Query psy9115
Match_columns 96
No_of_seqs 100 out of 1002
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 19:19:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9115hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0233 Frr Ribosome recycling 99.9 7.1E-28 1.5E-32 182.1 7.2 74 15-89 98-171 (187)
2 PRK00083 frr ribosome recyclin 99.9 7.9E-26 1.7E-30 168.7 7.5 74 15-89 96-169 (185)
3 TIGR00496 frr ribosome recycli 99.9 9.3E-26 2E-30 167.2 7.5 74 15-89 87-160 (176)
4 cd00520 RRF Ribosome recycling 99.9 6.7E-25 1.4E-29 162.2 7.5 73 16-89 93-165 (179)
5 PF01765 RRF: Ribosome recycli 99.9 4.5E-22 9.7E-27 144.4 6.8 74 15-89 78-151 (165)
6 KOG4759|consensus 99.6 1.5E-15 3.2E-20 120.0 6.6 71 16-89 177-247 (263)
7 PF12685 SpoIIIAH: SpoIIIAH-li 74.2 11 0.00025 27.9 5.6 49 35-83 83-131 (196)
8 cd02640 R3H_NRF R3H domain of 73.8 3.1 6.7E-05 26.2 2.1 25 16-40 17-42 (60)
9 cd02646 R3H_G-patch R3H domain 71.5 3.8 8.2E-05 25.1 2.1 26 16-41 16-41 (58)
10 PF02216 B: B domain; InterPr 70.9 5.1 0.00011 25.5 2.6 22 18-39 16-37 (54)
11 cd06007 R3H_DEXH_helicase R3H 70.3 4 8.7E-05 25.7 2.1 27 15-41 15-42 (59)
12 PF04695 Pex14_N: Peroxisomal 69.0 3.5 7.7E-05 29.2 1.8 49 29-82 2-50 (136)
13 PF13801 Metal_resist: Heavy-m 65.4 32 0.00069 21.7 7.8 62 21-83 39-100 (125)
14 PF00816 Histone_HNS: H-NS his 62.9 20 0.00043 23.4 4.4 43 30-72 1-43 (93)
15 PF05957 DUF883: Bacterial pro 59.3 21 0.00045 23.3 4.0 64 28-93 10-74 (94)
16 PF08910 Aida_N: Aida N-termin 59.2 34 0.00073 24.3 5.2 63 20-95 43-105 (106)
17 KOG0871|consensus 58.9 34 0.00073 25.9 5.5 44 31-79 83-126 (156)
18 PF09851 SHOCT: Short C-termin 57.6 18 0.00039 19.7 3.0 26 54-79 4-29 (31)
19 PF00804 Syntaxin: Syntaxin; 56.9 45 0.00098 20.7 5.7 54 29-88 47-100 (103)
20 cd02641 R3H_Smubp-2_like R3H d 55.4 12 0.00025 23.3 2.2 24 17-40 18-42 (60)
21 PF05008 V-SNARE: Vesicle tran 54.3 51 0.0011 20.5 6.3 30 21-50 15-44 (79)
22 PF03480 SBP_bac_7: Bacterial 54.3 54 0.0012 24.7 6.0 61 23-86 218-281 (286)
23 PRK14562 haloacid dehalogenase 52.9 58 0.0012 24.6 6.0 28 26-53 17-44 (204)
24 PF10281 Ish1: Putative stress 52.7 11 0.00024 21.2 1.6 20 19-39 18-37 (38)
25 PRK10404 hypothetical protein; 51.6 42 0.00091 23.1 4.6 62 31-94 20-82 (101)
26 PF06518 DUF1104: Protein of u 51.6 72 0.0016 21.8 5.8 59 24-89 22-81 (93)
27 PRK04195 replication factor C 51.0 41 0.00088 27.9 5.3 52 11-62 321-378 (482)
28 COG4575 ElaB Uncharacterized c 50.5 27 0.00059 24.7 3.6 61 34-95 26-86 (104)
29 PF09440 eIF3_N: eIF3 subunit 47.8 72 0.0016 22.9 5.5 58 18-75 60-126 (133)
30 PF05120 GvpG: Gas vesicle pro 47.3 76 0.0017 21.1 5.2 45 34-79 17-61 (79)
31 COG1638 DctP TRAP-type C4-dica 47.2 67 0.0014 26.0 5.9 68 22-92 248-316 (332)
32 COG5404 SulA SOS-response cell 42.3 21 0.00045 27.2 2.1 17 21-37 120-136 (169)
33 PF07564 DUF1542: Domain of Un 40.5 77 0.0017 19.5 4.2 33 20-52 8-40 (70)
34 smart00393 R3H Putative single 40.1 30 0.00065 21.9 2.4 23 17-39 37-59 (79)
35 cd02325 R3H R3H domain. The na 40.0 34 0.00073 19.0 2.4 24 16-39 17-40 (59)
36 cd07022 S49_Sppa_36K_type Sign 39.8 74 0.0016 23.5 4.7 42 20-61 143-184 (214)
37 PF00701 DHDPS: Dihydrodipicol 38.2 39 0.00084 25.8 3.1 34 3-39 255-288 (289)
38 TIGR01837 PHA_granule_1 poly(h 37.5 1.4E+02 0.003 20.7 5.8 27 54-83 83-109 (118)
39 PF04423 Rad50_zn_hook: Rad50 37.5 48 0.001 19.7 2.8 20 23-42 29-48 (54)
40 PF02866 Ldh_1_C: lactate/mala 37.3 93 0.002 22.1 4.8 30 19-48 143-172 (174)
41 TIGR00674 dapA dihydrodipicoli 37.0 46 0.00099 25.6 3.3 33 3-38 252-284 (285)
42 PF12614 RRF_GI: Ribosome recy 36.8 50 0.0011 24.1 3.3 44 16-59 4-47 (128)
43 COG1698 Uncharacterized protei 36.5 33 0.00071 24.0 2.2 42 20-62 6-47 (93)
44 cd02639 R3H_RRM R3H domain of 36.0 33 0.00072 21.6 2.0 26 16-41 17-43 (60)
45 KOG3813|consensus 35.1 37 0.00081 30.5 2.8 36 17-52 266-303 (640)
46 PRK04330 hypothetical protein; 33.6 38 0.00082 23.3 2.2 16 47-62 28-43 (88)
47 TIGR03249 KdgD 5-dehydro-4-deo 33.2 56 0.0012 25.4 3.3 32 4-38 263-294 (296)
48 PF03685 UPF0147: Uncharacteri 32.9 40 0.00087 23.0 2.2 16 47-62 25-40 (85)
49 cd07930 bacterial_phosphagen_k 32.5 61 0.0013 25.1 3.4 32 10-42 10-42 (232)
50 PF12875 DUF3826: Protein of u 32.2 60 0.0013 25.2 3.3 17 21-37 122-138 (188)
51 PF05529 Bap31: B-cell recepto 31.8 1E+02 0.0022 22.4 4.3 19 68-87 173-191 (192)
52 KOG4709|consensus 31.4 1.5E+02 0.0032 23.6 5.3 36 26-61 48-84 (217)
53 PRK06569 F0F1 ATP synthase sub 31.0 1.6E+02 0.0035 21.8 5.3 25 36-60 67-91 (155)
54 PF07946 DUF1682: Protein of u 30.6 2.8E+02 0.0061 22.1 7.2 51 29-79 264-314 (321)
55 COG1460 Uncharacterized protei 29.8 64 0.0014 23.2 2.9 66 15-82 44-111 (114)
56 cd07023 S49_Sppa_N_C Signal pe 28.8 1.3E+02 0.0029 21.8 4.5 42 20-61 136-177 (208)
57 PRK10132 hypothetical protein; 28.4 1.4E+02 0.003 20.8 4.3 54 37-94 33-88 (108)
58 cd07018 S49_SppA_67K_type Sign 27.7 1.8E+02 0.004 21.5 5.2 41 22-62 151-191 (222)
59 PRK03620 5-dehydro-4-deoxygluc 27.0 1.2E+02 0.0025 23.8 4.2 34 3-39 264-297 (303)
60 PF01997 Translin: Translin fa 26.7 91 0.002 23.1 3.4 29 27-55 2-30 (200)
61 PF01343 Peptidase_S49: Peptid 25.8 2.2E+02 0.0047 19.9 5.0 43 19-61 75-117 (154)
62 PF04147 Nop14: Nop14-like fam 25.7 1.1E+02 0.0023 28.0 4.2 27 29-55 779-805 (840)
63 PRK14861 tatA twin arginine tr 25.5 1.7E+02 0.0038 18.4 4.0 29 31-59 28-56 (61)
64 TIGR02609 doc_partner putative 25.5 1.3E+02 0.0027 19.1 3.5 36 14-50 37-72 (74)
65 KOG2147|consensus 25.4 90 0.0019 29.1 3.6 28 28-55 746-773 (823)
66 PF00244 14-3-3: 14-3-3 protei 25.4 1.4E+02 0.003 22.8 4.2 32 21-52 31-62 (236)
67 TIGR00706 SppA_dom signal pept 24.5 2.7E+02 0.0058 20.4 5.5 42 20-61 131-172 (207)
68 PRK03170 dihydrodipicolinate s 24.4 1.1E+02 0.0023 23.5 3.5 34 3-39 255-288 (292)
69 PF00140 Sigma70_r1_2: Sigma-7 24.2 87 0.0019 17.5 2.3 25 20-44 13-37 (37)
70 PRK09174 F0F1 ATP synthase sub 24.2 2.7E+02 0.0058 21.1 5.5 36 26-61 137-172 (204)
71 PLN02417 dihydrodipicolinate s 23.6 1.1E+02 0.0024 23.6 3.5 34 3-39 244-277 (280)
72 PF06831 H2TH: Formamidopyrimi 23.6 1.2E+02 0.0025 20.1 3.1 36 2-43 46-81 (92)
73 PF12137 RapA_C: RNA polymeras 23.2 91 0.002 26.0 3.0 70 19-90 270-348 (362)
74 TIGR00013 taut 4-oxalocrotonat 23.1 1.1E+02 0.0023 17.9 2.6 26 16-41 2-29 (63)
75 TIGR02313 HpaI-NOT-DapA 2,4-di 23.0 1.2E+02 0.0025 23.7 3.5 34 3-39 256-289 (294)
76 PF09036 Bcr-Abl_Oligo: Bcr-Ab 23.0 1.9E+02 0.0041 19.7 4.0 26 32-57 27-52 (79)
77 PF09932 DUF2164: Uncharacteri 22.7 1.3E+02 0.0027 19.8 3.1 20 23-42 2-21 (76)
78 KOG0225|consensus 22.6 98 0.0021 26.5 3.1 34 52-86 314-348 (394)
79 COG4847 Uncharacterized protei 22.3 72 0.0016 22.6 2.0 14 40-53 75-88 (103)
80 COG3937 Uncharacterized conser 22.2 2.7E+02 0.0059 19.9 4.9 54 24-83 18-74 (108)
81 PF11069 DUF2870: Protein of u 22.0 1.5E+02 0.0033 20.8 3.5 22 21-42 44-65 (98)
82 PF12732 YtxH: YtxH-like prote 21.9 2.1E+02 0.0046 17.8 7.0 34 20-53 19-52 (74)
83 TIGR00242 mraZ protein. Member 21.7 36 0.00078 24.1 0.4 21 3-23 71-91 (142)
84 PF06160 EzrA: Septation ring 21.7 2.6E+02 0.0056 24.1 5.6 54 34-94 410-466 (560)
85 COG2863 Cytochrome c553 [Energ 21.6 76 0.0017 22.8 2.0 56 17-83 46-101 (121)
86 PF02234 CDI: Cyclin-dependent 21.2 1.1E+02 0.0024 18.4 2.4 21 75-96 24-44 (51)
87 PF01496 V_ATPase_I: V-type AT 21.2 2.4E+02 0.0051 25.0 5.3 48 11-59 210-257 (759)
88 KOG0100|consensus 21.2 4E+02 0.0087 24.0 6.6 61 23-83 539-609 (663)
89 PF13257 DUF4048: Domain of un 21.2 1.5E+02 0.0032 23.8 3.7 30 27-60 77-106 (253)
90 PRK05602 RNA polymerase sigma 20.9 1.5E+02 0.0032 20.7 3.4 25 47-71 161-185 (186)
91 COG1349 GlpR Transcriptional r 20.9 1.4E+02 0.003 22.9 3.4 33 24-56 2-42 (253)
92 PF03623 Focal_AT: Focal adhes 20.9 1.1E+02 0.0024 22.5 2.8 27 19-45 94-120 (139)
93 PF10925 DUF2680: Protein of u 20.7 2.3E+02 0.005 17.7 6.1 49 24-83 1-49 (59)
94 cd00951 KDGDH 5-dehydro-4-deox 20.7 1.4E+02 0.003 23.1 3.4 32 3-37 257-288 (289)
95 PF12297 EVC2_like: Ellis van 20.5 4.9E+02 0.011 22.7 6.9 56 28-83 362-417 (429)
96 PRK10328 DNA binding protein, 20.4 2E+02 0.0043 20.8 4.0 24 50-73 53-76 (134)
97 PF08220 HTH_DeoR: DeoR-like h 20.2 98 0.0021 18.5 2.0 21 36-56 17-37 (57)
98 PRK04147 N-acetylneuraminate l 20.1 1.5E+02 0.0033 22.8 3.6 35 3-40 257-291 (293)
99 PRK11032 hypothetical protein; 20.1 3.8E+02 0.0082 20.0 5.5 48 31-81 10-57 (160)
100 PF01198 Ribosomal_L31e: Ribos 20.1 43 0.00093 22.4 0.5 10 2-11 52-61 (83)
101 PRK13509 transcriptional repre 20.1 1.7E+02 0.0036 22.3 3.8 28 26-53 4-39 (251)
No 1
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=7.1e-28 Score=182.07 Aligned_cols=74 Identities=24% Similarity=0.314 Sum_probs=71.7
