYLTAS 37 (97)
T ss_pred HHhHHHHhhhhhHHHHHH------HHHHHHH
Confidence 467889999999999874 4455554
No 45
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=34.51 E-value=1.5e+02 Score=32.94 Aligned_cols=92 Identities=17% Similarity=0.197 Sum_probs=49.0
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHH--HhhHhhc
Q 026691 133 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL--ASFYSKA 210 (235)
Q Consensus 133 ~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsL--AGHYsSf 210 (235)
..|..|++.|.++.+.... + |.+.+ .+.+=+--..|.|-+..-...+.-.-.|.|.+-..-|+.| .|-...|
T Consensus 539 ~~~~~y~~t~~EM~~~F~~---l-~~~~a--~e~~i~Nt~~IA~~c~~~~~~~~~~~~P~~~~~~~~L~~l~~~~~~~~y 612 (1213)
T TIGR01405 539 EVPELHFRTTNEMLDEFSF---L-GEEKA--YEIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIY 612 (1213)
T ss_pred CCcccccCCHHHHHHHHhh---c-chhhh--hHHHHHHHHHHHHHhhcccccCCCCCCCCCCCHHHHHHHHHHHHHHHHc
Confidence 3677899999999887664 2 22211 1111111222333332211111112233333333344443 4566667
Q ss_pred CCCCCCChhHHHHHHHHHHHHH
Q 026691 211 GPSAPLPGEVKSEILNDLDTAE 232 (235)
Q Consensus 211 Gp~rPLPeklK~RLLqEL~~AE 232 (235)
| .|+|+..++||.+||+-..
T Consensus 613 g--~~l~~~v~~RLe~EL~~I~ 632 (1213)
T TIGR01405 613 G--DPLPEIVEQRIEKELKSII 632 (1213)
T ss_pred C--CCCcHHHHHHHHHHHHHHH
Confidence 6 3689999999999998764
No 46
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=33.41 E-value=1.1e+02 Score=27.16 Aligned_cols=47 Identities=17% Similarity=0.291 Sum_probs=31.0
Q ss_pred CCCchHHHHHHHHHHHHHHHHhcC-CCCCchHHHHhHHHHHHHHHHHHHhhh
Q 026691 132 KVLPKAYLKSARELVKTLRESLKE-DPKDIANFRRNADSAKESIRDYLSNWR 182 (235)
Q Consensus 132 ~~LPkdY~kdT~~VV~tLReaLel-Dp~D~~~~~~aa~~AKe~InDyVSrYR 182 (235)
|-=|..+ ..+++.+.++|.. ||.+....++..+...+.+.+--.+|+
T Consensus 98 Wldp~n~----~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~ 145 (264)
T cd01020 98 WYDPETM----SKVANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIA 145 (264)
T ss_pred ecCHhHH----HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777777 6666677777764 888877666666666666555444443
No 47
>PF07030 DUF1320: Protein of unknown function (DUF1320); InterPro: IPR009752 This entry is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.39 E-value=2.7e+02 Score=22.45 Aligned_cols=63 Identities=16% Similarity=0.154 Sum_probs=42.3
Q ss_pred CCchHHHHhHHHHHHHHHHHH-HhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCC--ChhHHHHHHH
Q 026691 158 KDIANFRRNADSAKESIRDYL-SNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL--PGEVKSEILN 226 (235)
Q Consensus 158 ~D~~~~~~aa~~AKe~InDyV-SrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPL--PeklK~RLLq 226 (235)
.|......+.+.|-..|+.|+ +||. -|. .+.=..+....-.+|-|+-.- +++. |+.+++|-.+
T Consensus 28 ~d~~~v~~Al~dA~~~Id~yL~~RY~-lPl---~~~p~~L~~~~~dIA~y~L~~--~~~~~~~e~~~~rY~~ 93 (130)
T PF07030_consen 28 IDPAVVEAALADASAEIDGYLRGRYD-LPL---APVPALLKRIACDIARYRLYD--RRPSQETEPVRERYKD 93 (130)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHhcC-CCc---ccccHHHHHHHHHHHHHHHHh--cCCccCcHHHHHHHHH
Confidence 467788999999999999999 6775 232 122234666667788887652 4443 6776665443
No 48
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=31.74 E-value=1.2e+02 Score=21.85 Aligned_cols=34 Identities=18% Similarity=0.443 Sum_probs=26.6
Q ss_pred HHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcC
Q 026691 173 SIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAG 211 (235)
Q Consensus 173 ~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfG 211 (235)
.+++++..|.+ ..-++.+++.+.++|..+|.+.|
T Consensus 18 ~l~~~~~~~~g-----~~l~~~~l~~~~~~l~~~y~~~G 51 (76)
T PF08479_consen 18 ELQAILAPYIG-----RCLTLADLQQLADALTNYYREKG 51 (76)
T ss_dssp HHHHHHGGGTT-----SBB-HHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHhcC-----CCcCHHHHHHHHHHHHHHHHHcC
Confidence 45566667754 45689999999999999999987
No 49
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=31.70 E-value=26 Score=31.16 Aligned_cols=44 Identities=23% Similarity=0.514 Sum_probs=33.6
Q ss_pred HhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCC------CCCCChhHHHHHH
Q 026691 165 RNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGP------SAPLPGEVKSEIL 225 (235)
Q Consensus 165 ~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp------~rPLPeklK~RLL 225 (235)
+.+...-..|+.|..+|.+++-+ |.|| |||. --.||+.+|+||-
T Consensus 49 ~~a~Dl~~~i~~y~~~w~~~~vv---------------LiGY--SFGADvlP~~~nrLp~~~r~~v~ 98 (192)
T PF06057_consen 49 QTAADLARIIRHYRARWGRKRVV---------------LIGY--SFGADVLPFIYNRLPAALRARVA 98 (192)
T ss_pred HHHHHHHHHHHHHHHHhCCceEE---------------EEee--cCCchhHHHHHhhCCHHHHhhee
Confidence 35668888999999999998877 6665 5564 2358999988873
No 50
>PRK09269 chorismate mutase; Provisional
Probab=31.23 E-value=1.7e+02 Score=25.97 Aligned_cols=64 Identities=14% Similarity=0.261 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhc---CCCCCc-hHHHHhHHHHHHHHHHHHHhhhCCCCCCC--chhHHHHHHHHHHHH
Q 026691 141 SARELVKTLRESLK---EDPKDI-ANFRRNADSAKESIRDYLSNWRGQKTVAG--EESYVELEKAIRSLA 204 (235)
Q Consensus 141 dT~~VV~tLReaLe---lDp~D~-~~~~~aa~~AKe~InDyVSrYRr~~~V~G--~~SFttM~TALNsLA 204 (235)
.=.+|++++++-.+ +||... +=++...+.+|..=+.|+++|+.++.... .++-.+++..|+.|.
