Query 028492
Match_columns 208
No_of_seqs 88 out of 90
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 12:21:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028492hhsearch_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 1.5E-64 3.3E-69 415.7 13.8 148 56-205 3-150 (150)
2 TIGR03044 PS_II_psb27 photosys 100.0 5.2E-44 1.1E-48 290.5 14.6 104 103-208 29-132 (135)
3 PF13326 PSII_Pbs27: Photosyst 100.0 8.7E-45 1.9E-49 296.2 9.4 145 44-208 1-145 (145)
4 PLN00064 photosystem II protei 100.0 1.9E-43 4.1E-48 294.5 14.3 98 110-208 65-162 (166)
5 TIGR02811 formate_TAT formate 93.5 0.086 1.9E-06 38.6 3.2 15 41-55 7-21 (66)
6 PF10518 TAT_signal: TAT (twin 90.6 0.24 5.1E-06 30.3 2.2 13 43-55 2-14 (26)
7 TIGR01409 TAT_signal_seq Tat ( 86.4 0.6 1.3E-05 28.7 2.0 12 44-55 2-13 (29)
8 PF07240 Turandot: Stress-indu 84.4 2.3 4.9E-05 33.0 4.8 34 170-203 9-42 (85)
9 PF10399 UCR_Fe-S_N: Ubiquitin 81.4 0.57 1.2E-05 31.6 0.4 29 39-68 5-33 (41)
10 PF12732 YtxH: YtxH-like prote 79.2 3.2 7E-05 29.9 3.8 49 103-152 23-73 (74)
11 COG1698 Uncharacterized protei 74.4 21 0.00045 28.4 7.3 86 104-205 4-89 (93)
12 PRK15102 trimethylamine N-oxid 70.1 3.3 7.1E-05 41.7 2.5 32 43-74 1-32 (825)
13 PRK07474 sulfur oxidation prot 66.0 3.5 7.6E-05 34.8 1.5 15 42-56 7-21 (154)
14 cd00040 CSF2 Granulocyte Macro 63.7 14 0.00031 30.4 4.6 25 164-188 68-92 (121)
15 TIGR02166 dmsA_ynfE anaerobic 58.8 8.8 0.00019 38.2 3.0 26 43-68 1-26 (797)
16 PRK10882 hydrogenase 2 protein 57.4 7.9 0.00017 35.9 2.3 13 43-55 1-13 (328)
17 PF15519 RBM39linker: linker b 55.0 4.5 9.7E-05 30.0 0.3 15 91-105 59-73 (73)
18 COG2822 Predicted periplasmic 51.6 51 0.0011 31.6 6.6 63 112-180 296-366 (376)
19 smart00040 CSF2 Granulocyte-ma 48.4 16 0.00035 30.1 2.5 26 164-189 68-93 (121)
20 TIGR03175 AllD ureidoglycolate 48.2 45 0.00098 31.3 5.8 81 87-189 260-347 (349)
21 PRK14990 anaerobic dimethyl su 47.1 15 0.00032 37.0 2.5 14 42-55 13-26 (814)
22 cd01018 ZntC Metal binding pro 46.4 46 0.001 28.9 5.2 98 102-203 112-215 (266)
23 cd08054 gp6 Head-Tail Connecto 45.1 1.1E+02 0.0023 21.6 6.3 76 120-195 3-85 (91)
24 PF09236 AHSP: Alpha-haemoglob 44.3 30 0.00065 27.3 3.3 36 167-203 31-68 (89)
25 PF09037 Sulphotransf: Stf0 su 44.2 18 0.0004 31.8 2.4 46 111-156 198-244 (245)
26 TIGR01480 copper_res_A copper- 43.9 16 0.00034 36.4 2.2 30 42-74 5-34 (587)
27 TIGR01405 polC_Gram_pos DNA po 43.6 94 0.002 33.9 7.9 92 106-205 539-632 (1213)
28 PRK10866 outer membrane biogen 42.5 2.1E+02 0.0046 24.8 8.7 80 117-198 50-168 (243)
29 PRK13474 cytochrome b6-f compl 41.6 13 0.00028 31.4 1.1 13 43-55 12-24 (178)
30 PF12318 FAD-SLDH: Membrane bo 40.2 24 0.00052 29.7 2.4 8 43-50 2-9 (168)
31 PF02899 Phage_int_SAM_1: Phag 38.5 1.3E+02 0.0028 20.6 7.5 58 110-181 21-78 (84)
32 PF08374 Protocadherin: Protoc 38.3 2.6 5.7E-05 37.7 -3.7 30 145-184 133-162 (221)
33 PF08542 Rep_fac_C: Replicatio 37.6 1.5E+02 0.0032 21.1 7.7 36 169-208 37-72 (89)
34 TIGR01560 put_DNA_pack unchara 37.2 1.4E+02 0.0031 22.0 6.0 58 121-182 4-62 (91)
35 TIGR02659 TTQ_MADH_Lt methylam 35.8 25 0.00054 31.0 1.9 21 41-61 20-40 (186)
36 PRK09269 chorismate mutase; Pr 35.3 1.5E+02 0.0033 25.7 6.6 64 114-177 67-136 (193)
37 PF13551 HTH_29: Winged helix- 34.3 1.2E+02 0.0025 21.9 5.0 57 133-203 15-72 (112)
38 PF04740 LXG: LXG domain of WX 33.7 2E+02 0.0043 23.6 6.8 66 140-206 44-113 (204)
39 PRK15488 thiosulfate reductase 32.9 33 0.00072 34.1 2.5 61 94-156 70-139 (759)
40 PRK14993 tetrathionate reducta 32.9 31 0.00067 30.4 2.1 13 43-55 3-15 (244)
41 TIGR03149 cyt_nit_nrfC cytochr 32.6 25 0.00053 30.5 1.4 12 43-54 2-13 (225)
42 PRK15219 carbonic anhydrase; P 32.5 20 0.00043 32.1 0.8 71 41-114 7-80 (245)
43 PLN00033 photosystem II stabil 32.3 33 0.00072 32.5 2.3 40 16-55 13-52 (398)
44 PF13333 rve_2: Integrase core 31.4 56 0.0012 21.9 2.7 25 138-163 18-42 (52)
45 PRK00035 hemH ferrochelatase; 31.2 1.4E+02 0.0031 26.7 6.0 57 145-201 20-87 (333)
46 TIGR01416 Rieske_proteo ubiqui 31.0 22 0.00048 29.9 0.8 24 44-68 1-24 (174)
47 PF08463 EcoEI_R_C: EcoEI R pr 30.3 50 0.0011 26.4 2.7 64 110-187 60-124 (164)
48 PRK03620 5-dehydro-4-deoxygluc 29.8 1E+02 0.0023 27.5 4.9 42 166-208 258-301 (303)
49 PF10163 EnY2: Transcription f 29.5 1.9E+02 0.0042 21.6 5.6 51 140-203 33-83 (86)
50 smart00167 VPS9 Domain present 29.3 62 0.0013 25.8 3.0 35 145-179 66-102 (117)
51 TIGR03743 SXT_TraD conjugative 29.1 2.5E+02 0.0054 28.4 7.8 87 92-185 235-330 (634)
52 cd01019 ZnuA Zinc binding prot 28.7 50 0.0011 29.2 2.6 97 104-203 123-226 (286)
53 cd01493 APPBP1_RUB Ubiquitin a 27.3 3.3E+02 0.0072 26.2 8.0 82 106-193 222-313 (425)
54 TIGR01553 formate-DH-alph form 26.9 49 0.0011 35.1 2.6 17 95-111 79-95 (1009)
55 PF04011 LemA: LemA family; I 26.9 1.1E+02 0.0025 25.3 4.3 65 112-176 64-130 (186)
56 PF14461 Prok-E2_B: Prokaryoti 26.9 1.1E+02 0.0025 24.1 4.1 57 91-160 74-130 (133)
57 PF09684 Tail_P2_I: Phage tail 26.7 3E+02 0.0064 21.6 6.5 66 130-200 2-67 (139)
58 cd01145 TroA_c Periplasmic bin 26.7 61 0.0013 27.0 2.7 49 104-155 110-158 (203)
59 PF12889 DUF3829: Protein of u 26.5 1E+02 0.0022 26.2 4.1 48 135-182 219-274 (276)
60 PRK00448 polC DNA polymerase I 26.5 2.2E+02 0.0047 31.9 7.4 92 106-205 764-857 (1437)
61 COG3211 PhoX Predicted phospha 26.1 40 0.00087 34.4 1.7 20 42-63 20-39 (616)
62 PF06761 IcmF-related: Intrace 25.8 4E+02 0.0087 23.6 7.8 84 100-189 192-299 (312)
63 cd01020 TroA_b Metal binding p 25.7 68 0.0015 27.9 2.9 95 105-203 98-204 (264)
64 PF10428 SOG2: RAM signalling 25.7 1.5E+02 0.0032 28.6 5.4 68 112-198 354-424 (445)
65 PF07030 DUF1320: Protein of u 25.6 3.4E+02 0.0073 21.4 7.0 63 131-199 28-93 (130)
66 cd03411 Ferrochelatase_N Ferro 25.5 2.6E+02 0.0056 22.6 6.1 57 145-203 15-83 (159)
67 PF12918 TcdB_N: TcdB toxin N- 25.5 2.5E+02 0.0055 20.4 5.4 45 116-160 4-49 (66)
68 PRK09545 znuA high-affinity zi 25.2 1.5E+02 0.0033 26.7 5.1 96 104-203 147-250 (311)
69 PF07240 Turandot: Stress-indu 25.1 38 0.00083 26.3 1.1 22 144-165 33-55 (85)
70 PRK09898 hypothetical protein; 25.0 28 0.00061 29.5 0.4 14 42-55 12-25 (208)
71 PF01109 GM_CSF: Granulocyte-m 24.3 41 0.00089 27.9 1.2 36 147-192 59-94 (122)
72 PF05823 Gp-FAR-1: Nematode fa 24.2 1.6E+02 0.0034 24.4 4.7 58 140-203 75-135 (154)
73 PF08802 CytB6-F_Fe-S: Cytochr 24.2 33 0.00072 23.2 0.5 26 42-68 5-30 (39)
74 cd01137 PsaA Metal binding pro 23.8 2.4E+02 0.0052 25.0 6.0 98 102-203 117-224 (287)
75 COG0339 Dcp Zn-dependent oligo 23.0 76 0.0016 32.9 3.0 30 167-199 512-541 (683)
76 cd01017 AdcA Metal binding pro 22.0 77 0.0017 27.7 2.6 96 104-203 115-218 (282)
77 PF06741 LsmAD: LsmAD domain; 22.0 1.1E+02 0.0024 22.9 3.0 24 90-114 2-26 (72)
78 PRK11032 hypothetical protein; 21.4 4.8E+02 0.01 22.3 7.1 19 107-129 4-22 (160)
79 PTZ00484 GTP cyclohydrolase I; 21.3 3E+02 0.0065 25.3 6.2 59 99-158 60-119 (259)
80 PTZ00477 rhoptry-associated pr 21.2 1.5E+02 0.0033 29.8 4.6 57 99-155 26-97 (524)
81 smart00288 VHS Domain present 21.2 4.2E+02 0.0091 20.9 6.5 51 116-176 79-129 (133)
82 TIGR00391 hydA hydrogenase (Ni 20.8 46 0.00099 31.8 0.9 33 42-75 14-46 (365)
83 PF09373 PMBR: Pseudomurein-bi 20.6 1.7E+02 0.0036 18.4 3.2 24 161-184 2-25 (33)
84 COG1930 CbiN ABC-type cobalt t 20.2 84 0.0018 25.2 2.1 26 80-105 34-63 (97)
85 PRK10911 oligopeptidase A; Pro 20.1 1.2E+02 0.0025 30.8 3.7 28 169-199 511-538 (680)
No 1
>PLN00061 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=1.5e-64 Score=415.70 Aligned_cols=148 Identities=78% Similarity=1.098 Sum_probs=143.5
Q ss_pred HHHHHHhhcCCCCchhhhhcccCCCCccccccccchhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchH
Q 028492 56 LVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN 135 (208)
Q Consensus 56 ~~a~~~~~~~~~p~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~ 135 (208)
++++++++|...|++++|++|+ +.++++||||||||||||||+||||++||++|++||++||++||++|+++|+|+++
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 3689999999999999999997 47777899999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHH
Q 028492 136 FRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAE 205 (208)
Q Consensus 136 ~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~AE 205 (208)
