Query 034596
Match_columns 90
No_of_seqs 106 out of 686
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:29:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00033 clpS ATP-dependent Cl 100.0 3.6E-38 7.9E-43 208.1 11.5 82 4-86 19-100 (100)
2 PRK13019 clpS ATP-dependent Cl 100.0 2.8E-35 6.1E-40 192.4 10.3 82 3-87 12-94 (94)
3 COG2127 Uncharacterized conser 100.0 4.2E-32 9.2E-37 180.9 9.4 81 4-85 20-106 (107)
4 PF02617 ClpS: ATP-dependent C 100.0 2.8E-29 6E-34 158.9 8.8 76 7-83 1-82 (82)
5 PF00542 Ribosomal_L12: Riboso 95.4 0.3 6.5E-06 29.9 8.3 67 13-84 2-68 (68)
6 PF10056 DUF2293: Uncharacteri 85.0 1 2.2E-05 29.0 2.6 31 31-61 2-32 (86)
7 PRK15109 antimicrobial peptide 82.1 6.3 0.00014 31.9 6.7 50 38-87 358-417 (547)
8 cd08502 PBP2_NikA_DppA_OppA_li 77.2 11 0.00024 29.4 6.5 49 38-86 314-368 (472)
9 CHL00083 rpl12 ribosomal prote 76.9 18 0.00039 25.0 6.7 70 10-83 61-130 (131)
10 cd08507 PBP2_SgrR_like The C-t 75.3 8.6 0.00019 30.0 5.4 51 36-86 278-333 (448)
11 TIGR00878 purM phosphoribosyla 72.0 20 0.00043 27.4 6.6 66 13-84 261-326 (332)
12 COG2875 CobM Precorrin-4 methy 71.7 17 0.00038 27.7 6.1 73 13-86 29-111 (254)
13 smart00546 CUE Domain that may 69.6 13 0.00028 20.0 3.9 25 26-50 3-27 (43)
14 cd08506 PBP2_clavulanate_OppA2 69.4 23 0.0005 27.5 6.6 49 38-86 301-354 (466)
15 PRK00157 rplL 50S ribosomal pr 68.8 29 0.00064 23.7 6.2 70 9-83 53-122 (123)
16 cd04449 DEP_DEPDC5-like DEP (D 68.3 12 0.00026 23.3 4.0 54 1-55 8-63 (83)
17 TIGR00855 L12 ribosomal protei 68.3 36 0.00078 23.4 6.8 70 9-83 56-125 (126)
18 cd00387 Ribosomal_L7_L12 Ribos 68.0 31 0.00067 23.5 6.2 70 10-83 58-127 (127)
19 cd08511 PBP2_NikA_DppA_OppA_li 67.1 28 0.0006 27.0 6.6 49 38-86 301-354 (467)
20 cd08513 PBP2_thermophilic_Hb8_ 66.5 20 0.00042 27.9 5.7 49 38-86 306-373 (482)
21 PF07745 Glyco_hydro_53: Glyco 65.0 19 0.00041 28.2 5.3 66 12-89 40-134 (332)
22 PF02845 CUE: CUE domain; Int 64.9 14 0.00029 19.9 3.3 24 27-50 3-26 (42)
23 cd08497 PBP2_NikA_DppA_OppA_li 64.6 28 0.00062 27.4 6.3 48 39-86 318-382 (491)
24 PF03474 DMA: DMRTA motif; In 64.4 10 0.00023 21.0 2.8 19 29-47 5-23 (39)
25 PF05036 SPOR: Sporulation rel 64.0 17 0.00037 20.7 3.9 46 39-84 13-75 (76)
26 COG4635 HemG Flavodoxin [Energ 63.5 8.4 0.00018 27.9 2.9 25 63-87 14-38 (175)
27 cd08494 PBP2_NikA_DppA_OppA_li 62.5 39 0.00084 25.9 6.6 49 38-86 297-351 (448)
28 cd08515 PBP2_NikA_DppA_OppA_li 61.9 40 0.00086 26.2 6.6 49 38-86 305-361 (460)
29 cd08508 PBP2_NikA_DppA_OppA_li 61.5 39 0.00084 26.4 6.5 49 38-86 307-361 (470)
30 cd08517 PBP2_NikA_DppA_OppA_li 59.2 47 0.001 25.7 6.6 49 38-86 310-370 (480)
31 cd08520 PBP2_NikA_DppA_OppA_li 58.5 48 0.001 25.8 6.5 49 38-86 301-365 (468)
32 cd08503 PBP2_NikA_DppA_OppA_li 57.9 49 0.0011 25.6 6.5 49 38-86 304-358 (460)
33 PF03129 HGTP_anticodon: Antic 57.7 25 0.00054 21.2 4.0 22 64-85 15-36 (94)
34 cd08496 PBP2_NikA_DppA_OppA_li 57.5 52 0.0011 25.5 6.6 49 38-86 297-350 (454)
35 cd08495 PBP2_NikA_DppA_OppA_li 57.3 51 0.0011 25.7 6.5 49 38-86 312-370 (482)
36 cd02196 PurM PurM (Aminoimidaz 56.7 81 0.0017 23.5 8.5 66 12-83 227-292 (297)
37 cd08492 PBP2_NikA_DppA_OppA_li 56.4 52 0.0011 25.5 6.4 49 38-86 313-380 (484)
38 KOG0059 Lipid exporter ABCA1 a 53.9 30 0.00065 30.2 5.1 51 14-75 718-769 (885)
39 PF03861 ANTAR: ANTAR domain; 53.5 19 0.00042 20.5 2.8 25 26-51 16-40 (56)
40 cd08499 PBP2_Ylib_like The sub 53.4 65 0.0014 25.0 6.5 49 38-86 300-354 (474)
41 cd08491 PBP2_NikA_DppA_OppA_li 52.8 64 0.0014 25.2 6.4 49 38-86 293-352 (473)
42 cd00995 PBP2_NikA_DppA_OppA_li 52.7 71 0.0015 24.3 6.5 49 38-86 302-359 (466)
43 cd08514 PBP2_AppA_like The sub 52.7 48 0.001 25.8 5.7 49 38-86 308-375 (483)
44 cd01781 AF6_RA_repeat2 Ubiquit 52.2 20 0.00044 23.6 3.0 38 7-46 11-48 (100)
45 cd08498 PBP2_NikA_DppA_OppA_li 52.1 66 0.0014 25.1 6.4 49 38-86 311-367 (481)
46 PRK15413 glutathione ABC trans 51.9 74 0.0016 25.3 6.7 49 38-86 328-383 (512)
47 cd08504 PBP2_OppA The substrat 51.1 77 0.0017 24.7 6.6 49 38-86 322-380 (498)
48 smart00099 btg1 tob/btg1 famil 50.1 39 0.00084 22.6 4.1 37 5-45 49-85 (108)
49 PRK05179 rpsM 30S ribosomal pr 49.7 13 0.00028 25.1 1.8 61 15-76 2-62 (122)
50 TIGR03629 arch_S13P archaeal r 49.6 15 0.00033 25.5 2.2 64 12-76 3-66 (144)
51 PF07305 DUF1454: Protein of u 49.5 8.5 0.00018 28.4 1.0 62 25-86 125-187 (200)
52 PRK10927 essential cell divisi 49.2 54 0.0012 25.9 5.4 46 39-84 256-314 (319)
53 cd08512 PBP2_NikA_DppA_OppA_li 49.2 89 0.0019 24.2 6.7 49 38-86 315-370 (476)
54 PLN02557 phosphoribosylformylg 48.2 1.1E+02 0.0024 24.4 7.1 56 12-73 304-359 (379)
55 TIGR02294 nickel_nikA nickel A 47.4 86 0.0019 24.7 6.4 49 38-86 311-378 (500)
56 cd08501 PBP2_Lpqw The substrat 47.3 65 0.0014 25.1 5.7 49 38-86 317-382 (486)
57 COG0150 PurM Phosphoribosylami 47.2 1.5E+02 0.0032 23.8 7.6 60 19-83 269-328 (345)
58 PF00610 DEP: Domain found in 47.2 51 0.0011 19.2 4.1 40 15-55 11-52 (74)
59 cd08516 PBP2_NikA_DppA_OppA_li 46.8 93 0.002 23.9 6.4 49 38-86 299-354 (457)
60 PF06200 tify: tify domain; I 46.2 20 0.00043 19.5 1.9 17 35-51 18-34 (36)
61 PF00496 SBP_bac_5: Bacterial 45.9 50 0.0011 24.4 4.7 48 39-86 267-330 (374)
62 PRK12757 cell division protein 44.5 1E+02 0.0022 23.5 6.2 47 39-85 193-253 (256)
63 PTZ00134 40S ribosomal protein 44.5 7.9 0.00017 27.3 0.2 66 10-76 10-75 (154)
64 COG1202 Superfamily II helicas 43.8 25 0.00055 30.6 3.0 30 53-82 439-468 (830)
65 PHA01813 hypothetical protein 43.6 23 0.00051 21.0 2.0 23 14-36 7-30 (58)
66 PRK05385 phosphoribosylaminoim 43.0 1.5E+02 0.0032 22.5 8.2 63 15-83 261-323 (327)
67 PF03395 Pox_P4A: Poxvirus P4A 41.7 27 0.00058 31.0 2.9 51 20-72 547-597 (888)
68 cd08493 PBP2_DppA_like The sub 41.5 1.2E+02 0.0026 23.6 6.3 49 38-86 316-375 (482)
69 PRK04053 rps13p 30S ribosomal 41.1 11 0.00025 26.3 0.5 66 10-76 5-70 (149)
70 cd08510 PBP2_Lactococcal_OppA_ 41.0 1.1E+02 0.0023 24.3 6.1 48 38-85 340-407 (516)
71 PF08812 YtxC: YtxC-like famil 41.0 33 0.00072 25.1 3.0 27 11-37 190-216 (221)
72 PF04989 CmcI: Cephalosporin h 40.9 10 0.00023 27.9 0.3 30 11-40 109-138 (206)
73 PRK08334 translation initiatio 40.8 1.1E+02 0.0024 24.4 6.1 46 42-87 178-228 (356)
74 PF13817 DDE_Tnp_IS66_C: IS66 40.7 45 0.00098 18.2 2.8 26 20-46 9-34 (39)
75 cd08500 PBP2_NikA_DppA_OppA_li 40.6 1.2E+02 0.0026 24.0 6.3 49 38-86 312-380 (499)
76 cd04443 DEP_GPR155 DEP (Dishev 40.4 87 0.0019 19.6 4.5 45 5-50 14-58 (83)
77 PF08014 DUF1704: Domain of un 40.1 84 0.0018 24.7 5.3 34 22-56 237-270 (349)
78 cd08490 PBP2_NikA_DppA_OppA_li 40.1 1.4E+02 0.003 23.0 6.5 49 38-86 291-357 (470)
79 cd00861 ProRS_anticodon_short 39.6 82 0.0018 18.7 4.6 18 66-83 19-36 (94)
80 cd08509 PBP2_TmCBP_oligosaccha 38.8 1.2E+02 0.0027 23.9 6.1 49 38-86 321-388 (509)
81 PF04412 DUF521: Protein of un 38.3 1.3E+02 0.0027 24.3 6.1 45 36-80 297-350 (400)
82 cd04371 DEP DEP domain, named 38.2 85 0.0018 18.4 4.2 40 11-51 18-57 (81)
83 PLN02363 phosphoribosylanthran 37.0 71 0.0015 24.0 4.3 41 39-79 83-123 (256)
84 PF02780 Transketolase_C: Tran 37.0 77 0.0017 20.3 4.0 28 57-84 13-41 (124)
85 cd04442 DEP_1_DEP6 DEP (Dishev 36.9 76 0.0016 19.9 3.8 42 8-50 15-56 (82)
