Query 030997
Match_columns 167
No_of_seqs 92 out of 94
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:41:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030997hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00061 photosystem II protei 100.0 2.5E-63 5.3E-68 396.7 13.2 139 24-164 12-150 (150)
2 TIGR03044 PS_II_psb27 photosys 100.0 1.5E-44 3.3E-49 285.0 11.9 104 62-167 29-132 (135)
3 PLN00064 photosystem II protei 100.0 1.9E-42 4.1E-47 280.2 11.3 103 64-167 60-162 (166)
4 PF13326 PSII_Pbs27: Photosyst 100.0 1.3E-41 2.8E-46 269.4 9.3 110 50-167 36-145 (145)
5 PF07240 Turandot: Stress-indu 80.2 4.3 9.3E-05 30.4 4.8 34 129-162 9-42 (85)
6 smart00040 CSF2 Granulocyte-ma 78.3 4 8.6E-05 32.4 4.3 25 123-147 68-92 (121)
7 cd00040 CSF2 Granulocyte Macro 77.8 4.5 9.7E-05 32.2 4.4 25 123-147 68-92 (121)
8 PF15519 RBM39linker: linker b 67.3 1.7 3.8E-05 31.1 -0.1 15 50-64 59-73 (73)
9 COG1698 Uncharacterized protei 61.0 17 0.00036 27.9 4.2 85 63-163 4-88 (93)
10 PRK10866 outer membrane biogen 58.2 90 0.002 26.2 8.6 80 76-157 50-168 (243)
11 PF02899 Phage_int_SAM_1: Phag 53.6 63 0.0014 21.4 7.1 59 68-140 20-78 (84)
12 TIGR01405 polC_Gram_pos DNA po 50.8 78 0.0017 33.4 8.3 111 46-164 520-632 (1213)
13 PTZ00477 rhoptry-associated pr 50.6 33 0.00071 33.3 5.3 68 47-114 10-97 (524)
14 cd08054 gp6 Head-Tail Connecto 49.6 81 0.0018 21.5 6.3 76 79-154 3-85 (91)
15 COG2822 Predicted periplasmic 46.7 71 0.0015 29.7 6.6 64 71-140 296-367 (376)
16 PF08479 POTRA_2: POTRA domain 44.1 63 0.0014 22.0 4.7 34 105-143 18-51 (76)
17 TIGR01560 put_DNA_pack unchara 44.1 1.1E+02 0.0023 21.9 6.0 59 80-142 4-63 (91)
18 TIGR03175 AllD ureidoglycolate 43.3 37 0.0008 30.8 4.2 80 47-148 261-347 (349)
19 PF09037 Sulphotransf: Stf0 su 43.0 22 0.00049 30.2 2.7 47 69-115 197-244 (245)
20 cd01018 ZntC Metal binding pro 42.5 61 0.0013 27.2 5.2 90 63-162 114-215 (266)
21 PF12889 DUF3829: Protein of u 41.9 52 0.0011 27.1 4.6 49 94-142 219-275 (276)
22 PF04011 LemA: LemA family; I 41.7 55 0.0012 26.2 4.6 65 71-135 64-130 (186)
23 PF13551 HTH_29: Winged helix- 41.6 83 0.0018 21.9 5.1 52 94-162 17-72 (112)
24 PF04740 LXG: LXG domain of WX 40.6 1.2E+02 0.0026 24.0 6.4 66 99-165 44-113 (204)
25 PHA00649 hypothetical protein 38.1 1.1E+02 0.0024 22.8 5.3 43 69-116 10-52 (83)
26 PF12108 SF3a60_bindingd: Spli 37.0 46 0.001 20.2 2.7 26 119-145 3-28 (28)
27 PF11546 CompInhib_SCIN: Staph 36.4 57 0.0012 25.9 3.8 82 52-141 22-107 (114)
28 PF14461 Prok-E2_B: Prokaryoti 36.3 55 0.0012 25.1 3.7 58 49-119 73-130 (133)
29 PF10163 EnY2: Transcription f 35.9 1.4E+02 0.003 21.5 5.5 50 100-162 34-83 (86)
30 PF09373 PMBR: Pseudomurein-bi 35.3 66 0.0014 19.5 3.2 24 120-143 2-25 (33)
31 PF12732 YtxH: YtxH-like prote 35.3 47 0.001 23.0 2.9 62 45-110 9-72 (74)
32 PRK00035 hemH ferrochelatase; 33.7 1.3E+02 0.0028 26.1 6.0 57 104-160 20-87 (333)
33 PF10428 SOG2: RAM signalling 33.3 98 0.0021 28.8 5.5 27 131-157 398-424 (445)
34 PF08463 EcoEI_R_C: EcoEI R pr 32.9 60 0.0013 25.1 3.4 63 69-145 60-123 (164)
35 PRK03620 5-dehydro-4-deoxygluc 31.5 95 0.0021 26.8 4.8 42 125-167 258-301 (303)
36 PRK09269 chorismate mutase; Pr 31.1 3.2E+02 0.0069 22.9 7.7 62 75-136 69-136 (193)
37 cd03568 VHS_STAM VHS domain fa 30.9 2E+02 0.0044 22.6 6.2 58 74-142 78-135 (144)
38 PF13524 Glyco_trans_1_2: Glyc 30.2 66 0.0014 21.9 3.0 49 48-108 31-79 (92)
39 TIGR02878 spore_ypjB sporulati 30.1 1.2E+02 0.0025 26.7 5.0 50 46-113 85-134 (233)
40 PF13333 rve_2: Integrase core 29.8 64 0.0014 20.9 2.7 25 97-122 18-42 (52)
41 smart00288 VHS Domain present 28.8 2.6E+02 0.0056 21.4 6.3 52 74-135 78-129 (133)
42 PF01109 GM_CSF: Granulocyte-m 28.8 31 0.00066 27.6 1.2 36 105-150 58-93 (122)
43 COG1931 Uncharacterized protei 28.8 62 0.0013 26.5 3.0 60 41-108 13-73 (140)
44 smart00167 VPS9 Domain present 28.3 69 0.0015 24.6 3.1 33 105-137 67-101 (117)
45 PRK14996 TetR family transcrip 26.8 3E+02 0.0064 21.2 9.9 87 78-166 98-191 (192)
46 PF09236 AHSP: Alpha-haemoglob 26.0 93 0.002 23.7 3.3 13 125-137 63-75 (89)
47 PRK00448 polC DNA polymerase I 25.9 3.1E+02 0.0066 29.8 8.1 107 46-164 749-857 (1437)
48 TIGR00683 nanA N-acetylneurami 25.6 3.8E+02 0.0083 23.0 7.4 35 125-161 249-287 (290)
49 cd03411 Ferrochelatase_N Ferro 25.4 2.8E+02 0.0061 21.6 6.1 57 104-162 15-83 (159)
50 cd01137 PsaA Metal binding pro 25.4 2.4E+02 0.0053 24.1 6.2 97 63-162 119-224 (287)
51 cd08311 Death_p75NR Death doma 24.8 1.9E+02 0.0041 20.7 4.6 47 84-138 24-70 (77)
52 cd01493 APPBP1_RUB Ubiquitin a 24.6 4.1E+02 0.0089 24.7 7.9 82 65-152 222-313 (425)
53 PRK13659 hypothetical protein; 24.5 24 0.00052 27.5 -0.1 23 145-167 47-69 (103)
54 PF08651 DASH_Duo1: DASH compl 24.4 1.2E+02 0.0027 21.9 3.6 39 73-111 12-50 (78)
55 PF06160 EzrA: Septation ring 24.3 5E+02 0.011 24.7 8.5 69 65-141 437-528 (560)
56 PF14010 PEPcase_2: Phosphoeno 24.2 2.6E+02 0.0056 27.1 6.6 58 71-138 288-345 (491)
57 TIGR02949 anti_SigH_actin anti 24.0 2.3E+02 0.005 20.2 4.9 18 145-162 62-79 (84)
58 PF06543 Lac_bphage_repr: Lact 23.1 74 0.0016 21.9 2.1 21 139-160 23-43 (49)
59 PRK13382 acyl-CoA synthetase; 22.8 5.4E+02 0.012 23.0 8.1 76 68-143 4-89 (537)
60 cd01019 ZnuA Zinc binding prot 22.1 4.2E+02 0.0092 22.5 7.0 96 64-162 124-226 (286)
61 KOG0419 Ubiquitin-protein liga 21.9 64 0.0014 26.6 1.9 65 44-112 67-140 (152)
62 KOG2856 Adaptor protein PACSIN 21.8 1.4E+02 0.003 28.5 4.3 40 96-137 41-80 (472)
63 PF08638 Med14: Mediator compl 21.7 1.4E+02 0.003 24.7 3.9 37 127-163 110-152 (195)
64 PF07030 DUF1320: Protein of u 21.6 3.7E+02 0.0081 20.5 7.2 62 91-158 29-93 (130)
65 cd03569 VHS_Hrs_Vps27p VHS dom 21.2 3.8E+02 0.0082 20.9 6.1 61 63-133 73-133 (142)
66 PF05105 Phage_holin_4: Holin 21.1 1.2E+02 0.0026 22.6 3.1 27 130-158 87-113 (118)
67 PF01411 tRNA-synt_2c: tRNA sy 20.5 1.8E+02 0.0039 27.8 4.8 54 91-159 354-407 (552)
68 PRK08055 chorismate mutase; Pr 20.5 4.5E+02 0.0098 21.9 6.7 90 75-164 62-178 (181)
69 PF04905 NCD2: NAB conserved r 20.3 1.4E+02 0.003 25.1 3.5 59 76-142 71-130 (164)
70 KOG4097 Succinate dehydrogenas 20.3 44 0.00095 28.3 0.7 20 41-60 155-174 (178)
71 COG0167 PyrD Dihydroorotate de 20.2 1.2E+02 0.0026 27.3 3.4 87 56-148 134-244 (310)
72 PF08542 Rep_fac_C: Replicatio 20.2 1.7E+02 0.0036 20.1 3.5 35 129-167 38-72 (89)
73 PF02913 FAD-oxidase_C: FAD li 20.1 50 0.0011 25.7 0.9 20 45-64 228-247 (248)
No 1
>PLN00061 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=2.5e-63 Score=396.71 Aligned_cols=139 Identities=81% Similarity=1.144 Sum_probs=133.2
Q ss_pred ccccccccccccccCccccccchhhhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHH
Q 030997 24 TLTPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAK 103 (167)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ak 103 (167)
+++|+++||++++ +.++++||||||||||||||+||||+.|||+|++||++||++||++|+++|+|+++|++++++||
T Consensus 12 ~~~~~~~~a~~e~--~~~~~~~~~~~~~~~fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~~~~aa~~Ak 89 (150)
T PLN00061 12 QMTPLQARAEEEA--KVEEGEGVVGAIKSLFDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAKFRRTADAAK 89 (150)
T ss_pred CCCCCcchHHHHh--cccccccHHHHHHHhcCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHHHHHHHHHHH
Confidence 4678887776655 77888899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCCChHHHHHHHHHHHHHH
Q 030997 104 ESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAE 164 (167)
Q Consensus 104 e~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyGp~~PLPek~K~Rll~EL~~AE 164 (167)
++|||||++||+++.|+|++||+||+||||+|||||++||||||||+++|+||++||++||
T Consensus 90 e~IndYisryR~~~~V~gl~SfttMqtALnsLAghYssyGpnrPLPe~lK~Rll~EL~~AE 150 (150)
T PLN00061 90 ESIREYLGNWRGQKTVAEEESYVELEKAIRSLASFYSKAGPSAPLPEDVKSEILDDLNKAE 150 (150)
T ss_pred HHHHHHHHHhcCCccccccchHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhccC
Confidence 9999999999999999999999999999999999999999999999999999999999997
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=1.5e-44 Score=285.02 Aligned_cols=104 Identities=30% Similarity=0.494 Sum_probs=98.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhh
Q 030997 62 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK 141 (167)
Q Consensus 62 sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYss 141 (167)
+.+.|+|+|.+||++||++||++|+|+.+|| ++++++++||++|||||++|||+++|+|++||+|||||||+|||||++
T Consensus 29 ~~~~Ltg~Y~~DT~~Vi~tlr~~i~lpkd~p-~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~s 107 (135)
T TIGR03044 29 AKTRLTGDYVEDTLAVIQTLREAIDLPDDDP-NKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKS 107 (135)
T ss_pred CcccccchHHHHHHHHHHHHHHHHcCCCCCc-cHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhcc
Confidence 4578999999999999999999999954555 669999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHhcC
Q 030997 142 AGPSAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 142 yGp~~PLPek~K~Rll~EL~~AE~aL 167 (167)