|++++++||++|||||++||+++.|+|++||+||+||||+|||||++|||||||||++|+||++||++||
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
>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=5.2e-44 Score=290.46 Aligned_cols=104 Identities=31% Similarity=0.520 Sum_probs=100.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhh
Q 028492 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 182 (208)
Q Consensus 103 sg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss 182 (208)
+.+.|+++|.+||++||++||++|++ |+|++++++++++||++|||||+||||+++|+|++||+|||||||+|||||++
T Consensus 29 ~~~~Ltg~Y~~DT~~Vi~tlr~~i~l-pkd~p~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~s 107 (135)
T TIGR03044 29 AKTRLTGDYVEDTLAVIQTLREAIDL-PDDDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKS 107 (135)
T ss_pred CcccccchHHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhcc
Confidence 34678999999999999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHhcC
Q 028492 183 AGPSAPLPGEVKSEILNDLDTAEKFL 208 (208)
Q Consensus 183 ~GpnrPLPeklK~RLlqEL~~AE~aL 208 (208)
|| |||||||+|+||+|||++||++|
T Consensus 108 y~-~rPlPeklk~Rl~~El~~AE~al 132 (135)
T TIGR03044 108 YA-NRPLPEKLKERLEKELKKAEKAL 132 (135)
T ss_pred CC-CCCCCHHHHHHHHHHHHHHHHHH
Confidence 95 99999999999999999999986
No 3
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=100.00 E-value=8.7e-45 Score=296.16 Aligned_cols=145 Identities=41% Similarity=0.550 Sum_probs=93.0
Q ss_pred hhHHHHHhhhhhHHHHHHhhcCCCCchhhhhcccCCCCccccccccchhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHH
Q 028492 44 SRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLR 123 (208)
Q Consensus 44 sRr~~l~~~~~~~~a~~~~~~~~~p~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLR 123 (208)
+||+||.+.+.++ .++++.+..+++.+++.....+ ++|. +||+ .|+++|++||++||++||
T Consensus 1 ~rr~~l~~~~~~~-~al~l~~~~~~l~~~~l~~c~~-----------~~s~-~~~~------~l~~~Y~~dt~~vv~~lr 61 (145)
T PF13326_consen 1 SRRRLLLAASSAL-LALTLSARGAALAVIALTACRA-----------AKSG-DPNA------GLTGDYVKDTRAVVKTLR 61 (145)
T ss_dssp ---------------------------------S------------------S--S------S--S-CHHHHHHHHHHHH
T ss_pred CcchhhhHHHHHH-HHHHHhhhhHHHHhhcchhhhh-----------cccC-Cccc------cccchHHHHHHHHHHHHH
Confidence 6999998888874 4555555555655544222110 4455 6665 455679999999999999
Q ss_pred HHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 124 ESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 124 eaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
++|++ |+|++++++++++||++|||||++|||+++|+|++||++||+|||+|||||++|||++|||+|+|+||++||++
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 79999999999999999999999999999999999999999999999999999998889999999999999999
Q ss_pred HHhcC
Q 028492 204 AEKFL 208 (208)
Q Consensus 204 AE~aL 208 (208)
||++|
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
>PLN00064 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=1.9e-43 Score=294.52 Aligned_cols=98 Identities=27% Similarity=0.555 Sum_probs=96.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCC
Q 028492 110 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL 189 (208)
Q Consensus 110 ~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPL 189 (208)
+|.+||.+||++||++|+| |+|+++++++++++|++|||||+||||+++|+|++||+|||||||+|||||++|||||||
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 7999999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHhcC
Q 028492 190 PGEVKSEILNDLDTAEKFL 208 (208)
Q Consensus 190 PeklK~RLlqEL~~AE~aL 208 (208)
|+|+|+||+|||++||++|
T Consensus 144 PeKlK~RL~qE~~~AEkal 162 (166)
T PLN00064 144 PAKRKARILEEMDTAEKAL 162 (166)
T ss_pred cHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999986
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=93.48 E-value=0.086 Score=38.57 Aligned_cols=15 Identities=27% Similarity=0.357 Sum_probs=11.9
Q ss_pred hhhhhHHHHHhhhhh
Q 028492 41 AASSRRHVISCSSTA 55 (208)
Q Consensus 41 ~~~sRr~~l~~~~~~ 55 (208)
...+||+||.+.+.+
T Consensus 7 ~~~sRR~Flk~lg~~ 21 (66)
T TIGR02811 7 ADPSRRDLLKGLGVG 21 (66)
T ss_pred CCccHHHHHHHHHHH
Confidence 356899999988765
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=90.61 E-value=0.24 Score=30.26 Aligned_cols=13 Identities=31% Similarity=0.417 Sum_probs=11.0
Q ss_pred hhhHHHHHhhhhh
Q 028492 43 SSRRHVISCSSTA 55 (208)
Q Consensus 43 ~sRr~~l~~~~~~ 55 (208)
.+||+||.++++.
T Consensus 2 ~sRR~fLk~~~a~ 14 (26)
T PF10518_consen 2 LSRRQFLKGGAAA 14 (26)
T ss_pred CcHHHHHHHHHHH
Confidence 4899999999765
No 7
>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=86.38 E-value=0.6 Score=28.75 Aligned_cols=12 Identities=33% Similarity=0.506 Sum_probs=10.3
Q ss_pred hhHHHHHhhhhh
Q 028492 44 SRRHVISCSSTA 55 (208)
Q Consensus 44 sRr~~l~~~~~~ 55 (208)
+||+||..++.+
T Consensus 2 sRR~Flk~~~~~ 13 (29)
T TIGR01409 2 SRRDFLKGAAAA 13 (29)
T ss_pred chhhhHHHHHHH
Confidence 799999999764
No 8
>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=84.37 E-value=2.3 Score=32.99 Aligned_cols=34 Identities=26% Similarity=0.419 Sum_probs=29.4
Q ss_pred HHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 170 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 170 ~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
..=+.+|-+||..|.|.-||++..|+++...+++
T Consensus 9 ~rni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~ 42 (85)
T PF07240_consen 9 IRNIQELIAFYEKYSPRLPLTPQDRQRIDRFIRR 42 (85)
T ss_pred HhhHHHHHHHHHHcCccCCCCHHHHHHHHHHHHH
Confidence 3447789999999999999999999999887765
No 9
>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=81.45 E-value=0.57 Score=31.64 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=16.1
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492 39 VEAASSRRHVISCSSTALVAILTFNCGLAP 68 (208)
Q Consensus 39 ~~~~~sRr~~l~~~~~~~~a~~~~~~~~~p 68 (208)
.....+||+||..+.++ ++++-.+++.+|
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 34567999999555443 566666666666
No 10
>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=79.25 E-value=3.2 Score=29.91 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=23.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcCCCCC--chHHHhhHHHHHHHHHHHHh
Q 028492 103 SGKVLPKAYLKSARELVKTLRESLKEDPKD--IANFRRNADSAKESIRDYLS 152 (208)
Q Consensus 103 sg~~LPk~Y~~dTr~VV~tLReaL~ldp~D--~~~~r~aa~~AKe~Indyvs 152 (208)
+|+.+=++-.+.+.++.+.+.+..+. -.+ ...+.+..+.+++.+++++.
T Consensus 23 sG~e~R~~l~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~~~~~e~~~e~~d 73 (74)
T PF12732_consen 23 SGKETREKLKDKAEDLKDKAKDLYEE-AKEKVKEKAEETADEAKEKAKELKD 73 (74)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45544444444444444444443332 111 12344466667777777653
No 11
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=74.40 E-value=21 Score=28.36 Aligned_cols=86 Identities=28% Similarity=0.400 Sum_probs=63.4
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhc
Q 028492 104 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 183 (208)
Q Consensus 104 g~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~ 183 (208)
|-.++.++.+.-..++..|++.+. |..=+.+.|+++.+|++..++ .|++.+.--.+||.-|=.--+
T Consensus 4 ~~~~~~d~~e~i~q~~~lL~~Ii~-DttVPRNIRraA~~a~e~L~~-----------e~e~p~vRaAtaIsiLeeisn-- 69 (93)
T COG1698 4 GQGLMNDSEEKINQVMQLLDEIIQ-DTTVPRNIRRAAEEAKEALNN-----------EGESPAVRAATAISILEEISN-- 69 (93)
T ss_pred hhcchhhhHHHHHHHHHHHHHHHc-cccccHHHHHHHHHHHHHHhC-----------CCCCchhHHHHHHHHHHHHhc--
Confidence 456778888888999999999555 666778899999999998864 467777777888888876533
Q ss_pred CCCCCCChHHHHHHHHHHHHHH
Q 028492 184 GPSAPLPGEVKSEILNDLDTAE 205 (208)
Q Consensus 184 GpnrPLPeklK~RLlqEL~~AE 205 (208)
-||-|+ -.|..|.+=+.+-|
T Consensus 70 DPNmP~--h~RT~iw~vis~LE 89 (93)
T COG1698 70 DPNMPL--HARTLIWNVISQLE 89 (93)
T ss_pred CCCCch--HHHHHHHHHHHHHH
Confidence 488654 56776666554433
No 12
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=70.11 E-value=3.3 Score=41.71 Aligned_cols=32 Identities=22% Similarity=0.092 Sum_probs=17.7
Q ss_pred hhhHHHHHhhhhhHHHHHHhhcCCCCchhhhh
Q 028492 43 SSRRHVISCSSTALVAILTFNCGLAPLPVQAE 74 (208)
Q Consensus 43 ~sRr~~l~~~~~~~~a~~~~~~~~~p~~~~A~ 74 (208)
.|||.||.+++++..+++.-++.+.+..++|.