Q ss_pred ccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 15 KFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 15 ~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
..++|+||+||+|||++|||.||+++|+|||+|||||||+|++|||++|++.||||+.++++++||++| |.||+
T Consensus 98 ~~IRv~~P~lTeErRkelvK~~k~~~EeakvaiRniRrda~d~iKK~~K~~~isEDe~k~~e~~iQKlT-d~yi~ 171 (187)
T COG0233 98 NVIRVPLPPLTEERRKELVKVAKKYAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEEIQKLT-DEYIK 171 (187)
T ss_pred CeEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHH-HHHHH
Confidence 358999999999999999999999999999999999999999999999999999999999999999999 99986
No 2
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=99.93 E-value=7.9e-26 Score=168.66 Aligned_cols=74 Identities=22% Similarity=0.286 Sum_probs=71.5
Q ss_pred ccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 15 KFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 15 ~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
..++|+||+||+|+|++|||.|++++|+||++||||||+++++||+++|++++|||+.++++++||++| |+||+
T Consensus 96 ~~Iri~iP~lT~E~R~elvK~~k~~~E~aKv~iRniRr~~~~~iKk~~k~~~iseD~~k~~e~eiQklt-d~~i~ 169 (185)
T PRK00083 96 TVIRLPIPPLTEERRKELVKQVKKEAEEAKVAIRNIRRDANDKLKKLEKDKEISEDELKRAEDEIQKLT-DKYIK 169 (185)
T ss_pred CEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHHHHHHH-HHHHH
Confidence 467999999999999999999999999999999999999999999999889999999999999999999 99986
No 3
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=99.92 E-value=9.3e-26 Score=167.21 Aligned_cols=74 Identities=24% Similarity=0.328 Sum_probs=71.5
Q ss_pred ccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 15 KFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 15 ~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
..++||||+||+|+|++|||.|++++|+||++||||||+++++||+++|++.+|||+.+.++++||++| |+||+
T Consensus 87 ~~Iri~iP~lT~E~RkelvK~~k~~~E~aKv~iRniRr~~~~~iKk~~k~~~iseD~~k~~~~~iQklt-d~~i~ 160 (176)
T TIGR00496 87 SVIRVNFPPLTEERRKELVKHAKKIAEQAKVAVRNVRRDANDKVKKLEKDKEISEDEERRLQEEIQKLT-DEYIK 160 (176)
T ss_pred CEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHH-HHHHH
Confidence 467999999999999999999999999999999999999999999999888999999999999999999 99986
No 4
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=99.91 E-value=6.7e-25 Score=162.23 Aligned_cols=73 Identities=26% Similarity=0.348 Sum_probs=71.0
Q ss_pred cCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 16 FQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 16 ~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
.++|+||+||+|+|++|||.||+++|+||++||||||++++.||++++++.+|||+.++++++||++| |+|++
T Consensus 93 ~iri~iP~lT~E~R~~lvK~~k~~~E~~Kv~iRniR~~~~~~lKk~~k~~~iseD~~k~~~~~iqklt-d~~i~ 165 (179)
T cd00520 93 VIRVNLPPLTEERRKELVKDAKKIAEEAKVAIRNIRRDANDKIKKLEKEKEISEDEVKKAEEDLQKLT-DEYIK 165 (179)
T ss_pred EEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCchHHHHHHHHHHHHH-HHHHH
Confidence 67999999999999999999999999999999999999999999999888899999999999999999 99986
No 5
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=99.86 E-value=4.5e-22 Score=144.38 Aligned_cols=74 Identities=26% Similarity=0.325 Sum_probs=68.4
Q ss_pred ccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 15 KFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 15 ~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
....|+||+||+|+|++|+|.||+++|+||++|||||+++++.+|+..+++.+|+|+.++++++||++| |+|++
T Consensus 78 ~~i~v~iP~~T~E~R~~l~k~~k~~~E~~k~~iR~iR~~~~~~lkk~~~~~~~s~D~~~~~~~~iq~l~-~~~~~ 151 (165)
T PF01765_consen 78 NTIRVPIPPPTEERRKELVKQAKKIAEEAKVSIRNIRRDAMKKLKKLKKSKEISEDDIKKLEKEIQKLT-DKYIK 151 (165)
T ss_dssp TEEEEE--SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH-HHHHH
T ss_pred cEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHHHH-HHHHH
Confidence 567899999999999999999999999999999999999999999999888899999999999999999 99986
No 6
>KOG4759|consensus
Probab=99.60 E-value=1.5e-15 Score=120.04 Aligned_cols=71 Identities=31% Similarity=0.361 Sum_probs=66.9
Q ss_pred cCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 16 FQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 16 ~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
...++||++|.|||++|+|.+++.+|++|++||+||++++++++|.++ .+++|+++.+|.++|+++ |.|++
T Consensus 177 ~l~vsiP~~T~E~Re~laK~~~~~~ee~K~slr~ir~~~~kk~~k~~~--~~~~D~vkkae~~l~~l~-k~~v~ 247 (263)
T KOG4759|consen 177 VLRVSIPPVTKESREKLAKVLKRYFEEYKQSLRKIRTKSIKKSKKNKK--SLSEDEVKKAEAELQKLA-KDAVN 247 (263)
T ss_pred EEEecCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--cCChhHHHHHHHHHHHHH-HHHHH
Confidence 467999999999999999999999999999999999999999999853 399999999999999999 99986
No 7
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=74.20 E-value=11 Score=27.87 Aligned_cols=49 Identities=12% Similarity=0.186 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 35 NAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 35 ~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
....+|.++|...-..|...++.|+....+...|++....+.+++..|+
T Consensus 83 ~~~~~f~~~rl~Re~~r~~~~e~L~~ii~~~~~s~~~k~~A~~~~~~l~ 131 (196)
T PF12685_consen 83 SGSDYFAEARLEREQSRSKQIETLKEIINNENASEEEKKEAQDKLLELT 131 (196)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 3346899999999999999999999999888999999999999999998
No 8
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=73.84 E-value=3.1 Score=26.23 Aligned_cols=25 Identities=20% Similarity=0.119 Sum_probs=21.3
Q ss_pred cCccCCCC-CCHHHHHHHHHHHHHHH
Q psy9115 16 FQDQSSFV-VTKEHRESLSKNAKALF 40 (96)
Q Consensus 16 ~~~i~iP~-LTeErRkeLVK~aKk~~ 40 (96)
-.++.||| ||.+.|+-+=..|.+++
T Consensus 17 ~~~l~f~p~lt~~eR~~vH~~a~~~g 42 (60)
T cd02640 17 IRDMVFSPEFSKEERALIHQIAQKYG 42 (60)
T ss_pred cceEEcCCCCCHHHHHHHHHHHHHcC
Confidence 57889999 99999998888887654
No 9
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=71.50 E-value=3.8 Score=25.08 Aligned_cols=26 Identities=19% Similarity=0.089 Sum_probs=21.6
Q ss_pred cCccCCCCCCHHHHHHHHHHHHHHHH
Q psy9115 16 FQDQSSFVVTKEHRESLSKNAKALFV 41 (96)
Q Consensus 16 ~~~i~iP~LTeErRkeLVK~aKk~~E 41 (96)
-..+.|||||...|+-+=+.|..+.=
T Consensus 16 ~~~~~fppm~~~~R~~vH~lA~~~~L 41 (58)
T cd02646 16 RDSLSFPPMDKHGRKTIHKLANCYNL 41 (58)
T ss_pred CceEecCCCCHHHHHHHHHHHHHcCC
Confidence 45679999999999999888887643
No 10
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=70.88 E-value=5.1 Score=25.50 Aligned_cols=22 Identities=18% Similarity=0.040 Sum_probs=17.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHH
Q psy9115 18 DQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 18 ~i~iP~LTeErRkeLVK~aKk~ 39 (96)
-+.+|-||+|.|..+++.+|.-
T Consensus 16 vl~~~nLteeQrn~yI~~lKdd 37 (54)
T PF02216_consen 16 VLHMPNLTEEQRNGYIQSLKDD 37 (54)
T ss_dssp HHCSTTS-HHHHHHHHHHHHH-
T ss_pred HHcCCCcCHHHHHhHHHHHhhC
Confidence 3678999999999999988753
No 11
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=70.30 E-value=4 Score=25.66 Aligned_cols=27 Identities=11% Similarity=0.101 Sum_probs=22.1
Q ss_pred ccCccCCCC-CCHHHHHHHHHHHHHHHH
Q psy9115 15 KFQDQSSFV-VTKEHRESLSKNAKALFV 41 (96)
Q Consensus 15 ~~~~i~iP~-LTeErRkeLVK~aKk~~E 41 (96)
.-.++.||| ||.+.|+-+=..|.+++=
T Consensus 15 ~~~~l~Fpp~ls~~eR~~vH~~a~~~gL 42 (59)
T cd06007 15 DNEEYEFPSSLTNHERAVIHRLCRKLGL 42 (59)
T ss_pred cccEEEcCCCCCHHHHHHHHHHHHHcCC
Confidence 356789998 999999998888877653
No 12
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=69.00 E-value=3.5 Score=29.20 Aligned_cols=49 Identities=18% Similarity=0.208 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHH
Q psy9115 29 RESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFE 82 (96)
Q Consensus 29 RkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQkl 82 (96)
|++|+.+|.++..+-+| |.-..++=..+.+++++|+||+..+-.....-
T Consensus 2 Re~li~~A~~FL~~p~V-----~~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 2 REDLIEQAVKFLQDPKV-----RNSPLEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HHHHHHHHHHHHCTTTC-----CCS-HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHhCCccc-----ccCCHHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 89999999999988763 44444443344556789999998877665443
No 13
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=65.39 E-value=32 Score=21.69 Aligned_cols=62 Identities=6% Similarity=0.064 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 21 SFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 21 iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
...||+|.+..+-....++..+....-++++. ....+..+-....+.++.+..+.+++....