T Consensus 67 RE~~VL~~v~~~A~~~gLdp~~v~~iF~~~I~aSk~iQ~~~~a~W~~~~~~~~~~~~dL~~~Rp~l~~L~ 136 (193)
T PRK09269 67 REAQVLANVEAQAPAHGVDPDYVRRFFRDQIEANKLVQYALLARWRLAGAAPPGPRPDLASIRPRLDRLQ 136 (193)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHH
Confidence 33677777777665 333332 34577888899999999999997755322 355557776666654
No 51
>cd01493 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
Probab=30.02 E-value=2.8e+02 Score=27.16 Aligned_cols=82 Identities=23% Similarity=0.448 Sum_probs=43.7
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHH---------HHHhhhCCCCCCCchhHHHHHHHHHHH
Q 026691 133 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRD---------YLSNWRGQKTVAGEESYVELEKAIRSL 203 (235)
Q Consensus 133 ~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InD---------yVSrYRr~~~V~G~~SFttM~TALNsL 203 (235)
.+|..|-+. .+.-+.+++ ......|.+++.++.+.+....+. -+..-+-..-....+.|-.|-.| |
T Consensus 222 ~~p~~~~ek-~~f~~~i~~-~~~~~~~eeNf~EA~~~~~~~~~~~~i~~~v~~~~~~~~~~~~~~~~~~fwi~~~a---l 296 (425)
T cd01493 222 QLPSTYKEK-KEFRDLVRS-LMRSNEDEENFEEAIKAVNKALNRTKIPSSVEEIFNDDRCENLTSQSSSFWIMARA---L 296 (425)
T ss_pred CCCCCHHHH-HHHHHHHHH-hcccCCCccchHHHHHHHHHhhCCCCCcHHHHHHHhchhcccCCCCCchHHHHHHH---H
Confidence 467776542 222222222 222135677888877766654433 33333322223345667777555 5
Q ss_pred HhhHhh-cCCCCCCChhH
Q 026691 204 ASFYSK-AGPSAPLPGEV 220 (235)
Q Consensus 204 AGHYsS-fGp~rPLPekl 220 (235)
-.||.. +| .-|||..+
T Consensus 297 k~F~~~~~g-~lPl~G~l 313 (425)
T cd01493 297 KEFVAEENG-LLPLPGTL 313 (425)
T ss_pred HHHHHhcCC-CCCCCCCC
Confidence 568877 66 67887643
No 52
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=29.99 E-value=1.1e+02 Score=28.18 Aligned_cols=89 Identities=16% Similarity=0.166 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHhc-CCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHh-------hcCCC
Q 026691 142 ARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYS-------KAGPS 213 (235)
Q Consensus 142 T~~VV~tLReaLe-lDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYs-------SfGp~ 213 (235)
+..+++.+.+.|. +||.+.+.+++..+...+.+++--.+||..-.-.....+-+--.|.+=++.-|. .-+|-
T Consensus 154 ~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~i~~H~af~Yf~~~ygl~~~~~~~~~~~ 233 (311)
T PRK09545 154 ARATAVAIHDKLVELMPQSKAKLDANLKDFEAQLAQTDKQIGNQLAPVKGKGYFVFHDAYGYFEKHYGLTPLGHFTVNPE 233 (311)
T ss_pred HHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEECchHHHHHHhCCCceeeeeccCCC
Confidence 3556666666665 489888888888888877777766666643111111222222233333333331 11244
Q ss_pred CCCChhHHHHHHHHHHH
Q 026691 214 APLPGEVKSEILNDLDT 230 (235)
Q Consensus 214 rPLPeklK~RLLqEL~~ 230 (235)
.+.+.+.-.+|.+.+++
T Consensus 234 ~eps~~~l~~l~~~ik~ 250 (311)
T PRK09545 234 IQPGAQRLHEIRTQLVE 250 (311)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 55566666666666553
No 53
>PF09684 Tail_P2_I: Phage tail protein (Tail_P2_I); InterPro: IPR006521 These sequences represent a family of phage tail proteins from phage P2 protein and related temperates phage of Gram-negative bacteria.
Probab=29.77 E-value=2.4e+02 Score=22.55 Aligned_cols=66 Identities=12% Similarity=0.102 Sum_probs=33.4
Q ss_pred CCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHH
Q 026691 157 PKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILND 227 (235)
Q Consensus 157 p~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLqE 227 (235)
|.|.....++.+.+-+.+.+.....+........+. ..|.-||..|.--+-..-+|++.|.++.++
T Consensus 2 P~nat~le~al~~~~~~~~~~~~~i~~~~~~~~~~~-----~~L~~LA~~~~v~~~~~~~~~~~kR~li~~ 67 (139)
T PF09684_consen 2 PPNATPLERALAALLARLQEDIDSIRTLWDPDTCPE-----ALLPWLAWELGVDEWDPAWPEEQKRRLIKN 67 (139)
T ss_pred ccCccHHHHHHHHHHhHHHhhhHHHHHhcCcccCCH-----HHHHHHHHHhCcCccCCCCCHHHHHHHHHH
Confidence 555555555555555555444443333222222222 466777777766111233677766666654
No 54
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=28.95 E-value=49 Score=34.77 Aligned_cols=28 Identities=29% Similarity=0.553 Sum_probs=23.4
Q ss_pred HHHHHHHHHhhHhhcCCCCCCChhHHHHHHH
Q 026691 196 LEKAIRSLASFYSKAGPSAPLPGEVKSEILN 226 (235)
Q Consensus 196 M~TALNsLAGHYsSfGp~rPLPeklK~RLLq 226 (235)
-..+|..+|+||.+ | -|||+++-+++++
T Consensus 514 ~p~vL~~~a~Hy~T-G--e~lP~~ll~k~la 541 (683)
T COG0339 514 EPEVLAKYARHYQT-G--EPLPKELLDKMLA 541 (683)
T ss_pred CHHHHHHHHHhhcc-C--CcCHHHHHHHHHH
Confidence 34679999999998 6 8999998888875
No 55
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=28.88 E-value=1.1e+02 Score=25.87 Aligned_cols=58 Identities=19% Similarity=0.343 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHhhhC--CCCCCC-chhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 167 ADSAKESIRDYLSNWRG--QKTVAG-EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 167 a~~AKe~InDyVSrYRr--~~~V~G-~~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
..++|+-+++++.+.|. ...++| .++...+....+.+...|.. ||++.|+.|.+.|=.