|| |||||+|+|+||++||++||++|
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
>PLN00064 photosystem II protein Psb27; Provisional
Probab=100.00 E-value=1.9e-42 Score=280.17 Aligned_cols=103 Identities=25% Similarity=0.525 Sum_probs=98.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcC
Q 030997 64 KVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAG 143 (167)
Q Consensus 64 ~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyG 143 (167)
...+|+|.+||.+||++||++|+|+.+|+++ +++++++|++|||||++|||+++|+|++||+|||||||+|||||++||
T Consensus 60 a~~~g~Y~~DT~aVi~~lr~tI~L~~ddp~~-a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SFttMyTALNaLAGHY~Sfg 138 (166)
T PLN00064 60 AASDEEYVKETKDVIGKVRSTINMDKTDPNV-ADAVAELRETSNSWVAKYRREKALLGRPSFRDMYSALNAVSGHYISFG 138 (166)
T ss_pred hccCCChHHHHHHHHHHHHHHHcCCCCCccH-HHHHHHHHHHHHHHHHHhcCCCcccCcccHHHHHHHHHHHHHHhhccC
Confidence 3568999999999999999999998777765 999999999999999999999999999999999999999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHHHhcC
Q 030997 144 PSAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 144 p~~PLPek~K~Rll~EL~~AE~aL 167 (167)
|+||||+|+|+||+|||++||++|
T Consensus 139 pnrPlPeKlK~RL~qE~~~AEkal 162 (166)
T PLN00064 139 PTAPIPAKRKARILEEMDTAEKAL 162 (166)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999986
No 4
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=100.00 E-value=1.3e-41 Score=269.38 Aligned_cols=110 Identities=44% Similarity=0.621 Sum_probs=91.5
Q ss_pred hhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHH
Q 030997 50 IKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE 129 (167)
Q Consensus 50 ~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~ 129 (167)
++|. +||+ .|+++|++||++||++||++|+|+++|+ ++++++++||++|||||++|||++.|+|++||++||
T Consensus 36 ~~s~-~~~~------~l~~~Y~~dt~~vv~~lr~~l~l~~d~~-~~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf~~m~ 107 (145)
T PF13326_consen 36 AKSG-DPNA------GLTGDYVKDTRAVVKTLREALELDKDDP-NRAEAAAEARELINDYVSRYRRGPSVSGLPSFTTMY 107 (145)
T ss_dssp -----S--S------S--S-CHHHHHHHHHHHHHHHCS-TT-T-THHHHHHHHHHHHHHHHCCCCCCHHCCTSHHHHHHH
T ss_pred cccC-Cccc------cccchHHHHHHHHHHHHHHHHcCCCCCc-cHHHHHHHHHHHHHHHHHHhCCCCCcCCcchHHHHH
Confidence 5566 7765 4667899999999999999999986666 559999999999999999999999999999999999
Q ss_pred HHHHHHHhhHhhcCCCCCCChHHHHHHHHHHHHHHhcC
Q 030997 130 KAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 130 tALNsLAGhYssyGp~~PLPek~K~Rll~EL~~AE~aL 167 (167)
+|||+|||||++|||++|||+|+|+||++||++||++|
T Consensus 108 tAln~LaghY~s~g~raPlP~k~k~rll~el~~Ae~aL 145 (145)
T PF13326_consen 108 TALNALAGHYSSYGNRAPLPEKLKERLLKELDQAEKAL 145 (145)
T ss_dssp HHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhcC
Confidence 99999999999999888999999999999999999986
No 5
>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=80.24 E-value=4.3 Score=30.43 Aligned_cols=34 Identities=26% Similarity=0.419 Sum_probs=29.0
Q ss_pred HHHHHHHHhhHhhcCCCCCCChHHHHHHHHHHHH
Q 030997 129 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 129 ~tALNsLAGhYssyGp~~PLPek~K~Rll~EL~~ 162 (167)
..=+.+|-+||..|-|.-||++..|+++...+.+
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 3446789999999988889999999999887765
No 6
>smart00040 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic activity of white blood cells.
Probab=78.35 E-value=4 Score=32.41 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=22.1
Q ss_pred chHHHHHHHHHHHHhhHhhcCCCCC
Q 030997 123 ESYVELEKAIRSLASFYSKAGPSAP 147 (167)
Q Consensus 123 ~SFttm~tALNsLAGhYssyGp~~P 147 (167)
-||+-+..+|+-+|.||..+-|-.|
T Consensus 68 Gslt~Lkg~LtmmA~hYkq~CppTp 92 (121)
T smart00040 68 GSLTKLKGPLTMMASHYKQHCPPTP 92 (121)
T ss_pred ccHHHhhcHHHHHHHHHHhcCCCCC
Confidence 3899999999999999999976555
No 7
>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=77.77 E-value=4.5 Score=32.18 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=22.1
Q ss_pred chHHHHHHHHHHHHhhHhhcCCCCC
Q 030997 123 ESYVELEKAIRSLASFYSKAGPSAP 147 (167)
Q Consensus 123 ~SFttm~tALNsLAGhYssyGp~~P 147 (167)
-|++-+..+|+-+|.||..+-|-.|
T Consensus 68 GsltkLkg~LtmmAshYkqhCppTp 92 (121)
T cd00040 68 GSLTKLKGPLTMMASHYKQHCPPTP 92 (121)
T ss_pred ccHHHhccHHHHHHHHHHhcCCCCC
Confidence 3899999999999999999976555
No 8
>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A.
Probab=67.28 E-value=1.7 Score=31.10 Aligned_cols=15 Identities=40% Similarity=0.760 Sum_probs=12.3
Q ss_pred hhhccCCCCCCcCCC
Q 030997 50 IKSLFDPNEKTKSGK 64 (167)
Q Consensus 50 ~~~~fdp~~~t~sg~ 64 (167)
||..|||.++|..+|
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 678999999999887
No 9
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=60.99 E-value=17 Score=27.89 Aligned_cols=85 Identities=27% Similarity=0.384 Sum_probs=59.5
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhc
Q 030997 63 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 142 (167)
Q Consensus 63 g~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssy 142 (167)
|-.++.++.+--.+|+..|++.+ .|-.=|.+.|+++.+|++.+++ .|++.+.--.+||--|=. .+.
T Consensus 4 ~~~~~~d~~e~i~q~~~lL~~Ii-~DttVPRNIRraA~~a~e~L~~-----------e~e~p~vRaAtaIsiLee--isn 69 (93)
T COG1698 4 GQGLMNDSEEKINQVMQLLDEII-QDTTVPRNIRRAAEEAKEALNN-----------EGESPAVRAATAISILEE--ISN 69 (93)
T ss_pred hhcchhhhHHHHHHHHHHHHHHH-ccccccHHHHHHHHHHHHHHhC-----------CCCCchhHHHHHHHHHHH--Hhc
Confidence 34567788888899999999944 4556678899999999988764 356666666777777755 456
Q ss_pred CCCCCCChHHHHHHHHHHHHH
Q 030997 143 GPSAPLPGEVKSEILNDLDTA 163 (167)
Q Consensus 143 Gp~~PLPek~K~Rll~EL~~A 163 (167)
-||-|+ -.|..|.+=+.+-
T Consensus 70 DPNmP~--h~RT~iw~vis~L 88 (93)
T COG1698 70 DPNMPL--HARTLIWNVISQL 88 (93)
T ss_pred CCCCch--HHHHHHHHHHHHH
Confidence 677554 5566665544443
No 10
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=58.23 E-value=90 Score=26.15 Aligned_cols=80 Identities=10% Similarity=0.175 Sum_probs=55.6
Q ss_pred HHHHHHHHHhcCCCcchHHHHHh-------------HHHHHHHHHHHHHhccCCCCcc------Ccc----------hH-
Q 030997 76 ELVKTLRESLKEDPKDIANFRRN-------------ADSAKESIRDYLSNWRGQKTVA------GEE----------SY- 125 (167)
Q Consensus 76 ~VV~tLReaL~ld~~D~~k~~~a-------------a~~Ake~IndyvsrYRr~~~V~------G~~----------SF- 125 (167)
+.+..++..+...|..+-. ..+ -+.|....+.|+..|-+++.+. |.. .|
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 QAITQLEALDNRYPFGPYS-QQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFF 128 (243)
T ss_pred HHHHHHHHHHHhCCCChHH-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhcc
Confidence 4456677777777766422 122 2567778888888887777665 221 11
Q ss_pred ---------HHHHHHHHHHHhhHhhcCCCCCCChHHHHHHH
Q 030997 126 ---------VELEKAIRSLASFYSKAGPSAPLPGEVKSEIL 157 (167)
Q Consensus 126 ---------ttm~tALNsLAGhYssyGp~~PLPek~K~Rll 157 (167)
+..+.|++.+..+=..| |+.+--++.+.||.
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 33578999999999999 99999998888764
No 11
>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=53.64 E-value=63 Score=21.36 Aligned_cols=59 Identities=22% Similarity=0.430 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHh
Q 030997 68 KAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYS 140 (167)
Q Consensus 68 gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYs 140 (167)
..|..+-...+.-+.+ ....+.. +--...|.+|+......+ -|-+|+...+++|-.||.
T Consensus 20 ~~Y~~~l~~f~~~~~~---~~~~~~~------~i~~~~v~~f~~~~~~~~-----~s~~T~~~~~~alr~f~~ 78 (84)
T PF02899_consen 20 RSYRRDLRRFIRWLEE---HGIIDWE------DITEEDVRDFLEYLAKEG-----LSPSTINRRLSALRAFFR 78 (84)
T ss_dssp HHHHHHHHHHHHHHHH---TTS-CGG------G--HHHHHHHHHHHHCTT-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhh---hhhhhhh------hhhhHHHHHHHHHHHccC-----CCHHHHHHHHHHHHHHHH
Confidence 3566665566655555 1122222 223457889999887655 888999999999999986
No 12
>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=50.75 E-value=78 Score=33.41 Aligned_cols=111 Identities=19% Similarity=0.237 Sum_probs=59.2
Q ss_pred hhhhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchH
Q 030997 46 VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESY 125 (167)
Q Consensus 46 ~~~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SF 125 (167)
|+-+++..+++......-...+..|++.|.++.+.... + +.+..+ ..+.+... .|.+-+..-...+.-.-.|.|
T Consensus 520 il~~~~~~~~~~~~~~~~~~~~~~y~~t~~EM~~~F~~-l---~~~~a~-e~~i~Nt~-~IA~~c~~~~~~~~~~~~P~~ 593 (1213)
T TIGR01405 520 ILVASQGLGNPLNRHFNPKEVPELHFRTTNEMLDEFSF-L---GEEKAY-EIVVENTN-KIADQIEEIQPIKDKLYTPKI 593 (1213)
T ss_pred HHHhhhccCCcccccccccCCcccccCCHHHHHHHHhh-c---chhhhh-HHHHHHHH-HHHHHhhcccccCCCCCCCCC
Confidence 34455554543332222223577899999999887764 2 222111 11222222 333333321222222234444
Q ss_pred HHHHHHHHHH--HhhHhhcCCCCCCChHHHHHHHHHHHHHH
Q 030997 126 VELEKAIRSL--ASFYSKAGPSAPLPGEVKSEILNDLDTAE 164 (167)
Q Consensus 126 ttm~tALNsL--AGhYssyGp~~PLPek~K~Rll~EL~~AE 164 (167)
.+-..-|..| .|....|| .|+|+.+++||..||+-..