T Consensus 39 ~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~-~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~ 100 (125)
T PF13801_consen 39 MLNLTPEQQAKLRALMDEFRQEMRALRQELRA-ARQELRALLAAPPPDEAAIEALLEEIREAQ 100 (125)
T ss_dssp HS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHCCSSS-HHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 35799999999888887777655544433332 344444444455688888888887777654
No 14
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=62.91 E-value=20 Score=23.39 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhh
Q psy9115 30 ESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDV 72 (96)
Q Consensus 30 keLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~ 72 (96)
++|..+.+++-.+.....+.-|..++..|+.+...-+||-+|+
T Consensus 1 ~eL~~~~~~l~~~~~~~~~~e~~~~~~~i~~~~~~~Gis~~el 43 (93)
T PF00816_consen 1 KELEAQIKELEKEIEERRKQEREEAIAEIRELMAEYGISPEEL 43 (93)
T ss_dssp -HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHTT--HHHC
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHh
Confidence 3566777777777777778888889999999888888998888
No 15
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=59.30 E-value=21 Score=23.32 Aligned_cols=64 Identities=13% Similarity=0.254 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhc-CCCChhhhhhhHHHHHHHhhcccccCCCC
Q psy9115 28 HRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKS-EGLSQDDVRSVSEQSAFESYHGFISGEPL 93 (96)
Q Consensus 28 rRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~-~~iSEDd~k~~e~~IQklT~d~yi~~~~~ 93 (96)
-+.++-..++..+..+...+..+|..+.+.+...... ..+.++ ...--.+.-.-| +.||...|+
T Consensus 10 l~~d~~~l~~~~~~~~~~~~~~~r~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~-~~~V~e~P~ 74 (94)
T PF05957_consen 10 LRADLEDLARSAADLAGEKADEARDRAEEALDDARDRAEDAADQ-AREQAREAAEQT-EDYVRENPW 74 (94)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-HHHHHHChH
Confidence 4555666666666667777777777766666554211 112222 222234444556 689988886
No 16
>PF08910 Aida_N: Aida N-terminus; InterPro: IPR015006 This entry represents the axin interactor, dorsalization-associated protein family AIDA [].; PDB: 1UG7_A.
Probab=59.24 E-value=34 Score=24.28 Aligned_cols=63 Identities=16% Similarity=0.291 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhcccccCCCCCC
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFISGEPLDG 95 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~~~~~~~ 95 (96)
.-+.+|++..+-+.|.|--+ .+|..+...+... ..+|+-++.+.++.-++.|. .|.+.-|+|+
T Consensus 43 ~~~~fte~qkk~i~Kia~cL---------~lRs~~Lq~~t~~--~~~i~ledlk~l~~~lk~ll--~~~~~FP~dv 105 (106)
T PF08910_consen 43 QDSDFTEDQKKTIGKIATCL---------ELRSKALQSLTGS--QEGITLEDLKKLEPILKNLL--DYNKEFPFDV 105 (106)
T ss_dssp S--SS-HHHHHHHHHHHHHH---------HHHHHHHH---S-----S--SHHHHTHHHHHHTTT--T--S--SS--
T ss_pred cCCCCCHHHHHHHHHHHHHH---------HHHHHHHHhhhcc--ccccCHHHHHHHHHHHHHhc--ccCCCCCCCC
Confidence 45788999999998887544 3555555543222 45799999999999999999 5669999986
No 17
>KOG0871|consensus
Probab=58.85 E-value=34 Score=25.89 Aligned_cols=44 Identities=11% Similarity=0.388 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHH
Q psy9115 31 SLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQS 79 (96)
Q Consensus 31 eLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~I 79 (96)
+++--|....++||....+ |+.-..++++ .+|||+++.+-+.++
T Consensus 83 eYiee~~~vl~~~K~~~~~-~~~kssk~e~----~Gi~eEEL~~qQqeL 126 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEAKK-RRRKSSKFEK----SGIPEEELLRQQQEL 126 (156)
T ss_pred HHHHHHHHHHHHHHHHHHH-hhhhhhhHHh----cCCCHHHHHHHHHHH
Confidence 5677788899999999998 5445666665 479999999877765
No 18
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=57.58 E-value=18 Score=19.74 Aligned_cols=26 Identities=8% Similarity=0.101 Sum_probs=19.4
Q ss_pred HHHHHHhhhhcCCCChhhhhhhHHHH
Q psy9115 54 YTKTVKNKEKSEGLSQDDVRSVSEQS 79 (96)
Q Consensus 54 a~~~iKK~eK~~~iSEDd~k~~e~~I 79 (96)
.+..++.+-..+.||+++......+|
T Consensus 4 ~L~~L~~l~~~G~IseeEy~~~k~~l 29 (31)
T PF09851_consen 4 RLEKLKELYDKGEISEEEYEQKKARL 29 (31)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 45567777777889999988766554
No 19
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=56.91 E-value=45 Score=20.71 Aligned_cols=54 Identities=24% Similarity=0.334 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhcccc
Q psy9115 29 RESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFI 88 (96)
Q Consensus 29 RkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi 88 (96)
=..|+..++..+..++..|+.+..... .......+.-+.+-...+++.|+ .+|.
T Consensus 47 l~~l~~~i~~~~~~~~~~lk~l~~~~~-----~~~~~~~~~~~~ri~~nq~~~L~-~kf~ 100 (103)
T PF00804_consen 47 LDELTDEIKQLFQKIKKRLKQLSKDNE-----DSEGEEPSSNEVRIRKNQVQALS-KKFQ 100 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHCTT--SHHHHHHHHHHHHHH-HHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh-----hhcccCCCcHHHHHHHHHHHHHH-HHHH
Confidence 356788888899999999999888744 11134567777787888888888 6664
No 20
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=55.36 E-value=12 Score=23.32 Aligned_cols=24 Identities=13% Similarity=-0.010 Sum_probs=19.9
Q ss_pred CccCCCC-CCHHHHHHHHHHHHHHH
Q psy9115 17 QDQSSFV-VTKEHRESLSKNAKALF 40 (96)
Q Consensus 17 ~~i~iP~-LTeErRkeLVK~aKk~~ 40 (96)
..+.||| ||...|.-+=..|.++.
T Consensus 18 ~~l~F~p~ls~~eR~~vH~lA~~~g 42 (60)
T cd02641 18 TELEFPPTLSSHDRLLVHELAEELG 42 (60)
T ss_pred CcEECCCCCCHHHHHHHHHHHHHcC
Confidence 5789999 99999998877777653
No 21
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=54.31 E-value=51 Score=20.49 Aligned_cols=30 Identities=17% Similarity=0.234 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9115 21 SFVVTKEHRESLSKNAKALFVKCKENIRDI 50 (96)
Q Consensus 21 iP~LTeErRkeLVK~aKk~~EeaKvaIRNI 50 (96)
+|..+.+-|+.++..+....++|...|...
T Consensus 15 ~~~~~~~~r~~~i~~~e~~l~ea~~~l~qM 44 (79)
T PF05008_consen 15 IKNLSGEQRKSLIREIERDLDEAEELLKQM 44 (79)
T ss_dssp GGGS-CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhccChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777899999999999999998887743
No 22
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=54.28 E-value=54 Score=24.72 Aligned_cols=61 Identities=16% Similarity=0.183 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCC---CChhhhhhhHHHHHHHhhcc
Q psy9115 23 VVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEG---LSQDDVRSVSEQSAFESYHG 86 (96)
Q Consensus 23 ~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~---iSEDd~k~~e~~IQklT~d~ 86 (96)
.|++|.|+-|.+.+..........+++...++.+.+.+. .-. +|+++...+.+..+.+. ++
T Consensus 218 ~L~~e~q~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--G~~v~~~s~~~~~~~~~~~~~~~-~e 281 (286)
T PF03480_consen 218 SLPDEDQEALDDAADEAEARAREYYEAEDEEALKELEEN--GVTVVELSDEELAAWREAAAPVW-EE 281 (286)
T ss_dssp HS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--T-EEEEGCHHHHHHHHHHHHHHH-HH
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--cCEEeCCCHHHHHHHHHHHHHHH-HH
Confidence 478999999999999999988888888888877777763 112 49999999999888887 66
No 23
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=52.92 E-value=58 Score=24.63 Aligned_cols=28 Identities=25% Similarity=0.305 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q psy9115 26 KEHRESLSKNAKALFVKCKENIRDIQNK 53 (96)
Q Consensus 26 eErRkeLVK~aKk~~EeaKvaIRNIRRd 53 (96)
.+.|++++|.++.+.-.+|.+|+.|-|.
T Consensus 17 ~~~RE~iik~sRdI~~~Sk~~I~~lHr~ 44 (204)
T PRK14562 17 DEAREEALKLSREIVRLSGDAIRAIHRG 44 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3689999999999999999999988874
No 24
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=52.69 E-value=11 Score=21.18 Aligned_cols=20 Identities=25% Similarity=0.076 Sum_probs=15.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHH
Q psy9115 19 QSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 19 i~iP~LTeErRkeLVK~aKk~ 39 (96)
|++|+-. ..|.+|++.|++.
T Consensus 18 i~~~~~~-~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 18 IPVPKSA-KTRDELLKLAKKN 37 (38)
T ss_pred CCCCCCC-CCHHHHHHHHHHh
Confidence 5666666 7899999999863
No 25
>PRK10404 hypothetical protein; Provisional
Probab=51.61 E-value=42 Score=23.05 Aligned_cols=62 Identities=8% Similarity=0.207 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhh-hcCCCChhhhhhhHHHHHHHhhcccccCCCCC
Q psy9115 31 SLSKNAKALFVKCKENIRDIQNKYTKTVKNKE-KSEGLSQDDVRSVSEQSAFESYHGFISGEPLD 94 (96)
Q Consensus 31 eLVK~aKk~~EeaKvaIRNIRRda~~~iKK~e-K~~~iSEDd~k~~e~~IQklT~d~yi~~~~~~ 94 (96)
++-.+.+.-++.++..+-.+|..+...|+... +-....++-..+. .+.-.-| |.||...|.-
T Consensus 20 dle~Ll~~~~~~a~e~~~~lR~r~~~~L~~ar~~l~~~~~~~~~~~-k~aa~~t-d~yV~e~Pw~ 82 (101)
T PRK10404 20 TLEEVLRSSGDPADQKYVELKARAEKALDDVKKRVSQASDSYYYRA-KQAVYRA-DDYVHEKPWQ 82 (101)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH-HHHHHHH-HHHHHhCcHH
Confidence 44455566677888889999998888887764 1122334333334 5666677 7999999863
No 26
>PF06518 DUF1104: Protein of unknown function (DUF1104); InterPro: IPR009488 This family consists of several hypothetical proteins of unknown function which appear to be found exclusively in Helicobacter pylori.; PDB: 2XRH_A.
Probab=51.60 E-value=72 Score=21.80 Aligned_cols=59 Identities=12% Similarity=0.128 Sum_probs=41.4
Q ss_pred CCHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 24 VTKEHRESLSKNAKALFV-KCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 24 LTeErRkeLVK~aKk~~E-eaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
==.+.+-|+-|.++++-. +++.--++++..+-+.+.+ +|..+.....++|.+-. ..-++
T Consensus 22 ~~~dy~~Ei~KR~~~m~~~~~k~f~~~~~~~~~kn~~~------ms~~e~~k~~~ev~k~~-~~~~~ 81 (93)
T PF06518_consen 22 DVPDYKMEIHKRLKKMKEKEAKDFKKQFKEAARKNLSK------MSVEERKKRREEVRKAL-EKRIK 81 (93)
T ss_dssp GHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHTT------S-HHHHHHHHHHHHHHH-HHT--
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH------CCHHHHHHHHHHHHHHH-HHHHH
Confidence 335789999999999988 8888888888776655554 58888887888877766 44433
No 27
>PRK04195 replication factor C large subunit; Provisional
Probab=50.96 E-value=41 Score=27.94 Aligned_cols=52 Identities=19% Similarity=0.132 Sum_probs=43.7
Q ss_pred ccccccCccCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhh
Q psy9115 11 CRRDKFQDQSSFVV------TKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKE 62 (96)
Q Consensus 11 ~~~~~~~~i~iP~L------TeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~e 62 (96)
+.+..|.++.+|.. |.+.|.-.-..+.+++....++-+.+|.+++.-+.-+-
T Consensus 321 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~ 378 (482)
T PRK04195 321 KKKRGFTRYQPPSYWRLLSKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLSIIF 378 (482)
T ss_pred ccCCCCCCcCCcHHHHHHhhhhHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 44678999999977 77888888888899999999999999999887776654
No 28
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=50.50 E-value=27 Score=24.74 Aligned_cols=61 Identities=16% Similarity=0.226 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHhhcccccCCCCCC
Q psy9115 34 KNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHGFISGEPLDG 95 (96)
Q Consensus 34 K~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT~d~yi~~~~~~~ 95 (96)
.+.+.-+..|+...-++|..+...||+..+.=+-+.|.+..-.++.-.-| |.|+...|.-|
T Consensus 26 evL~ssg~~a~~e~~~lR~r~~~~Lk~~r~rl~~~~d~v~~~sk~a~~~t-D~yV~e~PWq~ 86 (104)
T COG4575 26 EVLKSSGSLAGDEAEELRSKAESALKEARDRLGDTGDAVVQRSKAAADAT-DDYVRENPWQG 86 (104)
T ss_pred HHHHhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-HHHHHcCCchH
Confidence 34455566677778888888888888764322234477777778888899 99999999643
No 29
>PF09440 eIF3_N: eIF3 subunit 6 N terminal domain; InterPro: IPR019010 This entry represents the N-terminal domain of subunit 6 (or e) (eIF3e) of the translation initiation factor eIF3. EIF3 is required in protein synthesis in mammalian cells and, together with other initiation factors, stimulates binding of initiator methionyl-tRNAi and mRNA to the 40S ribosomal subunit to form the 48 S initiation complex []. The eIF3 complex also prevents premature association of the 40 and 60 S ribosomal subunits and interacts with other initiation factors involved in start codon selection. EIF3 has at least 13 protein components (eIF3a-m or 1-13), where subunits h, i, k, and m are likely to be on the periphery of the complex []. Subunit 6 is produced by the int6 gene, one of the frequent integration sites for mouse mammary tumor viruses [].