T Consensus 75 ~peak~Fv~~li~~~~~l~~~~~~G~~~~~~~lk~~~k~~~~~yka------Ls~~ak~dL~k~FP~ 135 (154)
T PF05823_consen 75 SPEAKAFVKELIAKARSLYAQYSAGEKPDLEELKQLAKKVIDSYKA------LSPEAKDDLKKNFPI 135 (154)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHT----THHHHHHH----HHHHT------S-HHHHHHHHHH-TT
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhhhHHHHHc------CCHHHHHHHHHHCcc
Confidence 34566666666655431 111122 34455555555555666665 899999999988743
No 56
>cd01137 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=28.36 E-value=1.5e+02 Score=26.72 Aligned_cols=96 Identities=16% Similarity=0.222 Sum_probs=53.2
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhc-CCCCCchHHHHhHHHHHHHHHHHHHhhhCC---------CCCCCchhHHHHHHHH
Q 026691 131 GKVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRGQ---------KTVAGEESYVELEKAI 200 (235)
Q Consensus 131 g~~LPkdY~kdT~~VV~tLReaLe-lDp~D~~~~~~aa~~AKe~InDyVSrYRr~---------~~V~G~~SFttM~TAL 200 (235)
-|-=|..+ ..+++.+.+.|. +||.+.+..++..+...+.+++--.+|+.. +-+...++|.=+-...
T Consensus 119 ~Wldp~~~----~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~~~v~~H~af~Y~~~~y 194 (287)
T cd01137 119 AWMSPKNA----IIYVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRKLVTSEGAFSYFAKAY 194 (287)
T ss_pred cCcCHHHH----HHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCEEEEecccHHHHHHHc
Confidence 47667777 455555555553 489888888888888877777777766631 1233334444333222
Q ss_pred HHHHhhHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 201 RSLASFYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 201 NsLAGHYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
+-=--.....+|..+.+.+.-.+|.+.+++
T Consensus 195 Gl~~~~~~~~~~~~eps~~~l~~l~~~ik~ 224 (287)
T cd01137 195 GLKEAYLWPINTEEEGTPKQVATLIEQVKK 224 (287)
T ss_pred CCeEeecccCCCCCCCCHHHHHHHHHHHHH
Confidence 110000122234555566666666666554
No 57
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=28.19 E-value=51 Score=32.90 Aligned_cols=43 Identities=21% Similarity=0.361 Sum_probs=35.9
Q ss_pred hHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHh
Q 026691 161 ANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLAS 205 (235)
Q Consensus 161 ~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAG 205 (235)
.+++++.+.=-+.+.+|..|||. -|..-++|.++.+|-|++-+
T Consensus 38 qERA~IEk~YaqqL~~wakkWr~--lvekgpqyGt~e~aW~~~~t 80 (472)
T KOG2856|consen 38 QERARIEKAYAQQLTDWAKKWRQ--LVEKGPQYGTVEKAWNAFMT 80 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHhcCcccchHHHHHHHHHH
Confidence 35666777777899999999986 68888999999999998754
No 58
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=28.12 E-value=39 Score=29.06 Aligned_cols=14 Identities=14% Similarity=0.249 Sum_probs=10.5
Q ss_pred hhhhHHHHHhhhhh
Q 026691 69 ASSRRHVISCSSTA 82 (235)
Q Consensus 69 ~~~RR~~L~~~~~~ 82 (235)
-++||+||..++.+
T Consensus 11 d~~RR~FL~~~~~~ 24 (178)
T PRK13474 11 SMGRRQFMNLLTFG 24 (178)
T ss_pred CccHHHHHHHHHHH
Confidence 36899999966544
No 59
>PRK00035 hemH ferrochelatase; Reviewed
Probab=28.10 E-value=1.7e+02 Score=26.71 Aligned_cols=47 Identities=21% Similarity=0.355 Sum_probs=27.6
Q ss_pred HHHHHHHHhhhCCCCCCCchhHHHH--------HHHHHHHHhhHhhcCCCCCCCh
Q 026691 172 ESIRDYLSNWRGQKTVAGEESYVEL--------EKAIRSLASFYSKAGPSAPLPG 218 (235)
Q Consensus 172 e~InDyVSrYRr~~~V~G~~SFttM--------~TALNsLAGHYsSfGp~rPLPe 218 (235)
+.|+.|+.++++++.+-+.+.+--- ..=...++.+|...|-..||.+
T Consensus 20 ~~v~~fl~~~~~d~~v~~~~~~~~~~~l~~~i~~~r~~~~~~~Y~~ig~gSPl~~ 74 (333)
T PRK00035 20 EDVRPFLKNFLSDRRVIDLPRPLWQPLLAGIILPERLPKVAKHYASIGGGSPLNV 74 (333)
T ss_pred HHHHHHHHHHcCCCCcccCCHHHHHHHHHHHhhhhhHHHHHHHHHHcCCCChhHH
Confidence 4566677777777777666543210 1223456677777766667663
No 60
>PRK10280 dipeptidyl carboxypeptidase II; Provisional
Probab=27.92 E-value=48 Score=34.17 Aligned_cols=33 Identities=21% Similarity=0.478 Sum_probs=27.2
Q ss_pred hhHHHHHHHHHHHHhhHhhcCCCCCCChhHHHHHHH
Q 026691 191 ESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILN 226 (235)
Q Consensus 191 ~SFttM~TALNsLAGHYsSfGp~rPLPeklK~RLLq 226 (235)
+.|..-...|..+|.||.+ | -|||+++-+++.+
T Consensus 506 E~w~~~~~vL~~~a~Hy~T-g--epiP~~l~~~l~~ 538 (681)
T PRK10280 506 EHWASHPQVFARYARHYQS-G--EAMPDELQEKMRN 538 (681)
T ss_pred HHHhcCHHHHHHHhhccCC-C--CCCCHHHHHHHHH
Confidence 4466667899999999998 5 5999999988864
No 61
>PF05135 Phage_connect_1: Phage gp6-like head-tail connector protein; InterPro: IPR021146 The members of this family contain a conserved QLRG motif. This family of phage proteins are largely uncharacterised, although Q97HW6 from SWISSPROT and Q9XJA2 from SWISSPROT suggest a role in DNA packaging.; PDB: 2KBZ_A 3JVO_M.
Probab=26.71 E-value=2.6e+02 Score=20.50 Aligned_cols=62 Identities=19% Similarity=0.201 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCC-CCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhh
Q 026691 146 VKTLRESLKEDP-KDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 209 (235)
Q Consensus 146 V~tLReaLelDp-~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsS 209 (235)
++.++.-|..|- .|++-.....+.|++.|..|+.+-- +......--..+..|+..+++||=.