T Consensus 594 ~~~~~~L~~l~~~~~~~~yg--~~l~~~v~~RLe~EL~~I~ 632 (1213)
T TIGR01405 594 EGADEKIRDLTYENAKKIYG--DPLPEIVEQRIEKELKSII 632 (1213)
T ss_pred CCHHHHHHHHHHHHHHHHcC--CCCcHHHHHHHHHHHHHHH
Confidence 4444445544 56777787 3799999999999998764
No 13
>PTZ00477 rhoptry-associated protein; Provisional
Probab=50.55 E-value=33 Score=33.25 Aligned_cols=68 Identities=18% Similarity=0.327 Sum_probs=49.4
Q ss_pred hhhhhhccCC-----CCCCcCCCCC----cHHHHHHHHHHHHHHHHH----------hcCCCcchHHHHH-hHHHHHHHH
Q 030997 47 VGAIKSLFDP-----NEKTKSGKVL----PKAYLKSARELVKTLRES----------LKEDPKDIANFRR-NADSAKESI 106 (167)
Q Consensus 47 ~~~~~~~fdp-----~~~t~sg~~L----~gdY~kdT~~VV~tLRea----------L~ld~~D~~k~~~-aa~~Ake~I 106 (167)
+-.|+|||-| +.++++|..| |+..+++|.+|++-+.+. |..-+.|+..+-+ ....+++.|
T Consensus 10 ~~~~~~l~~~~~~v~~~~~~~~~~~~~~~t~~~~d~t~~~~~~v~~l~~v~~~Ms~yLs~~~~d~~~fC~~~~~~C~~~V 89 (524)
T PTZ00477 10 LLLIYSLFRYANGVTLKKRNGGAGLKSQNTEEFVDETEKVVREVNHLRMVSDKMTDYLSKNKYDPSMFCEGDLETCHTLV 89 (524)
T ss_pred HHHHHHHhcccchhhhccCCcccCCCCCCccchhhhhhHHHHhhhHHHhccHHHHHHHHhCCCChHHhhcCchhHHHHHH
Confidence 3456888888 5678888885 888999999998877665 3333556655555 344889999
Q ss_pred HHHHHhcc
Q 030997 107 RDYLSNWR 114 (167)
Q Consensus 107 ndyvsrYR 114 (167)
+.|+.|=.
T Consensus 90 ~~YveRC~ 97 (524)
T PTZ00477 90 NRYVERCK 97 (524)
T ss_pred HHHHHHhc
Confidence 99998863
No 14
>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=49.64 E-value=81 Score=21.50 Aligned_cols=76 Identities=24% Similarity=0.225 Sum_probs=47.7
Q ss_pred HHHHHHhcCCCcc-hHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhc-C-----CCCCCChH
Q 030997 79 KTLRESLKEDPKD-IANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA-G-----PSAPLPGE 151 (167)
Q Consensus 79 ~tLReaL~ld~~D-~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssy-G-----p~~PLPek 151 (167)
+.+++-|..+-++ .+......+.|++.|..|+.+--......+..-...+..|+..|++|+=.+ + ...++|.-
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 3455555554333 455667788888888888876644333446666778888888888876443 1 24566665
Q ss_pred HHH
Q 030997 152 VKS 154 (167)
Q Consensus 152 ~K~ 154 (167)
++.
T Consensus 83 v~~ 85 (91)
T cd08054 83 VES 85 (91)
T ss_pred HHH
Confidence 544
No 15
>COG2822 Predicted periplasmic lipoprotein involved in iron transport [Inorganic ion transport and metabolism]
Probab=46.73 E-value=71 Score=29.67 Aligned_cols=64 Identities=25% Similarity=0.401 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHH--------HHHHHHHHhhHh
Q 030997 71 LKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVEL--------EKAIRSLASFYS 140 (167)
Q Consensus 71 ~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm--------~tALNsLAGhYs 140 (167)
++-+..|++.+|-+|+- +|..- .+-.+..=..+++-+++||... |-.||..+ ...||+||.--+
T Consensus 296 VeGsqki~dl~rp~Lek--~dk~L-~~kid~nF~kv~~~LakYkt~d---g~esydklt~~dr~al~~~itaLaE~la 367 (376)
T COG2822 296 VEGSQKIVDLFRPALEK--KDKDL-LDKIDANFKKVNTILAKYRTKD---GFESYDKLTKADRKALKDPITALAEDLA 367 (376)
T ss_pred chhHHHHHHHHHHHHhh--ccHHH-HHHHHHHHHHHHHHHHHhccCC---cceeHHHhhHHHHHHHhhHHHHHHHHHH
Confidence 45578899999999974 45533 3446666679999999999765 88888765 455666665443
No 16
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=44.12 E-value=63 Score=22.04 Aligned_cols=34 Identities=15% Similarity=0.384 Sum_probs=26.2
Q ss_pred HHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcC
Q 030997 105 SIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAG 143 (167)
Q Consensus 105 ~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyG 143 (167)
.+++++..|- ...-++.+++.+.+.|..+|..-|
T Consensus 18 ~l~~~~~~~~-----g~~l~~~~l~~~~~~l~~~y~~~G 51 (76)
T PF08479_consen 18 ELQAILAPYI-----GRCLTLADLQQLADALTNYYREKG 51 (76)
T ss_dssp HHHHHHGGGT-----TSBB-HHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHhc-----CCCcCHHHHHHHHHHHHHHHHHcC
Confidence 4556666663 345699999999999999999987
No 17
>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=44.07 E-value=1.1e+02 Score=21.92 Aligned_cols=59 Identities=17% Similarity=0.125 Sum_probs=36.8
Q ss_pred HHHHHhcCCCc-chHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhc
Q 030997 80 TLRESLKEDPK-DIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 142 (167)
Q Consensus 80 tLReaL~ld~~-D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssy 142 (167)
.++.-|..|.+ |..-.....+.|++.|..++++.-.. .......+..|+..|++|+=.+
T Consensus 4 ~vK~~LrId~d~dD~li~~~i~aA~~~i~~~ig~~~~~----~~~~~~~~~~Avl~lv~~~Yen 63 (91)
T TIGR01560 4 EVKLSLRIDHDDDDELIKLMIAAAQDYIQSAIGTGVKD----SFDSKPLFKLACIKLVAHYYEN 63 (91)
T ss_pred HHHhHhcCCCCccHHHHHHHHHHHHHHHHHHhCCCccc----ccccCHHHHHHHHHHHHHHHHC
Confidence 34455554443 33344566788888888888765322 2334446778999998887544
No 18
>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=43.30 E-value=37 Score=30.80 Aligned_cols=80 Identities=16% Similarity=0.241 Sum_probs=50.1
Q ss_pred hhhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCC-------CcchHHHHHhHHHHHHHHHHHHHhccCCCCc
Q 030997 47 VGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKED-------PKDIANFRRNADSAKESIRDYLSNWRGQKTV 119 (167)
Q Consensus 47 ~~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld-------~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V 119 (167)
+|.+--..||.--. =..+|.+...++++.||.+--.+ |.|.+.. ..++ ..-
T Consensus 261 ~G~~~iaIDP~~F~-----~~~~f~~~~~~~~~~~r~~~~a~g~~~V~~PGe~e~~----~~~~-------------~~~ 318 (349)
T TIGR03175 261 LGQLHLVINPAFFT-----DCELFKKHISQMMQELNSVPPAEGFKQVYYPGEDGDL----KQKK-------------ADM 318 (349)
T ss_pred cceEEEEEChHHcC-----CHHHHHHHHHHHHHHHhcCCCCCCCCceECCCcHHHH----HHHH-------------HHc
Confidence 45566677875331 13579999999999998873222 4444321 1111 123
Q ss_pred cCcchHHHHHHHHHHHHhhHhhcCCCCCC
Q 030997 120 AGEESYVELEKAIRSLASFYSKAGPSAPL 148 (167)
Q Consensus 120 ~G~~SFttm~tALNsLAGhYssyGp~~PL 148 (167)
.|-+==..+...|+.|+-||++|-..-|.
T Consensus 319 ~GI~l~~~~~~~L~~la~~~~~~~~~~~~ 347 (349)
T TIGR03175 319 EGIEIVDDIYQYLVSDAVHYKSYEGKNPF 347 (349)
T ss_pred cCCccCHHHHHHHHHHHHHHHhccCCCcC
Confidence 45555567788899999999999656554
No 19
>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=42.95 E-value=22 Score=30.16 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcchH-HHHHhHHHHHHHHHHHHHhccC
Q 030997 69 AYLKSARELVKTLRESLKEDPKDIA-NFRRNADSAKESIRDYLSNWRG 115 (167)
Q Consensus 69 dY~kdT~~VV~tLReaL~ld~~D~~-k~~~aa~~Ake~IndyvsrYRr 115 (167)
+.++|-..+++.|-+.|..++..+. .....+..+-+.+.||+.|||.
T Consensus 197 dL~~dp~~~~~~Vl~fLgv~~~~~~~~~~~~~kqsd~~s~eW~~ry~~ 244 (245)
T PF09037_consen 197 DLLADPQKTVARVLDFLGVDPPLAPIVKPPLKKQSDERSEEWVERYRA 244 (245)
T ss_dssp HHHHHHHHHHHHHHHHTTS-GGGS----------------HHHHHHHH
T ss_pred HHHhCHHHHHHHHHHHhCCCCcccccCCCCceecCCCChHHHHHHHhc
Confidence 4455556788888888888664432 1123334444568889999985
No 20
>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=42.45 E-value=61 Score=27.20 Aligned_cols=90 Identities=13% Similarity=0.087 Sum_probs=50.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCC-------CCccCcchHHHHHHHHHHH
Q 030997 63 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQ-------KTVAGEESYVELEKAIRSL 135 (167)
Q Consensus 63 g~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~-------~~V~G~~SFttm~tALNsL 135 (167)
-|-=|.++.+-+..+.+.|.+ ++|...+.+++.++...+.+.+.-..|+.. .-+..-++|.=+
T Consensus 114 ~Wldp~~~~~~a~~I~~~L~~---~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~------- 183 (266)
T cd01018 114 IWLSPANAKIMAENIYEALAE---LDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMVYHPAWGYF------- 183 (266)
T ss_pred cCcCHHHHHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEECchhHHH-------
Confidence 455577775444444444422 467777777777777777777776666532 223344444443
Q ss_pred HhhHhhc-----CCCCCCChHHHHHHHHHHHH
Q 030997 136 ASFYSKA-----GPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 136 AGhYssy-----Gp~~PLPek~K~Rll~EL~~ 162 (167)
+..|.=- ++....+.+.-.+|.+.+++
T Consensus 184 ~~~ygl~~~~~~~~~~eps~~~l~~l~~~ik~ 215 (266)
T cd01018 184 ARDYGLTQIPIEEEGKEPSPADLKRLIDLAKE 215 (266)
T ss_pred HHHcCCEEEecCCCCCCCCHHHHHHHHHHHHH
Confidence 3333211 34556666666777766654
No 21
>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=41.91 E-value=52 Score=27.05 Aligned_cols=49 Identities=29% Similarity=0.310 Sum_probs=33.2
Q ss_pred HHHHhHHHHHHHHHHHHHhccC--------CCCccCcchHHHHHHHHHHHHhhHhhc
Q 030997 94 NFRRNADSAKESIRDYLSNWRG--------QKTVAGEESYVELEKAIRSLASFYSKA 142 (167)
Q Consensus 94 k~~~aa~~Ake~IndyvsrYRr--------~~~V~G~~SFttm~tALNsLAGhYssy 142 (167)
.+...+...+..+++||.+.|. -..-....|+..|....|.|-.-|++.