T Consensus 1 ~sRR~flk~~~~~~~~~~~g~~~~~~~~~~~~ 32 (825)
T PRK15102 1 ASRRRFLKGLGGLSAAGMLGPSLLTPRSALAA 32 (825)
T ss_pred CCHHHHHHHHHHHHHHHhhcccccchhhhhhc
Confidence 37999999887642222222234445555554
No 13
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=66.03 E-value=3.5 Score=34.78 Aligned_cols=15 Identities=40% Similarity=0.483 Sum_probs=12.1
Q ss_pred hhhhHHHHHhhhhhH
Q 028492 42 ASSRRHVISCSSTAL 56 (208)
Q Consensus 42 ~~sRr~~l~~~~~~~ 56 (208)
..+||+||+..++++
T Consensus 7 ~~~rr~~l~~~~~~~ 21 (154)
T PRK07474 7 ALSRRQALALGGGAL 21 (154)
T ss_pred CcCHHHHHHHHHHHH
Confidence 478999999987663
No 14
>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=63.71 E-value=14 Score=30.38 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=22.3
Q ss_pred chHHHHHHHHHHHHhhhhhcCCCCC
Q 028492 164 ESYVELEKAIRSLASFYSKAGPSAP 188 (208)
Q Consensus 164 ~SFttM~TALNsLAGhYss~GpnrP 188 (208)
-|++-+..+|+-+|.||..+-|..|
T Consensus 68 GsltkLkg~LtmmAshYkqhCppTp 92 (121)
T cd00040 68 GSLTKLKGPLTMMASHYKQHCPPTP 92 (121)
T ss_pred ccHHHhccHHHHHHHHHHhcCCCCC
Confidence 3899999999999999999877665
No 15
>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=58.78 E-value=8.8 Score=38.17 Aligned_cols=26 Identities=23% Similarity=0.114 Sum_probs=15.5
Q ss_pred hhhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492 43 SSRRHVISCSSTALVAILTFNCGLAP 68 (208)
Q Consensus 43 ~sRr~~l~~~~~~~~a~~~~~~~~~p 68 (208)
.+||+||.+++++.+++++.+|+..+
T Consensus 1 ~~RR~Flk~~~~~~~~~~~~~~~~~~ 26 (797)
T TIGR02166 1 ISRRHFLKTSAALGGLAAASGALSLP 26 (797)
T ss_pred CCHHHHHHHHHHHHHHHHHhhccccc
Confidence 37999999776543333334444433
No 16
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=57.43 E-value=7.9 Score=35.91 Aligned_cols=13 Identities=23% Similarity=0.463 Sum_probs=10.1
Q ss_pred hhhHHHHHhhhhh
Q 028492 43 SSRRHVISCSSTA 55 (208)
Q Consensus 43 ~sRr~~l~~~~~~ 55 (208)
++||+||.+++++
T Consensus 1 ~~RR~fl~~~~~~ 13 (328)
T PRK10882 1 MNRRNFLKAASAG 13 (328)
T ss_pred CCHHHHHHHHHHH
Confidence 4799999987553
No 17
>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A.
Probab=55.04 E-value=4.5 Score=30.01 Aligned_cols=15 Identities=40% Similarity=0.760 Sum_probs=12.4
Q ss_pred hhcccCCCCcCcCCC
Q 028492 91 IKSLFDPNEKTKSGK 105 (208)
Q Consensus 91 ~~~~fdp~~~~ksg~ 105 (208)
||..|||.++|..+|
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 688999999998887
No 18
>COG2822 Predicted periplasmic lipoprotein involved in iron transport [Inorganic ion transport and metabolism]
Probab=51.64 E-value=51 Score=31.59 Aligned_cols=63 Identities=25% Similarity=0.443 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHH--------HHHHHHHhhh
Q 028492 112 LKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE--------KAIRSLASFY 180 (208)
Q Consensus 112 ~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~--------TALNsLAGhY 180 (208)
++-+..|++.+|-.|+- +| ....+-.+..=..+++-+++||... |-.||..+- ..||+||+--
T Consensus 296 VeGsqki~dl~rp~Lek--~d-k~L~~kid~nF~kv~~~LakYkt~d---g~esydklt~~dr~al~~~itaLaE~l 366 (376)
T COG2822 296 VEGSQKIVDLFRPALEK--KD-KDLLDKIDANFKKVNTILAKYRTKD---GFESYDKLTKADRKALKDPITALAEDL 366 (376)
T ss_pred chhHHHHHHHHHHHHhh--cc-HHHHHHHHHHHHHHHHHHHHhccCC---cceeHHHhhHHHHHHHhhHHHHHHHHH
Confidence 56678999999999995 23 3445567788889999999999866 888998764 4556665543
No 19
>smart00040 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic activity of white blood cells.
Probab=48.39 E-value=16 Score=30.06 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=22.6
Q ss_pred chHHHHHHHHHHHHhhhhhcCCCCCC
Q 028492 164 ESYVELEKAIRSLASFYSKAGPSAPL 189 (208)
Q Consensus 164 ~SFttM~TALNsLAGhYss~GpnrPL 189 (208)
-||+-+..+|+-+|.||..+-|..|=
T Consensus 68 Gslt~Lkg~LtmmA~hYkq~CppTpE 93 (121)
T smart00040 68 GSLTKLKGPLTMMASHYKQHCPPTPE 93 (121)
T ss_pred ccHHHhhcHHHHHHHHHHhcCCCCCC
Confidence 38999999999999999998776653
No 20
>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=48.23 E-value=45 Score=31.25 Aligned_cols=81 Identities=15% Similarity=0.252 Sum_probs=53.1
Q ss_pred cccchhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHHHHhcCC-------CCCchHHHhhHHHHHHHHHHHHhhccCCCC
Q 028492 87 VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKED-------PKDIANFRRNADSAKESIRDYLSNWRGQKT 159 (208)
Q Consensus 87 ~~~~~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLReaL~ld-------p~D~~~~r~aa~~AKe~IndyvsrYRr~~~ 159 (208)
.+|.+--..||.--.. ..+|.+...++++.||.+--.+ |.|.+...+ .+..
T Consensus 260 ~~G~~~iaIDP~~F~~-----~~~f~~~~~~~~~~~r~~~~a~g~~~V~~PGe~e~~~~-----------------~~~~ 317 (349)
T TIGR03175 260 NLGQLHLVINPAFFTD-----CELFKKHISQMMQELNSVPPAEGFKQVYYPGEDGDLKQ-----------------KKAD 317 (349)
T ss_pred CcceEEEEEChHHcCC-----HHHHHHHHHHHHHHHhcCCCCCCCCceECCCcHHHHHH-----------------HHHH
Confidence 4677777889964421 3479999999999999873221 444433111 1123
Q ss_pred CCCcchHHHHHHHHHHHHhhhhhcCCCCCC
Q 028492 160 VAGEESYVELEKAIRSLASFYSKAGPSAPL 189 (208)
Q Consensus 160 V~G~~SFttM~TALNsLAGhYss~GpnrPL 189 (208)
-.|-+==..+...|+.|+-||++|-.+-|.
T Consensus 318 ~~GI~l~~~~~~~L~~la~~~~~~~~~~~~ 347 (349)
T TIGR03175 318 MEGIEIVDDIYQYLVSDAVHYKSYEGKNPF 347 (349)
T ss_pred ccCCccCHHHHHHHHHHHHHHHhccCCCcC
Confidence 345555567778889999999999666654
No 21
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=47.11 E-value=15 Score=36.96 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=11.9
Q ss_pred hhhhHHHHHhhhhh
Q 028492 42 ASSRRHVISCSSTA 55 (208)
Q Consensus 42 ~~sRr~~l~~~~~~ 55 (208)
..+||.||.+++++
T Consensus 13 ~~sRR~FLk~~~~~ 26 (814)
T PRK14990 13 EVSRRGLVKTTAIG 26 (814)
T ss_pred CccHHHHHHHHHHH
Confidence 67999999988765
No 22
>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=46.36 E-value=46 Score=28.86 Aligned_cols=98 Identities=13% Similarity=0.140 Sum_probs=54.6
Q ss_pred cCCCCCcHHHHHHHHHHHHHHHHHhcC-CCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhh
Q 028492 102 KSGKVLPKAYLKSARELVKTLRESLKE-DPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFY 180 (208)
Q Consensus 102 ksg~~LPk~Y~~dTr~VV~tLReaL~l-dp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhY 180 (208)
|--|-=|.++ ..+++++.+.|.. ||.+...+++..+...+.+.+.-..|+..-.-.....|-+.-.|++=|+..|
T Consensus 112 PH~Wldp~~~----~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~y 187 (266)
T cd01018 112 PHIWLSPANA----KIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMVYHPAWGYFARDY 187 (266)
T ss_pred CccCcCHHHH----HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEECchhHHHHHHc
Confidence 4467778888 4555555555553 7888888888887777777777766663211111112222223444444433
Q ss_pred hhc-----CCCCCCChHHHHHHHHHHHH
Q 028492 181 SKA-----GPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 181 ss~-----GpnrPLPeklK~RLlqEL~~ 203 (208)
.=- ++....+.+.-.+|.+.+++
T Consensus 188 gl~~~~~~~~~~eps~~~l~~l~~~ik~ 215 (266)
T cd01018 188 GLTQIPIEEEGKEPSPADLKRLIDLAKE 215 (266)
T ss_pred CCEEEecCCCCCCCCHHHHHHHHHHHHH
Confidence 211 24455556666666666654
No 23
>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=45.10 E-value=1.1e+02 Score=21.62 Aligned_cols=76 Identities=24% Similarity=0.225 Sum_probs=49.2
Q ss_pred HHHHHHhcCCC-CCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhc-C-----CCCCCChH
Q 028492 120 KTLRESLKEDP-KDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA-G-----PSAPLPGE 192 (208)
Q Consensus 120 ~tLReaL~ldp-~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~-G-----pnrPLPek 192 (208)
+.+++-|..|. .|+.-....-+.|++.|..|+.+--......+..-...+..|+..|++|+=.+ + ...++|.-
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 34555555533 34566777788888888888887655443456677778888999888876432 1 13466655
Q ss_pred HHH
Q 028492 193 VKS 195 (208)
Q Consensus 193 lK~ 195 (208)
++.
T Consensus 83 v~~ 85 (91)
T cd08054 83 VES 85 (91)
T ss_pred HHH
Confidence 543
No 24
>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=44.26 E-value=30 Score=27.28 Aligned_cols=36 Identities=11% Similarity=0.243 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCC--hHHHHHHHHHHHH
Q 028492 167 VELEKAIRSLASFYSKAGPSAPLP--GEVKSEILNDLDT 203 (208)
Q Consensus 167 ttM~TALNsLAGhYss~GpnrPLP--eklK~RLlqEL~~ 203 (208)
..|.|.+|-.-.||.+|+ ...+. +.-++|.++||.+
T Consensus 31 e~MvtvV~DwvnfYINYy-~~~~~GeqqeqdrAlqel~q 68 (89)
T PF09236_consen 31 EAMVTVVNDWVNFYINYY-KKQMTGEQQEQDRALQELQQ 68 (89)
T ss_dssp HHHHHHHHHHHHHHHHHH-HTT--SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH-HHHhcCChHHHHHHHHHHHH
Confidence 344445555555555544 22222 3334455555543
No 25
>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=44.21 E-value=18 Score=31.76 Aligned_cols=46 Identities=15% Similarity=0.203 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCchH-HHhhHHHHHHHHHHHHhhccC
Q 028492 111 YLKSARELVKTLRESLKEDPKDIAN-FRRNADSAKESIRDYLSNWRG 156 (208)
Q Consensus 111 Y~~dTr~VV~tLReaL~ldp~D~~~-~r~aa~~AKe~IndyvsrYRr 156 (208)
..+|-..+++.+-+.|..|+...+. ....+..+-+.+.||+.|||.
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 3445456777788888886654431 233444555678999999985
No 26
>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=43.91 E-value=16 Score=36.41 Aligned_cols=30 Identities=23% Similarity=0.151 Sum_probs=16.1
Q ss_pred hhhhHHHHHhhhhhHHHHHHhhcCCCCchhhhh
Q 028492 42 ASSRRHVISCSSTALVAILTFNCGLAPLPVQAE 74 (208)
Q Consensus 42 ~~sRr~~l~~~~~~~~a~~~~~~~~~p~~~~A~ 74 (208)
+.+||+||++.+++ ++.++|+..|.++|++
T Consensus 5 ~~~rr~~~~~~~~~---~~~~~~~~~~~~~~~~ 34 (587)
T TIGR01480 5 AFDRRRFLQGLASG---GAAAGLGLWATAAWAE 34 (587)
T ss_pred cccHHHHHHHHHHH---HHHHHhhccccchhhc
Confidence 56899999655432 3333444443344433
No 27
>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=43.59 E-value=94 Score=33.93 Aligned_cols=92 Identities=17% Similarity=0.197 Sum_probs=49.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHH--Hhhhhhc
Q 028492 106 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL--ASFYSKA 183 (208)
Q Consensus 106 ~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsL--AGhYss~ 183 (208)
..|..|++.|.++.+.... + |.+.+. +.+=.--..|.|-+..-...+.---.|.|.+-..-|+.| .|....|
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-GEEKAY--EIVVENTNKIADQIEEIQPIKDKLYTPKIEGADEKIRDLTYENAKKIY 612 (1213)
T ss_pred CCcccccCCHHHHHHHHhh---c-chhhhh--HHHHHHHHHHHHHhhcccccCCCCCCCCCCCHHHHHHHHHHHHHHHHc
Confidence 3677899999998887654 2 222211 111111222333332211221122234443344445444 4566677
Q ss_pred CCCCCCChHHHHHHHHHHHHHH
Q 028492 184 GPSAPLPGEVKSEILNDLDTAE 205 (208)
Q Consensus 184 GpnrPLPeklK~RLlqEL~~AE 205 (208)
|. |+|+.+++||..||+-..