T Consensus 6 Le~vK~~Lrid~d~dD~~l~~li~~A~~~i~~~~~~~~--~~~~~~~~~~~~~~av~~l~~~~y~ 68 (101)
T PF05135_consen 6 LEEVKQHLRIDDDDDDDLLELLIDAAEEYIENYTGRSF--DFPDDDEIPPLFKLAVLLLVAHYYN 68 (101)
T ss_dssp HHHCHHHCTTTTTTTHHHHHHHHHHHHHHHHCCCT-ST--TTTSGCGS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCccHHHHHHHHHHHHHHHHHHhhhhh--cccccccCCHHHHHHHHHHHHHHHH
Confidence 667777777633 3344445555555555555444311 3445566667888999999988754
No 62
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.89 E-value=3.2e+02 Score=22.79 Aligned_cols=66 Identities=20% Similarity=0.288 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCCchhH-HHHHHHHHHHHhhHhhcCC--CCCCChhHHH-HHHHHHHHHHh
Q 026691 167 ADSAKESIRDYLSNWRGQKTVAGEESY-VELEKAIRSLASFYSKAGP--SAPLPGEVKS-EILNDLDTAEK 233 (235)
Q Consensus 167 a~~AKe~InDyVSrYRr~~~V~G~~SF-ttM~TALNsLAGHYsSfGp--~rPLPeklK~-RLLqEL~~AEk 233 (235)
.-.|-++|+.|++.... |-+.|...+ .++..+++.+..++..+.+ ++-|+++..+ .|.+.+++++.
T Consensus 44 kGka~dsiK~y~~~vh~-pll~~~~~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~ 113 (204)
T PF04740_consen 44 KGKAYDSIKNYFSEVHI-PLLQGLILLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKE 113 (204)
T ss_pred hhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHH
Confidence 44677788888887554 455566555 5566888888888888873 5668888666 77777766553
No 63
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=25.64 E-value=2.3e+02 Score=32.26 Aligned_cols=92 Identities=18% Similarity=0.227 Sum_probs=49.2
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHH--HhhHhhc
Q 026691 133 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL--ASFYSKA 210 (235)
Q Consensus 133 ~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsL--AGHYsSf 210 (235)
..|..|++.|.++.+.... + |.+. ..+.+=+--..|.|-+......+.-.-.|.|.+-..-|+.| .|-...|
T Consensus 764 ~~~~~yl~tt~EM~~~f~~---l-~~~~--~~e~vi~Nt~~Ia~~~~~i~~~~~~~~~P~~~~a~~~L~~l~~~~a~~~y 837 (1437)
T PRK00448 764 PLPELHFRTTDEMLDEFAF---L-GEEL--AKEIVVENTNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIY 837 (1437)
T ss_pred cCCccccCCHHHHHHHhhh---c-chhh--hHHHHHHHHHHHHHhcceecccCCCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 4578899999998887653 2 2211 11111122233334333222221111223333333344433 3555566
Q ss_pred CCCCCCChhHHHHHHHHHHHHH
Q 026691 211 GPSAPLPGEVKSEILNDLDTAE 232 (235)
Q Consensus 211 Gp~rPLPeklK~RLLqEL~~AE 232 (235)
| .|+|+..++||.+||+-..
T Consensus 838 g--~~lp~~v~~RLe~EL~~I~ 857 (1437)
T PRK00448 838 G--EPLPEIVEKRIEKELNSII 857 (1437)
T ss_pred C--CCCcHHHHHHHHHHHHHHH
Confidence 6 4799999999999998754
No 64
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=25.20 E-value=48 Score=28.68 Aligned_cols=96 Identities=14% Similarity=0.178 Sum_probs=55.5
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhC-------CCCCCCchhHHHHHHHHHHH
Q 026691 131 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG-------QKTVAGEESYVELEKAIRSL 203 (235)
Q Consensus 131 g~~LPkdY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr-------~~~V~G~~SFttM~TALNsL 203 (235)
-|-=|..+.+-+..+.+.|.+ +||.+.+..++..+...+.+++.-.+|+. .+-+...++|.-+.+.++-=
T Consensus 94 ~Wldp~~~~~~~~~Ia~~L~~---~~P~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~h~~~~Y~~~~~gl~ 170 (256)
T PF01297_consen 94 VWLDPENAKKMAEAIADALSE---LDPANKDYYEKNAEKYLKELDELDAEIKEKLAKLPGRPVVVYHDAFQYFAKRYGLK 170 (256)
T ss_dssp GGGSHHHHHHHHHHHHHHHHH---HTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGGEEEEEESTTHHHHHHTT-E
T ss_pred hHHHHHHHHHHHHHHHHHHHH---hCccchHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCeEEEEChHHHHHHHhcCCc
Confidence 456677775555555555444 38988888888888888888877777763 23344455555444443210
Q ss_pred -HhhHhhcCCCCCCChhHHHHHHHHHHH
Q 026691 204 -ASFYSKAGPSAPLPGEVKSEILNDLDT 230 (235)
Q Consensus 204 -AGHYsSfGp~rPLPeklK~RLLqEL~~ 230 (235)
.+.. .-+|..+...+.-.+|.+.+++
T Consensus 171 ~~~~~-~~~~~~~ps~~~l~~l~~~ik~ 197 (256)
T PF01297_consen 171 VIGVI-EISPGEEPSPKDLAELIKLIKE 197 (256)
T ss_dssp EEEEE-SSSSSSSS-HHHHHHHHHHHHH
T ss_pred eeeee-ccccccCCCHHHHHHHHHHhhh
Confidence 0111 1245566667777777776665
No 65
>TIGR00831 a_cpa1 Na+/H+ antiporter, bacterial form. This model is specific for the bacterial members of this family.
Probab=25.20 E-value=6.8e+02 Score=24.80 Aligned_cols=29 Identities=21% Similarity=0.293 Sum_probs=21.8
Q ss_pred HHHhhHhhcCCCCCCChhHHHHHHHHHHHHHhc
Q 026691 202 SLASFYSKAGPSAPLPGEVKSEILNDLDTAEKF 234 (235)
Q Consensus 202 sLAGHYsSfGp~rPLPeklK~RLLqEL~~AEka 234 (235)
+|-..++. .-++++.-.++++|+|.-|..
T Consensus 494 ~l~~~~~~----~~i~~~~~~~~~~~ld~~e~~ 522 (525)
T TIGR00831 494 AVVDLRAG----GLISQEVLLELMRELDLKEAE 522 (525)
T ss_pred HHHHHHHc----CCCCHHHHHHHHHHhhHHHHh
Confidence 34455554 479999999999999987653
No 66
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=25.12 E-value=68 Score=27.24 Aligned_cols=47 Identities=21% Similarity=0.386 Sum_probs=32.2
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc-CCCCCchHHHHhHHHHHHHHHHHHHhhh
Q 026691 132 KVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWR 182 (235)
Q Consensus 132 ~~LPkdY~kdT~~VV~tLReaLe-lDp~D~~~~~~aa~~AKe~InDyVSrYR 182 (235)
|-=|.... .+++++.+.|. +||.+.+..++..+...+.+++--.+|+
T Consensus 111 Wldp~~~~----~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~ 158 (203)
T cd01145 111 WLDPNNAP----ALAKALADALIELDPSEQEEYKENLRVFLAKLNKLLREWE 158 (203)
T ss_pred ecCHHHHH----HHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66677774 44555555554 4898888888877777777777666665
No 67
>TIGR01480 copper_res_A copper-resistance protein, CopA family. This model represents the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechansism of resistance by packaging and export.