86 PF09397 Ftsk_gamma: Ftsk gamm 36.8 61 0.0013 19.6 3.2 26 30-56 24-49 (65)
87 cd00860 ThrRS_anticodon ThrRS 36.7 71 0.0015 18.7 3.6 20 41-60 14-33 (91)
88 PF05822 UMPH-1: Pyrimidine 5' 36.6 35 0.00075 25.8 2.5 24 11-36 223-246 (246)
89 PF13117 Cag12: Cag pathogenic 36.5 79 0.0017 21.2 4.0 71 11-84 36-110 (113)
90 PF12122 DUF3582: Protein of u 36.2 92 0.002 20.2 4.3 28 61-88 7-34 (101)
91 PF09413 DUF2007: Domain of un 36.0 87 0.0019 17.9 3.8 29 58-86 3-31 (67)
92 cd08518 PBP2_NikA_DppA_OppA_li 36.0 1.7E+02 0.0037 22.7 6.5 49 38-86 296-362 (464)
93 PF09868 DUF2095: Uncharacteri 35.8 1E+02 0.0022 21.2 4.5 49 26-82 65-113 (128)
94 cd08519 PBP2_NikA_DppA_OppA_li 35.1 1.3E+02 0.0028 23.4 5.6 49 38-86 306-364 (469)
95 PF13189 Cytidylate_kin2: Cyti 35.0 1E+02 0.0022 21.3 4.5 40 10-54 113-152 (179)
96 PF14528 LAGLIDADG_3: LAGLIDAD 35.0 76 0.0017 18.5 3.5 28 57-84 24-51 (77)
97 KOG3261 Uncharacterized conser 34.9 22 0.00048 26.0 1.2 29 1-29 145-176 (202)
98 smart00049 DEP Domain found in 34.8 77 0.0017 18.6 3.5 51 11-85 10-60 (77)
99 PRK08535 translation initiatio 34.6 1.1E+02 0.0025 23.3 5.2 47 42-88 131-181 (310)
100 cd00859 HisRS_anticodon HisRS 34.3 79 0.0017 18.0 3.5 18 43-60 16-33 (91)
101 cd06402 PB1_p62 The PB1 domain 34.2 1.1E+02 0.0024 19.5 4.3 56 7-64 11-66 (87)
102 PF09759 Atx10homo_assoc: Spin 34.1 1.1E+02 0.0024 20.0 4.4 55 20-88 40-96 (102)
103 cd08489 PBP2_NikA The substrat 33.4 1.6E+02 0.0035 22.9 5.9 49 38-86 303-370 (488)
104 PF11110 Phage_hub_GP28: Basep 33.2 69 0.0015 22.7 3.4 36 18-53 12-47 (151)
105 CHL00137 rps13 ribosomal prote 32.9 36 0.00079 22.9 2.0 60 15-75 2-61 (122)
106 PRK09755 putative ABC transpor 32.6 1.4E+02 0.0029 24.1 5.5 49 38-86 356-413 (535)
107 KOG2599 Pyridoxal/pyridoxine/p 32.6 40 0.00088 26.4 2.4 49 19-68 145-193 (308)
108 PRK09756 PTS system N-acetylga 32.6 1.7E+02 0.0037 20.3 6.4 62 11-72 29-97 (158)
109 PF12964 DUF3853: Protein of u 32.5 95 0.002 20.4 3.8 41 20-61 39-85 (96)
110 cd08505 PBP2_NikA_DppA_OppA_li 32.5 2.1E+02 0.0045 23.0 6.6 49 38-86 354-416 (528)
111 PRK11633 cell division protein 32.4 67 0.0014 23.9 3.5 24 63-86 159-182 (226)
112 cd00738 HGTP_anticodon HGTP an 32.3 73 0.0016 18.7 3.1 21 42-62 18-38 (94)
113 cd04437 DEP_Epac DEP (Dishevel 32.1 1.3E+02 0.0029 20.3 4.7 52 3-55 12-64 (125)
114 COG0309 HypE Hydrogenase matur 32.1 1.7E+02 0.0037 23.3 5.8 63 11-83 241-304 (339)
115 cd02144 iodotyrosine_dehalogen 31.8 61 0.0013 21.9 3.0 31 44-74 129-159 (193)
116 smart00027 EH Eps15 homology d 31.7 1.3E+02 0.0027 18.5 4.2 61 21-83 25-86 (96)
117 KOG0331 ATP-dependent RNA heli 31.6 1.8E+02 0.0038 24.5 6.1 69 11-81 295-368 (519)
118 COG0514 RecQ Superfamily II DN 31.2 83 0.0018 26.8 4.2 34 51-84 227-260 (590)
119 cd02149 NfsB_like_nitroreducta 30.6 37 0.00079 22.6 1.7 23 44-66 94-116 (157)
120 TIGR00963 secA preprotein tran 30.2 1.4E+02 0.0029 26.3 5.4 35 51-85 401-436 (745)
121 PRK05752 uroporphyrinogen-III 29.8 92 0.002 22.5 3.8 31 54-84 2-32 (255)
122 TIGR00614 recQ_fam ATP-depende 29.8 1.7E+02 0.0037 23.3 5.6 30 54-83 226-255 (470)
123 cd04441 DEP_2_DEP6 DEP (Dishev 29.5 1.2E+02 0.0025 19.3 3.8 45 5-50 16-60 (85)
124 TIGR00512 salvage_mtnA S-methy 29.2 2E+02 0.0044 22.5 5.8 45 43-87 166-215 (331)
125 PRK15320 transcriptional activ 28.4 1.3E+02 0.0029 22.8 4.4 59 14-72 3-66 (251)
126 PRK11776 ATP-dependent RNA hel 28.2 1.8E+02 0.004 22.8 5.5 33 51-83 239-271 (460)
127 cd00051 EFh EF-hand, calcium b 28.2 92 0.002 15.8 5.0 40 21-60 15-54 (63)
128 PRK08335 translation initiatio 27.9 1.7E+02 0.0036 22.4 5.0 46 42-88 120-170 (275)
129 TIGR00511 ribulose_e2b2 ribose 27.8 1.5E+02 0.0033 22.6 4.8 46 42-87 126-175 (301)
130 cd02150 NADPH_oxidoreductase_1 27.8 98 0.0021 20.6 3.5 23 44-66 96-118 (166)
131 PRK13104 secA preprotein trans 27.5 1.5E+02 0.0032 26.7 5.2 35 50-84 439-474 (896)
132 PF08544 GHMP_kinases_C: GHMP 27.3 1.1E+02 0.0025 17.7 3.3 24 55-78 59-83 (85)
133 cd04439 DEP_1_P-Rex DEP (Dishe 27.1 1.5E+02 0.0032 18.4 3.9 46 5-51 12-57 (81)
134 PRK05443 polyphosphate kinase; 27.1 4.2E+02 0.009 23.0 8.3 65 16-81 341-425 (691)
135 TIGR00524 eIF-2B_rel eIF-2B al 26.8 1E+02 0.0022 23.7 3.7 46 42-87 137-187 (303)
136 PF05614 DUF782: Circovirus pr 26.7 56 0.0012 21.1 2.0 18 7-24 61-78 (104)
137 PRK11192 ATP-dependent RNA hel 26.7 1.1E+02 0.0023 23.8 3.9 31 53-83 244-274 (434)
138 TIGR02421 QEGLA conserved hypo 26.7 1.4E+02 0.003 23.9 4.5 34 22-56 260-293 (366)
139 PF01465 GRIP: GRIP domain; I 26.7 87 0.0019 17.4 2.5 27 20-47 19-45 (46)
140 PF13166 AAA_13: AAA domain 26.5 34 0.00073 28.4 1.1 18 12-29 527-544 (712)
141 PF10975 DUF2802: Protein of u 26.5 94 0.002 18.9 2.9 19 29-48 47-65 (70)
142 PF15517 TBPIP_N: TBP-interact 26.4 54 0.0012 21.6 1.8 28 61-89 46-73 (99)
143 PRK12757 cell division protein 26.3 1.2E+02 0.0026 23.1 4.0 33 55-87 183-218 (256)
144 cd04450 DEP_RGS7-like DEP (Dis 26.1 1.7E+02 0.0036 18.1 4.4 39 11-50 18-56 (88)
145 COG0114 FumC Fumarase [Energy 26.0 46 0.001 27.5 1.7 23 36-58 412-434 (462)
146 PF14635 HHH_7: Helix-hairpin- 25.9 62 0.0013 21.4 2.1 35 24-59 44-78 (104)
147 PF10415 FumaraseC_C: Fumarase 25.8 12 0.00026 21.8 -1.2 21 38-58 8-28 (55)
148 PF08564 CDC37_C: Cdc37 C term 25.5 46 0.00099 21.8 1.4 32 29-60 37-68 (99)
149 PF12668 DUF3791: Protein of u 25.5 1.3E+02 0.0028 17.5 3.2 23 27-50 6-28 (62)
150 PRK11057 ATP-dependent DNA hel 25.4 1.5E+02 0.0032 24.7 4.6 33 51-83 233-265 (607)
151 PF12367 PFO_beta_C: Pyruvate 25.3 78 0.0017 19.2 2.3 54 18-75 4-60 (67)
152 PF11112 PyocinActivator: Pyoc 25.1 85 0.0018 19.5 2.5 41 30-70 19-68 (76)
153 cd04446 DEP_DEPDC4 DEP (Dishev 24.9 2E+02 0.0044 18.6 5.3 47 9-55 15-68 (95)
154 PRK12326 preprotein translocas 24.9 1.2E+02 0.0027 26.7 4.2 35 50-84 422-457 (764)
155 COG1184 GCD2 Translation initi 24.8 1.9E+02 0.0041 22.6 4.9 45 43-87 131-179 (301)
156 COG0222 RplL Ribosomal protein 24.6 2.2E+02 0.0049 19.5 4.7 68 11-83 56-123 (124)
157 PF13833 EF-hand_8: EF-hand do 24.4 1.3E+02 0.0028 16.1 3.3 33 27-60 9-43 (54)
158 TIGR00537 hemK_rel_arch HemK-r 24.1 2.3E+02 0.005 19.0 6.4 38 51-88 130-167 (179)
159 PF15574 Imm28: Immunity prote 24.1 1.3E+02 0.0029 20.6 3.5 23 28-51 55-77 (123)
160 KOG3052 Cytochrome c1 [Energy 23.9 74 0.0016 24.8 2.5 29 22-52 109-138 (311)
161 COG4778 PhnL ABC-type phosphon 23.8 3.1E+02 0.0067 20.6 5.6 53 12-75 170-223 (235)
162 cd02143 NADH_nitroreductase Ni 23.7 1.1E+02 0.0023 20.2 3.0 24 43-66 82-105 (147)
163 PRK14129 heat shock protein Hs 23.7 32 0.00068 23.1 0.4 26 6-31 45-71 (105)
164 COG4152 ABC-type uncharacteriz 23.6 2.6E+02 0.0057 21.9 5.4 49 15-75 151-201 (300)
165 PHA02593 62 clamp loader small 23.6 1.4E+02 0.0029 22.0 3.7 44 11-55 110-153 (191)
166 cd04448 DEP_PIKfyve DEP (Dishe 23.6 1.9E+02 0.0041 17.8 4.0 39 11-50 18-56 (81)
167 cd02139 Nitroreductase_3 Nitro 23.5 1E+02 0.0022 20.4 2.9 23 44-66 101-123 (164)
168 cd02135 Arsenite_oxidase Nitro 23.5 78 0.0017 20.6 2.3 20 44-63 113-132 (160)
169 COG0458 CarB Carbamoylphosphat 23.0 3.8E+02 0.0083 21.8 6.4 71 11-81 28-131 (400)
170 TIGR00426 competence protein C 23.0 1.6E+02 0.0035 17.0 3.4 33 21-55 9-41 (69)
171 PRK12928 lipoyl synthase; Prov 23.0 3.4E+02 0.0074 20.6 6.6 28 28-55 174-201 (290)