Probab=47.81 E-value=72 Score=22.87 Aligned_cols=58 Identities=16% Similarity=0.285 Sum_probs=45.4
Q ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHHH---------HHHHHHhhHHHHHHHhhhhcCCCChhhhhhh
Q psy9115 18 DQSSFVVTKEHRESLSKNAKALFVKCK---------ENIRDIQNKYTKTVKNKEKSEGLSQDDVRSV 75 (96)
Q Consensus 18 ~i~iP~LTeErRkeLVK~aKk~~EeaK---------vaIRNIRRda~~~iKK~eK~~~iSEDd~k~~ 75 (96)
+-.+|.=..++|+++++..+.+.+++- ..+.++|+|....+.-++++-+|+.|.+..+
T Consensus 60 ~~e~p~e~~~kr~~Vl~~l~~l~~~~~~v~~~~~~~ev~~~l~~dk~~nl~~L~~~h~it~e~id~L 126 (133)
T PF09440_consen 60 DDEVPAELAEKREEVLAELKELEEETEPVLELLEDPEVVKNLRSDKKQNLEYLEENHGITPEMIDAL 126 (133)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHccHHHHHHHHHHhcCCCHHHHHHH
Confidence 345888889999999999999888764 4567888887777777766777888776544
No 30
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=47.28 E-value=76 Score=21.14 Aligned_cols=45 Identities=4% Similarity=0.068 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHH
Q psy9115 34 KNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQS 79 (96)
Q Consensus 34 K~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~I 79 (96)
++++..++.==-..-+||+.-..---.+ ..+.||+++....++++
T Consensus 17 e~I~~~Ae~E~~Dp~~i~~~L~~L~~~~-e~GEIseeEf~~~E~eL 61 (79)
T PF05120_consen 17 EQIQEQAERELYDPAAIRRELAELQEAL-EAGEISEEEFERREDEL 61 (79)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHHHHH-HcCCCCHHHHHHHHHHH
Confidence 3344444444445678888755443344 36889999999888775
No 31
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=47.19 E-value=67 Score=25.96 Aligned_cols=68 Identities=12% Similarity=0.134 Sum_probs=49.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhh-hHHHHHHHhhcccccCCC
Q psy9115 22 FVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRS-VSEQSAFESYHGFISGEP 92 (96)
Q Consensus 22 P~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~-~e~~IQklT~d~yi~~~~ 92 (96)
=.|++|.|+-|-+.|+..++..+..+...=..+.+.+++. .-.+.+.+... ..+-.+.+. +.|.+..|
T Consensus 248 ~~L~~e~q~il~~aa~e~~~~~~~~~~~~e~~~~e~lk~~--Gv~v~~~~~~~~~~~~~~~~~-~~~~~~~~ 316 (332)
T COG1638 248 DSLPEEDQTILLEAAKEAAEEQRKLVEELEDELLEKLKEA--GVEVVEPDAAEAFREAAKPVY-DEFAKKAG 316 (332)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCEEecCCchHHHHHHHHHHH-HHHHhhch
Confidence 3689999999999999999888887777777777777664 12355544443 667777777 88887765
No 32
>COG5404 SulA SOS-response cell division inhibitor, blocks FtsZ ring formation [Cell division and chromosome partitioning]
Probab=42.31 E-value=21 Score=27.18 Aligned_cols=17 Identities=35% Similarity=0.333 Sum_probs=15.0
Q ss_pred CCCCCHHHHHHHHHHHH
Q psy9115 21 SFVVTKEHRESLSKNAK 37 (96)
Q Consensus 21 iP~LTeErRkeLVK~aK 37 (96)
+|+||+|-|.+|+..||
T Consensus 120 l~eLte~~r~~L~~AAk 136 (169)
T COG5404 120 LAELTEEERAELVDAAK 136 (169)
T ss_pred cchhcHHHHHHHHHHHH
Confidence 58999999999998765
No 33
>PF07564 DUF1542: Domain of Unknown Function (DUF1542); InterPro: IPR011439 This domain is found in several cell surface proteins. Some are involved in antibiotic resistance (e.g. Q9RL69 from SWISSPROT and Q9LCJ9 from SWISSPROT) [] and/or cellular adhesion (e.g. Q931R6 from SWISSPROT) []. In some proteins it is repeated more than fifteen times.
Probab=40.49 E-value=77 Score=19.52 Aligned_cols=33 Identities=9% Similarity=0.184 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQN 52 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRR 52 (96)
.-|.+|.|-+......+.....++...|-+...
T Consensus 8 ~~~~~T~eEK~~A~~~v~~~~~~a~~~I~~a~t 40 (70)
T PF07564_consen 8 NNPNATDEEKQAAKQKVDQILNQAINAINQATT 40 (70)
T ss_pred cCCcCCHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 358999999999999999999999998887763
No 34
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=40.14 E-value=30 Score=21.91 Aligned_cols=23 Identities=9% Similarity=0.005 Sum_probs=18.7
Q ss_pred CccCCCCCCHHHHHHHHHHHHHH
Q psy9115 17 QDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 17 ~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
..+.|||||...|+-+=..|..+
T Consensus 37 ~~~~~~pm~~~~R~~iH~~a~~~ 59 (79)
T smart00393 37 ESVELPPMNSYERKIVHELAEKY 59 (79)
T ss_pred CeEEcCCCCHHHHHHHHHHHHHc
Confidence 56899999999999877766654
No 35
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=39.98 E-value=34 Score=19.04 Aligned_cols=24 Identities=8% Similarity=-0.096 Sum_probs=19.9
Q ss_pred cCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 16 FQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 16 ~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
...+.||++|...|.-+-..|..+
T Consensus 17 ~~~~~~~p~~~~~R~~vH~la~~~ 40 (59)
T cd02325 17 GKSLELPPMNSYERKLIHDLAEYY 40 (59)
T ss_pred CCeEEcCCCCHHHHHHHHHHHHHC
Confidence 567889999999999887777655
No 36
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=39.83 E-value=74 Score=23.46 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=37.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNK 61 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~ 61 (96)
|+.++|+|.|+.+-..+..+.+..-..|..=|....++++..
T Consensus 143 ~~~~~s~~~re~~~~~l~~~~~~f~~~V~~~R~~~~~~~~~~ 184 (214)
T cd07022 143 PDEPLSDEARARLQAEVDALYAMFVAAVARNRGLSAAAVRAT 184 (214)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHh
Confidence 566899999999999999999999999999998777777665
No 37
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=38.18 E-value=39 Score=25.83 Aligned_cols=34 Identities=24% Similarity=0.220 Sum_probs=23.6
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
+++.+|+..-. -+.|+.+||+|.+++|-+..++.
T Consensus 255 ~l~~~G~~~g~---~R~Pl~~l~~~~~~~l~~~l~~~ 288 (289)
T PF00701_consen 255 ALELRGLIAGP---VRPPLLPLSDEEKEELKEILKEA 288 (289)
T ss_dssp HHHHTTSSSSB-----TTS-SS-HHHHHHHHHHHHHT
T ss_pred HHHHCCCCCCC---CCCCCCCCCHHHHHHHHHHHHhC
Confidence 46677775543 67899999999999999888765
No 38
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=37.47 E-value=1.4e+02 Score=20.70 Aligned_cols=27 Identities=7% Similarity=0.112 Sum_probs=20.4
Q ss_pred HHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 54 YTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 54 a~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
..+.+..+ +..|.+|+..++..|+.|+
T Consensus 83 v~~~L~~l---g~~tk~ev~~L~~RI~~Le 109 (118)
T TIGR01837 83 VEQALNRL---NIPSREEIEALSAKIEQLA 109 (118)
T ss_pred HHHHHHHc---CCCCHHHHHHHHHHHHHHH
Confidence 33444554 5689999999999999887
No 39
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=37.45 E-value=48 Score=19.65 Aligned_cols=20 Identities=30% Similarity=0.388 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHHHHHHH
Q psy9115 23 VVTKEHRESLSKNAKALFVK 42 (96)
Q Consensus 23 ~LTeErRkeLVK~aKk~~Ee 42 (96)
+|++++|.+|++..+...+.
T Consensus 29 ~l~~e~~~~li~~~~~~i~~ 48 (54)
T PF04423_consen 29 PLDEEHRQELIKKYKSEIEE 48 (54)
T ss_dssp EE-HHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHh
Confidence 68999999998877665544
No 40
>PF02866 Ldh_1_C: lactate/malate dehydrogenase, alpha/beta C-terminal domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR022383 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle. This entry represents the C-terminal, and is thought to be an is an unusual alpha+beta fold.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 4MDH_B 5MDH_A 1GV0_A 1GUZ_D 2EWD_B 2FRM_D 2FNZ_B 2FN7_B 2FM3_A 1LTH_T ....
Probab=37.28 E-value=93 Score=22.06 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=23.9
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy9115 19 QSSFVVTKEHRESLSKNAKALFVKCKENIR 48 (96)
Q Consensus 19 i~iP~LTeErRkeLVK~aKk~~EeaKvaIR 48 (96)
+..|+||++-++.|-+.|+.+-+..+.+..
T Consensus 143 ~~~~~L~~~E~~~l~~sa~~l~~~i~~~~~ 172 (174)
T PF02866_consen 143 VEDLPLSEEEQEKLKESAKELKKEIEKGLE 172 (174)
T ss_dssp ECSBSSTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455789999999999998888777666554
No 41
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=37.03 E-value=46 Score=25.57 Aligned_cols=33 Identities=24% Similarity=0.100 Sum_probs=25.2
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKA 38 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk 38 (96)
+|+.+|+..- ..+.|+++||.+.+++|.+.++.
T Consensus 252 ~l~~~G~~~g---~~R~P~~~l~~~~~~~l~~~l~~ 284 (285)
T TIGR00674 252 ALALLGLIEG---ELRLPLTELSEEHRNKLRDVLKD 284 (285)
T ss_pred HHHHcCCCCC---CCCCCCCCCCHHHHHHHHHHHHh
Confidence 4566776432 46889999999999999887753
No 42
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=36.84 E-value=50 Score=24.12 Aligned_cols=44 Identities=11% Similarity=-0.009 Sum_probs=33.5
Q ss_pred cCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q psy9115 16 FQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVK 59 (96)
Q Consensus 16 ~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iK 59 (96)
.+-|++|.|=---=.+-||.++..|-++.=.+..|||.=|-+|.