T Consensus 613 g~--~l~~~v~~RLe~EL~~I~ 632 (1213)
T TIGR01405 613 GD--PLPEIVEQRIEKELKSII 632 (1213)
T ss_pred CC--CCcHHHHHHHHHHHHHHH
Confidence 63 689999999999998764
No 28
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=42.50 E-value=2.1e+02 Score=24.81 Aligned_cols=80 Identities=10% Similarity=0.163 Sum_probs=57.2
Q ss_pred HHHHHHHHHhcCCCCCchHHHhh-------------HHHHHHHHHHHHhhccCCCCCC------Ccc----------hH-
Q 028492 117 ELVKTLRESLKEDPKDIANFRRN-------------ADSAKESIRDYLSNWRGQKTVA------GEE----------SY- 166 (208)
Q Consensus 117 ~VV~tLReaL~ldp~D~~~~r~a-------------a~~AKe~IndyvsrYRr~~~V~------G~~----------SF- 166 (208)
+.++.+++.++..|... -...+ -+.|....+.|+..|-+++.+. |.. .|
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 44566777777756443 32222 3678889999999998888876 221 11
Q ss_pred ---------HHHHHHHHHHHhhhhhcCCCCCCChHHHHHHH
Q 028492 167 ---------VELEKAIRSLASFYSKAGPSAPLPGEVKSEIL 198 (208)
Q Consensus 167 ---------ttM~TALNsLAGhYss~GpnrPLPeklK~RLl 198 (208)
+..+.|++.|..+=..| |+.+.-++.+.||.
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 33578999999999997 99999999988764
No 29
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=41.57 E-value=13 Score=31.38 Aligned_cols=13 Identities=15% Similarity=0.240 Sum_probs=10.2
Q ss_pred hhhHHHHHhhhhh
Q 028492 43 SSRRHVISCSSTA 55 (208)
Q Consensus 43 ~sRr~~l~~~~~~ 55 (208)
++||.||..+..+
T Consensus 12 ~~RR~FL~~~~~~ 24 (178)
T PRK13474 12 MGRRQFMNLLTFG 24 (178)
T ss_pred ccHHHHHHHHHHH
Confidence 5899999966554
No 30
>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=40.17 E-value=24 Score=29.66 Aligned_cols=8 Identities=38% Similarity=0.659 Sum_probs=6.6
Q ss_pred hhhHHHHH
Q 028492 43 SSRRHVIS 50 (208)
Q Consensus 43 ~sRr~~l~ 50 (208)
.|||+||+
T Consensus 2 ~sRR~~L~ 9 (168)
T PF12318_consen 2 LSRRRLLA 9 (168)
T ss_pred CcHHHHHH
Confidence 48999993
No 31
>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=38.49 E-value=1.3e+02 Score=20.56 Aligned_cols=58 Identities=22% Similarity=0.424 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhh
Q 028492 110 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYS 181 (208)
Q Consensus 110 ~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYs 181 (208)
.|..+-...++-+.+ . ...+. .+--...|.+|+....... -|-+|+...+++|-.||.
T Consensus 21 ~Y~~~l~~f~~~~~~--~-~~~~~------~~i~~~~v~~f~~~~~~~~-----~s~~T~~~~~~alr~f~~ 78 (84)
T PF02899_consen 21 SYRRDLRRFIRWLEE--H-GIIDW------EDITEEDVRDFLEYLAKEG-----LSPSTINRRLSALRAFFR 78 (84)
T ss_dssp HHHHHHHHHHHHHHH--T-TS-CG------GG--HHHHHHHHHHHHCTT-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhh--h-hhhhh------hhhhhHHHHHHHHHHHccC-----CCHHHHHHHHHHHHHHHH
Confidence 566666666666655 1 11122 1224567889999887755 888999999999999985
No 32
>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=38.33 E-value=2.6 Score=37.72 Aligned_cols=30 Identities=20% Similarity=0.224 Sum_probs=21.2
Q ss_pred HHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcC
Q 028492 145 ESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAG 184 (208)
Q Consensus 145 e~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~G 184 (208)
++.++=+++|.+-.---|.+. ||-||++.+
T Consensus 133 ~~~~~~~~~~~pt~~~P~sPD----------LarHYkS~S 162 (221)
T PF08374_consen 133 ELEEDSMGKYLPTTFKPDSPD----------LARHYKSAS 162 (221)
T ss_pred ccCCCCcccccCCCCCCCCcc----------hhhhcccCC
Confidence 667788888865544444443 999999854
No 33
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=37.61 E-value=1.5e+02 Score=21.08 Aligned_cols=36 Identities=25% Similarity=0.332 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHhcC
Q 028492 169 LEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208 (208)
Q Consensus 169 M~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~AE~aL 208 (208)
...-|+.|......+ .+|+..|.+|++.+.++|..|
T Consensus 37 ~~~Il~~l~~~l~~~----~~~~~~k~~i~~~la~~e~rl 72 (89)
T PF08542_consen 37 ASDILKQLHEVLVES----DIPDSQKAEILKILAEIEYRL 72 (89)
T ss_dssp HHHHHHHHHHHHHTS----TSSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHh----hccHHHHHHHHHHHHHHhHHH
Confidence 345566666666663 789999999999999998653
No 34
>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=37.25 E-value=1.4e+02 Score=21.99 Aligned_cols=58 Identities=17% Similarity=0.129 Sum_probs=38.8
Q ss_pred HHHHHhcCCC-CCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhh
Q 028492 121 TLRESLKEDP-KDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 182 (208)
Q Consensus 121 tLReaL~ldp-~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss 182 (208)
.++.-|..|. .|++-.....+.|++.|..++.+.-.. .......+..|+..|.+|+=.
T Consensus 4 ~vK~~LrId~d~dD~li~~~i~aA~~~i~~~ig~~~~~----~~~~~~~~~~Avl~lv~~~Ye 62 (91)
T TIGR01560 4 EVKLSLRIDHDDDDELIKLMIAAAQDYIQSAIGTGVKD----SFDSKPLFKLACIKLVAHYYE 62 (91)
T ss_pred HHHhHhcCCCCccHHHHHHHHHHHHHHHHHHhCCCccc----ccccCHHHHHHHHHHHHHHHH
Confidence 3455555533 355566677888999999998875332 333445678899999998744
No 35
>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=35.79 E-value=25 Score=30.97 Aligned_cols=21 Identities=33% Similarity=0.281 Sum_probs=16.2
Q ss_pred hhhhhHHHHHhhhhhHHHHHH
Q 028492 41 AASSRRHVISCSSTALVAILT 61 (208)
Q Consensus 41 ~~~sRr~~l~~~~~~~~a~~~ 61 (208)
.-.+||.||+-.+.+||.+.+
T Consensus 20 ~~tsRRs~l~~lG~~l~g~a~ 40 (186)
T TIGR02659 20 GKTSRRGFIGRLGTALAGSAL 40 (186)
T ss_pred hccchHHHHHHHHHHHhhhhh
Confidence 367999999999887655544
No 36
>PRK09269 chorismate mutase; Provisional
Probab=35.31 E-value=1.5e+02 Score=25.70 Aligned_cols=64 Identities=14% Similarity=0.261 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHhc---CCCCCc-hHHHhhHHHHHHHHHHHHhhccCCCCCCC--cchHHHHHHHHHHHH
Q 028492 114 SARELVKTLRESLK---EDPKDI-ANFRRNADSAKESIRDYLSNWRGQKTVAG--EESYVELEKAIRSLA 177 (208)
Q Consensus 114 dTr~VV~tLReaL~---ldp~D~-~~~r~aa~~AKe~IndyvsrYRr~~~V~G--~~SFttM~TALNsLA 177 (208)
.=.+|++.+++--+ +||... .=|+...+.+|..-+.|+++|+.++.... -+.-.+++..|..|.
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 333222 33888899999999999999997655332 355557777766654
No 37
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.34 E-value=1.2e+02 Score=21.88 Aligned_cols=57 Identities=19% Similarity=0.318 Sum_probs=32.7
Q ss_pred chHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHh-hhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 133 IANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLAS-FYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 133 ~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAG-hYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
..+.++.-.-.+..|..|+.+|+... +..|-. .+..-.|..+|+++.++.|.+.+.+
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~G--------------~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREGG--------------IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHccc--------------HHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 33444455566889999999998644 111222 2222122333778888877766653
No 38
>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=33.66 E-value=2e+02 Score=23.65 Aligned_cols=66 Identities=20% Similarity=0.288 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCcchH-HHHHHHHHHHHhhhhhcC--CCCCCChHHHH-HHHHHHHHHHh
Q 028492 140 ADSAKESIRDYLSNWRGQKTVAGEESY-VELEKAIRSLASFYSKAG--PSAPLPGEVKS-EILNDLDTAEK 206 (208)
Q Consensus 140 a~~AKe~IndyvsrYRr~~~V~G~~SF-ttM~TALNsLAGhYss~G--pnrPLPeklK~-RLlqEL~~AE~ 206 (208)
.-.|-+.|+.|++.... |-+.|...| ..+..+++.+..|+..+. ++.-|.++.-+ .|.+.++++..
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 45666777777777544 556666665 556688888999999887 35668887666 77777766543
No 39
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=32.90 E-value=33 Score=34.11 Aligned_cols=61 Identities=11% Similarity=0.131 Sum_probs=32.2
Q ss_pred ccCCCCcCcCCCCCcHHHHHHHHHHH---HHHHHHhcC-CCCCchH-----HHhhHHHHHHHHHHHHhhccC
Q 028492 94 LFDPNEKTKSGKVLPKAYLKSARELV---KTLRESLKE-DPKDIAN-----FRRNADSAKESIRDYLSNWRG 156 (208)
Q Consensus 94 ~fdp~~~~ksg~~LPk~Y~~dTr~VV---~tLReaL~l-dp~D~~~-----~r~aa~~AKe~IndyvsrYRr 156 (208)
.=||+..+-.|+.|+|.+.- .+.+ +.|+.=+-- +++...+ -.+|-+...+.+++...+|-+
T Consensus 70 ~g~~~~p~n~g~~C~kG~~~--~~~~y~p~Rl~~Pl~R~~~rg~g~~~~iSWdEAl~~ia~~l~~i~~~~G~ 139 (759)
T PRK15488 70 QGNPKAKSFGTKVCARGGSG--HSLLYDPQRIVKPLKRVGERGEGKWQEISWDEAYQEIAAKLNAIKQQHGP 139 (759)
T ss_pred ECCCCCCCCCCccCccchhH--HHhhcCcchhccceeecCCCCCCCeEEeCHHHHHHHHHHHHHHHHHHhCC
Confidence 45777777789999997531 1111 122222211 1221112 345666667777777777743
No 40
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=32.88 E-value=31 Score=30.44 Aligned_cols=13 Identities=23% Similarity=0.279 Sum_probs=10.1
Q ss_pred hhhHHHHHhhhhh
Q 028492 43 SSRRHVISCSSTA 55 (208)
Q Consensus 43 ~sRr~~l~~~~~~ 55 (208)
.+||+||..++++
T Consensus 3 ~~RR~flk~~~~~ 15 (244)
T PRK14993 3 SSKRQFLQQLGVL 15 (244)
T ss_pred ccHHHHHHHHHHH
Confidence 5899999976543
No 41
>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=32.64 E-value=25 Score=30.47 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=9.6
Q ss_pred hhhHHHHHhhhh
Q 028492 43 SSRRHVISCSST 54 (208)
Q Consensus 43 ~sRr~~l~~~~~ 54 (208)
.+||+||++.+.