Probab=25.10 E-value=52 Score=33.42 Aligned_cols=12 Identities=25% Similarity=0.285 Sum_probs=8.9
Q ss_pred hhhhHHHHHhhh
Q 026691 69 ASSRRHVISCSS 80 (235)
Q Consensus 69 ~~~RR~~L~~~~ 80 (235)
+.+||+||++.+
T Consensus 5 ~~~rr~~~~~~~ 16 (587)
T TIGR01480 5 AFDRRRFLQGLA 16 (587)
T ss_pred cccHHHHHHHHH
Confidence 567999996544
No 68
>PF04011 LemA: LemA family; InterPro: IPR007156 The members of this family are related to the LemA protein P71452 from SWISSPROT. The exact molecular function of this protein is uncertain. It is predicted to be a transmembrane protein with an extracellular N terminus [].; PDB: 2ETD_A.
Probab=24.60 E-value=1.3e+02 Score=25.41 Aligned_cols=65 Identities=15% Similarity=0.249 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHhc-C-CCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHH
Q 026691 140 KSARELVKTLRESLK-E-DPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLA 204 (235)
Q Consensus 140 kdT~~VV~tLReaLe-l-Dp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLA 204 (235)
+++..-|-.+|+... + ++.+..++.++....-+.++....--.+-|.....++|.+|++.|...-
T Consensus 65 ~~~l~~v~~~R~~~~~~~~~~~~~~~~~~~~~l~~al~~l~~~~e~yP~Lka~~~~~~l~~~l~~~E 131 (186)
T PF04011_consen 65 KETLTKVTKARSQANNLSDSADIQEFQQAEAELSQALSRLLAVVENYPELKADENFQQLMAQLEETE 131 (186)
T ss_dssp HHHHHHHHHHHHHHH---H--SHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHH
Confidence 445555666666666 2 3455666667777777777766655556688888899999888776543
No 69
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=24.07 E-value=3.7e+02 Score=28.20 Aligned_cols=28 Identities=7% Similarity=0.012 Sum_probs=17.1
Q ss_pred ccccccccCCCCcc--hhhhhHHHHHhhhh
Q 026691 54 KLHSRTHVVLPPVE--AASSRRHVISCSST 81 (235)
Q Consensus 54 k~~~~~~~~~p~~~--~~~~RR~~L~~~~~ 81 (235)
+-.-+|...|...+ ....||.+|...-.
T Consensus 118 RCc~~CGg~~~~~~~~~~~c~R~~l~~~L~ 147 (806)
T PF05478_consen 118 RCCGNCGGRMHQRDKKNDACRRGCLGILLL 147 (806)
T ss_pred ccCCCcCCccccccccccccchHHHHHHHH
Confidence 34567777664333 33567998887643
No 70
>PF01109 GM_CSF: Granulocyte-macrophage colony-stimulating factor; InterPro: IPR000773 Granulocyte-macrophage colony-stimulating factor (GMCSF) is a cytokine that acts in hematopoiesis to stimulate growth and differentiation of hematopoietic precursor cells from various lineages including granulocytes, macrophages, eosinophils and erythrocytes [, ]. GMCSF is a glycoprotein of ~120 residues that contains 4 conserved cysteines that participate in disulphide bond formation. The crystal structure of recombinant human GMCSF has been determined []. There are two molecules in the asymmetric unit, which are related by an approximate non-crystallographic 2-fold axis. The overall structure, which is highly compact and globular with a predominantly hydrophobic core, is characterised by a 4-alpha-helix bundle. The helices are arranged in a left-handed anti-parallel fashion, with two overhand connections. Within the connections is a two-stranded anti-parallel beta-sheet. The tertiary structure has a topology similar to that of Sus scrofa (pig) growth factor and interferon-beta. Most of the proposed critical regions for receptor binding are located on a continuous surface at one end of the molecule that includes the C terminus [].; GO: 0005129 granulocyte macrophage colony-stimulating factor receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 3CXE_B 1CSG_A 2GMF_B.
Probab=23.88 E-value=43 Score=28.27 Aligned_cols=37 Identities=24% Similarity=0.472 Sum_probs=22.8
Q ss_pred HHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhcCCCCCCChh
Q 026691 173 SIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGE 219 (235)
Q Consensus 173 ~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSfGp~rPLPek 219 (235)
-++=|...-|+ |++.+..+|+-+|.||.++- -|.||.