T Consensus 4 ~i~I~LpSlIHRig~~~~k~~ka~A~q~~CeLKRVRRSRnWql~ 47 (128)
T PF12614_consen 4 DITIPLPSLIHRIGREAVKQAKALARQHGCELKRVRRSRNWQLS 47 (128)
T ss_pred ceeeccHHHHHHhhHHHHHHHHHHHHHhCchHHHHHHhhhhHHh
Confidence 34566666643333788999999999999999999997666554
No 43
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.51 E-value=33 Score=23.99 Aligned_cols=42 Identities=7% Similarity=0.052 Sum_probs=30.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhh
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKE 62 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~e 62 (96)
..|.+++|.=++.+-.......+.-| =|||||-|.+.+.++.
T Consensus 6 ~~~~d~~e~i~q~~~lL~~Ii~DttV-PRNIRraA~~a~e~L~ 47 (93)
T COG1698 6 GLMNDSEEKINQVMQLLDEIIQDTTV-PRNIRRAAEEAKEALN 47 (93)
T ss_pred cchhhhHHHHHHHHHHHHHHHccccc-cHHHHHHHHHHHHHHh
Confidence 35667777777777776666555544 4999999988888874
No 44
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=35.97 E-value=33 Score=21.63 Aligned_cols=26 Identities=12% Similarity=-0.027 Sum_probs=21.2
Q ss_pred cCccCCCC-CCHHHHHHHHHHHHHHHH
Q psy9115 16 FQDQSSFV-VTKEHRESLSKNAKALFV 41 (96)
Q Consensus 16 ~~~i~iP~-LTeErRkeLVK~aKk~~E 41 (96)
-.++.||+ ||.+.|+-+-..|..++=
T Consensus 17 ~~eL~Fp~~ls~~eRriih~la~~lGL 43 (60)
T cd02639 17 RDELAFPSSLSPAERRIVHLLASRLGL 43 (60)
T ss_pred ceEEEcCCCCCHHHHHHHHHHHHHcCC
Confidence 45677777 999999999999988753
No 45
>KOG3813|consensus
Probab=35.08 E-value=37 Score=30.48 Aligned_cols=36 Identities=19% Similarity=0.299 Sum_probs=27.4
Q ss_pred CccCCCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHhh
Q psy9115 17 QDQSSFVVTKEHRESLSKNAKA--LFVKCKENIRDIQN 52 (96)
Q Consensus 17 ~~i~iP~LTeErRkeLVK~aKk--~~EeaKvaIRNIRR 52 (96)
.++.+|+++.-||..|.|.+.- +--+-|..+|.||+
T Consensus 266 ~~v~Lqpip~rrRraLLkaSGVrkIDaeEK~elralRn 303 (640)
T KOG3813|consen 266 SNVSLQPIPQRRRRALLKASGVRKIDAEEKDELRALRN 303 (640)
T ss_pred hccccCCCCHHHHHHHHHhccccccchhhHHHHHHHHh
Confidence 4577999999999999998654 33344777777775
No 46
>PRK04330 hypothetical protein; Provisional
Probab=33.60 E-value=38 Score=23.32 Aligned_cols=16 Identities=19% Similarity=0.077 Sum_probs=13.2
Q ss_pred HHHHhhHHHHHHHhhh
Q psy9115 47 IRDIQNKYTKTVKNKE 62 (96)
Q Consensus 47 IRNIRRda~~~iKK~e 62 (96)
=|||||-|.+.+..+.
T Consensus 28 PRNIRraa~ea~~~L~ 43 (88)
T PRK04330 28 PRNIRRAATEAKEILL 43 (88)
T ss_pred ChHHHHHHHHHHHHHh
Confidence 3999999888888774
No 47
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=33.19 E-value=56 Score=25.35 Aligned_cols=32 Identities=22% Similarity=0.032 Sum_probs=24.3
Q ss_pred hhhccccccccccCccCCCCCCHHHHHHHHHHHHH
Q psy9115 4 LWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKA 38 (96)
Q Consensus 4 ~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk 38 (96)
|..+|+.+ ..-|.|+++||.+.|+.|.+..+.
T Consensus 263 l~~~G~~~---g~~R~Pl~~l~~~~~~~i~~~l~~ 294 (296)
T TIGR03249 263 MEIVGLPA---GPVRPPLTDLTKEEYAQLEVILKK 294 (296)
T ss_pred HHHcCCCC---CCCCCCCCCCCHHHHHHHHHHHHh
Confidence 44567643 356899999999999998877654
No 48
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=32.86 E-value=40 Score=23.04 Aligned_cols=16 Identities=13% Similarity=0.100 Sum_probs=13.1
Q ss_pred HHHHhhHHHHHHHhhh
Q psy9115 47 IRDIQNKYTKTVKNKE 62 (96)
Q Consensus 47 IRNIRRda~~~iKK~e 62 (96)
=|||||-+.+.+..+.
T Consensus 25 PRNIRr~a~ea~~~L~ 40 (85)
T PF03685_consen 25 PRNIRRAAEEAKEILN 40 (85)
T ss_dssp -HHHHHHHHHHHHHCT
T ss_pred ChHHHHHHHHHHHHHh
Confidence 3999999988888874
No 49
>cd07930 bacterial_phosphagen_kinase Phosphagen (guanidino) kinases found in bacteria. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, such as phosphocreatine (PCr) or phosphoarginine, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. This subfamily is specific to bacteria and lacks an N-terminal domain, which otherwise forms part of the substrate binding site. Most of the catalytic residues are found in the larger C-terminal domain, however, which appears conserved in these bacterial proteins. Their functions have not been characterized.
Probab=32.49 E-value=61 Score=25.09 Aligned_cols=32 Identities=6% Similarity=0.103 Sum_probs=24.3
Q ss_pred cccccccCccCCCC-CCHHHHHHHHHHHHHHHHH
Q psy9115 10 ECRRDKFQDQSSFV-VTKEHRESLSKNAKALFVK 42 (96)
Q Consensus 10 ~~~~~~~~~i~iP~-LTeErRkeLVK~aKk~~Ee 42 (96)
.|.| .+.++|||+ ||.+.|.++...+++....
T Consensus 10 rlaR-Nl~g~~Fp~~ls~~~~~~v~~~v~~~l~~ 42 (232)
T cd07930 10 RLAR-NLKGYPFPNKLSEEQAADVLEKVEKALSN 42 (232)
T ss_pred EEEE-ccCCCCCCccCCHHHHHHHHHHHHHHHhc
Confidence 3444 366788887 9999999999988877543
No 50
>PF12875 DUF3826: Protein of unknown function (DUF3826); InterPro: IPR024284 This is a putative sugar-binding family.; PDB: 3KDW_A 3G6I_A.
Probab=32.18 E-value=60 Score=25.19 Aligned_cols=17 Identities=18% Similarity=0.116 Sum_probs=10.8
Q ss_pred CCCCCHHHHHHHHHHHH
Q psy9115 21 SFVVTKEHRESLSKNAK 37 (96)
Q Consensus 21 iP~LTeErRkeLVK~aK 37 (96)
||.||+|.+..+....+
T Consensus 122 vP~Lteeek~~I~~~L~ 138 (188)
T PF12875_consen 122 VPSLTEEEKAQILTWLK 138 (188)
T ss_dssp -TT--HHHHHHHHHHHH
T ss_pred cCcccHHHHHHHHHHHH
Confidence 79999999988765443
No 51
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=31.80 E-value=1e+02 Score=22.43 Aligned_cols=19 Identities=11% Similarity=0.260 Sum_probs=13.2
Q ss_pred ChhhhhhhHHHHHHHhhccc
Q psy9115 68 SQDDVRSVSEQSAFESYHGF 87 (96)
Q Consensus 68 SEDd~k~~e~~IQklT~d~y 87 (96)
.+.+...+.+|+..++ .+|
T Consensus 173 ~~~~~~~LkkQ~~~l~-~ey 191 (192)
T PF05529_consen 173 KEKEIEALKKQSEGLQ-KEY 191 (192)
T ss_pred HHHHHHHHHHHHHHHH-hhc
Confidence 5566677777777777 665
No 52
>KOG4709|consensus
Probab=31.41 E-value=1.5e+02 Score=23.56 Aligned_cols=36 Identities=11% Similarity=0.245 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HhhHHHHHHHhh
Q psy9115 26 KEHRESLSKNAKALFVKCKENIRD-IQNKYTKTVKNK 61 (96)
Q Consensus 26 eErRkeLVK~aKk~~EeaKvaIRN-IRRda~~~iKK~ 61 (96)
-|||+.-.+.+++..-.-++.+|. +|...+..|...
T Consensus 48 veRrK~Aqeqikeq~ReerielRk~~rqerkr~LeEr 84 (217)
T KOG4709|consen 48 VERRKAAQEQIKEQLREERIELRKERRQERKRMLEER 84 (217)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367777778888888888888887 555555555443
No 53
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=30.98 E-value=1.6e+02 Score=21.80 Aligned_cols=25 Identities=8% Similarity=0.150 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHhhHHHHHHHh
Q psy9115 36 AKALFVKCKENIRDIQNKYTKTVKN 60 (96)
Q Consensus 36 aKk~~EeaKvaIRNIRRda~~~iKK 60 (96)
..+...+|+.....||.++.+.+..
T Consensus 67 ye~~L~~Ar~eA~~I~~e~~~~~~a 91 (155)
T PRK06569 67 YNEEIDKTNTEIDRLKKEKIDSLES 91 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555566666665555443
No 54
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=30.58 E-value=2.8e+02 Score=22.11 Aligned_cols=51 Identities=16% Similarity=0.137 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHH
Q psy9115 29 RESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQS 79 (96)
Q Consensus 29 RkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~I 79 (96)
|++..+...+..++.+..-+.-|+..-+.-++..+-..+|.++.+++++.-
T Consensus 264 R~~~~~~~~K~~~~~r~E~~~~~k~e~kr~e~~~~~~~lspeeQrK~eeKe 314 (321)
T PF07946_consen 264 REEEEEKILKEAHQERQEEAQEKKEEKKREERERKLSKLSPEEQRKYEEKE 314 (321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 444444444444444444444444333333332223457778887777643
No 55
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.84 E-value=64 Score=23.17 Aligned_cols=66 Identities=18% Similarity=0.140 Sum_probs=44.9
Q ss_pred ccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhh-cC-CCChhhhhhhHHHHHHH
Q psy9115 15 KFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEK-SE-GLSQDDVRSVSEQSAFE 82 (96)
Q Consensus 15 ~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK-~~-~iSEDd~k~~e~~IQkl 82 (96)
+|..+. |.-..|-.++|++..+ +-|.+-+.|=.|-=...+.|+..-- .. .+|.|++..+-+-+.++
T Consensus 44 kFakld-pe~a~e~veEL~~i~~-~~e~~avkIadI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky 111 (114)
T COG1460 44 KFAKLD-PEKARELVEELLSIVK-MSEKIAVKIADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKY 111 (114)
T ss_pred HHhcCC-HHHHHHHHHHHHhhcc-ccHHHHHHHHHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 677777 7777888888888888 7888888887777777777766322 22 26666666655555443
No 56
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=28.77 E-value=1.3e+02 Score=21.84 Aligned_cols=42 Identities=10% Similarity=0.114 Sum_probs=35.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNK 61 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~ 61 (96)
|++++|++.|+.+-..+..+.+.....|..=|....+.++..
T Consensus 136 ~~~~~s~~~~e~~~~~l~~~~~~f~~~Va~~R~~~~~~~~~~ 177 (208)
T cd07023 136 PDRPLTEEERAILQALVDDIYDQFVDVVAEGRGMSGERLDKL 177 (208)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHh
Confidence 478999999999999999999999999998886555555554
No 57
>PRK10132 hypothetical protein; Provisional
Probab=28.45 E-value=1.4e+02 Score=20.80 Aligned_cols=54 Identities=11% Similarity=0.094 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCC--hhhhhhhHHHHHHHhhcccccCCCCC
Q psy9115 37 KALFVKCKENIRDIQNKYTKTVKNKEKSEGLS--QDDVRSVSEQSAFESYHGFISGEPLD 94 (96)
Q Consensus 37 Kk~~EeaKvaIRNIRRda~~~iKK~eK~~~iS--EDd~k~~e~~IQklT~d~yi~~~~~~ 94 (96)
+..+..+...+..+|..+...|+.... .++ ++..... .+.-..| +.||...|+-
T Consensus 33 ~~~~~~~~~~~~~lR~r~~~~L~~ar~--~l~~~~~~~~~~-~~a~~~~-~~~V~~~Pw~ 88 (108)
T PRK10132 33 KSWGSDAKGEAEAARRKAQALLKETRA--RMHGRTRVQQAA-RDAVGCA-DTFVRERPWC 88 (108)
T ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHH--HHhhhHHHHHHH-HHHHHHH-HHHHHhCcHH
Confidence 444566677788889888888877631 122 2322222 5556678 8999999863
No 58
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=27.70 E-value=1.8e+02 Score=21.52 Aligned_cols=41 Identities=10% Similarity=0.047 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhh
Q psy9115 22 FVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKE 62 (96)
Q Consensus 22 P~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~e 62 (96)
+++|+|.|+.+-..+..+.+.....|-.-|.-..+.++...