T Consensus 2 ~~rr~~l~~~~~ 13 (225)
T TIGR03149 2 CSRRNFLAGVGA 13 (225)
T ss_pred ccHHHHHHHHHH
Confidence 489999988754
No 42
>PRK15219 carbonic anhydrase; Provisional
Probab=32.49 E-value=20 Score=32.10 Aligned_cols=71 Identities=23% Similarity=0.205 Sum_probs=38.5
Q ss_pred hhhhhHHHHHhhhhhHHHHHHhhcCC---CCchhhhhcccCCCCccccccccchhcccCCCCcCcCCCCCcHHHHHH
Q 028492 41 AASSRRHVISCSSTALVAILTFNCGL---APLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKS 114 (208)
Q Consensus 41 ~~~sRr~~l~~~~~~~~a~~~~~~~~---~p~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~~ksg~~LPk~Y~~d 114 (208)
...+||++|.++.+...++ +.+++ +|..+.+..-...+. +.-.--.+|+.|++=|.++..|...+.+|...
T Consensus 7 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-~~~~p~~al~~L~~GN~rF~~~~~~~~~~~~~ 80 (245)
T PRK15219 7 NQPSRRAVLKAALAMTAAS--VIGLAGLGVPQISYAASLTKEER-DKMTPDQIIESLKQGNKRFRSGKPAQHDYLAQ 80 (245)
T ss_pred cchHHHHHHHHHHHHHHHh--hhhccccccchhhhhhccccccc-CCCCHHHHHHHHHHHHHHHHhcCcCCchhhHH
Confidence 3568999997665432222 22222 233222221111000 11122346899999999999998777777654
No 43
>PLN00033 photosystem II stability/assembly factor; Provisional
Probab=32.30 E-value=33 Score=32.46 Aligned_cols=40 Identities=13% Similarity=0.052 Sum_probs=29.8
Q ss_pred cccchhhhHhhhhcccCcccCCchhhhhhhHHHHHhhhhh
Q 028492 16 PLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTA 55 (208)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~sRr~~l~~~~~~ 55 (208)
+.....-.+..+..++++...+.......||+|+...++.
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 52 (398)
T PLN00033 13 ASNNRAAFSTVSKTVSSNVNELSSNSSENRRSFLRQTATA 52 (398)
T ss_pred ccccccccccccceeecCCccccccccchhhhHHHhhhHh
Confidence 3333444455667788888888899999999999887665
No 44
>PF13333 rve_2: Integrase core domain
Probab=31.39 E-value=56 Score=21.92 Aligned_cols=25 Identities=16% Similarity=0.505 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHHHHhhccCCCCCCCc
Q 028492 138 RNADSAKESIRDYLSNWRGQKTVAGE 163 (208)
Q Consensus 138 ~aa~~AKe~IndyvsrYRr~~~V~G~ 163 (208)
...+++++.|.+||-.| +..+..|+
T Consensus 18 ~t~eel~~~I~~YI~~y-N~~Rl~~l 42 (52)
T PF13333_consen 18 KTREELKQAIDEYIDYY-NNERLKGL 42 (52)
T ss_pred chHHHHHHHHHHHHHHh-ccCCCCCc
Confidence 35789999999999999 55555443
No 45
>PRK00035 hemH ferrochelatase; Reviewed
Probab=31.21 E-value=1.4e+02 Score=26.73 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=36.7
Q ss_pred HHHHHHHhhccCCCCCCCcchHHHH--------HHHHHHHHhhhhhcCCCCCCCh---HHHHHHHHHH
Q 028492 145 ESIRDYLSNWRGQKTVAGEESYVEL--------EKAIRSLASFYSKAGPSAPLPG---EVKSEILNDL 201 (208)
Q Consensus 145 e~IndyvsrYRr~~~V~G~~SFttM--------~TALNsLAGhYss~GpnrPLPe---klK~RLlqEL 201 (208)
+.|..|+.+++.++.+-+.+.+.-- ..=+..++.+|...|-..||.. +.-+.|.+.|
T Consensus 20 ~~v~~fl~~~~~d~~v~~~~~~~~~~~l~~~i~~~r~~~~~~~Y~~ig~gSPl~~~t~~q~~~L~~~l 87 (333)
T PRK00035 20 EDVRPFLKNFLSDRRVIDLPRPLWQPLLAGIILPERLPKVAKHYASIGGGSPLNVITRRQAEALQAEL 87 (333)
T ss_pred HHHHHHHHHHcCCCCcccCCHHHHHHHHHHHhhhhhHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHH
Confidence 5677888888888888877764321 2233467788888887778774 3334444444
No 46
>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=31.04 E-value=22 Score=29.90 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=14.4
Q ss_pred hhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492 44 SRRHVISCSSTALVAILTFNCGLAP 68 (208)
Q Consensus 44 sRr~~l~~~~~~~~a~~~~~~~~~p 68 (208)
+||+||..+..+ +..+.....++|
T Consensus 1 ~RR~fl~~~~~~-~~~~~~~~~~~p 24 (174)
T TIGR01416 1 TRRDFLYAATGA-VGAVGAAAAAVP 24 (174)
T ss_pred ChHHHHHHHHHH-HHHHHHHHHHHH
Confidence 699999877654 344444444445
No 47
>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=30.31 E-value=50 Score=26.42 Aligned_cols=64 Identities=14% Similarity=0.303 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHH-HHHHHHHhhhhhcCCCC
Q 028492 110 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE-KAIRSLASFYSKAGPSA 187 (208)
Q Consensus 110 ~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~-TALNsLAGhYss~Gpnr 187 (208)
.|.+...++++-||..+.+|.+=. .+ .+.+.+..++|+..+. |+..| .-|+.|-.||..+|--.
T Consensus 60 ~~~~~~~dl~~~ir~i~g~d~~l~-tr---~erv~~~~~~~l~~~~----------~~~~Q~~~L~~i~~~~~~~G~~~ 124 (164)
T PF08463_consen 60 TYEAIDADLFDFIRHILGLDTPLL-TR---RERVEEAFSKFLNQHQ----------FNAEQREFLERILDYYAQNGIIE 124 (164)
T ss_pred hcccccCCHHHHHHHHHhcCCCCC-CH---HHHHHHHHHHHHHhcC----------CCHHHHHHHHHHHHHHHHhCccc
Confidence 555566778899999988841111 12 2333335588886653 66666 77899999999988443
No 48
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=29.82 E-value=1e+02 Score=27.47 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHhcC
Q 028492 166 YVELEKAIRSLASFYSKA--GPSAPLPGEVKSEILNDLDTAEKFL 208 (208)
Q Consensus 166 FttM~TALNsLAGhYss~--GpnrPLPeklK~RLlqEL~~AE~aL 208 (208)
+..+..|++. -|+...+ -|-.||+++.|++|.+.|+...+.|
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 4665432 1344589999999999998877654
No 49
>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=29.47 E-value=1.9e+02 Score=21.55 Aligned_cols=51 Identities=27% Similarity=0.469 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 140 ADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 140 a~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
.+..|+.+++.+.. ++.. ..+|.++...|---| ..-+|+.+|+.|++...+
T Consensus 33 ~d~vr~~~re~i~~-~g~~----~~~~~~l~~~i~P~A--------r~~VP~~vk~ell~~Ir~ 83 (86)
T PF10163_consen 33 RDEVRQLCREIIRE-RGID----NLTFEDLLEEITPKA--------RAMVPDEVKKELLQRIRA 83 (86)
T ss_dssp HHHHHHHHHHHHHH-H-TT----TSBHHHHHHHHHHHH--------HHCS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHh-hCCC----CCCHHHHHHHHHHHH--------HHHCCHHHHHHHHHHHHH
Confidence 34555555555555 3333 457777776665433 567999999999988765
No 50
>smart00167 VPS9 Domain present in VPS9. Domain present in yeast vacuolar sorting protein 9 and other proteins.
Probab=29.31 E-value=62 Score=25.77 Aligned_cols=35 Identities=17% Similarity=0.350 Sum_probs=27.5
Q ss_pred HHHHHHHhhccCCCCCCCcchH--HHHHHHHHHHHhh
Q 028492 145 ESIRDYLSNWRGQKTVAGEESY--VELEKAIRSLASF 179 (208)
Q Consensus 145 e~IndyvsrYRr~~~V~G~~SF--ttM~TALNsLAGh 179 (208)
.+--.||.+||......|+..| |+++.|+.-+-.+
T Consensus 66 ~sn~~yI~~f~~~~~l~gE~gY~lT~l~aAv~fi~~l 102 (117)
T smart00167 66 LLNAEYMEEFLEPSLLTGEGGYYLTSLSAALALIKGL 102 (117)
T ss_pred HHHHHHHHHHCCccccccHHHHHHHHHHHHHHHHHHC
Confidence 3446899999988888999875 8889998766544
No 51
>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily. Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.
Probab=29.11 E-value=2.5e+02 Score=28.40 Aligned_cols=87 Identities=17% Similarity=0.166 Sum_probs=57.0
Q ss_pred hcccCCCCcCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHH
Q 028492 92 KSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEK 171 (208)
Q Consensus 92 ~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~T 171 (208)
--.|||...+.|..--|=.|+.+..+|++.+-..+.. ..+.+.|++.+..+-..+-.-+-.++.. +||.++..