172 PF13241 NAD_binding_7: Putati 22.9 1.8E+02 0.004 18.1 3.9 33 52-84 4-36 (103)
173 COG1587 HemD Uroporphyrinogen- 22.7 1.5E+02 0.0033 21.4 3.9 31 55-85 1-31 (248)
174 PF01922 SRP19: SRP19 protein; 22.7 1.1E+02 0.0025 19.5 2.8 22 66-87 30-51 (95)
175 COG0747 DdpA ABC-type dipeptid 22.6 2.1E+02 0.0045 22.2 4.8 49 38-86 363-425 (556)
176 TIGR03714 secA2 accessory Sec 22.6 3.1E+02 0.0067 24.2 6.1 35 50-84 419-454 (762)
177 PRK08811 uroporphyrinogen-III 22.4 1.6E+02 0.0035 21.8 4.0 30 53-82 16-45 (266)
178 PRK06371 translation initiatio 22.3 3.3E+02 0.0071 21.4 5.8 45 43-87 156-205 (329)
179 smart00843 Ftsk_gamma This dom 22.2 1.4E+02 0.0029 18.0 2.9 25 30-55 23-47 (63)
180 PF07775 PaRep2b: PaRep2b prot 22.2 1.5E+02 0.0033 24.9 4.1 35 54-88 104-140 (512)
181 KOG1438 Anthranilate phosphori 22.1 81 0.0018 25.1 2.4 25 55-79 218-242 (373)
182 PRK00076 recR recombination pr 22.1 1.3E+02 0.0028 22.0 3.4 44 23-75 4-47 (196)
183 PF11097 DUF2883: Protein of u 22.1 1E+02 0.0023 19.1 2.4 29 36-64 11-39 (75)
184 COG0099 RpsM Ribosomal protein 22.0 81 0.0017 21.6 2.1 60 15-75 2-61 (121)
185 cd02148 Nitroreductase_5 Nitro 22.0 59 0.0013 22.3 1.5 28 46-74 123-150 (185)
186 PRK13844 recombination protein 22.0 1.5E+02 0.0032 21.8 3.6 43 24-75 9-51 (200)
187 PRK08445 hypothetical protein; 21.9 1.6E+02 0.0034 22.9 4.0 33 30-62 169-202 (348)
188 PRK14461 ribosomal RNA large s 21.9 2.5E+02 0.0054 22.5 5.1 49 38-86 283-349 (371)
189 TIGR01389 recQ ATP-dependent D 21.6 3.3E+02 0.0071 22.3 5.9 31 53-83 223-253 (591)
190 TIGR00615 recR recombination p 21.6 1.5E+02 0.0033 21.6 3.6 43 24-75 5-47 (195)
191 PF11360 DUF3110: Protein of u 21.5 2.3E+02 0.0049 17.9 4.7 12 76-87 66-77 (86)
192 cd03757 proteasome_beta_type_1 21.5 1.6E+02 0.0035 20.8 3.7 26 26-51 142-177 (212)
193 PRK05720 mtnA methylthioribose 21.3 3.5E+02 0.0077 21.2 5.8 45 43-87 166-215 (344)
194 COG0337 AroB 3-dehydroquinate 21.1 77 0.0017 25.3 2.1 63 22-85 244-306 (360)
195 COG0593 DnaA ATPase involved i 20.8 1.4E+02 0.0031 24.1 3.6 47 40-86 193-244 (408)
196 TIGR02223 ftsN cell division p 20.8 3.4E+02 0.0074 21.0 5.6 45 39-83 236-295 (298)
197 PRK05298 excinuclease ABC subu 20.8 2.7E+02 0.0058 23.6 5.4 33 52-84 444-476 (652)
198 cd02146 NfsA_FRP This family c 20.7 1.3E+02 0.0029 21.4 3.1 21 44-64 114-134 (229)
199 PRK08734 lipid A biosynthesis 20.7 1.6E+02 0.0034 22.1 3.7 24 27-50 46-69 (305)
200 PRK11634 ATP-dependent RNA hel 20.4 2.7E+02 0.0059 23.5 5.3 36 48-83 239-274 (629)
201 PRK10927 essential cell divisi 20.4 1.4E+02 0.0029 23.7 3.3 34 54-87 245-281 (319)
202 TIGR00036 dapB dihydrodipicoli 20.4 2.7E+02 0.0058 20.6 4.8 32 37-68 100-131 (266)
203 TIGR03631 bact_S13 30S ribosom 20.3 60 0.0013 21.5 1.2 54 21-75 6-59 (113)
204 COG1753 Predicted antotoxin, c 20.2 1.8E+02 0.0038 18.3 3.2 23 29-51 41-63 (74)
205 COG1764 osmC Organic hydropero 20.2 1E+02 0.0022 21.3 2.4 41 13-53 84-124 (143)
206 PF02022 Integrase_Zn: Integra 20.1 1.1E+02 0.0025 16.7 2.1 20 29-49 12-31 (40)
207 cd04444 DEP_PLEK2 DEP (Disheve 20.0 2.1E+02 0.0046 19.1 3.8 44 11-55 21-64 (109)
208 PF11256 DUF3055: Protein of u 20.0 1.4E+02 0.0031 19.0 2.8 32 16-52 48-79 (81)
209 PF13041 PPR_2: PPR repeat fam 20.0 1.6E+02 0.0034 15.6 3.7 30 23-55 4-33 (50)
No 1
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=100.00 E-value=3.6e-38 Score=208.06 Aligned_cols=82 Identities=27% Similarity=0.333 Sum_probs=79.3
Q ss_pred CCCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 4 KRGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 4 ~~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
+++.+.|++|+|||||||+||||||+++|+++| |+|.++|++||++||++|+|+||+|++|+||+++++|+++||+|+|
T Consensus 19 ~~~~~~~~~y~ViL~NDd~ntmd~Vv~vL~~vf-~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l~~~~L~~~i 97 (100)
T PRK00033 19 EPKLKPPPMYKVLLHNDDYTPMEFVVYVLQKFF-GYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQVHQHGLLCTM 97 (100)
T ss_pred ccccCCCCceEEEEEcCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHHHcCCCeEEE
Confidence 456788899999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred EeC
Q 034596 84 EPD 86 (90)
Q Consensus 84 ep~ 86 (90)
||+
T Consensus 98 e~~ 100 (100)
T PRK00033 98 EKD 100 (100)
T ss_pred eeC
Confidence 986
No 2
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=100.00 E-value=2.8e-35 Score=192.41 Aligned_cols=82 Identities=27% Similarity=0.412 Sum_probs=75.3
Q ss_pred CCCCCCCCCceEEEEEcCCCCCHHHHH-HHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCee
Q 034596 3 DKRGTGSGDSYRVLLIDDTRHSEKLVA-KVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRS 81 (90)
Q Consensus 3 ~~~~~~~~~~y~ViL~NDd~~t~e~Vi-~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~ 81 (90)
-+++...|++|+|||||||+||||||| .+|+.+| ++|.++|++||++||++|+|+||+|++|+||+++.+|+++||
T Consensus 12 ~~~~~~~p~~ykViL~NDd~~t~dfVi~~vl~~vf-~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~gl-- 88 (94)
T PRK13019 12 TKPKLERYPLYKVIVLNDDFNTFEHVVNCLLKAIP-GMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGL-- 88 (94)
T ss_pred ccccccCCCceEEEEEcCCCCCHHHHHHHHHHHhc-CCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHccc--
Confidence 356788899999999999999999999 5666677 999999999999999999999999999999999999999997
Q ss_pred EEEeCC
Q 034596 82 TIEPDS 87 (90)
Q Consensus 82 ~iep~~ 87 (90)
++||++
T Consensus 89 t~e~~~ 94 (94)
T PRK13019 89 TMAPEE 94 (94)
T ss_pred ccCCCC
Confidence 777764
No 3
>COG2127 Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=4.2e-32 Score=180.91 Aligned_cols=81 Identities=28% Similarity=0.373 Sum_probs=74.4
Q ss_pred CCCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcC-----
Q 034596 4 KRGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGG----- 78 (90)
Q Consensus 4 ~~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~g----- 78 (90)
++.+++|++|+|||+|||+|+|+||+.+|+++| ++|.++|.+||++||++|+|+||+|++|+||+|+.+++.+|
T Consensus 20 ~t~~~~p~~ykVillNDd~T~mefVv~vL~~~F-~~s~e~A~~lMl~VH~~G~av~gv~t~evAEtk~~~v~~~g~~~~~ 98 (107)
T COG2127 20 KTKTKPPKMYKVILLNDDYTPMEFVVYVLQKFF-GMSEERATKLMLQVHREGKAVVGVYTREVAETKVAQVRDAGLEATH 98 (107)
T ss_pred CcccCCCCceeEEEecCCCcHHHHHHHHHHHHh-ccCHHHHHHHHHHHHhcCcEEEEEccHHHHHHHHHHHHHHHHHccC
Confidence 355889999999999999999999999999999 99999999999999999999999999999999999998655
Q ss_pred -CeeEEEe
Q 034596 79 -LRSTIEP 85 (90)
Q Consensus 79 -L~~~iep 85 (90)
|.|++||
T Consensus 99 pl~~~~e~ 106 (107)
T COG2127 99 PLLCTMEE 106 (107)
T ss_pred ChhhhccC
Confidence 5555554
No 4
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=99.96 E-value=2.8e-29 Score=158.94 Aligned_cols=76 Identities=38% Similarity=0.521 Sum_probs=65.4
Q ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcC------Ce
Q 034596 7 TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGG------LR 80 (90)
Q Consensus 7 ~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~g------L~ 80 (90)
|+.+++|+|||||||+|||+||+++|+++| |+|.++|.++|++||++|+|+|+.+++++||.++.+|+++| |+
T Consensus 1 ~~~~~~~~vvL~NDe~ht~~~Vi~~L~~~~-~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~~g~~~~~PL~ 79 (82)