T Consensus 219 ~~~~~~~~~~~~~~~~i~~vr~~~~~~~~~~~~~~~~~~~~~l~~~yn~lI~~yN~~ 275 (276)
T PF12889_consen 219 SFMSSADSFKSSAKSFIRRVRDLQQSESNWMSGEPTEGSPEKLLKSYNDLISDYNRL 275 (276)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH-------------HCTTSS--HHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcchhhhhhcccCCCCCHHHHHHHHHHHHHHhccC
Confidence 4566788888888889999988 333344668888888888888888764
No 22
>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=41.66 E-value=55 Score=26.23 Aligned_cols=65 Identities=15% Similarity=0.250 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHhc--CCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHH
Q 030997 71 LKSARELVKTLRESLK--EDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL 135 (167)
Q Consensus 71 ~kdT~~VV~tLReaL~--ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsL 135 (167)
.+++..-|-.+|.... .++.++.++.++....-+.++..+.--..-|.......|.+|++.|..+
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 4566666777777776 1245566666777777777776665555668888889999988777544
No 23
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.56 E-value=83 Score=21.89 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=31.7
Q ss_pred HHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHh-hc---CCCCCCChHHHHHHHHHHHH
Q 030997 94 NFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYS-KA---GPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 94 k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYs-sy---Gp~~PLPek~K~Rll~EL~~ 162 (167)
..++.-.-.+..|..|+.+|+... +++... +. -|..+|+++.++.|.+.+.+
T Consensus 17 ~ia~~lg~s~~Tv~r~~~~~~~~G-----------------~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 17 EIARRLGISRRTVYRWLKRYREGG-----------------IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHHHCcCHHHHHHHHHHHHccc-----------------HHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 334444456778999999998655 333333 22 12333778888877766653
No 24
>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=40.57 E-value=1.2e+02 Score=24.04 Aligned_cols=66 Identities=20% Similarity=0.288 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHhccCCCCccCcchH-HHHHHHHHHHHhhHhhcC--CCCCCChHHHH-HHHHHHHHHHh
Q 030997 99 ADSAKESIRDYLSNWRGQKTVAGEESY-VELEKAIRSLASFYSKAG--PSAPLPGEVKS-EILNDLDTAEK 165 (167)
Q Consensus 99 a~~Ake~IndyvsrYRr~~~V~G~~SF-ttm~tALNsLAGhYssyG--p~~PLPek~K~-Rll~EL~~AE~ 165 (167)
.-.|-.+|+.|++.... |-+.|...| ..+..+++.+..|+..+. +++-|.++..+ .|.+.++++..
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 44556667777777544 455555555 556688899999999997 35668888666 77677766543
No 25
>PHA00649 hypothetical protein
Probab=38.05 E-value=1.1e+02 Score=22.84 Aligned_cols=43 Identities=21% Similarity=0.175 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCC
Q 030997 69 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQ 116 (167)
Q Consensus 69 dY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~ 116 (167)
...+.+-..|+..-++|..|.+||.++++. |+-++ |..+||..
T Consensus 10 acqEAA~rAV~~~~~~LGVD~~~P~~VEEF----r~D~~-~~Rr~RKA 52 (83)
T PHA00649 10 ACQEAADRAVKKVFAILGVDVDVPEQVEEF----REDLR-FGRRMRKA 52 (83)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHH----HHHHH-HHHHHHHH
Confidence 455667777888889999999999876443 43332 78888853
No 26
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=36.96 E-value=46 Score=20.23 Aligned_cols=26 Identities=12% Similarity=0.523 Sum_probs=15.7
Q ss_pred ccCcchHHHHHHHHHHHHhhHhhcCCC
Q 030997 119 VAGEESYVELEKAIRSLASFYSKAGPS 145 (167)
Q Consensus 119 V~G~~SFttm~tALNsLAGhYssyGp~ 145 (167)
++|-.-|...|.=|+.+=.|+.+| ||
T Consensus 3 is~~d~f~eFY~rlk~Ike~Hrr~-Pn 28 (28)
T PF12108_consen 3 ISGGDPFSEFYERLKEIKEYHRRY-PN 28 (28)
T ss_dssp --S--HHHHHHHHHHHHHHHHHS---S
T ss_pred CCCCChHHHHHHHHHHHHHHHHhC-CC
Confidence 455566778888888888888887 54
No 27
>PF11546 CompInhib_SCIN: Staphylococcal complement inhibitor SCIN ; InterPro: IPR021612 SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface []. An 18 residue stretch 31-48 is crucial for SCIN activity []. ; PDB: 3L3O_P 3OHX_P 3NMS_M 3L5N_M 3T49_C 3T4A_H 2WIN_P 2QFF_A 3T48_B 3T47_B ....
Probab=36.42 E-value=57 Score=25.88 Aligned_cols=82 Identities=15% Similarity=0.211 Sum_probs=41.7
Q ss_pred hccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhH----HHHHHHHHHHHHhccCCCCccCcchHHH
Q 030997 52 SLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNA----DSAKESIRDYLSNWRGQKTVAGEESYVE 127 (167)
Q Consensus 52 ~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa----~~Ake~IndyvsrYRr~~~V~G~~SFtt 127 (167)
++|+-|+.+-+- +....|.=.-.++++.|++.|+. .|....+..- -.=.=.++.|.+++ +....-|..
T Consensus 22 ~~~~~n~a~Ast-~~~t~~Ey~~q~la~eLk~Ll~~--s~vn~LA~~sl~~yyKr~i~~~~y~AK~-----alks~n~~q 93 (114)
T PF11546_consen 22 SVLSGNEAEAST-KYITASEYQDQKLADELKSLLDN--SNVNALAAGSLNAYYKRTIMMAEYRAKA-----ALKSKNFDQ 93 (114)
T ss_dssp -----------------HHHHHHHHHHHHHHHHHHT--HHHHHHHGGCS-HHHHHHHHHHHHHHHH-----HHHHT-HHH
T ss_pred hhhccchhhhcc-ccchHHHHHHHHHHHHHHHHHHH--hhHHHHHhccccHHHHHHHHHHHHHHHH-----HHhhccHHH
Confidence 578889877766 56666555557788999999973 3332211100 00112466677776 445567999
Q ss_pred HHHHHHHHHhhHhh
Q 030997 128 LEKAIRSLASFYSK 141 (167)
Q Consensus 128 m~tALNsLAGhYss 141 (167)
|-+|.+.|-.-|+.
T Consensus 94 M~~Ak~~Le~IY~e 107 (114)
T PF11546_consen 94 MAEAKVRLENIYNE 107 (114)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998875
No 28
>PF14461 Prok-E2_B: Prokaryotic E2 family B
Probab=36.34 E-value=55 Score=25.06 Aligned_cols=58 Identities=14% Similarity=0.095 Sum_probs=33.9
Q ss_pred hhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCc
Q 030997 49 AIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTV 119 (167)
Q Consensus 49 ~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V 119 (167)
+..=++|+ +-...-+...+.+ .++++.....|+....+.+ -++.+.||.+.|.+...+
T Consensus 73 G~LCl~~~-~~~~D~~~P~~~~----~~~l~~a~~lL~~~~~~~~--------~~d~~~Ef~sYW~~~~~~ 130 (133)
T PF14461_consen 73 GKLCLLDE-ELVLDPWDPEGII----ADCLERAIRLLEDGLSGDN--------EDDFADEFQSYWNRQCDV 130 (133)
T ss_pred CeEEEecC-CcccCccCHHHHH----HHHHHHHHHHHHHhhcCCc--------hHHHHHHHHHHHhhcccc
Confidence 44456666 5555555555555 4445555555543333332 456889999999876543
No 29
>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=35.88 E-value=1.4e+02 Score=21.54 Aligned_cols=50 Identities=28% Similarity=0.482 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCCChHHHHHHHHHHHH
Q 030997 100 DSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 100 ~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyGp~~PLPek~K~Rll~EL~~ 162 (167)
+..|+.+++.+.. ++.. ..+|.++...|---| ..-+|+.+|..|++...+
T Consensus 34 d~vr~~~re~i~~-~g~~----~~~~~~l~~~i~P~A--------r~~VP~~vk~ell~~Ir~ 83 (86)
T PF10163_consen 34 DEVRQLCREIIRE-RGID----NLTFEDLLEEITPKA--------RAMVPDEVKKELLQRIRA 83 (86)
T ss_dssp HHHHHHHHHHHHH-H-TT----TSBHHHHHHHHHHHH--------HHCS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh-hCCC----CCCHHHHHHHHHHHH--------HHHCCHHHHHHHHHHHHH
Confidence 4445555555555 3333 457888777665443 667999999999988765
No 30
>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=35.35 E-value=66 Score=19.50 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=18.2
Q ss_pred cCcchHHHHHHHHHHHHhhHhhcC
Q 030997 120 AGEESYVELEKAIRSLASFYSKAG 143 (167)
Q Consensus 120 ~G~~SFttm~tALNsLAGhYssyG 143 (167)
+|.-|+.++-.++.-+-.||.++|
T Consensus 2 ~~~i~~~~~~d~a~rv~~f~~~ng 25 (33)
T PF09373_consen 2 SGTISKEEYLDMASRVNNFYESNG 25 (33)
T ss_pred CceecHHHHHHHHHHHHHHHHHcC
Confidence 355677777778888888888887
No 31
>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=35.28 E-value=47 Score=23.00 Aligned_cols=62 Identities=27% Similarity=0.367 Sum_probs=33.8
Q ss_pred chhhhhh-hccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcc-hHHHHHhHHHHHHHHHHHH
Q 030997 45 GVVGAIK-SLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKD-IANFRRNADSAKESIRDYL 110 (167)
Q Consensus 45 ~~~~~~~-~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D-~~k~~~aa~~Ake~Indyv 110 (167)
+++|++. -||-| ++|+.+-.+-.+-+.++.+.+.+..+.-... -++.....+.+++.+++++
T Consensus 9 a~~Ga~~glL~aP----~sG~e~R~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~e~~~e~~ 72 (74)
T PF12732_consen 9 AAAGAAAGLLFAP----KSGKETREKLKDKAEDLKDKAKDLYEEAKEKVKEKAEETADEAKEKAKELK 72 (74)
T ss_pred HHHHHHHHHHhCC----CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455444 45676 6788776666555555555555555421110 1233445666777776665
No 32
>PRK00035 hemH ferrochelatase; Reviewed
Probab=33.71 E-value=1.3e+02 Score=26.06 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=38.2
Q ss_pred HHHHHHHHhccCCCCccCcchHHHH--------HHHHHHHHhhHhhcCCCCCCCh---HHHHHHHHHH
Q 030997 104 ESIRDYLSNWRGQKTVAGEESYVEL--------EKAIRSLASFYSKAGPSAPLPG---EVKSEILNDL 160 (167)
Q Consensus 104 e~IndyvsrYRr~~~V~G~~SFttm--------~tALNsLAGhYssyGp~~PLPe---k~K~Rll~EL 160 (167)
+.|+.|+.+++.++.+-+.+.+.-- ..=+..++.+|...|-..||.. +.-+.|.+.|
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 4788888888888888887765321 2233467889999987788874 3334444444
No 33
>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=33.35 E-value=98 Score=28.84 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=21.0
Q ss_pred HHHHHHhhHhhcCCCCCCChHHHHHHH
Q 030997 131 AIRSLASFYSKAGPSAPLPGEVKSEIL 157 (167)
Q Consensus 131 ALNsLAGhYssyGp~~PLPek~K~Rll 157 (167)
++=+|++-++..+...|||.++|.++-
T Consensus 398 s~i~l~~~iK~~~~~~~l~~dvr~~L~ 424 (445)
T PF10428_consen 398 SWISLLAKIKEIMKDLPLPPDVRARLR 424 (445)
T ss_pred HHHHHHHHHHHHhccCCCCHHHHHHHH
Confidence 445567777777889999999998763
No 34
>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=32.85 E-value=60 Score=25.09 Aligned_cols=63 Identities=14% Similarity=0.327 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHH-HHHHHHHhhHhhcCCC
Q 030997 69 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE-KAIRSLASFYSKAGPS 145 (167)
Q Consensus 69 dY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~-tALNsLAGhYssyGp~ 145 (167)
.|......++.-||..+.++..=..+ .+.|.+..++|+..+. |+..+ .-|+.|-.||..+|--
T Consensus 60 ~~~~~~~dl~~~ir~i~g~d~~l~tr----~erv~~~~~~~l~~~~----------~~~~Q~~~L~~i~~~~~~~G~~ 123 (164)
T PF08463_consen 60 TYEAIDADLFDFIRHILGLDTPLLTR----RERVEEAFSKFLNQHQ----------FNAEQREFLERILDYYAQNGII 123 (164)
T ss_pred hcccccCCHHHHHHHHHhcCCCCCCH----HHHHHHHHHHHHHhcC----------CCHHHHHHHHHHHHHHHHhCcc
Confidence 55566677889999998884111122 2333345588886653 66666 7789999999999843
No 35
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=31.52 E-value=95 Score=26.77 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhhHhhc--CCCCCCChHHHHHHHHHHHHHHhcC
Q 030997 125 YVELEKAIRSLASFYSKA--GPSAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 125 Fttm~tALNsLAGhYssy--Gp~~PLPek~K~Rll~EL~~AE~aL 167 (167)
+..+..|++. -|+...+ -|-.||+++.|++|.+.|....+.|
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 5668888874 5765433 1444589999999999998876643
No 36
>PRK09269 chorismate mutase; Provisional
Probab=31.08 E-value=3.2e+02 Score=22.94 Aligned_cols=62 Identities=15% Similarity=0.270 Sum_probs=41.9
Q ss_pred HHHHHHHHHHhc---CCCcch-HHHHHhHHHHHHHHHHHHHhccCCCCcc--CcchHHHHHHHHHHHH
Q 030997 75 RELVKTLRESLK---EDPKDI-ANFRRNADSAKESIRDYLSNWRGQKTVA--GEESYVELEKAIRSLA 136 (167)
Q Consensus 75 ~~VV~tLReaL~---ld~~D~-~k~~~aa~~Ake~IndyvsrYRr~~~V~--G~~SFttm~tALNsLA 136 (167)
.+|++.++.-.+ ++|+.. .=|+...+.+|..=+.|++.|+.++... -.+.-.+++..|..|.