T Consensus 235 ~~~f~~~~p~~S~~~NPl~~~~~~~eva~~i~~ll~~-~g~~~~f~~~a~~~l~~~~~alv~~~~~------~s~~~i~~ 307 (634)
T TIGR03743 235 FYYFHPAFPEISVRYNPLGNFSRISEVASRIAQLLPG-EGESAAFKEFAWRFVNIVARGLVYIGQR------PSYKLILR 307 (634)
T ss_pred EEEEecCCCCcCcCcChhhhcCChHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHHHHHhccC------CCHHHHHH
Confidence 4578988877777777888888888999998888875 3355566555554444444444344322 57777776
Q ss_pred HHH---------HHHhhhhhcCC
Q 028492 172 AIR---------SLASFYSKAGP 185 (208)
Q Consensus 172 ALN---------sLAGhYss~Gp 185 (208)
=++ .+..+|..++|
T Consensus 308 ~i~~~i~~L~~~~~~~~~~~~~~ 330 (634)
T TIGR03743 308 YVESGIEPLLEKYLEKFFTQHYP 330 (634)
T ss_pred HHhccHHHHHHHHHHHHHHhhCc
Confidence 444 25667777654
No 52
>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=28.75 E-value=50 Score=29.19 Aligned_cols=97 Identities=12% Similarity=0.134 Sum_probs=51.4
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccC-------CCCCCCcchHHHHHHHHHHH
Q 028492 104 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG-------QKTVAGEESYVELEKAIRSL 176 (208)
Q Consensus 104 g~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr-------~~~V~G~~SFttM~TALNsL 176 (208)
-|-=|.++.+-+..+.+.|.+ +||.+...+++..+...+.+++..++|+. ..-+..-++|.=+-..++-=
T Consensus 123 iWldp~n~~~~a~~I~~~L~~---~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Yl~~~~gl~ 199 (286)
T cd01019 123 LWLSPENAAEVAQAVAEKLSA---LDPDNAATYAANLEAFNARLAELDATIKERLAPVKTKPFFVFHDAYGYFEKRYGLT 199 (286)
T ss_pred cCCCHHHHHHHHHHHHHHHHH---HCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHHHHcCCc
Confidence 477788885554444444442 47888878877777777777776666653 22334444444433332110
Q ss_pred HhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 177 ASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 177 AGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
--.+..-.+......+.-.+|.+.+++
T Consensus 200 ~~~~~~~~~~~eps~~~l~~l~~~ik~ 226 (286)
T cd01019 200 QAGVFTIDPEIDPGAKRLAKIRKEIKE 226 (286)
T ss_pred eeeeecCCCCCCCCHHHHHHHHHHHHH
Confidence 000111123445555555566665543
No 53
>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=27.25 E-value=3.3e+02 Score=26.18 Aligned_cols=82 Identities=23% Similarity=0.445 Sum_probs=45.2
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHH---------HHHhhccCCCCCCCcchHHHHHHHHHHH
Q 028492 106 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIR---------DYLSNWRGQKTVAGEESYVELEKAIRSL 176 (208)
Q Consensus 106 ~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~In---------dyvsrYRr~~~V~G~~SFttM~TALNsL 176 (208)
.+|..|-+ .+..+.+-........|.++|.+|.+.+....+ +-+..-+-..-......|-.|-.| |
T Consensus 222 ~~p~~~~e--k~~f~~~i~~~~~~~~~eeNf~EA~~~~~~~~~~~~i~~~v~~~~~~~~~~~~~~~~~~fwi~~~a---l 296 (425)
T cd01493 222 QLPSTYKE--KKEFRDLVRSLMRSNEDEENFEEAIKAVNKALNRTKIPSSVEEIFNDDRCENLTSQSSSFWIMARA---L 296 (425)
T ss_pred CCCCCHHH--HHHHHHHHHHhcccCCCccchHHHHHHHHHhhCCCCCcHHHHHHHhchhcccCCCCCchHHHHHHH---H
Confidence 37877654 222333222233213577888888877665443 333333322223345668888655 5
Q ss_pred Hhhhhh-cCCCCCCChHH
Q 028492 177 ASFYSK-AGPSAPLPGEV 193 (208)
Q Consensus 177 AGhYss-~GpnrPLPekl 193 (208)
-.||.. +| .-|||..+
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 65 67887643
No 54
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=26.92 E-value=49 Score=35.10 Aligned_cols=17 Identities=29% Similarity=0.495 Sum_probs=13.6
Q ss_pred cCCCCcCcCCCCCcHHH
Q 028492 95 FDPNEKTKSGKVLPKAY 111 (208)
Q Consensus 95 fdp~~~~ksg~~LPk~Y 111 (208)
=||+...-.|+.|+|..
T Consensus 79 g~~~~Pvn~G~lC~KG~ 95 (1009)
T TIGR01553 79 GDPDHPINRGSLCPKGA 95 (1009)
T ss_pred CCCCCCCCCCccCHhHH
Confidence 47777777899999976
No 55
>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=26.91 E-value=1.1e+02 Score=25.26 Aligned_cols=65 Identities=15% Similarity=0.235 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHhc-C-CCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHH
Q 028492 112 LKSARELVKTLRESLK-E-DPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL 176 (208)
Q Consensus 112 ~~dTr~VV~tLReaL~-l-dp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsL 176 (208)
.+++..-|-.+|.... + ++.+..++.++....-+.++..+.--...|.......|.+|++.|..+
T Consensus 64 E~~~l~~v~~~R~~~~~~~~~~~~~~~~~~~~~l~~al~~l~~~~e~yP~Lka~~~~~~l~~~l~~~ 130 (186)
T PF04011_consen 64 EKETLTKVTKARSQANNLSDSADIQEFQQAEAELSQALSRLLAVVENYPELKADENFQQLMAQLEET 130 (186)
T ss_dssp -HHHHHHHHHHHHHHH---H--SHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHH
Confidence 3445555666666666 2 345666777788888888887776666778999999999998877644
No 56
>PF14461 Prok-E2_B: Prokaryotic E2 family B
Probab=26.87 E-value=1.1e+02 Score=24.14 Aligned_cols=57 Identities=14% Similarity=0.094 Sum_probs=30.8
Q ss_pred hhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCC
Q 028492 91 IKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTV 160 (208)
Q Consensus 91 ~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V 160 (208)
..=++|+ +-...-+..-..+ +++++.....|+..+.+.. -++.+.||.+.|.+...+
T Consensus 74 ~LCl~~~-~~~~D~~~P~~~~----~~~l~~a~~lL~~~~~~~~--------~~d~~~Ef~sYW~~~~~~ 130 (133)
T PF14461_consen 74 KLCLLDE-ELVLDPWDPEGII----ADCLERAIRLLEDGLSGDN--------EDDFADEFQSYWNRQCDV 130 (133)
T ss_pred eEEEecC-CcccCccCHHHHH----HHHHHHHHHHHHHhhcCCc--------hHHHHHHHHHHHhhcccc
Confidence 3445555 3333333333333 4445555555553233332 567889999999886654
No 57
>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=26.67 E-value=3e+02 Score=21.65 Aligned_cols=66 Identities=12% Similarity=0.102 Sum_probs=36.6
Q ss_pred CCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q 028492 130 PKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILND 200 (208)
Q Consensus 130 p~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqE 200 (208)
|.+...+.++.+.+-+.|.+.+...+........+. ..|.-||..|.=-+=..-+|++.|.++.++
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 555556666666666666555444443332222222 567777777776111233777777777665
No 58
>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=26.66 E-value=61 Score=27.03 Aligned_cols=49 Identities=20% Similarity=0.321 Sum_probs=33.8
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhcc
Q 028492 104 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWR 155 (208)
Q Consensus 104 g~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYR 155 (208)
-|-=|.++..-+..+.+.|.+ +||.+...+++..+...+.+++--.+|+
T Consensus 110 ~Wldp~~~~~~a~~I~~~L~~---~dP~~~~~y~~N~~~~~~~l~~l~~~~~ 158 (203)
T cd01145 110 VWLDPNNAPALAKALADALIE---LDPSEQEEYKENLRVFLAKLNKLLREWE 158 (203)
T ss_pred eecCHHHHHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 388888885555555555432 3788888888877777777777666665
No 59
>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=26.52 E-value=1e+02 Score=26.21 Aligned_cols=48 Identities=29% Similarity=0.324 Sum_probs=32.8
Q ss_pred HHHhhHHHHHHHHHHHHhhccC--------CCCCCCcchHHHHHHHHHHHHhhhhh
Q 028492 135 NFRRNADSAKESIRDYLSNWRG--------QKTVAGEESYVELEKAIRSLASFYSK 182 (208)
Q Consensus 135 ~~r~aa~~AKe~IndyvsrYRr--------~~~V~G~~SFttM~TALNsLAGhYss 182 (208)
.+......-+..+++||.+.|. ...-....|+..|....|.|-.-|++
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 5566788888888888888888 33344566788888888888888876
No 60
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=26.49 E-value=2.2e+02 Score=31.88 Aligned_cols=92 Identities=20% Similarity=0.244 Sum_probs=49.8
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHH--Hhhhhhc
Q 028492 106 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL--ASFYSKA 183 (208)
Q Consensus 106 ~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsL--AGhYss~ 183 (208)
..|..|+..|.++.+.... + |.+.. .+.+=.--..|.+-+......+.---.|.|.+-..-|+.| .|-...|
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-GEELA--KEIVVENTNKIADLIEEIEPIKDKLYTPKIEGAEEEIRELTYKKAHEIY 837 (1437)
T ss_pred cCCccccCCHHHHHHHhhh---c-chhhh--HHHHHHHHHHHHHhcceecccCCCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 3577899999888876653 2 22111 1112222223333333222222222233443344445544 3555667
Q ss_pred CCCCCCChHHHHHHHHHHHHHH
Q 028492 184 GPSAPLPGEVKSEILNDLDTAE 205 (208)
Q Consensus 184 GpnrPLPeklK~RLlqEL~~AE 205 (208)
| .|||+.+++||.+||+-..
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 3689999999999998764
No 61
>COG3211 PhoX Predicted phosphatase [General function prediction only]
Probab=26.06 E-value=40 Score=34.38 Aligned_cols=20 Identities=35% Similarity=0.454 Sum_probs=13.9
Q ss_pred hhhhHHHHHhhhhhHHHHHHhh
Q 028492 42 ASSRRHVISCSSTALVAILTFN 63 (208)
Q Consensus 42 ~~sRr~~l~~~~~~~~a~~~~~ 63 (208)
+.+||+||.+++++ ++++++
T Consensus 20 ~lsRR~fl~gsaa~--~aia~g 39 (616)
T COG3211 20 ALSRRKFLKGSAAA--AAIALG 39 (616)
T ss_pred hhhhhhhhhhhHHH--HHHHhc
Confidence 79999999975443 444444
No 62
>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=25.80 E-value=4e+02 Score=23.65 Aligned_cols=84 Identities=23% Similarity=0.411 Sum_probs=43.5
Q ss_pred cCcCCCC----CcHHHHHHHH-HHH-HHHHH----HhcCC-----C-----CCchHHHhhHHHHHH-HHHHHHhhccC--
Q 028492 100 KTKSGKV----LPKAYLKSAR-ELV-KTLRE----SLKED-----P-----KDIANFRRNADSAKE-SIRDYLSNWRG-- 156 (208)
Q Consensus 100 ~~ksg~~----LPk~Y~~dTr-~VV-~tLRe----aL~ld-----p-----~D~~~~r~aa~~AKe-~IndyvsrYRr-- 156 (208)
+.++|+. +|+-|..+.- +++ ..+.. ....+ . .++....+..+..++ =.+||+..|+.
T Consensus 192 ~~~s~~~l~~~Ipg~yT~~G~~~~~~~~~~~~~~~~~~e~~WVlg~~~~~~~~~~~~~~L~~~v~~~Y~~DY~~~W~~~L 271 (312)
T PF06761_consen 192 TRKSGKPLSDGIPGLYTRQGFEDYFLPALPKLAEALRSEDDWVLGDSEDSDASEADLEQLRQDVRKLYFQDYIAAWDDFL 271 (312)
T ss_pred ecCCCcccccCCChhhhHHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556644 9998887765 222 22222 22222 1 122233334444443 36899999994
Q ss_pred -CCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCC
Q 028492 157 -QKTVAGEESYVELEKAIRSLASFYSKAGPSAPL 189 (208)
Q Consensus 157 -~~~V~G~~SFttM~TALNsLAGhYss~GpnrPL 189 (208)
+=++..-.+..+....++.|+ +|+.||
T Consensus 272 ~~i~v~~~~~l~~a~~~l~~Ls------~~~SPl 299 (312)
T PF06761_consen 272 NDIRVQPFADLSQAVDQLRLLS------SPDSPL 299 (312)
T ss_pred hcCcccCCCCHHHHHHHHHHHc------CCCCHH
Confidence 445555555555555555554 355565
No 63
>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=25.72 E-value=68 Score=27.88 Aligned_cols=95 Identities=16% Similarity=0.237 Sum_probs=49.7
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcC-CCCCchHHHhhHHHHHHHHHHHHhh-------ccCCCCCCCcchHHHHHHHHH--
Q 028492 105 KVLPKAYLKSARELVKTLRESLKE-DPKDIANFRRNADSAKESIRDYLSN-------WRGQKTVAGEESYVELEKAIR-- 174 (208)
Q Consensus 105 ~~LPk~Y~~dTr~VV~tLReaL~l-dp~D~~~~r~aa~~AKe~Indyvsr-------YRr~~~V~G~~SFttM~TALN-- 174 (208)
|-=|.++ ..+++.+.++|.. ||.+...+++..+...+.+.+--.. +.+.+-+..-+.|.-+...+.