T PF02617_consen 1 TKEPDMYRVVLWNDEVHTFEQVIDVLRRVF-GCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQRAGRDSGHPLR 79 (82)
T ss_dssp -BS--EEEEEEE--SSSBHHHHHHHHHHHC----HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHHHHHHTT---E
T ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHHHhhccCCCeE
Confidence 467899999999999999999999999999 99999999999999999999999999999999999999888 99
Q ss_pred eEE
Q 034596 81 STI 83 (90)
Q Consensus 81 ~~i 83 (90)
++|
T Consensus 80 ~ti 82 (82)
T PF02617_consen 80 ATI 82 (82)
T ss_dssp EEE
T ss_pred EeC
Confidence 987
No 5
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=95.40 E-value=0.3 Score=29.92 Aligned_cols=67 Identities=19% Similarity=0.198 Sum_probs=49.4
Q ss_pred eEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 13 YRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 13 y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
|.|+|-.= -.-.=-||..++.+. |++..+|..+...+ -..+-...+++.||....+|...|-.+.|+
T Consensus 2 f~V~L~~~-~~~ki~vIK~vR~~t-gl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~Le~aGa~v~l~ 68 (68)
T PF00542_consen 2 FDVVLKSF-GEKKIKVIKEVREIT-GLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKLEAAGAKVELK 68 (68)
T ss_dssp EEEEEEE--TTGHHHHHHHHHHHC----HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHHHCCT-EEEEE
T ss_pred eEEEEeec-ccchHHHHHHHHHHh-CCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 55666555 666667999999998 99999999987666 455666788999999999999999888774
No 6
>PF10056 DUF2293: Uncharacterized conserved protein (DUF2293); InterPro: IPR018744 Proteins in this entry are found the bacteria and fungi, they have no known function.
Probab=85.02 E-value=1 Score=29.01 Aligned_cols=31 Identities=19% Similarity=0.290 Sum_probs=28.9
Q ss_pred HHHHhCCCCCHHHHHHHHHHHhhCCcEEEEe
Q 034596 31 VLPQVVPSVTPDDARKLFHESREHGMAIVIV 61 (90)
Q Consensus 31 ~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~ 61 (90)
.|.+.||+++..+|.+|...+=..|..-||.
T Consensus 2 al~~lfP~~P~~d~~~I~~hA~~~gs~rvgr 32 (86)
T PF10056_consen 2 ALRRLFPRCPAEDAEAILAHAFPKGSGRVGR 32 (86)
T ss_pred hHHHHccCCCHHHHHHHHHHHHhcCCCCCCC
Confidence 5788999999999999999999999999985
No 7
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=82.07 E-value=6.3 Score=31.90 Aligned_cols=50 Identities=14% Similarity=0.249 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHhhCCcEEEEee----------eHHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 38 SVTPDDARKLFHESREHGMAIVIVT----------VKEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~v~~~----------~~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
..+.++|.++..++-.+|..+-..+ ..+.|+.++++|++.|+.++|++..
T Consensus 358 ~yd~~kAk~lL~eAG~~~~~l~i~~~~~~~~~~~~~~~~a~~iq~~l~~iGI~v~i~~~~ 417 (547)
T PRK15109 358 EYNPEKSREQLKALGLENLTLKLWVPTASQAWNPSPLKTAELIQADLAQVGVKVVIVPVE 417 (547)
T ss_pred CCCHHHHHHHHHHcCCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHHHcCCEEEEEEcc
Confidence 4789999999999999887765433 2689999999999999999998743
No 8
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=77.17 E-value=11 Score=29.44 Aligned_cols=49 Identities=27% Similarity=0.315 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhCCcEEEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHGMAIVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-..|+.+...+ ..+.|+.++++|++.|+.+.+++.
T Consensus 314 ~~d~~kA~~lL~~aG~~g~~l~l~~~~~~~~~~~~a~~i~~~l~~iGI~v~v~~~ 368 (472)
T cd08502 314 KPDLEKAKKLLKEAGYDGEPIVILTPTDYAYLYNAALVAAQQLKAAGFNVDLQVM 368 (472)
T ss_pred cCCHHHHHHHHHHcCCCCceEEEEECCCCcchhhHHHHHHHHHHhcCcEEEEEEe
Confidence 5899999999999988887654322 257899999999999999999874
No 9
>CHL00083 rpl12 ribosomal protein L12
Probab=76.88 E-value=18 Score=24.98 Aligned_cols=70 Identities=20% Similarity=0.205 Sum_probs=57.6
Q ss_pred CCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 10 GDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 10 ~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
...|.|+|-+-|-..-==||..++.+. |++.-+|..+...+ .+-+--..++++||....+|...|-.++|
T Consensus 61 KT~F~V~L~~~~~~~Ki~vIK~vr~it-~lgLkeaK~lVe~~---P~~ike~v~KeeAe~ik~~le~~Ga~v~l 130 (131)
T CHL00083 61 KTEFDVILEEVPADKRIAVLKVVRSLT-GLGLKEAKELVESL---PKTIKEGISKEEAEEAKKQLEEAGAKVII 130 (131)
T ss_pred cceeeEEEeecCCcchHHHHHHHHHHc-CCCHHHHHHHHHhC---CHHHHhCCCHHHHHHHHHHHHHcCCEEEe
Confidence 367999999876667778999999998 99999999986544 34444467899999999999999987765
No 10
>cd08507 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery f
Probab=75.30 E-value=8.6 Score=29.99 Aligned_cols=51 Identities=25% Similarity=0.418 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHhhCCcEEEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 36 VPSVTPDDARKLFHESREHGMAIVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 36 ~p~~s~~~A~~i~~~vH~~G~a~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
+|..+.++|.++..++=..|..+...+ ..+.|+.++++++..|+.+++++.
T Consensus 278 ~p~~d~~~Ak~lL~eaG~~~~~~~l~~~~~~~~~~~a~~l~~~l~~~Gi~v~l~~~ 333 (448)
T cd08507 278 LPEWPREKIRRLLKESEYPGEELTLATYNQHPHREDAKWIQQRLAKHGIRLEIHIL 333 (448)
T ss_pred CCccCHHHHHhhccccCCCCceEEEEEcCCCchHHHHHHHHHHHHHcCcEEEEEee
Confidence 333689999999998877775555443 478999999999999999999874
No 11
>TIGR00878 purM phosphoribosylaminoimidazole synthetase. This enzyme is found as a homodimeric monofunctional protein in prokaryotes and as part of a larger, multifunctional protein, sometimes with two copies of this enzyme in tandem, in eukaryotes.
Probab=72.03 E-value=20 Score=27.44 Aligned_cols=66 Identities=11% Similarity=0.209 Sum_probs=47.4
Q ss_pred eEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 13 YRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 13 y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
..+.+.-+.+.-.+ .+..+.+-+ +.+.++++++. +.|.+++.+.+.|.|+...+.+++.|+.+++.
T Consensus 261 ~g~~I~~~~ipi~~-~~~~~~e~~-~~~~~e~~~~~----~~g~glli~v~~e~~~~~~~~l~~~gi~a~vI 326 (332)
T TIGR00878 261 LKAVIDMSSWPQPP-IFKWIQEAG-NVEEEEMYRTF----NMGVGFVVIVPEEEVDKALALLNARGEKAWVI 326 (332)
T ss_pred ceEEEecCCCCCCH-HHHHHHHCC-CCChHHHHHHH----hccCCEEEEECHHHHHHHHHHHHhcCCCcEEE
Confidence 34455555543323 556666655 78887777655 57888899999999999999999999877653
No 12
>COG2875 CobM Precorrin-4 methylase [Coenzyme metabolism]
Probab=71.68 E-value=17 Score=27.72 Aligned_cols=73 Identities=15% Similarity=0.128 Sum_probs=51.9
Q ss_pred eEEEEEcCCCCCHHHHHHHH-----HHhCCCCCHHHHHHHHHHHhhCCcEEEE--eeeHHHHHHHHHHH---hhcCCeeE
Q 034596 13 YRVLLIDDTRHSEKLVAKVL-----PQVVPSVTPDDARKLFHESREHGMAIVI--VTVKEHAEFYAQMM---VRGGLRST 82 (90)
Q Consensus 13 y~ViL~NDd~~t~e~Vi~~L-----~~v~p~~s~~~A~~i~~~vH~~G~a~v~--~~~~e~AE~~~~~l---~~~gL~~~ 82 (90)
.-|++|-+..-+-|..-++= ..-- ++|.++-..+|..+|..|+-++- +|+..+=-...+|+ .++|+-.+
T Consensus 29 advviYAGSLV~~elL~~~~~~aei~nSa-~~tLeeIi~~m~~a~~~Gk~VvRLhSGDpsiYgA~~EQm~~L~~~gI~ye 107 (254)
T COG2875 29 ADVVIYAGSLVPPELLEYCRPDAEIVNSA-SLTLEEIIDLMVDAVREGKDVVRLHSGDPSIYGALAEQMRELEALGIPYE 107 (254)
T ss_pred CCEEEECCCcCCHHHHhhcCCCCEEEecC-cCCHHHHHHHHHHHHHcCCeEEEeecCChhHHHHHHHHHHHHHHcCCCeE
Confidence 34667766666655443321 1112 68999999999999999999986 67766655666665 47899999
Q ss_pred EEeC
Q 034596 83 IEPD 86 (90)
Q Consensus 83 iep~ 86 (90)
+.|.