T Consensus 69 ~~VL~~v~~~A~~~gLdp~~v~~iF~~~I~aSk~iQ~~~~a~W~~~~~~~~~~~~dL~~~Rp~l~~L~ 136 (193)
T PRK09269 69 AQVLANVEAQAPAHGVDPDYVRRFFRDQIEANKLVQYALLARWRLAGAAPPGPRPDLASIRPRLDRLQ 136 (193)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHH
Confidence 677777777665 433332 3378888899999999999999765422 2355557777766654
No 37
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=30.88 E-value=2e+02 Score=22.60 Aligned_cols=58 Identities=9% Similarity=0.244 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhc
Q 030997 74 ARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA 142 (167)
Q Consensus 74 T~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssy 142 (167)
++++++.|...+.- +.+ ......+.+.|..|...++++ +++.-|+.+.+.|-..+-.|
T Consensus 78 sk~Fl~eL~kl~~~-~~~----~~Vk~kil~li~~W~~~f~~~------~~l~~i~~~y~~L~~~G~~f 135 (144)
T cd03568 78 SRDFTQELKKLIND-RVH----PTVKEKLREVVKQWADEFKND------PSLSLMSDLYKKLKNEGPDL 135 (144)
T ss_pred hHHHHHHHHHHhcc-cCC----HHHHHHHHHHHHHHHHHhCCC------cccHHHHHHHHHHHHcCCCC
Confidence 45677777777753 222 346778888888888888654 45555666666665555555
No 38
>PF13524 Glyco_trans_1_2: Glycosyl transferases group 1
Probab=30.20 E-value=66 Score=21.86 Aligned_cols=49 Identities=20% Similarity=0.331 Sum_probs=34.2
Q ss_pred hhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHH
Q 030997 48 GAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRD 108 (167)
Q Consensus 48 ~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~Ind 108 (167)
.++..+|++.+. .-++.+..++++.++..++ |++..++.+..|++.|.+
T Consensus 31 ~~~~~~~~~~~~--------~~~~~~~~el~~~i~~ll~----~~~~~~~ia~~a~~~v~~ 79 (92)
T PF13524_consen 31 PGLREIFEDGEH--------IITYNDPEELAEKIEYLLE----NPEERRRIAKNARERVLK 79 (92)
T ss_pred HHHHHHcCCCCe--------EEEECCHHHHHHHHHHHHC----CHHHHHHHHHHHHHHHHH
Confidence 456666777652 3344477888888888886 666667788888877764
No 39
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=30.06 E-value=1.2e+02 Score=26.72 Aligned_cols=50 Identities=28% Similarity=0.381 Sum_probs=39.3
Q ss_pred hhhhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhc
Q 030997 46 VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNW 113 (167)
Q Consensus 46 ~~~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrY 113 (167)
||+||.|-.+| |=..|.+--...+..|..+..- .|...| ++.+|+|++.|
T Consensus 85 avDA~~s~~qP---------LW~~~e~~im~~f~~mk~a~~~--~~~~~f-------~~~ln~Fl~~Y 134 (233)
T TIGR02878 85 AVDAIVSRSQP---------LWGSLEKPVMEAFTELEKAAQK--EDSQAF-------QEKLNEFLSLY 134 (233)
T ss_pred HHHHhcCCCcc---------hHHHHHHHHHHHHHHHHHHHHc--CCHHHH-------HHHHHHHHHHh
Confidence 67888777766 7788888888999999988874 466555 45889999998
No 40
>PF13333 rve_2: Integrase core domain
Probab=29.83 E-value=64 Score=20.87 Aligned_cols=25 Identities=16% Similarity=0.505 Sum_probs=18.7
Q ss_pred HhHHHHHHHHHHHHHhccCCCCccCc
Q 030997 97 RNADSAKESIRDYLSNWRGQKTVAGE 122 (167)
Q Consensus 97 ~aa~~Ake~IndyvsrYRr~~~V~G~ 122 (167)
...+++++.|.+||..| ...+..|+
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 35689999999999999 54544443
No 41
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=28.80 E-value=2.6e+02 Score=21.36 Aligned_cols=52 Identities=12% Similarity=0.228 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHH
Q 030997 74 ARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSL 135 (167)
Q Consensus 74 T~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsL 135 (167)
+.++++.|...+.- +.+... ..+.+.+.|.+|-..+++ .++|.-|+.+.+.|
T Consensus 78 s~~fl~~L~~l~~~-~~~~~~---Vk~kil~li~~W~~~f~~------~~~~~~i~~~y~~L 129 (133)
T smart00288 78 SKEFLNELVKLIKP-KYPLPL---VKKRILELIQEWADAFKN------DPDLSQIVDVYDLL 129 (133)
T ss_pred hHHHHHHHHHHHcC-CCCcHH---HHHHHHHHHHHHHHHHcC------CCCchHHHHHHHHH
Confidence 56677788877763 333222 567777778888777765 34444444444443
No 42
>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=28.79 E-value=31 Score=27.64 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=23.6
Q ss_pred HHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCCCh
Q 030997 105 SIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPG 150 (167)
Q Consensus 105 ~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyGp~~PLPe 150 (167)
-++=|...-|+ |++.+..+|+-+|.||.++= -|.||
T Consensus 58 rLkly~qGLrg--------nlT~L~g~L~~mAshy~~~C--PptpE 93 (122)
T PF01109_consen 58 RLKLYKQGLRG--------NLTRLKGPLTMMASHYKQHC--PPTPE 93 (122)
T ss_dssp HHHHHHHT--G--------GGGGGHHHHHHHHHHHHHCS-------
T ss_pred HHHHHHHHccc--------cchhhhhhHHHHHHHhccCC--CCCCC
Confidence 34556666655 78999999999999999984 45555
No 43
>COG1931 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.78 E-value=62 Score=26.47 Aligned_cols=60 Identities=25% Similarity=0.222 Sum_probs=42.2
Q ss_pred ccccchhhhhhhccCCCCCCcCCCCCc-HHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHH
Q 030997 41 EKEEGVVGAIKSLFDPNEKTKSGKVLP-KAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRD 108 (167)
Q Consensus 41 ~~~~~~~~~~~~~fdp~~~t~sg~~L~-gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~Ind 108 (167)
|+.+-|..||.-+|++-+-+....... .--...|+.-..+|++.|- .++..|.||..+..
T Consensus 13 ED~~KV~kAi~NlFp~~~ie~~~~~~~~~~~~~~~~~sL~~l~elLr--------~qrIlDtAR~~l~k 73 (140)
T COG1931 13 EDPEKVLKAILNLFPGAEIEVEDEDYEILVGEGRTLKSLERLRELLR--------KQRILDTARMVLEK 73 (140)
T ss_pred CCHHHHHHHHHhcCCchheEeeccceeeeeeccchHHHHHHHHHHHH--------HhHHHHHHHHHHHc
Confidence 455689999999999998888777220 0112345677888888884 36788999865544
No 44
>smart00167 VPS9 Domain present in VPS9. Domain present in yeast vacuolar sorting protein 9 and other proteins.
Probab=28.35 E-value=69 Score=24.60 Aligned_cols=33 Identities=18% Similarity=0.379 Sum_probs=25.7
Q ss_pred HHHHHHHhccCCCCccCcchH--HHHHHHHHHHHh
Q 030997 105 SIRDYLSNWRGQKTVAGEESY--VELEKAIRSLAS 137 (167)
Q Consensus 105 ~IndyvsrYRr~~~V~G~~SF--ttm~tALNsLAG 137 (167)
+--.||.+||......|+..| |+++.|+.-+-.
T Consensus 67 sn~~yI~~f~~~~~l~gE~gY~lT~l~aAv~fi~~ 101 (117)
T smart00167 67 LNAEYMEEFLEPSLLTGEGGYYLTSLSAALALIKG 101 (117)
T ss_pred HHHHHHHHHCCccccccHHHHHHHHHHHHHHHHHH
Confidence 334699999988888999875 888898876544
No 45
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=26.76 E-value=3e+02 Score=21.15 Aligned_cols=87 Identities=13% Similarity=0.110 Sum_probs=55.1
Q ss_pred HHHHHHHhcCCCcchH---HHHHhHHHHHHHHHHHHHhccCCCCccCcchHH----HHHHHHHHHHhhHhhcCCCCCCCh
Q 030997 78 VKTLRESLKEDPKDIA---NFRRNADSAKESIRDYLSNWRGQKTVAGEESYV----ELEKAIRSLASFYSKAGPSAPLPG 150 (167)
Q Consensus 78 V~tLReaL~ld~~D~~---k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFt----tm~tALNsLAGhYssyGp~~PLPe 150 (167)
+....+...+...|+. .+.+..+.-.+.+.+++.++..+..+.....-. .|...++.+.|.+... ..+.++
T Consensus 98 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~~~~~~~a~~l~~~~~g~~g~~~~~--~~~~~~ 175 (192)
T PRK14996 98 IRLWREAQILADRDPEIKDAYLLTMQMWHQETVAIIEQGKAAGEFRSTSNATDIAWRLIALVCGLDGIYVLG--IPGLAD 175 (192)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHhHHhhhHhhC--CCCCcH
Confidence 3344444444444553 233344556778888888887666665544433 3346667777888776 348888
Q ss_pred HHHHHHHHHHHHHHhc
Q 030997 151 EVKSEILNDLDTAEKF 166 (167)
Q Consensus 151 k~K~Rll~EL~~AE~a 166 (167)
+...++++++-..|-+
T Consensus 176 ~~~~~~~~~~~~~~~~ 191 (192)
T PRK14996 176 PAFKRHLDRMITLELF 191 (192)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999988877753
No 46
>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=25.98 E-value=93 Score=23.73 Aligned_cols=13 Identities=31% Similarity=0.544 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHh
Q 030997 125 YVELEKAIRSLAS 137 (167)
Q Consensus 125 Fttm~tALNsLAG 137 (167)
-..++.-||.||.