T Consensus 151 ~~~s~~~r~~~~~~l~~~~~~f~~~Va~~R~~~~~~~~~~~ 191 (222)
T cd07018 151 DDMSPEAREQTQALLDSLWDQYLADVAASRGLSPDALEALI 191 (222)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 47999999999999999999999999998876666666554
No 59
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=27.03 E-value=1.2e+02 Score=23.75 Aligned_cols=34 Identities=15% Similarity=-0.092 Sum_probs=25.4
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
+|+-+|+. ...-|.|+.+||.|.|..+.+..+..
T Consensus 264 al~~~G~~---~g~~R~Pl~~l~~~~~~~i~~~l~~~ 297 (303)
T PRK03620 264 GARLVGLD---AGPVRAPLTDLTPEELAELAALIAKG 297 (303)
T ss_pred HHHHcCCC---CCCCCCCCCCCCHHHHHHHHHHHHHh
Confidence 45667873 23568999999999999988776653
No 60
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=26.72 E-value=91 Score=23.08 Aligned_cols=29 Identities=17% Similarity=0.165 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Q psy9115 27 EHRESLSKNAKALFVKCKENIRDIQNKYT 55 (96)
Q Consensus 27 ErRkeLVK~aKk~~EeaKvaIRNIRRda~ 55 (96)
++|+.++|..+.....+|.+|.-+.|--.
T Consensus 2 d~RE~iik~sRdi~~~Sk~~I~~lhr~~~ 30 (200)
T PF01997_consen 2 DRRERIIKLSRDITRLSKKIIFALHRIDQ 30 (200)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCTCTT
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 68999999999999999999888776433
No 61
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=25.77 E-value=2.2e+02 Score=19.90 Aligned_cols=43 Identities=14% Similarity=0.168 Sum_probs=33.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q psy9115 19 QSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNK 61 (96)
Q Consensus 19 i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~ 61 (96)
.+.-++|+|.|+.+-..+..+.+.....|..=|.-..+.++..
T Consensus 75 ~~~~~~s~~~r~~~~~~l~~~~~~f~~~Va~~R~~~~~~v~~~ 117 (154)
T PF01343_consen 75 FPRDPMSEEERENLQELLDELYDQFVNDVAEGRGLSPDDVEEI 117 (154)
T ss_dssp CTTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCH
T ss_pred CcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHH
Confidence 5788999999999999999999999999998886555555543
No 62
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=25.67 E-value=1.1e+02 Score=27.98 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHH
Q psy9115 29 RESLSKNAKALFVKCKENIRDIQNKYT 55 (96)
Q Consensus 29 RkeLVK~aKk~~EeaKvaIRNIRRda~ 55 (96)
|.++.|+-+++-.+-|=|||.||+|+.
T Consensus 779 r~E~~KLk~q~KkErKGA~RELRKD~~ 805 (840)
T PF04147_consen 779 RAELRKLKAQLKKERKGAMRELRKDNR 805 (840)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999975
No 63
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=25.55 E-value=1.7e+02 Score=18.44 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q psy9115 31 SLSKNAKALFVKCKENIRDIQNKYTKTVK 59 (96)
Q Consensus 31 eLVK~aKk~~EeaKvaIRNIRRda~~~iK 59 (96)
++++.+.+..-+.|.++..++++..+..+
T Consensus 28 ~l~r~~G~~~~~fk~~~~~~~~~~~~~~~ 56 (61)
T PRK14861 28 ELGKALGKTLREFKKATKELTDDDFQEKK 56 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHhhh
Confidence 45555655555556666665555444433
No 64
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=25.53 E-value=1.3e+02 Score=19.15 Aligned_cols=36 Identities=11% Similarity=0.141 Sum_probs=27.2
Q ss_pred cccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9115 14 DKFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDI 50 (96)
Q Consensus 14 ~~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNI 50 (96)
+.+.=.+.++ +++..+++.+.+.+..++.+.++|.+
T Consensus 37 ~~iii~~~~~-~~~~~~~~~~~~~~~~~~y~~~l~~L 72 (74)
T TIGR02609 37 GGLKLKRFDE-GKELEKKMQMAVERAMSKYDEALKEL 72 (74)
T ss_pred CEEEEEECCC-CccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344554 67999999999999999999888754
No 65
>KOG2147|consensus
Probab=25.42 E-value=90 Score=29.10 Aligned_cols=28 Identities=25% Similarity=0.285 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHH
Q psy9115 28 HRESLSKNAKALFVKCKENIRDIQNKYT 55 (96)
Q Consensus 28 rRkeLVK~aKk~~EeaKvaIRNIRRda~ 55 (96)
.|.++-|+.+++=.+.|=|||-||+|+-
T Consensus 746 ~r~e~kKL~~klKrE~kGAiRElRKD~~ 773 (823)
T KOG2147|consen 746 ERSELKKLKAKLKRERKGAIRELRKDAA 773 (823)
T ss_pred hHHHHHHHHHHHHHHhhhhHHHHHhhHH
Confidence 4778888888889999999999999964
No 66
>PF00244 14-3-3: 14-3-3 protein; InterPro: IPR023410 The 14-3-3 proteins are a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimeric within all eukaryotic cells [, ]. There is a high degree of sequence identity and conservation between all the 14-3-3 isotypes, particularly in the regions which form the dimer interface or line the central ligand binding channel of the dimeric molecule. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins. The monomer consists of nine helices organised in an antiparallel manner, forming an L-shaped structure. The interior of the L-structure is composed of four helices: H3 and H5, which contain many charged and polar amino acids, and H7 and H9, which contain hydrophobic amino acids. These four helices form the concave amphipathic groove that interacts with target peptides. 14-3-3 proteins mainly bind proteins containing phosphothreonine or phosphoserine motifs however exceptions to this rule do exist. Extensive investigation of the 14-3-3 binding site of the mammalian serine/threonine kinase Raf-1 has produced a consensus sequence for 14-3-3-binding, RSxpSxP (in the single-letter amino-acid code, where x denotes any amino acid and p indicates that the next residue is phosphorylated). 14-3-3 proteins appear to effect intracellular signalling in one of three ways - by direct regulation of the catalytic activity of the bound protein, by regulating interactions between the bound protein and other molecules in the cell by sequestration or modification or by controlling the subcellular localisation of the bound ligand. Proteins appear to initially bind to a single dominant site and then subsequently to many, much weaker secondary interaction sites. The 14-3-3 dimer is capable of changing the conformation of its bound ligand whilst itself undergoing minimal structural alteration. This entry represents the structural domain found in 14-3-3 proteins.; PDB: 2O8P_A 3AXY_D 2C74_A 2C63_A 4DX0_A 1YWT_A 3P1O_A 3P1N_A 4DAU_A 3U9X_A ....
Probab=25.39 E-value=1.4e+02 Score=22.84 Aligned_cols=32 Identities=22% Similarity=0.180 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy9115 21 SFVVTKEHRESLSKNAKALFVKCKENIRDIQN 52 (96)
Q Consensus 21 iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRR 52 (96)
-|.||.|.|.-|+-..|...-.-+-++|-|..
T Consensus 31 ~~eLt~eERnLlsvayKn~i~~~R~s~R~l~~ 62 (236)
T PF00244_consen 31 NPELTEEERNLLSVAYKNVIGSRRASWRILSS 62 (236)
T ss_dssp SS---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHhccccchHHHHhhhh
Confidence 68999999999999999999999999988854
No 67
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=24.51 E-value=2.7e+02 Score=20.43 Aligned_cols=42 Identities=17% Similarity=0.133 Sum_probs=34.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNK 61 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~ 61 (96)
|+-++|+|.|+.+-..+..+.+.....|-.=|.-..+.++..
T Consensus 131 ~~~~~s~~~~e~~~~~l~~~~~~f~~~va~~R~~~~~~~~~~ 172 (207)
T TIGR00706 131 PTRELTPEERDILQNLVNESYEQFVQVVAKGRNLPVEDVKKF 172 (207)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 345799999999999999999999999988887666666654
No 68
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=24.38 E-value=1.1e+02 Score=23.50 Aligned_cols=34 Identities=21% Similarity=0.074 Sum_probs=26.2
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
+++.+|+.+- --+.|+++||++.++.+.+..++.
T Consensus 255 ~l~~~G~~~g---~~R~P~~~l~~~~~~~i~~~l~~~ 288 (292)
T PRK03170 255 ALNLLGLIEG---ELRLPLVPLSEEEKEKLRAALKEA 288 (292)
T ss_pred HHHHcCCCCC---CCCCCCCCCCHHHHHHHHHHHHHc
Confidence 4667888543 168899999999999998887753
No 69
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=24.24 E-value=87 Score=17.50 Aligned_cols=25 Identities=12% Similarity=0.046 Sum_probs=19.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCK 44 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaK 44 (96)
.+|-||.|.=.+|++.++.-.+.+|
T Consensus 13 ~~~LLt~eeE~~LA~~i~~g~~~ar 37 (37)
T PF00140_consen 13 RYPLLTAEEEIELARRIRKGDEAAR 37 (37)
T ss_dssp HS-EETTHHHHHHHHHHHHHHHHH-
T ss_pred CCCCCCHHHHHHHHHHHHHhHHhcC
Confidence 3688999999999999988776664
No 70
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=24.15 E-value=2.7e+02 Score=21.05 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q psy9115 26 KEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNK 61 (96)
Q Consensus 26 eErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~ 61 (96)
++-+.++-..+.++.++++..|...|..++..|+..
T Consensus 137 e~~~~~a~~ea~~~l~~Ae~~I~~ek~~A~~el~~~ 172 (204)
T PRK09174 137 EAERAAIEASLEKKLKEAEARIAAIKAKAMADVGSI 172 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666677777777777777777777654
No 71
>PLN02417 dihydrodipicolinate synthase
Probab=23.58 E-value=1.1e+02 Score=23.56 Aligned_cols=34 Identities=18% Similarity=0.063 Sum_probs=24.9
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
.|+.+|+.+- --|.|+++||.+.++.|.+..+.+
T Consensus 244 al~~~G~~~g---~~R~Pl~~l~~~~~~~l~~~l~~~ 277 (280)
T PLN02417 244 ALAQLGLIRP---VFRLPYVPLDLAKRAEFVALVKAI 277 (280)
T ss_pred HHHHcCCCCC---CCCCCCCCCCHHHHHHHHHHHHHc
Confidence 3455676432 138899999999999998887653
No 72
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=23.56 E-value=1.2e+02 Score=20.06 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=26.3
Q ss_pred hhhhhccccccccccCccCCCCCCHHHHHHHHHHHHHHHHHH
Q psy9115 2 EMLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKALFVKC 43 (96)
Q Consensus 2 ~~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~~Eea 43 (96)
|.||.-|+.=. -++-.||++....|...++.....+
T Consensus 46 EiLf~a~i~P~------~~~~~L~~~~~~~l~~~~~~vl~~a 81 (92)
T PF06831_consen 46 EILFRAGIHPE------RPASSLSEEELRRLHEAIKRVLREA 81 (92)
T ss_dssp HHHHHTTB-TT------SBGGGSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHcCCCcc------CccccCCHHHHHHHHHHHHHHHHHH
Confidence 67888777533 3567899999999988888776554
No 73
>PF12137 RapA_C: RNA polymerase recycling family C-terminal; InterPro: IPR022737 This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with PF00271 from PFAM, PF00176 from PFAM. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3DMQ_A.