T Consensus 108 vvPG 111 (254)
T COG2875 108 VVPG 111 (254)
T ss_pred EeCC
Confidence 9885
No 13
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=69.60 E-value=13 Score=20.04 Aligned_cols=25 Identities=8% Similarity=0.210 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 26 KLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 26 e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
+-.+..|+..||+++.+....+-..
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~ 27 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEA 27 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 4578899999999999998876554
No 14
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=69.43 E-value=23 Score=27.48 Aligned_cols=49 Identities=27% Similarity=0.425 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHhhCCcEEEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHGMAIVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=..|..+...+ ..+.|+.++++|++.|+.+.+++-
T Consensus 301 ~~d~ekAk~lL~~aG~~g~~l~~~~~~~~~~~~~a~~i~~~l~~iGI~v~i~~~ 354 (466)
T cd08506 301 KGDPDKAKELLAEAGVPGLKLTLAYRDTAVDKKIAEALQASLARAGIDVTLKPI 354 (466)
T ss_pred CCCHHHHHHHHHHcCCCCceEEEEeCCCchHHHHHHHHHHHHHHcCCeEEEEEc
Confidence 5789999999998876676555533 367999999999999999999764
No 15
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=68.75 E-value=29 Score=23.68 Aligned_cols=70 Identities=16% Similarity=0.212 Sum_probs=54.9
Q ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 9 SGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 9 ~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
....|.|+|-.- -..-==||..++.+. |++.-+|..+...+ -+-+--..+++.||....+|...|-.++|
T Consensus 53 Ekt~f~V~L~~~-~~kKi~vIK~vR~it-gLgLkEAK~lVe~~---P~~ike~v~keeAe~ik~~Le~aGa~vel 122 (123)
T PRK00157 53 EKTEFDVVLKSA-GDKKIAVIKAVREIT-GLGLKEAKDLVEGA---PKVVKEGVSKEEAEEIKKKLEEAGAKVEL 122 (123)
T ss_pred cccceeEEEecc-chhhHHHHHHHHHHh-CCCHHHHHHHHHhC---CHHHHhCCCHHHHHHHHHHHHHcCCEEee
Confidence 345688988855 345667999999999 99999999987665 22233457899999999999999987766
No 16
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=68.33 E-value=12 Score=23.27 Aligned_cols=54 Identities=20% Similarity=0.144 Sum_probs=32.3
Q ss_pred CCCCCC-CCCCCceEEEEEcCCCCCHHHHHHHHHHhCC-CCCHHHHHHHHHHHhhCC
Q 034596 1 MKDKRG-TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVP-SVTPDDARKLFHESREHG 55 (90)
Q Consensus 1 ~~~~~~-~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p-~~s~~~A~~i~~~vH~~G 55 (90)
|+|..+ .-...+|+-.++.+.+.-.|-|-..+. -++ -.|+++|..+....-.+|
T Consensus 8 m~~~~~~~i~~r~~~~~~~~~cF~G~e~VdWL~~-~~~~~~~r~eAv~lgq~Ll~~g 63 (83)
T cd04449 8 MRDPSGIGIFDRSWHKGLPSNCFIGSEAVSWLIN-NFEDVDTREEAVELGQELMNEG 63 (83)
T ss_pred HhCCCCCceeechhcCccCCcceEhHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHCC
Confidence 445444 233456888888999888888775554 442 255555555555444443
No 17
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=68.25 E-value=36 Score=23.37 Aligned_cols=70 Identities=17% Similarity=0.236 Sum_probs=56.0
Q ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 9 SGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 9 ~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
....|.|+|-..+-+ -==||..++.+. |+..-+|..+...+ .+.+--..++++||....+|...|-.++|
T Consensus 56 EKt~f~V~L~~~~~~-Ki~vIK~vR~it-gLgLkEAK~lVe~~---P~~ike~vsKeeAe~ik~~Le~aGa~vei 125 (126)
T TIGR00855 56 EKTEFDVILKGAGDN-KIAVIKVVREIT-GLGLKEAKDLVEGA---PKVLKEGVSKEEAEELKKKLEEAGAKVEV 125 (126)
T ss_pred ccceeeEEEecCCcc-hhHHHHHHHHHc-CCcHHHHHHHHHhC---cHHHHhCCCHHHHHHHHHHHHHcCCEEEe
Confidence 345699999865444 777999999998 99999999986543 44455567899999999999999987766
No 18
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=68.05 E-value=31 Score=23.52 Aligned_cols=70 Identities=16% Similarity=0.177 Sum_probs=56.8
Q ss_pred CCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 10 GDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 10 ~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
...|.|+|-.=|-..-==||..++.+. |++.-+|..+...+= +-+--.-++++||....+|...|-.++|
T Consensus 58 Kt~F~V~L~~~~~~~Ki~vIK~VR~it-~LgLkEAK~lVe~~P---~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 58 KTEFDVVLESFGAAKKIAVIKEVREIT-GLGLKEAKDLVESAP---KVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred cceEEEEEeeCCchhhHHHHHHHHHHh-CCChHHHHHHHHhCc---HHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 467999998877767778999999999 999999999865543 3333457899999999999999977653
No 19
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is mos
Probab=67.07 E-value=28 Score=26.96 Aligned_cols=49 Identities=18% Similarity=0.325 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHhhCCcEEEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHGMAIVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++-.++...+..+...+ ..+.|+..+++|++.|+.+++.+.
T Consensus 301 ~~d~~~A~~lL~~aG~~~~~l~i~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~~~ 354 (467)
T cd08511 301 GRDPAKAKALLAEAGVPTVTFELTTANTPTGRQLAQVIQAMAAEAGFTVKLRPT 354 (467)
T ss_pred CCCHHHHHHHHHHcCCCCceEEEEecCCCchhHHHHHHHHHHHhcCcEeEEEEc
Confidence 5789999999888766654444322 257899999999999999999763
No 20
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=66.54 E-value=20 Score=27.94 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhC-----------CcEEEE-----e---eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GMAIVI-----V---TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~a~v~-----~---~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |+-+-. . ...+.|+.++++|++.|+.+.+++-
T Consensus 306 ~~d~~kAk~lL~eaG~~~~~~g~~~~~~g~~l~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~~~~~ 373 (482)
T cd08513 306 EYDPEKAKQLLDEAGWKLGPDGGIREKDGTPLSFTLLTTSGNAVRERVAELIQQQLAKIGIDVEIENV 373 (482)
T ss_pred CCCHHHHHHHHHHcCCccCCCCcEEcCCCcEEEEEEEeCCCChHHHHHHHHHHHHHHHcCCEEEEeeC
Confidence 56899999999998653 543221 1 1257899999999999999999873
No 21
>PF07745 Glyco_hydro_53: Glycosyl hydrolase family 53; InterPro: IPR011683 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain is found in family 53 of the glycosyl hydrolase classification []. These enzymes are endo-1,4- beta-galactanases (3.2.1.89 from EC). The structure of this domain is known [] and has a TIM barrel fold.; GO: 0015926 glucosidase activity; PDB: 1HJQ_A 1HJS_A 1HJU_B 1FHL_A 1FOB_A 2GFT_A 1UR4_B 1UR0_A 1R8L_B 2CCR_A ....
Probab=64.98 E-value=19 Score=28.23 Aligned_cols=66 Identities=11% Similarity=0.107 Sum_probs=44.1
Q ss_pred ceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHH-------------------HHHHH--
Q 034596 12 SYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKE-------------------HAEFY-- 70 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e-------------------~AE~~-- 70 (90)
.-|+.||||+.+ --..+.+.+.+++.+++..|..+...+.+. .++..
T Consensus 40 ~vRlRvwv~P~~------------~g~~~~~~~~~~akrak~~Gm~vlldfHYSD~WaDPg~Q~~P~aW~~~~~~~l~~~ 107 (332)
T PF07745_consen 40 AVRLRVWVNPYD------------GGYNDLEDVIALAKRAKAAGMKVLLDFHYSDFWADPGKQNKPAAWANLSFDQLAKA 107 (332)
T ss_dssp EEEEEE-SS-TT------------TTTTSHHHHHHHHHHHHHTT-EEEEEE-SSSS--BTTB-B--TTCTSSSHHHHHHH
T ss_pred eEEEEeccCCcc------------cccCCHHHHHHHHHHHHHCCCeEEEeecccCCCCCCCCCCCCccCCCCCHHHHHHH
Confidence 358999999999 225788999999999999999999877662 22222
Q ss_pred --------HHHHhhcCCeeEEEeCCCC
Q 034596 71 --------AQMMVRGGLRSTIEPDSST 89 (90)
Q Consensus 71 --------~~~l~~~gL~~~iep~~~~ 89 (90)
...|++.|+...|...+++
T Consensus 108 v~~yT~~vl~~l~~~G~~pd~VQVGNE 134 (332)
T PF07745_consen 108 VYDYTKDVLQALKAAGVTPDMVQVGNE 134 (332)
T ss_dssp HHHHHHHHHHHHHHTT--ESEEEESSS
T ss_pred HHHHHHHHHHHHHHCCCCccEEEeCcc
Confidence 2456688888877776665
No 22
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=64.89 E-value=14 Score=19.93 Aligned_cols=24 Identities=8% Similarity=0.267 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 27 LVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 27 ~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
--+..|+.+||+++.+.-..+-.+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~ 26 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQA 26 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH
Confidence 357889999999999887765543
No 23
>cd08497 PBP2_NikA_DppA_OppA_like_14 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=64.64 E-value=28 Score=27.43 Aligned_cols=48 Identities=15% Similarity=0.171 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHhhC-----------CcEEEE--e----eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 39 VTPDDARKLFHESREH-----------GMAIVI--V----TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~-----------G~a~v~--~----~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
.+.++|.++..++-.. |+.+-. . .....|+.++++|++.|+.+.+++-
T Consensus 318 ~d~~kAk~lL~~aG~~~~~g~~~~~~~G~~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 382 (491)
T cd08497 318 FNLRKALELLAEAGWTVRGGDILVNADGEPLSFEILLDSPTFERVLLPYVRNLKKLGIDASLRLV 382 (491)
T ss_pred CCHHHHHHHHHHcCCccCCCCEEECCCCCEEEEEEEeCCCcHHHHHHHHHHHHHhcCceEEEeec
Confidence 6899999999998753 433221 1 1366899999999999999999874
No 24
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=64.43 E-value=10 Score=21.03 Aligned_cols=19 Identities=16% Similarity=0.256 Sum_probs=14.7
Q ss_pred HHHHHHhCCCCCHHHHHHH
Q 034596 29 AKVLPQVVPSVTPDDARKL 47 (90)
Q Consensus 29 i~~L~~v~p~~s~~~A~~i 47 (90)
+++|+++||++.+..=+.+
T Consensus 5 idiL~rvFP~~kr~~Le~i 23 (39)
T PF03474_consen 5 IDILTRVFPHQKRSVLELI 23 (39)
T ss_pred HHHHHHHCCCCChHHHHHH
Confidence 5789999999887765543
No 25
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=64.03 E-value=17 Score=20.71 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhCCcE-------------EEEee---eHHHHHHHHHHHh-hcCCeeEEE
Q 034596 39 VTPDDARKLFHESREHGMA-------------IVIVT---VKEHAEFYAQMMV-RGGLRSTIE 84 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G~a-------------~v~~~---~~e~AE~~~~~l~-~~gL~~~ie 84 (90)
.+.+.|.+...+....|-. .|..| +++.|+..+.+|+ ..|..|.|.