T Consensus 63 lqel~qeL~tla~ 75 (89)
T PF09236_consen 63 LQELQQELNTLAN 75 (89)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3345555555554
No 47
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=25.87 E-value=3.1e+02 Score=29.80 Aligned_cols=107 Identities=20% Similarity=0.259 Sum_probs=58.0
Q ss_pred hhhhhhhccCCCCCCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchH
Q 030997 46 VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESY 125 (167)
Q Consensus 46 ~~~~~~~~fdp~~~t~sg~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SF 125 (167)
|+-+++..+++... ...|..|++.|.++.+.... | +.+-.. ..+.+.. ..|.+-+......+.-.-.|.|
T Consensus 749 il~~~~~~~~~~~~----~~~~~~yl~tt~EM~~~f~~-l---~~~~~~-e~vi~Nt-~~Ia~~~~~i~~~~~~~~~P~~ 818 (1437)
T PRK00448 749 ILVASQGGGNPLNR----HPLPELHFRTTDEMLDEFAF-L---GEELAK-EIVVENT-NKIADLIEEIEPIKDKLYTPKI 818 (1437)
T ss_pred HHHHhhcCCCcccc----ccCCccccCCHHHHHHHhhh-c---chhhhH-HHHHHHH-HHHHHhcceecccCCCCCCCCC
Confidence 34455555554322 23578899999998887653 2 111111 1112222 2344444323322222233444
Q ss_pred HHHHHHHHHH--HhhHhhcCCCCCCChHHHHHHHHHHHHHH
Q 030997 126 VELEKAIRSL--ASFYSKAGPSAPLPGEVKSEILNDLDTAE 164 (167)
Q Consensus 126 ttm~tALNsL--AGhYssyGp~~PLPek~K~Rll~EL~~AE 164 (167)
.+-..-|..| .|-...|| .|||+.+++||.+||+-..
T Consensus 819 ~~a~~~L~~l~~~~a~~~yg--~~lp~~v~~RLe~EL~~I~ 857 (1437)
T PRK00448 819 EGAEEEIRELTYKKAHEIYG--EPLPEIVEKRIEKELNSII 857 (1437)
T ss_pred CCHHHHHHHHHHHHHHHHhC--CCCcHHHHHHHHHHHHHHH
Confidence 4444445544 36666787 4799999999999998764
No 48
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=25.59 E-value=3.8e+02 Score=22.97 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhhHhhcCCCCCCC----hHHHHHHHHHHH
Q 030997 125 YVELEKAIRSLASFYSKAGPSAPLP----GEVKSEILNDLD 161 (167)
Q Consensus 125 Fttm~tALNsLAGhYssyGp~~PLP----ek~K~Rll~EL~ 161 (167)
+..+..|++.+ |....+ ++.||. ++.+++|.+++.
T Consensus 249 ~~~~K~~l~~~-G~~~g~-~R~Pl~~~~~~~~~~~~~~~~~ 287 (290)
T TIGR00683 249 YLTIKELLKLE-GVDAGY-CREPMTSKATPEQKAKAKDLKA 287 (290)
T ss_pred CHHHHHHHHHc-CCCCCC-cCCCCCCCCCHHHHHHHHHHHH
Confidence 56799999855 665444 788864 577777777663
No 49
>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=25.42 E-value=2.8e+02 Score=21.62 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=33.9
Q ss_pred HHHHHHHHhccCCCCccCcchHHHHHHHH---------HHHHhhHhhcCCCCCC---ChHHHHHHHHHHHH
Q 030997 104 ESIRDYLSNWRGQKTVAGEESYVELEKAI---------RSLASFYSKAGPSAPL---PGEVKSEILNDLDT 162 (167)
Q Consensus 104 e~IndyvsrYRr~~~V~G~~SFttm~tAL---------NsLAGhYssyGp~~PL---Pek~K~Rll~EL~~ 162 (167)
+.|+.|+.+-..++.|-..+.+. +..| ..++.+|.+.|-..|| .++..+.|.+.|++
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 35556666666666665555442 2222 3478889999856666 45555666666653
No 50
>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=25.37 E-value=2.4e+02 Score=24.08 Aligned_cols=97 Identities=14% Similarity=0.232 Sum_probs=54.1
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccC---------CCCccCcchHHHHHHHHH
Q 030997 63 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG---------QKTVAGEESYVELEKAIR 133 (167)
Q Consensus 63 g~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr---------~~~V~G~~SFttm~tALN 133 (167)
-|-=|.++..-+..+.+.|. +++|.+.+.+++..+...+.+++.-..|+. .+-+..-++|.=+-..++
T Consensus 119 ~Wldp~~~~~~a~~Ia~~L~---~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~~~v~~H~af~Y~~~~yG 195 (287)
T cd01137 119 AWMSPKNAIIYVKNIAKALS---EADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRKLVTSEGAFSYFAKAYG 195 (287)
T ss_pred cCcCHHHHHHHHHHHHHHHH---HHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCEEEEecccHHHHHHHcC
Confidence 47667777544444444443 356777777777777777777776666653 122344445554443332
Q ss_pred HHHhhHhhcCCCCCCChHHHHHHHHHHHH
Q 030997 134 SLASFYSKAGPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 134 sLAGhYssyGp~~PLPek~K~Rll~EL~~ 162 (167)
-=--.....+|..+.+.+.-.+|.+.+++
T Consensus 196 l~~~~~~~~~~~~eps~~~l~~l~~~ik~ 224 (287)
T cd01137 196 LKEAYLWPINTEEEGTPKQVATLIEQVKK 224 (287)
T ss_pred CeEeecccCCCCCCCCHHHHHHHHHHHHH
Confidence 11111123445666677777777766654
No 51
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=24.81 E-value=1.9e+02 Score=20.70 Aligned_cols=47 Identities=19% Similarity=0.321 Sum_probs=33.2
Q ss_pred HhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhh
Q 030997 84 SLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASF 138 (167)
Q Consensus 84 aL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGh 138 (167)
-|..+..+...+..-.+++++.+++|..+ . | ++...|.+||+.+.-.
T Consensus 24 ~LG~~~~~I~~i~~~~~p~~~lL~~W~~r--~-----~-ATv~~L~~aL~~i~R~ 70 (77)
T cd08311 24 ELGYEDEAIDTFGREESPVRTLLADWSAQ--E-----G-ATLDALCTALRRIQRE 70 (77)
T ss_pred HcCCCHHHHHHHHcChhHHHHHHHHHHHC--c-----C-chHHHHHHHHHHcChH
Confidence 34444445556666678999999999984 2 2 7888999999887543
No 52
>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=24.59 E-value=4.1e+02 Score=24.71 Aligned_cols=82 Identities=23% Similarity=0.432 Sum_probs=43.5
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHH---------HHHhccCCCCccCcchHHHHHHHHHHH
Q 030997 65 VLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRD---------YLSNWRGQKTVAGEESYVELEKAIRSL 135 (167)
Q Consensus 65 ~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~Ind---------yvsrYRr~~~V~G~~SFttm~tALNsL 135 (167)
.+|..|.+ ....+.+-........|.++|.+|.+.+...++. -+..-+-..-......|-.|-.| |
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 36777654 2222222222332225667888877766644433 33222222222344567777555 5
Q ss_pred HhhHhh-cCCCCCCChHH
Q 030997 136 ASFYSK-AGPSAPLPGEV 152 (167)
Q Consensus 136 AGhYss-yGp~~PLPek~ 152 (167)
-.||.. +| .-|||..+
T Consensus 297 k~F~~~~~g-~lPl~G~l 313 (425)
T cd01493 297 KEFVAEENG-LLPLPGTL 313 (425)
T ss_pred HHHHHhcCC-CCCCCCCC
Confidence 568888 87 77887643
No 53
>PRK13659 hypothetical protein; Provisional
Probab=24.51 E-value=24 Score=27.50 Aligned_cols=23 Identities=17% Similarity=0.398 Sum_probs=19.4
Q ss_pred CCCCChHHHHHHHHHHHHHHhcC
Q 030997 145 SAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 145 ~~PLPek~K~Rll~EL~~AE~aL 167 (167)
++.|=.|+-.|+++||+++++|.
T Consensus 47 Tr~LR~KVN~R~EKefDK~D~A~ 69 (103)
T PRK13659 47 TRSLRQKVNKRVEKEFDKADRAF 69 (103)
T ss_pred HHHHHHHHhhHHHhhhhHHHHhh
Confidence 56677889999999999998873
No 54
>PF08651 DASH_Duo1: DASH complex subunit Duo1; InterPro: IPR013960 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=24.44 E-value=1.2e+02 Score=21.89 Aligned_cols=39 Identities=10% Similarity=0.326 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHH
Q 030997 73 SARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLS 111 (167)
Q Consensus 73 dT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~Indyvs 111 (167)
.--.||..+.++|.--.++-+++.++.+.+-.+++.|++
T Consensus 12 ~IN~~ie~~~~~L~~a~~~~~~v~~~~~~t~~LLd~w~~ 50 (78)
T PF08651_consen 12 KINPVIEGLIETLRSAKSNMNRVQETVESTNTLLDKWIR 50 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777777765556778899999999999998875
No 55
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=24.33 E-value=5e+02 Score=24.73 Aligned_cols=69 Identities=16% Similarity=0.467 Sum_probs=43.3
Q ss_pred CCcHH---HHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHH--------------------HHHHhccCCCCccC
Q 030997 65 VLPKA---YLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIR--------------------DYLSNWRGQKTVAG 121 (167)
Q Consensus 65 ~L~gd---Y~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~In--------------------dyvsrYRr~~~V~G 121 (167)
+||.+ |+.++.+-|.+|...|+..|=|.....+-...|...|. .|-.|||++.
T Consensus 437 Glp~~y~~~~~~~~~~i~~l~~~L~~~pinm~~v~~~l~~a~~~v~~L~~~t~~li~~A~L~E~~iQYaNRYR~~~---- 512 (560)
T PF06160_consen 437 GLPEDYLDYFFDVSDEIEELSDELNQVPINMDEVNKQLEEAEDDVETLEEKTEELIDNATLAEQLIQYANRYRSDN---- 512 (560)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCC----
Confidence 45666 55667777888888888878776554444444433332 3899998643
Q ss_pred cchHHHHHHHHHHHHhhHhh
Q 030997 122 EESYVELEKAIRSLASFYSK 141 (167)
Q Consensus 122 ~~SFttm~tALNsLAGhYss 141 (167)
-.+..||..-=-.|..
T Consensus 513 ----~~v~~al~~Ae~~F~~ 528 (560)
T PF06160_consen 513 ----PEVDEALTEAEDLFRN 528 (560)
T ss_pred ----HHHHHHHHHHHHHHHh
Confidence 4666666655555555
No 56
>PF14010 PEPcase_2: Phosphoenolpyruvate carboxylase; PDB: 3ODM_C.