Probab=23.17 E-value=91 Score=26.00 Aligned_cols=70 Identities=13% Similarity=0.160 Sum_probs=41.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHH--------HHHHHHHHhhHHHHHHHhhhh-cCCCChhhhhhhHHHHHHHhhccccc
Q psy9115 19 QSSFVVTKEHRESLSKNAKALFVK--------CKENIRDIQNKYTKTVKNKEK-SEGLSQDDVRSVSEQSAFESYHGFIS 89 (96)
Q Consensus 19 i~iP~LTeErRkeLVK~aKk~~Ee--------aKvaIRNIRRda~~~iKK~eK-~~~iSEDd~k~~e~~IQklT~d~yi~ 89 (96)
-.+.+.....=..+++.|.+.|+. |+..+..--..-++-++.+.+ +..|.+|++..++++.+.++ .+|.
T Consensus 270 ~~~i~~~~~~i~~ll~~ae~~A~~~~~~~~~~A~~~~~~~l~~Ei~RL~aL~~vNp~IR~~EI~~l~~~~~~~~--~~i~ 347 (362)
T PF12137_consen 270 RKVIKALRPLIEELLEKAEKLAEAQLQALIEEAKQRMQQELDAEIERLKALQKVNPNIRDEEIEALEQQRQQLL--QAID 347 (362)
T ss_dssp GGGTTTTHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS--THHHHHHHHHHHHHH--HHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcCHHHHHHHHHHHHHHH--HHHH
Confidence 344555566666677766666554 444444444333444444433 56699999999999999988 6665
Q ss_pred C
Q psy9115 90 G 90 (96)
Q Consensus 90 ~ 90 (96)
.
T Consensus 348 ~ 348 (362)
T PF12137_consen 348 Q 348 (362)
T ss_dssp T
T ss_pred h
Confidence 4
No 74
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=23.13 E-value=1.1e+02 Score=17.88 Aligned_cols=26 Identities=15% Similarity=0.187 Sum_probs=18.3
Q ss_pred cCccCCC--CCCHHHHHHHHHHHHHHHH
Q psy9115 16 FQDQSSF--VVTKEHRESLSKNAKALFV 41 (96)
Q Consensus 16 ~~~i~iP--~LTeErRkeLVK~aKk~~E 41 (96)
|..|.+. ..|.|.++.|++.+-....
T Consensus 2 ~i~i~i~~~grt~eqK~~l~~~it~~l~ 29 (63)
T TIGR00013 2 FVNIYILKEGRTDEQKRQLIEGVTEAMA 29 (63)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHH
Confidence 3445555 4799999999988766554
No 75
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=23.02 E-value=1.2e+02 Score=23.71 Aligned_cols=34 Identities=18% Similarity=0.001 Sum_probs=25.5
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKAL 39 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~ 39 (96)
.|..+|+.+ ..-|.|+++|+.+.|+++.+.++++
T Consensus 256 al~~~G~~~---g~~R~Pl~~l~~~~~~~l~~~l~~~ 289 (294)
T TIGR02313 256 ALGMMGLIE---KELRPPLGLPSDALEEEIRDMAEKY 289 (294)
T ss_pred HHHHcCCCC---CCcCCCCCCCCHHHHHHHHHHHHHc
Confidence 345577743 2368999999999999998877653
No 76
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion []. Brc displays serine/threonine protein kinase activity (2.7.11.1 from EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells []. The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein []. ; GO: 0004674 protein serine/threonine kinase activity, 0005096 GTPase activator activity, 0006468 protein phosphorylation, 0007165 signal transduction; PDB: 1K1F_C.
Probab=23.02 E-value=1.9e+02 Score=19.66 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHH
Q psy9115 32 LSKNAKALFVKCKENIRDIQNKYTKT 57 (96)
Q Consensus 32 LVK~aKk~~EeaKvaIRNIRRda~~~ 57 (96)
-|-..-...|.||.+||.+.+..|+.
T Consensus 27 svgd~e~eLerCK~sirrLeqevnkE 52 (79)
T PF09036_consen 27 SVGDIEQELERCKASIRRLEQEVNKE 52 (79)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhccHHHHHHHHHHHHHHHHHHHHHH
Confidence 34446788999999999999998875
No 77
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=22.70 E-value=1.3e+02 Score=19.81 Aligned_cols=20 Identities=20% Similarity=0.395 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHHHHHHHH
Q psy9115 23 VVTKEHRESLSKNAKALFVK 42 (96)
Q Consensus 23 ~LTeErRkeLVK~aKk~~Ee 42 (96)
.||+|.|..|+..++.++.+
T Consensus 2 ~l~ke~k~~li~~iq~yf~~ 21 (76)
T PF09932_consen 2 KLSKEEKAELIDKIQRYFAE 21 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHH
Confidence 58999999999999998754
No 78
>KOG0225|consensus
Probab=22.63 E-value=98 Score=26.51 Aligned_cols=34 Identities=6% Similarity=0.128 Sum_probs=26.2
Q ss_pred hHHHHHHHhhh-hcCCCChhhhhhhHHHHHHHhhcc
Q psy9115 52 NKYTKTVKNKE-KSEGLSQDDVRSVSEQSAFESYHG 86 (96)
Q Consensus 52 Rda~~~iKK~e-K~~~iSEDd~k~~e~~IQklT~d~ 86 (96)
||-|..+|+.. ..+..+|++++.++++|.+.- |+
T Consensus 314 RDPI~~lk~~li~~~late~ELKai~k~irkeV-de 348 (394)
T KOG0225|consen 314 RDPIEGLKKRLIELGLATEEELKAIDKEIRKEV-DE 348 (394)
T ss_pred cChHHHHHHHHHHhcccCHHHHHHHHHHHHHHH-HH
Confidence 67778887743 345589999999999998887 54
No 79
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.31 E-value=72 Score=22.64 Aligned_cols=14 Identities=29% Similarity=0.496 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHhhH
Q psy9115 40 FVKCKENIRDIQNK 53 (96)
Q Consensus 40 ~EeaKvaIRNIRRd 53 (96)
.|+++.+||++|..
T Consensus 75 seeake~irq~rq~ 88 (103)
T COG4847 75 SEEAKESIRQVRQE 88 (103)
T ss_pred cHHHHHHHHHHHHH
Confidence 57899999999985
No 80
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=22.16 E-value=2.7e+02 Score=19.86 Aligned_cols=54 Identities=13% Similarity=0.114 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhh---HHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 24 VTKEHRESLSKNAKALFVKCKENIRDIQN---KYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 24 LTeErRkeLVK~aKk~~EeaKvaIRNIRR---da~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
++.+..+.+.|++..+..+++.+-=..++ |.+..++.. +.+-....+.+|+.++
T Consensus 18 ~~a~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k~~------~~e~e~K~~r~i~~ml 74 (108)
T COG3937 18 LAAETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAKEA------QGELEEKIPRKIEEML 74 (108)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH------hhhHHHhhhHHHHHHH
Confidence 45566666666777776666665544444 233333322 2333333566666666
No 81
>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function.
Probab=21.97 E-value=1.5e+02 Score=20.79 Aligned_cols=22 Identities=9% Similarity=0.042 Sum_probs=17.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH
Q psy9115 21 SFVVTKEHRESLSKNAKALFVK 42 (96)
Q Consensus 21 iP~LTeErRkeLVK~aKk~~Ee 42 (96)
=|.+++|.|+.|.-.+-+..|+
T Consensus 44 Ep~isee~qk~mm~~~~rrqEE 65 (98)
T PF11069_consen 44 EPVISEEEQKAMMAYYYRRQEE 65 (98)
T ss_pred CCCCCHHHHHHHHHHHHHHHHH
Confidence 3889999999998877665543
No 82
>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=21.90 E-value=2.1e+02 Score=17.78 Aligned_cols=34 Identities=29% Similarity=0.256 Sum_probs=23.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q psy9115 20 SSFVVTKEHRESLSKNAKALFVKCKENIRDIQNK 53 (96)
Q Consensus 20 ~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRd 53 (96)
.-|.-=+|.|+.|...+..+.+.+.....++...
T Consensus 19 ~aP~sG~e~R~~l~~~~~~~~~~~~~~~~~~~~~ 52 (74)
T PF12732_consen 19 FAPKSGKETREKLKDKAEDLKDKAKDLYEEAKEK 52 (74)
T ss_pred hCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3477778888888888877766666655555443
No 83
>TIGR00242 mraZ protein. Members of this family contain two tandem copies of a domain described by pfam02381. This protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc.
Probab=21.70 E-value=36 Score=24.15 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=18.7
Q ss_pred hhhhccccccccccCccCCCC
Q psy9115 3 MLWSRGLECRRDKFQDQSSFV 23 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~ 23 (96)
.|.+...+|.=|+-+||.||+
T Consensus 71 ~l~~~a~~~~~D~~GRi~iP~ 91 (142)
T TIGR00242 71 LIFGHATECEMDTAGRVLIAN 91 (142)
T ss_pred HHhcCCeeeeeCCCCeEeCCH
Confidence 567888999999999999996
No 84
>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=21.65 E-value=2.6e+02 Score=24.12 Aligned_cols=54 Identities=24% Similarity=0.379 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChh---hhhhhHHHHHHHhhcccccCCCCC
Q psy9115 34 KNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQD---DVRSVSEQSAFESYHGFISGEPLD 94 (96)
Q Consensus 34 K~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSED---d~k~~e~~IQklT~d~yi~~~~~~ 94 (96)
+.|++.....+..+++|+|. +.+.- =-++|++ ....+.++|+.+. ......|++
T Consensus 410 ~~Ar~~l~~~~~~l~~ikR~----lek~n-LPGlp~~y~~~~~~~~~~i~~l~--~~L~~~pin 466 (560)
T PF06160_consen 410 KEAREKLQKLKQKLREIKRR----LEKSN-LPGLPEDYLDYFFDVSDEIEELS--DELNQVPIN 466 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHH----HHHcC-CCCCCHHHHHHHHHHHHHHHHHH--HHHhcCCcC
Confidence 45677777777777777774 33220 1358876 7778888888887 444445543
No 85
>COG2863 Cytochrome c553 [Energy production and conversion]
Probab=21.60 E-value=76 Score=22.80 Aligned_cols=56 Identities=16% Similarity=0.148 Sum_probs=43.6
Q ss_pred CccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 17 QDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 17 ~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
.-..+|+|---.+..|.+..+.+-...+.+- .|..+.. .+|++|+..+...+..+.
T Consensus 46 ~~~~~P~Lagq~~~yl~~~L~a~k~g~r~~~------vM~~~a~-----~LsD~Di~~lAa~~a~~~ 101 (121)
T COG2863 46 PAPGYPKLAGQSEAYLEKQLKAYKDGKRPGP------VMNAIAS-----GLSDEDIADLAAYYAAQK 101 (121)
T ss_pred ccCCCCCcCCCCHHHHHHHHHHHHcCCCCcc------hHHHHHH-----hCCHHHHHHHHHHHHhCC
Confidence 3456899999999999999998877766554 5666654 489999998888877665
No 86
>PF02234 CDI: Cyclin-dependent kinase inhibitor; InterPro: IPR003175 Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.; GO: 0004861 cyclin-dependent protein kinase inhibitor activity, 0007050 cell cycle arrest, 0005634 nucleus; PDB: 1H27_E 1JSU_C.
Probab=21.24 E-value=1.1e+02 Score=18.43 Aligned_cols=21 Identities=33% Similarity=0.444 Sum_probs=14.7
Q ss_pred hHHHHHHHhhcccccCCCCCCC
Q psy9115 75 VSEQSAFESYHGFISGEPLDGR 96 (96)
Q Consensus 75 ~e~~IQklT~d~yi~~~~~~~~ 96 (96)
.+...++-. =.|..+.||+||
T Consensus 24 ~e~~~~kWN-FDF~~~~PL~Gr 44 (51)
T PF02234_consen 24 REEFSEKWN-FDFVNDTPLPGR 44 (51)
T ss_dssp THHHHHHHT-EETTTTEE-SSS
T ss_pred HHHHHHhcC-CCCCCCccCCCC
Confidence 455566777 578899999886
No 87
>PF01496 V_ATPase_I: V-type ATPase 116kDa subunit family ; InterPro: IPR002490 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the 116kDa subunit (or subunit a) and subunit I found in the V0 or A0 complex of V- or A-ATPases, respectively. The 116kDa subunit is a transmembrane glycoprotein required for the assembly and proton transport activity of the ATPase complex. Several isoforms of the 116kDa subunit exist, providing a potential role in the differential targeting and regulation of the V-ATPase for specific organelles []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 2RPW_X 2NVJ_A 2JTW_A 3RRK_A.