T Consensus 13 ~~~~~A~~~~~~l~~~g~~~~~~~~~~~~~~yrV~~G~f~~~~~A~~~~~~l~~~~~~~~~vv 75 (76)
T PF05036_consen 13 SSEENAERLLAKLKKKGPDAYVVQVSKGGPWYRVRVGPFSSREEAEAALRKLKKAAGPDAFVV 75 (76)
T ss_dssp S-HHHHHHHHHHHHHHT-----EEEEEETTCEEEEECCECTCCHHHHHHHHHHHHHTS--EEE
T ss_pred CCHHHHHHHHHHHHhcCCCcceEEEecCCceEEEEECCCCCHHHHHHHHHHHhHhhCCCCEEE
Confidence 4677777777777777753 23333 3678999999998 788777663
No 26
>COG4635 HemG Flavodoxin [Energy production and conversion / Coenzyme metabolism]
Probab=63.53 E-value=8.4 Score=27.89 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=22.4
Q ss_pred eHHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 63 VKEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 63 ~~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.+++|+..+.+|++.|+.|+|++-.
T Consensus 14 T~kIA~~iA~~L~e~g~qvdi~dl~ 38 (175)
T COG4635 14 TRKIAEYIASHLRESGIQVDIQDLH 38 (175)
T ss_pred HHHHHHHHHHHhhhcCCeeeeeehh
Confidence 3789999999999999999999853
No 27
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=62.48 E-value=39 Score=25.88 Aligned_cols=49 Identities=22% Similarity=0.342 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHhhCC-cEEEEe-----eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG-MAIVIV-----TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G-~a~v~~-----~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-..+ ..+-.. ...+.|+.++++|++.|+.+.+++.
T Consensus 297 ~~d~~kA~~lL~~aG~~~g~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~~~ 351 (448)
T cd08494 297 PYDPDKARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKIEVV 351 (448)
T ss_pred CCCHHHHHHHHHHcCCCCCeEEEEEecCCcchhHHHHHHHHHHHhcCcEEEEEEe
Confidence 578999999998876544 343321 2467999999999999999999863
No 28
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=61.91 E-value=40 Score=26.15 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHhh-CCcEEEEee-------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESRE-HGMAIVIVT-------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~-~G~a~v~~~-------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-. .|..+-..+ ..+.|+.++++|++.|+.+.+++.
T Consensus 305 ~~d~~~A~~lL~~aG~~~g~~l~l~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~~~ 361 (460)
T cd08515 305 PYDPEKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAEAIVGMWKAVGINAELNVL 361 (460)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCCCCchHHHHHHHHHHHHHhCceEEEEEe
Confidence 5688999999988765 565554321 367999999999999999999875
No 29
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=61.53 E-value=39 Score=26.41 Aligned_cols=49 Identities=14% Similarity=0.282 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |..+-..+ ....|+.++++|++.|+.+.+++-
T Consensus 307 ~~d~~kA~~lL~eaG~~~g~~l~~~~~~~~~~~~~a~~l~~~l~~~Gi~v~~~~~ 361 (470)
T cd08508 307 PYDPAKAKALLAEAGFPNGLTLTFLVSPAAGQQSIMQVVQAQLAEAGINLEIDVV 361 (470)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCchHHHHHHHHHHHHHhcCcEEEEEEc
Confidence 46889999999988543 54444322 367899999999999999999863
No 30
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=59.21 E-value=47 Score=25.67 Aligned_cols=49 Identities=18% Similarity=0.277 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhC----CcE--EEE-e---ee--HHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH----GMA--IVI-V---TV--KEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~----G~a--~v~-~---~~--~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |.- +-. . .+ .+.|+.++++|++.|+.+++++.
T Consensus 310 ~~d~~~A~~lL~~aG~~~~~~G~~~~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 370 (480)
T cd08517 310 PFDVAKAEALLDEAGYPRGADGIRFKLRLDPLPYGEFWKRTAEYVKQALKEVGIDVELRSQ 370 (480)
T ss_pred CCCHHHHHHHHHHcCCCcCCCCceEEEEEEecCCCchHHHHHHHHHHHHHHcCCEEEEEEe
Confidence 46789999999988653 422 211 1 12 67899999999999999999863
No 31
>cd08520 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=58.45 E-value=48 Score=25.77 Aligned_cols=49 Identities=18% Similarity=0.319 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHhh---------CCcE--EEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESRE---------HGMA--IVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~---------~G~a--~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=. .|+. +...+ ..+.|+.++++|++.|+.+++++.
T Consensus 301 ~~d~~kAk~lL~eaG~~~~~~~~~~~g~~l~l~l~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 365 (468)
T cd08520 301 PYDPEKAKELLKGLGYTDNGGDGEKDGEPLSLELLTSSSGDEVRVAELIKEQLERVGIKVNVKSL 365 (468)
T ss_pred CCCHHHHHHHHHHcCCcccCCCCCcCCceEEEEEEecCCchHHHHHHHHHHHHHHcCceEEEEec
Confidence 5789999999998754 4643 22211 257899999999999999999874
No 32
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=57.88 E-value=49 Score=25.63 Aligned_cols=49 Identities=20% Similarity=0.380 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHhhCCcEEEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHGMAIVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-..|.-+...+ ....|+.++++|++.|+.++++..
T Consensus 304 ~~d~~~A~~lL~eaG~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~~~ 358 (460)
T cd08503 304 EYDPDKAKALLAEAGLPDLEVELVTSDAAPGAVDAAVLFAEQAAQAGININVKRV 358 (460)
T ss_pred CCCHHHHHHHHHHcCCCCceEEEEecCCCccHHHHHHHHHHHHHhhCCEEEEEEe
Confidence 5789999999988876665544332 366899999999999999999863
No 33
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=57.71 E-value=25 Score=21.22 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhcCCeeEEEe
Q 034596 64 KEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 64 ~e~AE~~~~~l~~~gL~~~iep 85 (90)
.+.|...+++|+..|+++.+..
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~ 36 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDD 36 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEES
T ss_pred HHHHHHHHHHHHHCCCEEEEEC
Confidence 4566677777777777777765
No 34
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=57.48 E-value=52 Score=25.45 Aligned_cols=49 Identities=27% Similarity=0.457 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEe----eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIV----TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~----~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |..+-.. ...+.|+.++++|++.|+.+++.+.
T Consensus 297 ~~d~~~A~~lL~~aG~~~g~~l~i~~~~~~~~~~a~~i~~~l~~iGi~v~~~~~ 350 (454)
T cd08496 297 PYDPEKAKELLAEAGYPNGFSLTIPTGAQNADTLAEIVQQQLAKVGIKVTIKPL 350 (454)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCchhHHHHHHHHHHHHcCceEEEEEe
Confidence 57899999999988654 5443332 2467999999999999999999864
No 35
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=57.32 E-value=51 Score=25.72 Aligned_cols=49 Identities=24% Similarity=0.287 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHhhCC---cEEEEee-------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG---MAIVIVT-------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G---~a~v~~~-------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.+++.++=..+ ..+...+ ..+.|+.++++|++.|+.+.+.+.
T Consensus 312 ~~d~~~Ak~lL~~aG~~~~~~l~l~~~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 370 (482)
T cd08495 312 KYDPDKARALLKEAGYGPGLTLKLRVSASGSGQMQPLPMNEFIQQNLAEIGIDLDIEVV 370 (482)
T ss_pred CCCHHHHHHHHHHcCCCCCCceEEEEecCCCCCCcHHHHHHHHHHHHHHcCceEEEEEc
Confidence 568999999998875433 2233322 267999999999999999998764
No 36
>cd02196 PurM PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis. The N-terminal domain of PurM is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP.
Probab=56.68 E-value=81 Score=23.53 Aligned_cols=66 Identities=12% Similarity=0.260 Sum_probs=47.7
Q ss_pred ceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 12 SYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
...+.+..|.+..-+.+ ..+++.+ +.++.+-..+. ..|-.++.+.+.+.++...+.++++|+.+++
T Consensus 227 ~~g~~Id~~~iPv~~~~-~~~~e~~-~~~p~~~~~~~----~~g~gll~~v~~~~~~~~~~~l~~~gi~a~~ 292 (297)
T cd02196 227 GLGAVIDLGSWEIPPIF-KWIQKAG-NVSEEEMYRTF----NMGIGMVLIVSEEDADEVLEILEKLGEKAYV 292 (297)
T ss_pred CceEEEecCCCCCCHHH-HHHHHhC-CCCHHHHHHHH----hCCCCEEEEECHHHHHHHHHHHHhcCCCeEE
Confidence 45567777776433333 6678877 88886644433 3565688888999999999999999998775
No 37
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=56.40 E-value=52 Score=25.51 Aligned_cols=49 Identities=14% Similarity=0.241 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhC-----------CcEEEEee--------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GMAIVIVT--------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~a~v~~~--------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+-+-... ....|+.++++|++.|+.+.+++.