T Consensus 98 Wldp~n~----~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~yGl~ 173 (264)
T cd01020 98 WYDPETM----SKVANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIAELSAKYKGAPVAATEPVFDYLLDALGMK 173 (264)
T ss_pred ecCHhHH----HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEeCchHHHHHHHCCCc
Confidence 8888888 5566666666664 7888766666666655555444444 433334444444444333221
Q ss_pred HHH-hhhhh-cCCCCCCChHHHHHHHHHHHH
Q 028492 175 SLA-SFYSK-AGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 175 sLA-GhYss-~GpnrPLPeklK~RLlqEL~~ 203 (208)
.++ .+|.. ..+-...+.+.-.+|.+.+++
T Consensus 174 ~~~~~~~~~~~~~~~~ps~~~l~~l~~~ik~ 204 (264)
T cd01020 174 ERTPKGYTATTESETEPSPADIAAFQNAIKN 204 (264)
T ss_pred ccCHHHHHhhhcCCCCCCHHHHHHHHHHHHh
Confidence 110 01111 113455566666666666554
No 64
>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=25.65 E-value=1.5e+02 Score=28.63 Aligned_cols=68 Identities=21% Similarity=0.284 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHhcCCC---CCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCC
Q 028492 112 LKSARELVKTLRESLKEDP---KDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAP 188 (208)
Q Consensus 112 ~~dTr~VV~tLReaL~ldp---~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrP 188 (208)
-..+.++.+.|++-|..-. +|+-.--+.+.+-.+.+|.||.-| =+|++-++..+...|
T Consensus 354 C~~~~~~T~~L~~rLs~ik~~~~ep~~~~~~~~~fwe~~~~Fiks~-------------------i~l~~~iK~~~~~~~ 414 (445)
T PF10428_consen 354 CNSAIDQTERLKSRLSTIKNQLKEPGGGIREQKEFWEDCNSFIKSW-------------------ISLLAKIKEIMKDLP 414 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccCCCCCccccHHHHHHHHHHHHHH-------------------HHHHHHHHHHhccCC
Confidence 3456666666666555411 121011123455567777777733 335556666677899
Q ss_pred CChHHHHHHH
Q 028492 189 LPGEVKSEIL 198 (208)
Q Consensus 189 LPeklK~RLl 198 (208)
||.++|.++-
T Consensus 415 l~~dvr~~L~ 424 (445)
T PF10428_consen 415 LPPDVRARLR 424 (445)
T ss_pred CCHHHHHHHH
Confidence 9999998763
No 65
>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=25.60 E-value=3.4e+02 Score=21.45 Aligned_cols=63 Identities=16% Similarity=0.154 Sum_probs=42.9
Q ss_pred CCchHHHhhHHHHHHHHHHHH-hhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCC--ChHHHHHHHH
Q 028492 131 KDIANFRRNADSAKESIRDYL-SNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL--PGEVKSEILN 199 (208)
Q Consensus 131 ~D~~~~r~aa~~AKe~Indyv-srYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPL--PeklK~RLlq 199 (208)
.|.....++.+.|-..|+.|+ +||. -|. ...=..+....--+|-||-.- +++. ++.+++|-.+
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 467789999999999999999 6776 232 122234667777788888752 4444 7776665443
No 66
>cd03411 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=25.47 E-value=2.6e+02 Score=22.60 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=32.2
Q ss_pred HHHHHHHhhccCCCCCCCcchHHHHHHHH---------HHHHhhhhhcCCCCCC---ChHHHHHHHHHHHH
Q 028492 145 ESIRDYLSNWRGQKTVAGEESYVELEKAI---------RSLASFYSKAGPSAPL---PGEVKSEILNDLDT 203 (208)
Q Consensus 145 e~IndyvsrYRr~~~V~G~~SFttM~TAL---------NsLAGhYss~GpnrPL---PeklK~RLlqEL~~ 203 (208)
+.|..|+.+-+.++.|-..+.+. +.-| ..++.+|.+.|-..|| .++..+.|.+.|++
T Consensus 15 ~~v~~yL~~~~~d~~vi~~p~~~--~~~l~~~I~~~r~~k~~~~Y~~ig~~SPL~~~t~~q~~~l~~~L~~ 83 (159)
T cd03411 15 EDVRPFLKNFLSDRRVIELPRPL--RPILAGIILPRRPPKVAKNYKKIGGGSPLNEITRAQAEALEKALDE 83 (159)
T ss_pred HHHHHHHHHHcCCCCcccCCHHH--HHHHHHHhcccccHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhc
Confidence 34555555555555554444442 2222 4567888888766676 45555566666653
No 67
>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=25.47 E-value=2.5e+02 Score=20.41 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=34.6
Q ss_pred HHHHHHHHHHh-cCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCC
Q 028492 116 RELVKTLRESL-KEDPKDIANFRRNADSAKESIRDYLSNWRGQKTV 160 (208)
Q Consensus 116 r~VV~tLReaL-~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V 160 (208)
..+++++-+-| .+.+.-.+.....-..++++|..|...|-.+..-
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 46788888888 7766666777788899999999999998765443
No 68
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=25.15 E-value=1.5e+02 Score=26.69 Aligned_cols=96 Identities=14% Similarity=0.103 Sum_probs=52.5
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhc-CCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhh--
Q 028492 104 GKVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFY-- 180 (208)
Q Consensus 104 g~~LPk~Y~~dTr~VV~tLReaL~-ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhY-- 180 (208)
=|-=|.+.. .+++++.+.|. +||.+...+++..+...+.+++--.+||..-.-.....|-+.-.|++=|+.-|
T Consensus 147 iWldp~~~~----~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~i~~H~af~Yf~~~ygl 222 (311)
T PRK09545 147 IWLSPEIAR----ATAVAIHDKLVELMPQSKAKLDANLKDFEAQLAQTDKQIGNQLAPVKGKGYFVFHDAYGYFEKHYGL 222 (311)
T ss_pred ccCCHHHHH----HHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEECchHHHHHHhCCC
Confidence 455566664 45555555554 48888888888887777777776666663211111122323333444444333
Q ss_pred -----hhcCCCCCCChHHHHHHHHHHHH
Q 028492 181 -----SKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 181 -----ss~GpnrPLPeklK~RLlqEL~~ 203 (208)
..-+|....+.+.-.+|.+.+++
T Consensus 223 ~~~~~~~~~~~~eps~~~l~~l~~~ik~ 250 (311)
T PRK09545 223 TPLGHFTVNPEIQPGAQRLHEIRTQLVE 250 (311)
T ss_pred ceeeeeccCCCCCCCHHHHHHHHHHHHH
Confidence 11234555666666666666553
No 69
>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=25.13 E-value=38 Score=26.29 Aligned_cols=22 Identities=14% Similarity=0.474 Sum_probs=19.1
Q ss_pred HHHHHHHHhhccCCC-CCCCcch
Q 028492 144 KESIRDYLSNWRGQK-TVAGEES 165 (208)
Q Consensus 144 Ke~IndyvsrYRr~~-~V~G~~S 165 (208)
|+.|++||.+|++.. .|.|.++
T Consensus 33 r~~~d~~i~~y~~~~~lVDGvPa 55 (85)
T PF07240_consen 33 RQRIDRFIRRYKEENNLVDGVPA 55 (85)
T ss_pred HHHHHHHHHHHHHHhhcccCcCC
Confidence 677999999999888 8888876
No 70
>PRK09898 hypothetical protein; Provisional
Probab=24.99 E-value=28 Score=29.51 Aligned_cols=14 Identities=14% Similarity=0.183 Sum_probs=11.2
Q ss_pred hhhhHHHHHhhhhh
Q 028492 42 ASSRRHVISCSSTA 55 (208)
Q Consensus 42 ~~sRr~~l~~~~~~ 55 (208)
..+||.||..++.+
T Consensus 12 ~~~RR~flk~~~~~ 25 (208)
T PRK09898 12 GLTRLEFLRISGKG 25 (208)
T ss_pred chhHHHHHHhhcch
Confidence 48999999987643
No 71
>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=24.27 E-value=41 Score=27.88 Aligned_cols=36 Identities=25% Similarity=0.487 Sum_probs=23.0
Q ss_pred HHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChH
Q 028492 147 IRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGE 192 (208)
Q Consensus 147 IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPek 192 (208)
++=|...-|+ |++.+..+|+-+|.||.++- -|.||.
T Consensus 59 Lkly~qGLrg--------nlT~L~g~L~~mAshy~~~C--PptpEt 94 (122)
T PF01109_consen 59 LKLYKQGLRG--------NLTRLKGPLTMMASHYKQHC--PPTPET 94 (122)
T ss_dssp HHHHHHT--G--------GGGGGHHHHHHHHHHHHHCS-------S
T ss_pred HHHHHHHccc--------cchhhhhhHHHHHHHhccCC--CCCCCc
Confidence 4446666655 78999999999999999964 455553
No 72
>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=24.19 E-value=1.6e+02 Score=24.42 Aligned_cols=58 Identities=19% Similarity=0.318 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhhcc--CCCCCCC-cchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 140 ADSAKESIRDYLSNWR--GQKTVAG-EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 140 a~~AKe~IndyvsrYR--r~~~V~G-~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
..++|+-+++++...| ....++| .++...|....+.+...|.. ||++.|+.|.+.|=.
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 4455555555555443 1122223 34455555555555566655 899999999988744
No 73
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=24.17 E-value=33 Score=23.20 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=14.0
Q ss_pred hhhhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492 42 ASSRRHVISCSSTALVAILTFNCGLAP 68 (208)
Q Consensus 42 ~~sRr~~l~~~~~~~~a~~~~~~~~~p 68 (208)
.++||+||--...+ +.+++..+.+.|
T Consensus 5 dm~RR~lmN~ll~G-ava~~a~~~lyP 30 (39)
T PF08802_consen 5 DMSRRQLMNLLLGG-AVAVPAGGMLYP 30 (39)
T ss_dssp -HHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHh-hHHHHHHHHhhh
Confidence 47899987665444 334444443333
No 74
>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=23.78 E-value=2.4e+02 Score=25.00 Aligned_cols=98 Identities=15% Similarity=0.234 Sum_probs=56.3
Q ss_pred cCCCCCcHHHHHHHHHHHHHHHHHhc-CCCCCchHHHhhHHHHHHHHHHHHhhccCC---------CCCCCcchHHHHHH
Q 028492 102 KSGKVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRGQ---------KTVAGEESYVELEK 171 (208)
Q Consensus 102 ksg~~LPk~Y~~dTr~VV~tLReaL~-ldp~D~~~~r~aa~~AKe~IndyvsrYRr~---------~~V~G~~SFttM~T 171 (208)
|--|-=|.++.. +++.+.+.|. +||.+...+++..+...+.+++.-..|+.. +-+..-++|.=+..