Probab=21.23 E-value=2.4e+02 Score=25.02 Aligned_cols=48 Identities=10% Similarity=0.105 Sum_probs=26.6
Q ss_pred ccccccCccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q psy9115 11 CRRDKFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVK 59 (96)
Q Consensus 11 ~~~~~~~~i~iP~LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iK 59 (96)
|+.-.|..+++|.. ...+.+..+.+.+..++.+..++.+.....+.++
T Consensus 210 l~~~~f~~~~~p~~-~~~p~e~~~~l~~~i~~l~~~~~~~~~~l~~~~~ 257 (759)
T PF01496_consen 210 LRSFGFERYDLPED-EGTPEEAIKELEEEIEELEKELEELEEELKKLLE 257 (759)
T ss_dssp HHTTT--B----GG-GGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhccCceecCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66777888999985 4456667777777777777777666665444333
No 88
>KOG0100|consensus
Probab=21.19 E-value=4e+02 Score=23.98 Aligned_cols=61 Identities=20% Similarity=0.219 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHH-----HHHHHHHhhHHHHHHHhhhh-----cCCCChhhhhhhHHHHHHHh
Q psy9115 23 VVTKEHRESLSKNAKALFVKC-----KENIRDIQNKYTKTVKNKEK-----SEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 23 ~LTeErRkeLVK~aKk~~Eea-----KvaIRNIRRda~~~iKK~eK-----~~~iSEDd~k~~e~~IQklT 83 (96)
.||+|.-+.+|+-|-++||+- |+.-||-=--+--.+|.+.. .+.+|+++...++.-+....
T Consensus 539 rLt~EdIerMv~eAekFAeeDk~~KekieaRN~LE~YayslKnqi~dkekLg~Kl~~edKe~~e~av~e~~ 609 (663)
T KOG0100|consen 539 RLTPEDIERMVNEAEKFAEEDKKLKEKIEARNELESYAYSLKNQIGDKEKLGGKLSDEDKETIEDAVEEAL 609 (663)
T ss_pred CCCHHHHHHHHHHHHHHhhhhHHHHHHHHhHHHHHHHHHHhhhccCchhHhcccCChhHHHHHHHHHHHHH
Confidence 589999999999999999964 45566655555555555432 23488888888877776655
No 89
>PF13257 DUF4048: Domain of unknown function (DUF4048)
Probab=21.16 E-value=1.5e+02 Score=23.83 Aligned_cols=30 Identities=20% Similarity=0.433 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHh
Q psy9115 27 EHRESLSKNAKALFVKCKENIRDIQNKYTKTVKN 60 (96)
Q Consensus 27 ErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK 60 (96)
-.++.||.-.|+|||+.|..+.. .++.|..
T Consensus 77 ~~~eal~rtgkQmAeDfK~GLWT----FvEDIRQ 106 (253)
T PF13257_consen 77 PQREALMRTGKQMAEDFKEGLWT----FVEDIRQ 106 (253)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence 56889999999999999999875 3444544
No 90
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.94 E-value=1.5e+02 Score=20.66 Aligned_cols=25 Identities=12% Similarity=0.187 Sum_probs=14.2
Q ss_pred HHHHhhHHHHHHHhhhhcCCCChhh
Q psy9115 47 IRDIQNKYTKTVKNKEKSEGLSQDD 71 (96)
Q Consensus 47 IRNIRRda~~~iKK~eK~~~iSEDd 71 (96)
|++.-..+...|++...+.+.|||+
T Consensus 161 V~~~l~Rar~~Lr~~l~~~~~~~~~ 185 (186)
T PRK05602 161 LESLLARGRRALRAQLADLPGSEDD 185 (186)
T ss_pred HHHHHHHHHHHHHHHHHhccccccc
Confidence 3333344666666655556677765
No 91
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=20.89 E-value=1.4e+02 Score=22.94 Aligned_cols=33 Identities=12% Similarity=0.093 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHH--------HHHHHHHHHHHHhhHHHH
Q psy9115 24 VTKEHRESLSKNAKA--------LFVKCKENIRDIQNKYTK 56 (96)
Q Consensus 24 LTeErRkeLVK~aKk--------~~EeaKvaIRNIRRda~~ 56 (96)
+.+||++.+++.+++ +++...|+-==||||.++
T Consensus 2 ~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~ 42 (253)
T COG1349 2 LKEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNE 42 (253)
T ss_pred ChHHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHH
Confidence 567899999988765 788899999999999443
No 92
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=20.87 E-value=1.1e+02 Score=22.49 Aligned_cols=27 Identities=22% Similarity=0.289 Sum_probs=23.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy9115 19 QSSFVVTKEHRESLSKNAKALFVKCKE 45 (96)
Q Consensus 19 i~iP~LTeErRkeLVK~aKk~~EeaKv 45 (96)
....+|-+|.|++++..|..+|-+||-
T Consensus 94 ~~~ttl~~eyrr~ml~aah~LA~daKn 120 (139)
T PF03623_consen 94 NSNTTLDEEYRRQMLSAAHVLAMDAKN 120 (139)
T ss_dssp TTTSTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCchHHHHHHHHHHHHHHHHHHhHHH
Confidence 345678899999999999999999995
No 93
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=20.72 E-value=2.3e+02 Score=17.70 Aligned_cols=49 Identities=10% Similarity=0.187 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 24 VTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 24 LTeErRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
||.+.-.+|-..-+++++.-|. -|.+..+.+.||.+....+.+.|+...
T Consensus 1 lT~~Qk~el~~l~~qm~e~kK~-----------~idk~Ve~G~iTqeqAd~ik~~id~~~ 49 (59)
T PF10925_consen 1 LTDQQKKELKALYKQMLELKKQ-----------IIDKYVEAGVITQEQADAIKKHIDQRQ 49 (59)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 6888888888888888775443 244566678999999998888887765
No 94
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=20.69 E-value=1.4e+02 Score=23.13 Aligned_cols=32 Identities=16% Similarity=-0.044 Sum_probs=23.6
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAK 37 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aK 37 (96)
.|+-+|+.+ ..-+.|+++||++.+..|-+..+
T Consensus 257 al~~~G~~~---g~~R~Pl~~l~~~~~~~i~~~l~ 288 (289)
T cd00951 257 GARLVGRDA---GPVRPPLTDLTEEELAQLTALIK 288 (289)
T ss_pred HHHHcCCCC---CCCCCCCCCCCHHHHHHHHHHHh
Confidence 356678743 34689999999999988876543
No 95
>PF12297 EVC2_like: Ellis van Creveld protein 2 like protein; InterPro: IPR022076 This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Probab=20.53 E-value=4.9e+02 Score=22.66 Aligned_cols=56 Identities=16% Similarity=0.236 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHHHh
Q psy9115 28 HRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFES 83 (96)
Q Consensus 28 rRkeLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQklT 83 (96)
+|+-||++....-.-.+--+--.=.....-|.+.+..+.++||...-+.+.+|+-.
T Consensus 362 ~R~~Lv~~~qs~e~~~~~llntaa~Ql~~li~k~erag~L~eeq~e~l~eraq~Ev 417 (429)
T PF12297_consen 362 QREYLVQNLQSQETRVSGLLNTAAAQLTSLIQKHERAGYLDEEQMEMLLERAQKEV 417 (429)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Confidence 68888887766655555555444445556778888888899999998888888754
No 96
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=20.41 E-value=2e+02 Score=20.78 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=17.1
Q ss_pred HhhHHHHHHHhhhhcCCCChhhhh
Q psy9115 50 IQNKYTKTVKNKEKSEGLSQDDVR 73 (96)
Q Consensus 50 IRRda~~~iKK~eK~~~iSEDd~k 73 (96)
-|..++.+|+.+-...+||-+|+-
T Consensus 53 er~~~l~~i~~~~~~~Git~eeL~ 76 (134)
T PRK10328 53 ERQEKINTWLELMKADGINPEELL 76 (134)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHh
Confidence 355567777777667789988883
No 97
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=20.18 E-value=98 Score=18.47 Aligned_cols=21 Identities=19% Similarity=0.113 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHhhHHHH
Q psy9115 36 AKALFVKCKENIRDIQNKYTK 56 (96)
Q Consensus 36 aKk~~EeaKvaIRNIRRda~~ 56 (96)
++.+++...||..-||||.+.
T Consensus 17 ~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 17 VKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 467888999999999998543
No 98
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=20.13 E-value=1.5e+02 Score=22.81 Aligned_cols=35 Identities=14% Similarity=0.111 Sum_probs=25.7
Q ss_pred hhhhccccccccccCccCCCCCCHHHHHHHHHHHHHHH
Q psy9115 3 MLWSRGLECRRDKFQDQSSFVVTKEHRESLSKNAKALF 40 (96)
Q Consensus 3 ~~~~~~~~~~~~~~~~i~iP~LTeErRkeLVK~aKk~~ 40 (96)
+|..+|+. ...-+.|+++||+|.++++-...+++.
T Consensus 257 ~l~~~G~~---~g~~R~Pl~~l~~~~~~~i~~~l~~~~ 291 (293)
T PRK04147 257 ILHYMGVD---AGLCRKPFKPVDEKYLPALKALAAKYL 291 (293)
T ss_pred HHHHcCCC---CCCcCCCCCCCCHHHHHHHHHHHHHHh
Confidence 34556753 234588999999999999988877654
No 99
>PRK11032 hypothetical protein; Provisional
Probab=20.13 E-value=3.8e+02 Score=20.00 Aligned_cols=48 Identities=15% Similarity=0.195 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhhhcCCCChhhhhhhHHHHHH
Q psy9115 31 SLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAF 81 (96)
Q Consensus 31 eLVK~aKk~~EeaKvaIRNIRRda~~~iKK~eK~~~iSEDd~k~~e~~IQk 81 (96)
.|+..++...+++...|..+=..+.+.+.. .+.+|+|+...+...++.
T Consensus 10 ~ll~~v~~~l~~~~~~l~~~ve~a~~~~~~---~~elT~dEl~lv~~ylkR 57 (160)
T PRK11032 10 ELVASLTERLRNGERDIDALVESARKRVDA---AGELTRDEVDLITRAVRR 57 (160)
T ss_pred HHHHHHHHHHHhCHHHHHHHHHHHHHHHHH---HHhcCHHHHHHHHHHHHH
Confidence 345555555555554444432222222222 356899998877766553
No 100
>PF01198 Ribosomal_L31e: Ribosomal protein L31e; InterPro: IPR000054 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of: Yeast L34 Archaeal L31 [] Plants L31 Mammalian L31 [] ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3G6E_X 3I56_X 1YIT_X 1NJI_Y 3CC4_X 1VQM_X 1KC8_Y 1VQ9_X 1VQN_X 1M1K_Y ....
Probab=20.09 E-value=43 Score=22.39 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=8.2
Q ss_pred hhhhhccccc
Q psy9115 2 EMLWSRGLEC 11 (96)
Q Consensus 2 ~~~~~~~~~~ 11 (96)
+.+||+|.+.
T Consensus 52 ~~IWsrGi~~ 61 (83)
T PF01198_consen 52 KAIWSRGIRK 61 (83)
T ss_dssp HHHHTTTSSS
T ss_pred HHHHhcccCC
Confidence 5689999875
No 101
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=20.07 E-value=1.7e+02 Score=22.34 Aligned_cols=28 Identities=4% Similarity=0.013 Sum_probs=23.0
Q ss_pred HHHHHHHHHH--------HHHHHHHHHHHHHHHhhH
Q psy9115 26 KEHRESLSKN--------AKALFVKCKENIRDIQNK 53 (96)
Q Consensus 26 eErRkeLVK~--------aKk~~EeaKvaIRNIRRd 53 (96)
+||++.+.+. ++.+++...|+..-||||
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRd 39 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRD 39 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 5788887766 456888899999999998
Done!