Probab=24.18 E-value=2.6e+02 Score=27.06 Aligned_cols=58 Identities=19% Similarity=0.370 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhh
Q 030997 71 LKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASF 138 (167)
Q Consensus 71 ~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGh 138 (167)
.++++.+|++|++.....|..-.. +-++.+.+.|..|.+.||+ -...+-..||.+|.|
T Consensus 288 ~~~v~~ai~~l~~~~~~~p~~~~~--ee~~~~~~ii~~~s~~Y~~--------~i~~la~~In~va~~ 345 (491)
T PF14010_consen 288 YEEVIKAIEKLNEAPRKKPRIIDE--EEEEILLEIIEKYSAEYRS--------QIEKLAPTINRVARY 345 (491)
T ss_dssp HHHHHHHHHHHHHGGG-------H--HHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhcccCCcccCCh--HHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHh
Confidence 467788888888866544433321 2235577788888888864 345555666666654
No 57
>TIGR02949 anti_SigH_actin anti-sigma factor, TIGR02949 family. This group of anti-sigma factors are associated in an apparent operon with a family of sigma-70 family sigma factors (TIGR02947). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria.
Probab=23.96 E-value=2.3e+02 Score=20.25 Aligned_cols=18 Identities=11% Similarity=0.274 Sum_probs=15.5
Q ss_pred CCCCChHHHHHHHHHHHH
Q 030997 145 SAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 145 ~~PLPek~K~Rll~EL~~ 162 (167)
..+.|+.+|+||+..+..
T Consensus 62 ~~~aP~~Lr~rI~~~l~~ 79 (84)
T TIGR02949 62 TEAAPEGLRSRLRLQIRV 79 (84)
T ss_pred CCCCCHHHHHHHHHHHHh
Confidence 457899999999999875
No 58
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=23.09 E-value=74 Score=21.85 Aligned_cols=21 Identities=24% Similarity=0.297 Sum_probs=15.9
Q ss_pred HhhcCCCCCCChHHHHHHHHHH
Q 030997 139 YSKAGPSAPLPGEVKSEILNDL 160 (167)
Q Consensus 139 YssyGp~~PLPek~K~Rll~EL 160 (167)
.-||| -+||++++|+-|-.=|
T Consensus 23 wvSf~-GrPltdevK~a~k~i~ 43 (49)
T PF06543_consen 23 WVSFD-GRPLTDEVKEAMKLIF 43 (49)
T ss_pred heeeC-CeeCCHHHHHHHHHHH
Confidence 45787 8999999998765433
No 59
>PRK13382 acyl-CoA synthetase; Provisional
Probab=22.83 E-value=5.4e+02 Score=23.00 Aligned_cols=76 Identities=18% Similarity=0.150 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcchHH-HHHhH------HHHHHHHHHHHHhccCCCCc---cCcchHHHHHHHHHHHHh
Q 030997 68 KAYLKSARELVKTLRESLKEDPKDIAN-FRRNA------DSAKESIRDYLSNWRGQKTV---AGEESYVELEKAIRSLAS 137 (167)
Q Consensus 68 gdY~kdT~~VV~tLReaL~ld~~D~~k-~~~aa------~~Ake~IndyvsrYRr~~~V---~G~~SFttm~tALNsLAG 137 (167)
+|-+.|+.....+|...+-..|..+.. +.... ....+.+..+..+|-....+ .+.-||.++....|.+|.
T Consensus 4 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~p~~~a~~~~~~~~Ty~el~~~~~~~A~ 83 (537)
T PRK13382 4 KDRLRDTLGLIATLRRAGLIAPMRPDRYLRIVAAMRREGMGPTSGFAIAAQRCPDRPGLIDELGTLTWRELDERSDALAA 83 (537)
T ss_pred chhHHHHHHHHHHHHhccCCCCCCchhHHHHHHHHHhhcCCHHHHHHHHHHhCCCCeEEEeCCCeecHHHHHHHHHHHHH
Confidence 456778888888888887665553221 11100 01333445555565443332 367899999999999999
Q ss_pred hHhhcC
Q 030997 138 FYSKAG 143 (167)
Q Consensus 138 hYssyG 143 (167)
+....|
T Consensus 84 ~L~~~g 89 (537)
T PRK13382 84 ALQALP 89 (537)
T ss_pred HHHHcC
Confidence 998765
No 60
>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=22.11 E-value=4.2e+02 Score=22.55 Aligned_cols=96 Identities=13% Similarity=0.150 Sum_probs=50.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccC-------CCCccCcchHHHHHHHHHHHH
Q 030997 64 KVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG-------QKTVAGEESYVELEKAIRSLA 136 (167)
Q Consensus 64 ~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr-------~~~V~G~~SFttm~tALNsLA 136 (167)
|-=|.++.+-+..+.+.|.+ ++|...+.+++.++...+.+++..++|+. ..-+..-++|.=+-..++-=-
T Consensus 124 Wldp~n~~~~a~~I~~~L~~---~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Yl~~~~gl~~ 200 (286)
T cd01019 124 WLSPENAAEVAQAVAEKLSA---LDPDNAATYAANLEAFNARLAELDATIKERLAPVKTKPFFVFHDAYGYFEKRYGLTQ 200 (286)
T ss_pred CCCHHHHHHHHHHHHHHHHH---HCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHHHHcCCce
Confidence 55577775555555544443 46777666777777777777776666642 223444444544443322100
Q ss_pred hhHhhcCCCCCCChHHHHHHHHHHHH
Q 030997 137 SFYSKAGPSAPLPGEVKSEILNDLDT 162 (167)
Q Consensus 137 GhYssyGp~~PLPek~K~Rll~EL~~ 162 (167)
-.+..-.|......+.-.+|.+.+++
T Consensus 201 ~~~~~~~~~~eps~~~l~~l~~~ik~ 226 (286)
T cd01019 201 AGVFTIDPEIDPGAKRLAKIRKEIKE 226 (286)
T ss_pred eeeecCCCCCCCCHHHHHHHHHHHHH
Confidence 00112223455556666666666543
No 61
>KOG0419 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.91 E-value=64 Score=26.61 Aligned_cols=65 Identities=22% Similarity=0.372 Sum_probs=34.6
Q ss_pred cchhhhhhhccCCCCCCcCCCCC-------cHHHHHHHHHHHHHHHHHhcCCC--cchHHHHHhHHHHHHHHHHHHHh
Q 030997 44 EGVVGAIKSLFDPNEKTKSGKVL-------PKAYLKSARELVKTLRESLKEDP--KDIANFRRNADSAKESIRDYLSN 112 (167)
Q Consensus 44 ~~~~~~~~~~fdp~~~t~sg~~L-------~gdY~kdT~~VV~tLReaL~ld~--~D~~k~~~aa~~Ake~Indyvsr 112 (167)
--+|--|...|-||----+.--| ...| |...+.-.+...|.. | ..|++ .+||.--++-=++|+.+
T Consensus 67 PP~VrFvs~mFHPNvya~G~iClDiLqNrWsp~Y--dva~ILtsiQslL~d-Pn~~sPaN-~eAA~Lf~e~~rey~rr 140 (152)
T KOG0419|consen 67 PPTVRFVSKMFHPNVYADGSICLDILQNRWSPTY--DVASILTSIQSLLND-PNPNSPAN-SEAARLFSENKREYERR 140 (152)
T ss_pred CCeeEeeeeccCCCcCCCCcchHHHHhcCCCCch--hHHHHHHHHHHHhcC-CCCCCccc-HHHHHHHhhChHHHHHH
Confidence 35777788888888665532222 3334 445555566666652 3 34444 34444444444555544
No 62
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=21.81 E-value=1.4e+02 Score=28.52 Aligned_cols=40 Identities=23% Similarity=0.409 Sum_probs=33.2
Q ss_pred HHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHh
Q 030997 96 RRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLAS 137 (167)
Q Consensus 96 ~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAG 137 (167)
+++...=-+++.+|..+||. -|..-++|.++.+|-|++-+
T Consensus 41 A~IEk~YaqqL~~wakkWr~--lvekgpqyGt~e~aW~~~~t 80 (472)
T KOG2856|consen 41 ARIEKAYAQQLTDWAKKWRQ--LVEKGPQYGTVEKAWNAFMT 80 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHhcCcccchHHHHHHHHHH
Confidence 56666677899999999984 57888999999999998744
No 63
>PF08638 Med14: Mediator complex subunit MED14; InterPro: IPR013947 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Saccharomyces cerevisiae (Baker's yeast) RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes, and sporulation. It is required for glucose repression, HO repression, RME1 repression and sporulation [, ]. This subunit is also found in higher eukaryotes and MED14 is the agreed unified nomenclature for this subunit []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=21.70 E-value=1.4e+02 Score=24.68 Aligned_cols=37 Identities=27% Similarity=0.293 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhh-Hh-----hcCCCCCCChHHHHHHHHHHHHH
Q 030997 127 ELEKAIRSLASF-YS-----KAGPSAPLPGEVKSEILNDLDTA 163 (167)
Q Consensus 127 tm~tALNsLAGh-Ys-----syGp~~PLPek~K~Rll~EL~~A 163 (167)
++-|||..|..= |. .|.|..||+++...+.+++|+..
T Consensus 110 Dl~tAldVL~tGr~p~~~~~~~~~~~~l~~~e~l~~l~~ln~~ 152 (195)
T PF08638_consen 110 DLPTALDVLSTGRLPWMPKDGFIPPPPLSPEEILKTLRRLNTL 152 (195)
T ss_pred chHHHHHHHhcCCcccccccccCCCCCCCHHHHHHHHHHHHHH
Confidence 577888888754 32 36788899999999999999864
No 64
>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=21.56 E-value=3.7e+02 Score=20.46 Aligned_cols=62 Identities=16% Similarity=0.168 Sum_probs=41.2
Q ss_pred chHHHHHhHHHHHHHHHHHH-HhccCCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCC--ChHHHHHHHH
Q 030997 91 DIANFRRNADSAKESIRDYL-SNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL--PGEVKSEILN 158 (167)
Q Consensus 91 D~~k~~~aa~~Ake~Indyv-srYRr~~~V~G~~SFttm~tALNsLAGhYssyGp~~PL--Pek~K~Rll~ 158 (167)
|+.....+.+.|-..|+.|+ +||. -|. ...=..+....-.+|-||-.- +++. |+.+++|-.+
T Consensus 29 d~~~v~~Al~dA~~~Id~yL~~RY~-lPl---~~~p~~L~~~~~dIA~y~L~~--~~~~~~~e~~~~rY~~ 93 (130)
T PF07030_consen 29 DPAVVEAALADASAEIDGYLRGRYD-LPL---APVPALLKRIACDIARYRLYD--RRPSQETEPVRERYKD 93 (130)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhcC-CCc---ccccHHHHHHHHHHHHHHHHh--cCCccCcHHHHHHHHH
Confidence 56788999999999999999 6775 222 112234666667788877644 4443 6776665443
No 65
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=21.19 E-value=3.8e+02 Score=20.94 Aligned_cols=61 Identities=15% Similarity=0.246 Sum_probs=36.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHH
Q 030997 63 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIR 133 (167)
Q Consensus 63 g~~L~gdY~kdT~~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALN 133 (167)
|..+-..+. ++++++.|...+.- ..+ .++.+.+.+.|..|-..++++ .+...|.++|..|.