T Consensus 58 rLkly~qGLrg--------nlT~L~g~L~~mAshy~~~C--PptpEt 94 (122)
T PF01109_consen 58 RLKLYKQGLRG--------NLTRLKGPLTMMASHYKQHC--PPTPET 94 (122)
T ss_dssp HHHHHHHT--G--------GGGGGHHHHHHHHHHHHHCS-------S
T ss_pred HHHHHHHHccc--------cchhhhhhHHHHHHHhccCC--CCCCCc
Confidence 34445555544 68889999999999999964 455553
No 71
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=23.54 E-value=60 Score=29.15 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=9.7
Q ss_pred hhhHHHHHhhhh
Q 026691 70 SSRRHVISCSST 81 (235)
Q Consensus 70 ~~RR~~L~~~~~ 81 (235)
.+||+||..+++
T Consensus 3 ~~RR~flk~~~~ 14 (244)
T PRK14993 3 SSKRQFLQQLGV 14 (244)
T ss_pred ccHHHHHHHHHH
Confidence 589999987654
No 72
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=23.15 E-value=1.6e+02 Score=26.75 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhhHhhc--CCCCCCChhHHHHHHHHHHHHHhcC
Q 026691 193 YVELEKAIRSLASFYSKA--GPSAPLPGEVKSEILNDLDTAEKFL 235 (235)
Q Consensus 193 FttM~TALNsLAGHYsSf--Gp~rPLPeklK~RLLqEL~~AEkaL 235 (235)
...+..|++. -|....+ -|-.|++++.|++|.+.++...+-|
T Consensus 258 ~~~~K~al~~-~G~~~g~~R~Pl~~l~~~~~~~i~~~l~~~~~~~ 301 (303)
T PRK03620 258 VSIVKAGARL-VGLDAGPVRAPLTDLTPEELAELAALIAKGGAQL 301 (303)
T ss_pred cHHHHHHHHH-cCCCCCCCCCCCCCCCHHHHHHHHHHHHHhhhhh
Confidence 4668888874 4665321 1344588999999999998877643
No 73
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=22.56 E-value=4.2e+02 Score=21.44 Aligned_cols=68 Identities=13% Similarity=0.101 Sum_probs=48.2
Q ss_pred HhHHHHHHHHHHHHHhhhCCCCCCCchhHH----HHHHHHHHHHhhHhhcCCCCCCChhHHHHHHHHHHHHHhc
Q 026691 165 RNADSAKESIRDYLSNWRGQKTVAGEESYV----ELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKF 234 (235)
Q Consensus 165 ~aa~~AKe~InDyVSrYRr~~~V~G~~SFt----tM~TALNsLAGHYsSfGp~rPLPeklK~RLLqEL~~AEka 234 (235)
+..+.-.+.+.+++.++..++.......-. .+...++.+.|.+.. ++ .+.+++...++++++-+.|-+
T Consensus 120 ~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~~a~~l~~~~~g~~g~~~~-~~-~~~~~~~~~~~~~~~~~~~~~ 191 (192)
T PRK14996 120 LTMQMWHQETVAIIEQGKAAGEFRSTSNATDIAWRLIALVCGLDGIYVL-GI-PGLADPAFKRHLDRMITLELF 191 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHhHHhhhHhh-CC-CCCcHHHHHHHHHHHHHHHHh
Confidence 344556788888898888777766554433 334667777888887 43 488888888999988877753
No 74
>PF13333 rve_2: Integrase core domain
Probab=22.44 E-value=1.1e+02 Score=20.91 Aligned_cols=24 Identities=17% Similarity=0.565 Sum_probs=17.9
Q ss_pred HhHHHHHHHHHHHHHhhhCCCCCCC
Q 026691 165 RNADSAKESIRDYLSNWRGQKTVAG 189 (235)
Q Consensus 165 ~aa~~AKe~InDyVSrYRr~~~V~G 189 (235)
...+++++.|.+||-.| +..+..|
T Consensus 18 ~t~eel~~~I~~YI~~y-N~~Rl~~ 41 (52)
T PF13333_consen 18 KTREELKQAIDEYIDYY-NNERLKG 41 (52)
T ss_pred chHHHHHHHHHHHHHHh-ccCCCCC
Confidence 35679999999999988 5445443
No 75
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=22.42 E-value=69 Score=32.49 Aligned_cols=62 Identities=11% Similarity=0.138 Sum_probs=33.3
Q ss_pred ccCCCCcccCCCCCchHHHHHHHHHH---HHHHHHhcC-CCCCch-----HHHHhHHHHHHHHHHHHHhhhCC
Q 026691 121 LFDPNEKTKSGKVLPKAYLKSARELV---KTLRESLKE-DPKDIA-----NFRRNADSAKESIRDYLSNWRGQ 184 (235)
Q Consensus 121 ~fdp~~~tkSg~~LPkdY~kdT~~VV---~tLReaLel-Dp~D~~-----~~~~aa~~AKe~InDyVSrYRr~ 184 (235)
.=||+...-.|+.++|...- .+.+ ++|+.=+-- +++... .-.++.+.+.+.+++...+|-++
T Consensus 70 ~g~~~~p~n~g~~C~kG~~~--~~~~y~p~Rl~~Pl~R~~~rg~g~~~~iSWdEAl~~ia~~l~~i~~~~G~~ 140 (759)
T PRK15488 70 QGNPKAKSFGTKVCARGGSG--HSLLYDPQRIVKPLKRVGERGEGKWQEISWDEAYQEIAAKLNAIKQQHGPE 140 (759)
T ss_pred ECCCCCCCCCCccCccchhH--HHhhcCcchhccceeecCCCCCCCeEEeCHHHHHHHHHHHHHHHHHHhCCc
Confidence 45777777788989887521 1111 223322221 121111 22567777777777777777443
No 76
>PF05105 Phage_holin_4: Holin family ; InterPro: IPR006480 This group of sequences describe one of the many mutually dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species []. This entry is represented by the Bacteriophage phi-29, Gp14 (holin). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.38 E-value=1e+02 Score=24.34 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=20.5
Q ss_pred HHHHHhhHhhcCCCCCCChhHHHHHHH
Q 026691 200 IRSLASFYSKAGPSAPLPGEVKSEILN 226 (235)
Q Consensus 200 LNsLAGHYsSfGp~rPLPeklK~RLLq 226 (235)
+-|+.+++..-| -|+|+.+|+++.+
T Consensus 89 ~~SI~EN~~~~G--~~iP~~l~~~l~~ 113 (118)
T PF05105_consen 89 LISILENLAEMG--VPIPKWLKKFLKQ 113 (118)
T ss_pred HHHHHHHHHHhC--CCchHHHHHHHHH
Confidence 567889999987 4899999988874
No 77
>PF06761 IcmF-related: Intracellular multiplication and human macrophage-killing; InterPro: IPR009612 This entry represents a conserved region within several bacterial proteins that resemble ImcF, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation, resulting in increased adherence to epithelial cells and increased conjugation frequency. Note that many entry members are hypothetical proteins.
Probab=22.13 E-value=5.3e+02 Score=23.32 Aligned_cols=79 Identities=20% Similarity=0.331 Sum_probs=40.1
Q ss_pred CcccCCCC----CchHHHHHHH-HHH-HHHHHH----hcCC-----C-----CCchHHHHhHHHHHHH-HHHHHHhhhC-
Q 026691 126 EKTKSGKV----LPKAYLKSAR-ELV-KTLRES----LKED-----P-----KDIANFRRNADSAKES-IRDYLSNWRG- 183 (235)
Q Consensus 126 ~~tkSg~~----LPkdY~kdT~-~VV-~tLRea----LelD-----p-----~D~~~~~~aa~~AKe~-InDyVSrYRr- 183 (235)
.+.+||+. +|+-|-++.= +++ ..+... ...+ . .++....+..+..++. .+||+..|++
T Consensus 191 f~~~s~~~l~~~Ipg~yT~~G~~~~~~~~~~~~~~~~~~e~~WVlg~~~~~~~~~~~~~~L~~~v~~~Y~~DY~~~W~~~ 270 (312)
T PF06761_consen 191 FTRKSGKPLSDGIPGLYTRQGFEDYFLPALPKLAEALRSEDDWVLGDSEDSDASEADLEQLRQDVRKLYFQDYIAAWDDF 270 (312)
T ss_pred eecCCCcccccCCChhhhHHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46667754 8888877765 222 222222 2222 1 1223333444444433 5789999994
Q ss_pred --CCCCCCchhHHHHHHHHHHHH
Q 026691 184 --QKTVAGEESYVELEKAIRSLA 204 (235)
Q Consensus 184 --~~~V~G~~SFttM~TALNsLA 204 (235)
+=++..-.+..+....++.|+
T Consensus 271 L~~i~v~~~~~l~~a~~~l~~Ls 293 (312)
T PF06761_consen 271 LNDIRVQPFADLSQAVDQLRLLS 293 (312)
T ss_pred HhcCcccCCCCHHHHHHHHHHHc
Confidence 444444444444445555554
No 78
>PF10428 SOG2: RAM signalling pathway protein; InterPro: IPR019487 The RAM signalling pathway regulates Ace2p transcription factor activity and cellular morphogenesis in Saccharomyces cerevisiae (Baker's yeast), and is thought to be conserved amongst eukaryotes []. This entry is found in one of the components of this pathway, the leucine-rich repeat-containing protein SOG2.