T Consensus 313 ~~d~~~A~~lL~~aG~~~~~~~g~~~~~g~~l~l~~~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 380 (484)
T cd08492 313 AYDPEKAKKLLDEAGWTARGADGIRTKDGKRLTLTFLYSTGQPQSQSVLQLIQAQLKEVGIDLQLKVL 380 (484)
T ss_pred CCCHHHHHHHHHHcCCCcCCCCceecCCCcEEEEEEecCCCCchHHHHHHHHHHHHHhhCeEEEEEEe
Confidence 46789999999988543 54322111 356889999999999999999864
No 38
>KOG0059 consensus Lipid exporter ABCA1 and related proteins, ABC superfamily [Lipid transport and metabolism; General function prediction only]
Probab=53.88 E-value=30 Score=30.20 Aligned_cols=51 Identities=20% Similarity=0.261 Sum_probs=38.5
Q ss_pred EEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEE-eeeHHHHHHHHHHHh
Q 034596 14 RVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVI-VTVKEHAEFYAQMMV 75 (90)
Q Consensus 14 ~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~-~~~~e~AE~~~~~l~ 75 (90)
.||++|.+-+-||-. ++...+.+-.++-++|+|++. +-+.|+||..|.++-
T Consensus 718 ~vi~LDEPstGmDP~-----------arr~lW~ii~~~~k~g~aiiLTSHsMeE~EaLCtR~a 769 (885)
T KOG0059|consen 718 SVILLDEPSTGLDPK-----------ARRHLWDIIARLRKNGKAIILTSHSMEEAEALCTRTA 769 (885)
T ss_pred CEEEecCCCCCCCHH-----------HHHHHHHHHHHHHhcCCEEEEEcCCHHHHHHHhhhhh
Confidence 588888887776642 334457777778889988886 555999999999884
No 39
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=53.48 E-value=19 Score=20.55 Aligned_cols=25 Identities=16% Similarity=0.278 Sum_probs=18.1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHH
Q 034596 26 KLVAKVLPQVVPSVTPDDARKLFHES 51 (90)
Q Consensus 26 e~Vi~~L~~v~p~~s~~~A~~i~~~v 51 (90)
+--..+||.-. |+|+++|++.....
T Consensus 16 ~~AkgiLm~~~-g~~e~~A~~~Lr~~ 40 (56)
T PF03861_consen 16 EQAKGILMARY-GLSEDEAYRLLRRQ 40 (56)
T ss_dssp HHHHHHHHHHH-T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHh-CcCHHHHHHHHHHH
Confidence 34467899999 99999999987653
No 40
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=53.45 E-value=65 Score=25.01 Aligned_cols=49 Identities=24% Similarity=0.331 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEe-----eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIV-----TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~-----~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |..+... ...+.|+.++++|++.|+.+.+++.
T Consensus 300 ~~d~~~A~~lL~eaG~~~~~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~~~ 354 (474)
T cd08499 300 EYDPEKAKELLAEAGYPDGFETTLWTNDNRERIKIAEFIQQQLAQIGIDVEIEVM 354 (474)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCCchhHHHHHHHHHHHHcCceEEEEec
Confidence 57899999999887543 5333322 2357899999999999999999864
No 41
>cd08491 PBP2_NikA_DppA_OppA_like_12 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=52.83 E-value=64 Score=25.21 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhCCcE----EEE-e------eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHGMA----IVI-V------TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a----~v~-~------~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-..|.. +.. . ...+.|+.++++|++.|+.++|++.
T Consensus 293 ~yd~~kA~~lL~~ag~~g~~~~~~l~i~~~~~~~~~~~~~a~~i~~~l~~~GI~v~i~~~ 352 (473)
T cd08491 293 PYDPEKAKALVAEAKADGVPVDTEITLIGRNGQFPNATEVMEAIQAMLQQVGLNVKLRML 352 (473)
T ss_pred CCCHHHHHHHHHHhhccCCCCCceEEEeccCCCCcchHHHHHHHHHHHHHhCeeEEEEEe
Confidence 46889999999999544542 211 1 1267899999999999999999874
No 42
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=52.73 E-value=71 Score=24.28 Aligned_cols=49 Identities=27% Similarity=0.404 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhCC---cEEEEe------eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG---MAIVIV------TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G---~a~v~~------~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=..+ ..+-.. .....|+.++++|++.|+.+++.+.
T Consensus 302 ~~d~~kA~~lL~~ag~~~~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 359 (466)
T cd00995 302 EYDPEKAKELLAEAGYKDGKGLELTLLYNSDGPTRKEIAEAIQAQLKEIGIKVEIEPL 359 (466)
T ss_pred CCCHHHHHHHHHHhCCCCCCceEEEEEeCCCCCcHHHHHHHHHHHHHHcCceEEEEEe
Confidence 468899999998886543 233222 2357899999999999999999863
No 43
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=52.65 E-value=48 Score=25.77 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHhhC-----------CcEEE--E---ee---eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GMAIV--I---VT---VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~a~v--~---~~---~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |+.+- . .+ ..+.|+.++++|++.|+.+++++.
T Consensus 308 ~~d~~~Ak~lL~eaG~~~~~~~~~~~~~G~~l~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 375 (483)
T cd08514 308 PYDPDKAKELLAEAGWVDGDDDGILDKDGKPFSFTLLTNQGNPVREQAATIIQQQLKEIGIDVKIRVL 375 (483)
T ss_pred CCCHHHHHHHHHHcCCCcCCCCceecCCCCEEEEEEEecCCCchHHHHHHHHHHHHHhcCcEEEEEEe
Confidence 46899999999888543 54321 1 11 257899999999999999999864
No 44
>cd01781 AF6_RA_repeat2 Ubiquitin domain of AT-6, second repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=52.21 E-value=20 Score=23.63 Aligned_cols=38 Identities=13% Similarity=0.340 Sum_probs=32.1
Q ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHH
Q 034596 7 TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARK 46 (90)
Q Consensus 7 ~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~ 46 (90)
...+.+|+.||.+-+-++.+-|.++|.++ |+..+++..
T Consensus 11 L~~~~~YKSIlvt~~~~a~~vV~eALeKy--gL~~e~p~~ 48 (100)
T cd01781 11 LVPTRPYKTILLSINDNADRIVGEALEKY--GLEKSDPDD 48 (100)
T ss_pred ccCCCCeEEEEecCCccHHHHHHHHHHHh--CCCccCccc
Confidence 34678999999999999999999999994 898886543
No 45
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=52.14 E-value=66 Score=25.09 Aligned_cols=49 Identities=24% Similarity=0.389 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHhh-CCcEEEEee-------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESRE-HGMAIVIVT-------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~-~G~a~v~~~-------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=. .|..+...+ ....|+.++++|++.|+.+.+++.
T Consensus 311 ~~d~~kAk~lL~~aG~~~g~~l~l~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~~~ 367 (481)
T cd08498 311 PYDPEKAKKLLAEAGYPDGFELTLHCPNDRYVNDEAIAQAVAGMLARIGIKVNLETM 367 (481)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEEcCCCCCcchHHHHHHHHHHHHhCceEEEEEe
Confidence 4689999999988754 454443321 357899999999999999999864
No 46
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=51.91 E-value=74 Score=25.27 Aligned_cols=49 Identities=18% Similarity=0.374 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |..+...+ ..+.|+.++++|++.|+.+.|++.
T Consensus 328 ~~D~ekAk~lL~~aG~~~g~~~~~~~~~~~~~~~~~a~~iq~~l~~iGI~v~i~~~ 383 (512)
T PRK15413 328 PYDPAKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAM 383 (512)
T ss_pred CCCHHHHHHHHHHcCCCCCeeEEEEecCCCccHHHHHHHHHHHHHhcCcEEEEEEe
Confidence 57999999999888653 53333211 257999999999999999999864
No 47
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=51.08 E-value=77 Score=24.67 Aligned_cols=49 Identities=27% Similarity=0.398 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhh-CC---cEEEEe-----eeHHHHHHHHHHHhh-cCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESRE-HG---MAIVIV-----TVKEHAEFYAQMMVR-GGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~-~G---~a~v~~-----~~~e~AE~~~~~l~~-~gL~~~iep~ 86 (90)
..+.++|.++..++=. .| ..+... ...+.|+.++++|++ .|+.+++++.
T Consensus 322 ~~d~~kA~~lL~~aG~~~~~~~~~l~i~~~~~~~~~~~a~~i~~~l~~~iGI~v~i~~~ 380 (498)
T cd08504 322 EYNPEKAKKLLAEAGYELGKNPLKLTLLYNTSENHKKIAEAIQQMWKKNLGVKVTLKNV 380 (498)
T ss_pred ccCHHHHHHHHHHcCcccCCCCceEEEEecCchhHHHHHHHHHHHHHHcCCCeEEEEec
Confidence 5689999999988743 34 233221 236899999999999 9999999864
No 48
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=50.08 E-value=39 Score=22.59 Aligned_cols=37 Identities=16% Similarity=0.188 Sum_probs=30.6
Q ss_pred CCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHH
Q 034596 5 RGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDAR 45 (90)
Q Consensus 5 ~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~ 45 (90)
.++..+..||.|..| +.+|=++..-.+-. |++.++=.
T Consensus 49 ~~P~kGqayRCIrIn---~~~Dp~l~~Aa~~s-Gl~~~~l~ 85 (108)
T smart00099 49 EKPYKGSGFRCIRIN---QKVDPVIEQACKES-GLDIDDLG 85 (108)
T ss_pred CCCCCCcceEEEEEC---CcCCHHHHHHHHHh-CCCHHHHH
Confidence 356677889999999 78999999888888 99987744
No 49
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=49.73 E-value=13 Score=25.11 Aligned_cols=61 Identities=10% Similarity=0.028 Sum_probs=52.1
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhh
Q 034596 15 VLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVR 76 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~ 76 (90)
|.++|=|+..-.-|...|..++ |.....|.+|...+.-...+.++.-+.+.-+.....|..
T Consensus 2 vrI~~~~l~~~k~v~~aL~~I~-GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~ 62 (122)
T PRK05179 2 ARIAGVDIPRNKRVVIALTYIY-GIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK 62 (122)
T ss_pred ceecCccCCCCcEEEeeecccc-cccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh
Confidence 3456666666666778899999 999999999999999999999999999988888888864
No 50
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=49.61 E-value=15 Score=25.55 Aligned_cols=64 Identities=17% Similarity=0.077 Sum_probs=58.6
Q ss_pred ceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhh
Q 034596 12 SYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVR 76 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~ 76 (90)
.|.|.++|=|+..-.-|...|..++ |.....|.+|...+--....-++.-+.+..+.....|..
T Consensus 3 ~~m~rI~~~~i~~~k~v~~aLt~I~-GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 3 KYIVRIADTDLDGNKPVEYALTGIK-GIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred ceeeeeeCccCCCCCEEEEeeccee-ccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh
Confidence 4778889999999999999999999 999999999999999999999999999999888888864
No 51
>PF07305 DUF1454: Protein of unknown function (DUF1454); InterPro: IPR009918 This family consists of several Enterobacterial sequences of around 200 residues in length, which are often known as YiiQ proteins. The function of this family is unknown.