T Consensus 73 G~~fh~eva--s~~fl~~l~~l~~~--~~~---~~Vk~kil~li~~W~~~f~~~---~~l~~i~~~y~~L~ 133 (142)
T cd03569 73 GTHFHDEVA--SREFMDELKDLIKT--TKN---EEVRQKILELIQAWALAFRNK---PQLKYVVDTYQILK 133 (142)
T ss_pred CHHHHHHHh--hHHHHHHHHHHHcc--cCC---HHHHHHHHHHHHHHHHHhCCC---cccHHHHHHHHHHH
Confidence 444444444 46777777776652 122 346778888888888888654 34445555555554
No 66
>PF05105 Phage_holin_4: Holin family ; InterPro: IPR006480 This group of sequences describe one of the many mutually dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species []. This entry is represented by the Bacteriophage phi-29, Gp14 (holin). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.06 E-value=1.2e+02 Score=22.64 Aligned_cols=27 Identities=19% Similarity=0.318 Sum_probs=21.8
Q ss_pred HHHHHHHhhHhhcCCCCCCChHHHHHHHH
Q 030997 130 KAIRSLASFYSKAGPSAPLPGEVKSEILN 158 (167)
Q Consensus 130 tALNsLAGhYssyGp~~PLPek~K~Rll~ 158 (167)
+=+-|+-+++...| -|+|+.+|+.|.+
T Consensus 87 ~E~~SI~EN~~~~G--~~iP~~l~~~l~~ 113 (118)
T PF05105_consen 87 NELISILENLAEMG--VPIPKWLKKFLKQ 113 (118)
T ss_pred HHHHHHHHHHHHhC--CCchHHHHHHHHH
Confidence 44667889999998 4999999988864
No 67
>PF01411 tRNA-synt_2c: tRNA synthetases class II (A); InterPro: IPR018164 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Alanyl-tRNA synthetase (6.1.1.7 from EC) is an alpha4 tetramer that belongs to class IIc. ; GO: 0000166 nucleotide binding, 0004813 alanine-tRNA ligase activity, 0005524 ATP binding, 0006419 alanyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3HY1_A 3HXZ_C 3HXY_A 3HXU_A 3HY0_B 3HXV_A 3HXX_A 3HXW_A 2E1B_A 2ZZG_B ....
Probab=20.52 E-value=1.8e+02 Score=27.85 Aligned_cols=54 Identities=17% Similarity=0.465 Sum_probs=39.9
Q ss_pred chHHHHHhHHHHHHHHHHHHHhccCCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCCChHHHHHHHHH
Q 030997 91 DIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILND 159 (167)
Q Consensus 91 D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G~~SFttm~tALNsLAGhYssyGp~~PLPek~K~Rll~E 159 (167)
..++|.+.-+...+.+.+.+.+....+.++|..-|. -|.+|| +|.++=..|.+|
T Consensus 354 EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsge~aF~-----------LYDTyG----fP~Dlt~eia~e 407 (552)
T PF01411_consen 354 EEERFLKTLERGLKLLEKLIKKLKKKKELSGEDAFK-----------LYDTYG----FPLDLTEEIAEE 407 (552)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCSEE-HHHHHH-----------HHHHH-------HHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhccccCCChHHhee-----------ehhccC----CCHHHHHHHHHH
Confidence 346788888888999999999988777777776664 399999 999988888775
No 68
>PRK08055 chorismate mutase; Provisional
Probab=20.48 E-value=4.5e+02 Score=21.88 Aligned_cols=90 Identities=23% Similarity=0.335 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhc---CCCcch-HHHHHhHHHHHHHHHHHHHhccCCCCccC-cchHHHHHHHHHHH--------HhhHhh
Q 030997 75 RELVKTLRESLK---EDPKDI-ANFRRNADSAKESIRDYLSNWRGQKTVAG-EESYVELEKAIRSL--------ASFYSK 141 (167)
Q Consensus 75 ~~VV~tLReaL~---ld~~D~-~k~~~aa~~Ake~IndyvsrYRr~~~V~G-~~SFttm~tALNsL--------AGhYss 141 (167)
.+|++.++.-.+ ++|+.. +=|+...+.+|..-+.|.+.|+..+.... -+.-++++-.|..| +.+-++
T Consensus 62 ~~VL~~v~~~A~~~GLdp~~i~~~F~~~I~asK~iQ~~~~a~W~~~~~~~~~~~dL~~vRp~l~~L~~~il~~ia~~l~~ 141 (181)
T PRK08055 62 QKVLAEAEEEAASNGLDPESIKPFIVAQMDAAKAIQYRYRADWLSQPEPSWPPQDLSDVRQRIRQLDTQILIQIAQRLKV 141 (181)
T ss_pred HHHHHHHHHHhhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 677888777664 433333 33778888899888999999986655422 33445555555443 433333
Q ss_pred cCC--------------CCCCChHHHHHHHHHHHHHH
Q 030997 142 AGP--------------SAPLPGEVKSEILNDLDTAE 164 (167)
Q Consensus 142 yGp--------------~~PLPek~K~Rll~EL~~AE 164 (167)
-|+ ..-|.+.-|++|..=|.++.
T Consensus 142 ~g~~~~~~~~~f~~~i~~~~ls~~dk~~l~~al~~i~ 178 (181)
T PRK08055 142 CGPFSHGDMAWFRSTINQPNLSEADKSAIFAALSQVR 178 (181)
T ss_pred cCCCCcchHHHHHHHHhcccCCHHHHHHHHHHHHHhh
Confidence 242 12355666666666666553
No 69
>PF04905 NCD2: NAB conserved region 2 (NCD2); InterPro: IPR006989 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents a NAB domain near the C terminus of the protein. It is necessary for transcriptional repression by the Nab proteins []. It is also required for transcription activation by Nab proteins at Nab-activated promoters [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2YUF_A.
Probab=20.34 E-value=1.4e+02 Score=25.10 Aligned_cols=59 Identities=20% Similarity=0.192 Sum_probs=34.6
Q ss_pred HHHHHHHHHhcCCCcchHHHHHhHHHHHHHHHHHHHhccCCCCccC-cchHHHHHHHHHHHHhhHhhc
Q 030997 76 ELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG-EESYVELEKAIRSLASFYSKA 142 (167)
Q Consensus 76 ~VV~tLReaL~ld~~D~~k~~~aa~~Ake~IndyvsrYRr~~~V~G-~~SFttm~tALNsLAGhYssy 142 (167)
.+-+.|...++|+.+||.+. +.|+-|.+=|.|...... ...-|.-+-++|+.|...-.+
T Consensus 71 K~~k~l~~v~~M~~~dp~r~--------eEiRkySaIygrfDskRr~~k~Lt~~E~~iNEAaaQlc~~ 130 (164)
T PF04905_consen 71 KLAKELEHVLEMSEDDPRRE--------EEIRKYSAIYGRFDSKRRPGKPLTLHEITINEAAAQLCRR 130 (164)
T ss_dssp HHHHHHTHHHHS-SS-HHHH--------HHHHHH--SSS-S---TT---S-SSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCChHHH--------HHHHHHHHHhCccccCCCCCCCccHHHHHHHHHHHHHHhc
Confidence 34566778888988888763 478999999976543332 334455567888888877776
No 70
>KOG4097 consensus Succinate dehydrogenase membrane anchor subunit and related proteins [Energy production and conversion; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.34 E-value=44 Score=28.27 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=16.4
Q ss_pred ccccchhhhhhhccCCCCCC
Q 030997 41 EKEEGVVGAIKSLFDPNEKT 60 (167)
Q Consensus 41 ~~~~~~~~~~~~~fdp~~~t 60 (167)
-+|-|++++||++||-|++-
T Consensus 155 tndvGl~~~vk~lW~~~~~~ 174 (178)
T KOG4097|consen 155 TNDVGLVKGVKKLWDSKGKD 174 (178)
T ss_pred ecchHHHHHHHHHHccCcch
Confidence 34669999999999988753
No 71
>COG0167 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]
Probab=20.21 E-value=1.2e+02 Score=27.28 Aligned_cols=87 Identities=25% Similarity=0.389 Sum_probs=48.6
Q ss_pred CCCCCcCCCCCcHH--HHHHHHHHHHHHHHHhc------CCCcchHHHHHhHHHHHHH-------HHHHHHhc-----c-
Q 030997 56 PNEKTKSGKVLPKA--YLKSARELVKTLRESLK------EDPKDIANFRRNADSAKES-------IRDYLSNW-----R- 114 (167)
Q Consensus 56 p~~~t~sg~~L~gd--Y~kdT~~VV~tLReaL~------ld~~D~~k~~~aa~~Ake~-------IndyvsrY-----R- 114 (167)
|| ||.|..|-.+ |+.+ |++.++.... +.| +...+.+.++.|.+. ||.-.++= .
T Consensus 134 Pn--t~g~~~l~~~~e~l~~---l~~~vk~~~~~Pv~vKl~P-~~~di~~iA~~~~~~g~Dgl~~~NT~~~~~~id~~~~ 207 (310)
T COG0167 134 PN--TPGGRALGQDPELLEK---LLEAVKAATKVPVFVKLAP-NITDIDEIAKAAEEAGADGLIAINTTKSGMKIDLETK 207 (310)
T ss_pred CC--CCChhhhccCHHHHHH---HHHHHHhcccCceEEEeCC-CHHHHHHHHHHHHHcCCcEEEEEeecccccccccccc
Confidence 77 8888888633 5544 4445555444 445 444555555555554 23222221 1
Q ss_pred ---CCCCccCcchHHHHHHHHHHHHhhHhhcCCCCCC
Q 030997 115 ---GQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL 148 (167)
Q Consensus 115 ---r~~~V~G~~SFttm~tALNsLAGhYssyGp~~PL 148 (167)
......|+.-=--+..|++-+...|...|+.-||
T Consensus 208 ~~~~~~~~GGLSG~~ikp~al~~v~~l~~~~~~~ipI 244 (310)
T COG0167 208 KPVLANETGGLSGPPLKPIALRVVAELYKRLGGDIPI 244 (310)
T ss_pred ccccCcCCCCcCcccchHHHHHHHHHHHHhcCCCCcE
Confidence 1112233333333458999999999999877765
No 72
>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=20.20 E-value=1.7e+02 Score=20.10 Aligned_cols=35 Identities=26% Similarity=0.353 Sum_probs=26.2
Q ss_pred HHHHHHHHhhHhhcCCCCCCChHHHHHHHHHHHHHHhcC
Q 030997 129 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 167 (167)
Q Consensus 129 ~tALNsLAGhYssyGp~~PLPek~K~Rll~EL~~AE~aL 167 (167)
..-|+.|......+ .+|+..|.+|++.+.++|..|
T Consensus 38 ~~Il~~l~~~l~~~----~~~~~~k~~i~~~la~~e~rl 72 (89)
T PF08542_consen 38 SDILKQLHEVLVES----DIPDSQKAEILKILAEIEYRL 72 (89)
T ss_dssp HHHHHHHHHHHHTS----TSSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHh----hccHHHHHHHHHHHHHHhHHH
Confidence 34455555555555 789999999999999998653
No 73
>PF02913 FAD-oxidase_C: FAD linked oxidases, C-terminal domain; InterPro: IPR004113 Some oxygen-dependent oxidoreductases are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. The region around the histidine that binds the FAD group is conserved in these enzymes (see IPR006093 from INTERPRO).; GO: 0003824 catalytic activity, 0050660 flavin adenine dinucleotide binding; PDB: 1WVE_B 1DII_B 1WVF_A 1DIQ_A 2UUU_B 2UUV_A 1W1M_A 1E8H_B 1E0Y_B 1DZN_B ....
Probab=20.13 E-value=50 Score=25.68 Aligned_cols=20 Identities=45% Similarity=0.665 Sum_probs=14.5
Q ss_pred chhhhhhhccCCCCCCcCCC
Q 030997 45 GVVGAIKSLFDPNEKTKSGK 64 (167)
Q Consensus 45 ~~~~~~~~~fdp~~~t~sg~ 64 (167)
.++.+||..||||.----||
T Consensus 228 ~~~~~iK~~~DP~~ilNPGk 247 (248)
T PF02913_consen 228 RLMRAIKQAFDPNGILNPGK 247 (248)
T ss_dssp HHHHHHHHHH-TTS-BSTTG
T ss_pred HHHHHhhhccCCccCCCCCC
Confidence 57889999999997665554
Done!