Probab=21.86 E-value=2e+02 Score=28.28 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=32.9
Q ss_pred HHHHHHhhh---CCC--CCCCchhHHHHH----HHHHHHHhhHhhcCCCCCCChhHHHHHH
Q 026691 174 IRDYLSNWR---GQK--TVAGEESYVELE----KAIRSLASFYSKAGPSAPLPGEVKSEIL 225 (235)
Q Consensus 174 InDyVSrYR---r~~--~V~G~~SFttM~----TALNsLAGHYsSfGp~rPLPeklK~RLL 225 (235)
.+.=++.-| .+| .......|-+.- +++=++++=++..+...|+|.++|.++-
T Consensus 364 L~~rLs~ik~~~~ep~~~~~~~~~fwe~~~~Fiks~i~l~~~iK~~~~~~~l~~dvr~~L~ 424 (445)
T PF10428_consen 364 LKSRLSTIKNQLKEPGGGIREQKEFWEDCNSFIKSWISLLAKIKEIMKDLPLPPDVRARLR 424 (445)
T ss_pred HHHHHHHHHhhccCCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHH
Confidence 344445555 333 444455554432 4556677777888889999999998763
No 79
>smart00167 VPS9 Domain present in VPS9. Domain present in yeast vacuolar sorting protein 9 and other proteins.
Probab=21.56 E-value=1.1e+02 Score=24.75 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=26.2
Q ss_pred HHHHHHHhhhCCCCCCCchhH--HHHHHHHHHHHhh
Q 026691 173 SIRDYLSNWRGQKTVAGEESY--VELEKAIRSLASF 206 (235)
Q Consensus 173 ~InDyVSrYRr~~~V~G~~SF--ttM~TALNsLAGH 206 (235)
+--.||.+||......|+.+| |+++.|+.-+-..
T Consensus 67 sn~~yI~~f~~~~~l~gE~gY~lT~l~aAv~fi~~l 102 (117)
T smart00167 67 LNAEYMEEFLEPSLLTGEGGYYLTSLSAALALIKGL 102 (117)
T ss_pred HHHHHHHHHCCccccccHHHHHHHHHHHHHHHHHHC
Confidence 345699999988888899885 7888888765443
No 80
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=21.47 E-value=80 Score=28.07 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=31.9
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc-CCCCCchHHHHhHHHHHHHHHHHHHhhhC
Q 026691 132 KVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRG 183 (235)
Q Consensus 132 ~~LPkdY~kdT~~VV~tLReaLe-lDp~D~~~~~~aa~~AKe~InDyVSrYRr 183 (235)
|-=|..+ ..+++.+.+.|. +||.+.+.+++..+...+.+++.-.+|+.
T Consensus 116 Wldp~~~----~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~ 164 (282)
T cd01017 116 WLSPVLA----IQQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRA 164 (282)
T ss_pred ccCHHHH----HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555 555666666665 48988877777777777777766666653
No 81
>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein. Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase.
Probab=21.36 E-value=55 Score=28.82 Aligned_cols=13 Identities=23% Similarity=0.353 Sum_probs=10.0
Q ss_pred hhhHHHHHhhhhh
Q 026691 70 SSRRHVISCSSTA 82 (235)
Q Consensus 70 ~~RR~~L~~~~~~ 82 (235)
.+||+||++.++.
T Consensus 2 ~~rr~~l~~~~~~ 14 (225)
T TIGR03149 2 CSRRNFLAGVGAL 14 (225)
T ss_pred ccHHHHHHHHHHH
Confidence 4899999887543
No 82
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=21.16 E-value=3.9e+02 Score=22.17 Aligned_cols=57 Identities=9% Similarity=0.242 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHHHHHHHHHhhHhhc
Q 026691 143 RELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 210 (235)
Q Consensus 143 ~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~TALNsLAGHYsSf 210 (235)
++.++.|+..+.- +.+ .+..+.+++.|..|-..++++ +++.-|+.+-+.|-...-.|
T Consensus 79 k~Fl~eL~kl~~~-~~~----~~Vk~kil~li~~W~~~f~~~------~~l~~i~~~y~~L~~~G~~f 135 (144)
T cd03568 79 RDFTQELKKLIND-RVH----PTVKEKLREVVKQWADEFKND------PSLSLMSDLYKKLKNEGPDL 135 (144)
T ss_pred HHHHHHHHHHhcc-cCC----HHHHHHHHHHHHHHHHHhCCC------cccHHHHHHHHHHHHcCCCC
Confidence 4555566665552 322 245668889999998888754 34444555555555444443
No 83
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=21.13 E-value=1.5e+02 Score=18.92 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=18.2
Q ss_pred CCchhHHHHHHHHHHHHhhHhhcC
Q 026691 188 AGEESYVELEKAIRSLASFYSKAG 211 (235)
Q Consensus 188 ~G~~SFttM~TALNsLAGHYsSfG 211 (235)
+|.-|+.++..+....-.||.++|
T Consensus 2 ~~~i~~~~~~d~a~rv~~f~~~ng 25 (33)
T PF09373_consen 2 SGTISKEEYLDMASRVNNFYESNG 25 (33)
T ss_pred CceecHHHHHHHHHHHHHHHHHcC
Confidence 356677777778888888888876
No 84
>PF14461 Prok-E2_B: Prokaryotic E2 family B
Probab=21.00 E-value=1.8e+02 Score=23.49 Aligned_cols=37 Identities=14% Similarity=0.209 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCC
Q 026691 143 RELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTV 187 (235)
Q Consensus 143 ~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V 187 (235)
+++++..+..|+..+.+.. -++.++||.|.|.+...+
T Consensus 94 ~~~l~~a~~lL~~~~~~~~--------~~d~~~Ef~sYW~~~~~~ 130 (133)
T PF14461_consen 94 ADCLERAIRLLEDGLSGDN--------EDDFADEFQSYWNRQCDV 130 (133)
T ss_pred HHHHHHHHHHHHHhhcCCc--------hHHHHHHHHHHHhhcccc
Confidence 4555555555553333332 567889999999887654
No 85