T Consensus 117 PH~Wldp~~~~~----~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~~~v~~H~af~Y~~~ 192 (287)
T cd01137 117 PHAWMSPKNAII----YVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRKLVTSEGAFSYFAK 192 (287)
T ss_pred CCcCcCHHHHHH----HHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCEEEEecccHHHHHH
Confidence 445888888854 4455555553 489888888888888777777777766631 22334445544433
Q ss_pred HHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 172 AIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 172 ALNsLAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
.++-=--.....+|....+.+.-.+|.+.+++
T Consensus 193 ~yGl~~~~~~~~~~~~eps~~~l~~l~~~ik~ 224 (287)
T cd01137 193 AYGLKEAYLWPINTEEEGTPKQVATLIEQVKK 224 (287)
T ss_pred HcCCeEeecccCCCCCCCCHHHHHHHHHHHHH
Confidence 32111001123345566666666667666654
No 75
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=23.00 E-value=76 Score=32.86 Aligned_cols=30 Identities=27% Similarity=0.469 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q 028492 167 VELEKAIRSLASFYSKAGPSAPLPGEVKSEILN 199 (208)
Q Consensus 167 ttM~TALNsLAGhYss~GpnrPLPeklK~RLlq 199 (208)
..-..+|..+|+||.+ | -|||+++-+++++
T Consensus 512 ~~~p~vL~~~a~Hy~T-G--e~lP~~ll~k~la 541 (683)
T COG0339 512 CWEPEVLAKYARHYQT-G--EPLPKELLDKMLA 541 (683)
T ss_pred hcCHHHHHHHHHhhcc-C--CcCHHHHHHHHHH
Confidence 3345789999999998 5 8999998888774
No 76
>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=22.03 E-value=77 Score=27.68 Aligned_cols=96 Identities=13% Similarity=0.185 Sum_probs=50.1
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhc-CCCCCchHHHhhHHHHHHHHHHHHhhccC-------CCCCCCcchHHHHHHHHHH
Q 028492 104 GKVLPKAYLKSARELVKTLRESLK-EDPKDIANFRRNADSAKESIRDYLSNWRG-------QKTVAGEESYVELEKAIRS 175 (208)
Q Consensus 104 g~~LPk~Y~~dTr~VV~tLReaL~-ldp~D~~~~r~aa~~AKe~IndyvsrYRr-------~~~V~G~~SFttM~TALNs 175 (208)
-|-=|..+. .+++.+.+.|. +||.+...+++..+...+.+++.-.+|+. .+-+..-++|.=+....+-
T Consensus 115 ~Wldp~~~~----~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~~gl 190 (282)
T cd01017 115 VWLSPVLAI----QQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKAKGKTFVTQHAAFGYLARRYGL 190 (282)
T ss_pred cccCHHHHH----HHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEEecccHHHHHHHCCC
Confidence 476777774 45555555554 47888877777777777776666666543 3334444444433332210
Q ss_pred HHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492 176 LASFYSKAGPSAPLPGEVKSEILNDLDT 203 (208)
Q Consensus 176 LAGhYss~GpnrPLPeklK~RLlqEL~~ 203 (208)
=--......+....+.+.-.+|.+.+++
T Consensus 191 ~~~~~~~~~~~~eps~~~l~~l~~~ik~ 218 (282)
T cd01017 191 KQIAIVGVSPEVEPSPKQLAELVEFVKK 218 (282)
T ss_pred eEEecccCCCCCCCCHHHHHHHHHHHHH
Confidence 0000011123455555555555555543
No 77
>PF06741 LsmAD: LsmAD domain; InterPro: IPR009604 This entry represents a conserved region approximately 250 residues long located on eukaryotic ataxin-2 []. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].
Probab=22.03 E-value=1.1e+02 Score=22.92 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=16.6
Q ss_pred chhcccCCC-CcCcCCCCCcHHHHHH
Q 028492 90 AIKSLFDPN-EKTKSGKVLPKAYLKS 114 (208)
Q Consensus 90 ~~~~~fdp~-~~~ksg~~LPk~Y~~d 114 (208)
+|+|-||+| |+||=++.=| .|.+.
T Consensus 2 GV~stydE~lYTT~Ld~~~~-~~k~~ 26 (72)
T PF06741_consen 2 GVKSTYDENLYTTPLDRSDP-DYKER 26 (72)
T ss_pred CCCCccCchhceeeccCCCc-chHHH
Confidence 478899998 6777777655 45433
No 78
>PRK11032 hypothetical protein; Provisional
Probab=21.43 E-value=4.8e+02 Score=22.26 Aligned_cols=19 Identities=42% Similarity=0.718 Sum_probs=12.8
Q ss_pred CcHHHHHHHHHHHHHHHHHhcCC
Q 028492 107 LPKAYLKSARELVKTLRESLKED 129 (208)
Q Consensus 107 LPk~Y~~dTr~VV~tLReaL~ld 129 (208)
|...| .+++..|++.|+.+
T Consensus 4 ~~~~Y----~~ll~~v~~~l~~~ 22 (160)
T PRK11032 4 VAQYY----RELVASLTERLRNG 22 (160)
T ss_pred HHHHH----HHHHHHHHHHHHhC
Confidence 44455 67777888877753
No 79
>PTZ00484 GTP cyclohydrolase I; Provisional
Probab=21.34 E-value=3e+02 Score=25.25 Aligned_cols=59 Identities=12% Similarity=0.188 Sum_probs=42.7
Q ss_pred CcCcCCCCCcHHHHHHHHHHHHHHHHHh-cCCCCCchHHHhhHHHHHHHHHHHHhhccCCC
Q 028492 99 EKTKSGKVLPKAYLKSARELVKTLRESL-KEDPKDIANFRRNADSAKESIRDYLSNWRGQK 158 (208)
Q Consensus 99 ~~~ksg~~LPk~Y~~dTr~VV~tLReaL-~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~ 158 (208)
++.+....+-+.=.+...+.|+.|-++| .+||.+ +...+.-...-+...++.+.|+-++
T Consensus 60 ~~~~~~~~~~~~~~~~ie~avr~iL~al~GeDp~R-egL~~TP~RVak~~~e~~~Gy~~~~ 119 (259)
T PTZ00484 60 ESSPTCATLMEEKKGAIESARRKILKSLEGEDPDR-DGLKKTPKRVAKALEFLTKGYHMSV 119 (259)
T ss_pred cCCccccccchhhHHHHHHHHHHHHHHhcCCCCCC-cchhhhHHHHHHHHHHHHhcccCCH
Confidence 5555666777777788889999999999 876655 3666666666666678888887544
No 80
>PTZ00477 rhoptry-associated protein; Provisional
Probab=21.25 E-value=1.5e+02 Score=29.85 Aligned_cols=57 Identities=12% Similarity=0.321 Sum_probs=36.6
Q ss_pred CcCcCCCC----CcHHHHHHHHHHHHHHHHH----------hcCCCCCchHHHh-hHHHHHHHHHHHHhhcc
Q 028492 99 EKTKSGKV----LPKAYLKSARELVKTLRES----------LKEDPKDIANFRR-NADSAKESIRDYLSNWR 155 (208)
Q Consensus 99 ~~~ksg~~----LPk~Y~~dTr~VV~tLRea----------L~ldp~D~~~~r~-aa~~AKe~IndyvsrYR 155 (208)
.++++|.. =|...+++|.+|++-+.+. |...+-|+..+-+ .....++.|+.|+.|=.
T Consensus 26 ~~~~~~~~~~~~~t~~~~d~t~~~~~~v~~l~~v~~~Ms~yLs~~~~d~~~fC~~~~~~C~~~V~~YveRC~ 97 (524)
T PTZ00477 26 KKRNGGAGLKSQNTEEFVDETEKVVREVNHLRMVSDKMTDYLSKNKYDPSMFCEGDLETCHTLVNRYVERCK 97 (524)
T ss_pred ccCCcccCCCCCCccchhhhhhHHHHhhhHHHhccHHHHHHHHhCCCChHHhhcCchhHHHHHHHHHHHHhc
Confidence 45555555 3566777777777665554 3334556555544 34489999999999874
No 81
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=21.23 E-value=4.2e+02 Score=20.94 Aligned_cols=51 Identities=12% Similarity=0.225 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHH
Q 028492 116 RELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL 176 (208)
Q Consensus 116 r~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsL 176 (208)
.+.++.|...+.- +.+.+. ..+.+.+.|.+|-..+++ .++|..|+.+.+.|
T Consensus 79 ~~fl~~L~~l~~~-~~~~~~---Vk~kil~li~~W~~~f~~------~~~~~~i~~~y~~L 129 (133)
T smart00288 79 KEFLNELVKLIKP-KYPLPL---VKKRILELIQEWADAFKN------DPDLSQIVDVYDLL 129 (133)
T ss_pred HHHHHHHHHHHcC-CCCcHH---HHHHHHHHHHHHHHHHcC------CCCchHHHHHHHHH
Confidence 4566667666663 444443 677888888888888866 44455555554444
No 82
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA). Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea.
Probab=20.76 E-value=46 Score=31.83 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=20.7
Q ss_pred hhhhHHHHHhhhhhHHHHHHhhcCCCCchhhhhc
Q 028492 42 ASSRRHVISCSSTALVAILTFNCGLAPLPVQAED 75 (208)
Q Consensus 42 ~~sRr~~l~~~~~~~~a~~~~~~~~~p~~~~A~~ 75 (208)
-.|||+||...++. .+++.|...+.|..+.|.+
T Consensus 14 g~sRR~FlK~~~~~-~a~~~l~~~~~~~~a~a~~ 46 (365)
T TIGR00391 14 GINRRDFLKLCAAL-ATTLGLSAKAAPEMAEAVE 46 (365)
T ss_pred CCCHHHHHHHHHHH-HHHhcCChhhhHHHHHHHh
Confidence 46899999988653 3455555555565555443
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=20.63 E-value=1.7e+02 Score=18.37 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=18.7
Q ss_pred CCcchHHHHHHHHHHHHhhhhhcC
Q 028492 161 AGEESYVELEKAIRSLASFYSKAG 184 (208)
Q Consensus 161 ~G~~SFttM~TALNsLAGhYss~G 184 (208)
+|.-++.++..+....-.||.++|
T Consensus 2 ~~~i~~~~~~d~a~rv~~f~~~ng 25 (33)
T PF09373_consen 2 SGTISKEEYLDMASRVNNFYESNG 25 (33)
T ss_pred CceecHHHHHHHHHHHHHHHHHcC
Confidence 456678888888888888888876
No 84
>COG1930 CbiN ABC-type cobalt transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=20.19 E-value=84 Score=25.18 Aligned_cols=26 Identities=35% Similarity=0.500 Sum_probs=18.6
Q ss_pred CCccccccccchh----cccCCCCcCcCCC
Q 028492 80 QDEKEEGVVGAIK----SLFDPNEKTKSGK 105 (208)
Q Consensus 80 ~~~~~~g~~~~~~----~~fdp~~~~ksg~ 105 (208)
.+++-|+|+-.|+ -.|-|=++.|||-
T Consensus 34 aD~~Ae~~I~ei~p~YePWF~Pl~EPpSGE 63 (97)
T COG1930 34 ADGEAEEVITEIKPGYEPWFQPLWEPPSGE 63 (97)
T ss_pred CcchhhHHHHHhCCCCCcccccccCCCCcc
Confidence 3444556766665 6788999999995
No 85
>PRK10911 oligopeptidase A; Provisional
Probab=20.10 E-value=1.2e+02 Score=30.77 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q 028492 169 LEKAIRSLASFYSKAGPSAPLPGEVKSEILN 199 (208)
Q Consensus 169 M~TALNsLAGhYss~GpnrPLPeklK~RLlq 199 (208)
-...|..+|.||.+ ..|||+++.+++++
T Consensus 511 ~~~vL~~~a~H~~t---geplp~~l~~~l~~ 538 (680)
T PRK10911 511 EPEALAFISGHYET---GEPLPKELLDKMLA 538 (680)
T ss_pred CHHHHHHHHHHhcC---CCCCCHHHHHHHHH
Confidence 34678889999997 46999999999887
Done!