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=20.87 E-value=4.2e+02 Score=21.34 Aligned_cols=38 Identities=13% Similarity=0.260 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhC
Q 026691 142 ARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG 183 (235)
Q Consensus 142 T~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr 183 (235)
+.+..+.|...+.- +.+.+. ..+.+.+.|.+|-..+++
T Consensus 78 s~~fl~~L~~l~~~-~~~~~~---Vk~kil~li~~W~~~f~~ 115 (133)
T smart00288 78 SKEFLNELVKLIKP-KYPLPL---VKKRILELIQEWADAFKN 115 (133)
T ss_pred hHHHHHHHHHHHcC-CCCcHH---HHHHHHHHHHHHHHHHcC
Confidence 35566777766663 444443 566788888888888866
No 86
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=20.67 E-value=2.7e+02 Score=26.75 Aligned_cols=85 Identities=15% Similarity=0.127 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCC---------CchhHHHHHHHHHHHHhhHh
Q 026691 138 YLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVA---------GEESYVELEKAIRSLASFYS 208 (235)
Q Consensus 138 Y~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~---------G~~SFttM~TALNsLAGHYs 208 (235)
+...|.+-++-|.+-... ..|. .+--|++.||+.|.-. -.++...++.-|.+.-.==+
T Consensus 164 ~~~~t~eai~~M~elA~e-a~D~------------~~~~~L~~Yrk~p~k~~~~~la~mL~~~kh~~~~~~l~e~l~~As 230 (299)
T PF12994_consen 164 NWPPTEEAIDVMEELARE-AGDK------------SYLKMLRLYRKHPSKRMARKLARMLHRKKHQKVYDLLIEKLQEAS 230 (299)
T ss_pred CCcCcHHHHHHHHHHHHH-hCcH------------HHHHHHHHHHhCCcHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHh
Confidence 344444555555554443 3342 2334777777766432 12444444444444444444
Q ss_pred hcCCCCCCChhHHHHHHHHHHHHHhcC
Q 026691 209 KAGPSAPLPGEVKSEILNDLDTAEKFL 235 (235)
Q Consensus 209 SfGp~rPLPeklK~RLLqEL~~AEkaL 235 (235)
+.+|+|-.-++..+|+.+..+++++.|
T Consensus 231 ~~Yp~R~fg~~~~~~~q~~~~~~~~~L 257 (299)
T PF12994_consen 231 SPYPRRDFGEDIDERIQKKRKQAENEL 257 (299)
T ss_pred ccCCcccccHHHHHHHHHHHHHHHHHH
Confidence 555788888999999999888887643
No 87
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=20.55 E-value=1.3e+02 Score=24.58 Aligned_cols=63 Identities=16% Similarity=0.351 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHHhHHHHHHHHHHHHHhhhCCCCCCCchhHHHHH-HHHHHHHhhHhhcCCC
Q 026691 137 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE-KAIRSLASFYSKAGPS 213 (235)
Q Consensus 137 dY~kdT~~VV~tLReaLelDp~D~~~~~~aa~~AKe~InDyVSrYRr~~~V~G~~SFttM~-TALNsLAGHYsSfGp~ 213 (235)
.|.+....++.-||..+.+|.+ ...++ +.+.+..++|+.++. |+..| .-|+.|..||..+|--
T Consensus 60 ~~~~~~~dl~~~ir~i~g~d~~-l~tr~---erv~~~~~~~l~~~~----------~~~~Q~~~L~~i~~~~~~~G~~ 123 (164)
T PF08463_consen 60 TYEAIDADLFDFIRHILGLDTP-LLTRR---ERVEEAFSKFLNQHQ----------FNAEQREFLERILDYYAQNGII 123 (164)
T ss_pred hcccccCCHHHHHHHHHhcCCC-CCCHH---HHHHHHHHHHHHhcC----------CCHHHHHHHHHHHHHHHHhCcc
Confidence 4555567788889999888411 11222 234445588886653 65555 7789999999998843
No 88
>PLN02382 probable sucrose-phosphatase
Probab=20.46 E-value=77 Score=30.45 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=28.8
Q ss_pred cccccccchhcccCCCCc--ccCCCCCchHHHHHHHHHHHHHHHHhc
Q 026691 110 KEEGVVGAIKSLFDPNEK--TKSGKVLPKAYLKSARELVKTLRESLK 154 (235)
Q Consensus 110 ~~~g~~~~~~~~fdp~~~--tkSg~~LPkdY~kdT~~VV~tLReaLe 154 (235)
++++++.++|+.|+||.+ +++|..|+.. +++..+|..=.
T Consensus 304 ~~~~~~~~l~~~~~p~~~~v~p~G~~~~~~------~~~~~~~~~~G 344 (413)
T PLN02382 304 NSDEVFQRLKSSCAPNGVFVHPSGVEKSLH------DSIDELRSCYG 344 (413)
T ss_pred CcHHHHHHHHHhcCCCeeEECCCcccCCHH------HHHHHHHHhhC
Confidence 556889999999999987 6888888764 34555555443
No 89
>PRK10911 oligopeptidase A; Provisional
Probab=20.36 E-value=1.1e+02 Score=31.42 Aligned_cols=29 Identities=24% Similarity=0.431 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhhHhhcCCCCCCChhHHHHHHH
Q 026691 195 ELEKAIRSLASFYSKAGPSAPLPGEVKSEILN 226 (235)
Q Consensus 195 tM~TALNsLAGHYsSfGp~rPLPeklK~RLLq 226 (235)
.-..+|..+|.||.+ ..|||+++.+++++
T Consensus 510 ~~~~vL~~~a~H~~t---geplp~~l~~~l~~ 538 (680)
T PRK10911 510 WEPEALAFISGHYET---GEPLPKELLDKMLA 538 (680)
T ss_pred cCHHHHHHHHHHhcC---CCCCCHHHHHHHHH
Confidence 334678889999997 46999999999887
No 90
>TIGR02949 anti_SigH_actin anti-sigma factor, TIGR02949 family. This group of anti-sigma factors are associated in an apparent operon with a family of sigma-70 family sigma factors (TIGR02947). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria.
Probab=20.20 E-value=2.7e+02 Score=21.00 Aligned_cols=19 Identities=11% Similarity=0.246 Sum_probs=15.9
Q ss_pred CCCCChhHHHHHHHHHHHH
Q 026691 213 SAPLPGEVKSEILNDLDTA 231 (235)
Q Consensus 213 ~rPLPeklK~RLLqEL~~A 231 (235)
..+-|+.+|+||+..+...
T Consensus 62 ~~~aP~~Lr~rI~~~l~~~ 80 (84)
T TIGR02949 62 TEAAPEGLRSRLRLQIRVI 80 (84)
T ss_pred CCCCCHHHHHHHHHHHHhh
Confidence 4578999999999998753
Done!