Probab=49.51 E-value=8.5 Score=28.43 Aligned_cols=62 Identities=19% Similarity=0.270 Sum_probs=45.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh-hcCCeeEEEeC
Q 034596 25 EKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV-RGGLRSTIEPD 86 (90)
Q Consensus 25 ~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~-~~gL~~~iep~ 86 (90)
.+|.+.+++.+-|.+|.+++.+--...=.+|++.=.-...+=|-+|+-.=. +.||+..|||.
T Consensus 125 ~~YmaAl~r~F~Ptls~eQs~~kl~~lL~~gk~~~yy~q~~GAiRYVvad~gekglTFAVEPI 187 (200)
T PF07305_consen 125 IEYMAALMRQFEPTLSPEQSQEKLQKLLTKGKGSRYYSQTEGAIRYVVADNGEKGLTFAVEPI 187 (200)
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHHHHHHcCCCCcceeeccCceEEEEecCCCceeEEEeeee
Confidence 579999999999999999999888888888887654444444444332222 55899999996
No 52
>PRK10927 essential cell division protein FtsN; Provisional
Probab=49.21 E-value=54 Score=25.91 Aligned_cols=46 Identities=15% Similarity=0.104 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHhhCC------------cEEEEee-eHHHHHHHHHHHhhcCCeeEEE
Q 034596 39 VTPDDARKLFHESREHG------------MAIVIVT-VKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G------------~a~v~~~-~~e~AE~~~~~l~~~gL~~~ie 84 (90)
.+.++|+++--.+...| +-.||-| +++.|+....+|...|+...|.
T Consensus 256 ~n~~nAE~LrAkLa~~G~~A~I~~~g~~~RVrVGPf~sr~eAe~a~~rLk~aGis~ci~ 314 (319)
T PRK10927 256 RGAEQAETVRAQLAFEGFDSKITTNNGWNRVVIGPVKGKENADSTLNRLKMAGHTNCIR 314 (319)
T ss_pred CCHHHHHHHHHHHHHcCCeeEEccCCcEEEEEeCCCCCHHHHHHHHHHHHHCCCCceee
Confidence 78888999988888888 3344433 4789999999999999877664
No 53
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=49.17 E-value=89 Score=24.23 Aligned_cols=49 Identities=18% Similarity=0.348 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEe------eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIV------TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~------~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |..+-.. ...+.|+.++++|++.|+.+.+++.
T Consensus 315 ~~d~~~A~~lL~eaG~~~g~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 370 (476)
T cd08512 315 KYDLEKAKELLAEAGYPNGFKLTLSYNSGNEPREDIAQLLQASLAQIGIKVEIEPV 370 (476)
T ss_pred CCCHHHHHHHHHHcCCCCCcEEEEEeCCCCcchHHHHHHHHHHHHHhCCeEEEEEc
Confidence 46889999999887553 6444321 2367999999999999999999864
No 54
>PLN02557 phosphoribosylformylglycinamidine cyclo-ligase
Probab=48.19 E-value=1.1e+02 Score=24.42 Aligned_cols=56 Identities=13% Similarity=0.164 Sum_probs=43.1
Q ss_pred ceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHH
Q 034596 12 SYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQM 73 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~ 73 (90)
...+.+.-|.+...+ ++..|++.+ +++.++ |.++.+.|.+.|.+-+.+.|+...+.
T Consensus 304 g~g~~Id~~~~pv~~-~f~~i~~~g-~i~~~e----m~~tfN~GiGmv~~V~~~~a~~~l~~ 359 (379)
T PLN02557 304 GLGAKIRTGSWEVPP-LFKWLQEAG-NIEDAE----MRRTFNMGIGMVLVVSPEAADRILEE 359 (379)
T ss_pred CeeEEEeCCCCCCCH-HHHHHHHhC-CCCHHH----HHHhcCCcccEEEEECHHHHHHHHHh
Confidence 455555555555444 558899999 999998 66689999999999999988876555
No 55
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=47.36 E-value=86 Score=24.69 Aligned_cols=49 Identities=16% Similarity=0.204 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhC-----------CcE--EEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GMA--IVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~a--~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+. +...+ ..+.|+.++++|++.|+.+++++.
T Consensus 311 ~~d~~kAk~lL~~aG~~~~~g~~~~~~~G~~l~l~l~~~~~~~~~~~~a~~l~~~l~~~GI~v~i~~~ 378 (500)
T TIGR02294 311 KYDVKKANALLDEAGWKLGKGKDVREKDGKPLELELYYDKTSALQKSLAEYLQAEWRKIGIKLSLIGE 378 (500)
T ss_pred CCCHHHHHHHHHHcCCcccCCCceEcCCCceEEEEEEEcCCChhhHHHHHHHHHHHHHcCCeEEEeec
Confidence 57999999999888652 543 22221 257899999999999999999874
No 56
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=47.32 E-value=65 Score=25.13 Aligned_cols=49 Identities=22% Similarity=0.413 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhC---------Cc--EEEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH---------GM--AIVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~---------G~--a~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.+++.++=.. |+ .+-..+ ....|+.++++|++.|+.+++++.
T Consensus 317 ~~d~~kAk~lL~~aG~~~~~~g~~~~g~~~~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 382 (486)
T cd08501 317 KYDPEAAKKLLDDAGYTLGGDGIEKDGKPLTLRIAYDGDDPTAVAAAELIQDMLAKAGIKVTVVSV 382 (486)
T ss_pred CCCHHHHHHHHHhcceeccCCccccCCcceEEEEEeCCCCHHHHHHHHHHHHHHHhcCCEEEeccc
Confidence 57899999999998543 22 222211 256899999999999999999874
No 57
>COG0150 PurM Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism]
Probab=47.22 E-value=1.5e+02 Score=23.75 Aligned_cols=60 Identities=17% Similarity=0.245 Sum_probs=48.4
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 19 DDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 19 NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
|++.=+-.-|-..|++.- +.+.++.++ +=+-|.+.|..-+.|.++...+.|.++|+.+.+
T Consensus 269 d~~~~~~p~iF~~i~~~G-~v~~~EM~r----tFNmGvG~v~iv~~e~~~~~~~~l~~~g~~a~~ 328 (345)
T COG0150 269 DKPSWPPPPIFKWLQKAG-NVEREEMYR----TFNMGVGMVLIVPEEDAEKALALLKEQGETAYV 328 (345)
T ss_pred cCCCCCCcHHHHHHHHhc-CCCHHHHHH----HhcCccceEEEEcHHHHHHHHHHHHhcCCceEE
Confidence 333333456777788877 788888766 779999999999999999999999999987765
No 58
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=47.18 E-value=51 Score=19.21 Aligned_cols=40 Identities=15% Similarity=0.100 Sum_probs=18.5
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCC--CCCHHHHHHHHHHHhhCC
Q 034596 15 VLLIDDTRHSEKLVAKVLPQVVP--SVTPDDARKLFHESREHG 55 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi~~L~~v~p--~~s~~~A~~i~~~vH~~G 55 (90)
...+.+-++-.|- |+-|++.++ ..++++|.+++...-..|
T Consensus 11 ~~~~~~~F~G~e~-v~WL~~~~~~~~~~r~eA~~l~q~Ll~~g 52 (74)
T PF00610_consen 11 LKTYPNCFTGSEA-VDWLMDNFEGFVRDREEAVQLGQELLDHG 52 (74)
T ss_dssp SEEECCEEEHHHH-HHHHHHTSCTSTSSHHHHHHHHHHHHHCT
T ss_pred CEEcCCEeEhHHH-HHHHHHhccccccCHHHHHHHHHHHHHCC
Confidence 3344444444443 344444332 355566655555554444
No 59
>cd08516 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=46.83 E-value=93 Score=23.86 Aligned_cols=49 Identities=20% Similarity=0.300 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEEe---e---eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVIV---T---VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~~---~---~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |..+-.. + ..+.|+.++++|++.|+.+.+++.
T Consensus 299 ~~d~~kA~~lL~~aG~~~g~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 354 (457)
T cd08516 299 KYDPEKAKALLAEAGYPNGFDFTILVTSQYGMHVDTAQVIQAQLAAIGINVEIELV 354 (457)
T ss_pred CCCHHHHHHHHHhcCCCCCceEEEEeCCCCccHHHHHHHHHHHHHHcCceEEEEEe
Confidence 57889999998887543 5443322 1 357899999999999999998753
No 60
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=46.25 E-value=20 Score=19.46 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=13.2
Q ss_pred hCCCCCHHHHHHHHHHH
Q 034596 35 VVPSVTPDDARKLFHES 51 (90)
Q Consensus 35 v~p~~s~~~A~~i~~~v 51 (90)
||.+.+.++|..||.-+
T Consensus 18 Vfd~v~~~Ka~~im~lA 34 (36)
T PF06200_consen 18 VFDDVPPDKAQEIMLLA 34 (36)
T ss_pred EeCCCCHHHHHHHHHHh
Confidence 45468899999999765
No 61
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=45.94 E-value=50 Score=24.38 Aligned_cols=48 Identities=23% Similarity=0.390 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHhhCCcE----------EEEeee------HHHHHHHHHHHhhcCCeeEEEeC
Q 034596 39 VTPDDARKLFHESREHGMA----------IVIVTV------KEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G~a----------~v~~~~------~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
.+.++|.++..++-..+.. +...+. ++.|+..+++|++.|+.+++++-
T Consensus 267 ~d~~~A~~lL~~ag~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~Gi~v~i~~~ 330 (374)
T PF00496_consen 267 YDPEKARELLEKAGYKKSDGGGWRKDPLPLIILYTSDDPIWKAIAEALQEQLKKIGIKVEIKPV 330 (374)
T ss_dssp HHHHHHHHHHHHTTHEESTTSEEEETEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred CCHHHHHHhHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHhhcceeEEEEEe
Confidence 3678899999988655442 333222 57899999999999999999874
No 62
>PRK12757 cell division protein FtsN; Provisional
Probab=44.48 E-value=1e+02 Score=23.53 Aligned_cols=47 Identities=13% Similarity=-0.004 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhCC------------cEEEEee-eHHHHHHHHHHHhhcCC-eeEEEe
Q 034596 39 VTPDDARKLFHESREHG------------MAIVIVT-VKEHAEFYAQMMVRGGL-RSTIEP 85 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G------------~a~v~~~-~~e~AE~~~~~l~~~gL-~~~iep 85 (90)
.+.+.|.++.-+....| +-.||-| +++.|+....+|+..|+ .|.+..
T Consensus 193 ~~~~nAe~L~arL~~~G~~a~I~~~gg~yRVrVGPf~sr~~A~~~~~rLk~~G~~~~iiva 253 (256)
T PRK12757 193 KGTEQAESVRAQLAFAGIESRITTGGGWNRVVLGPYNSKAAADKMLQRLKGAGHSGCIPLA 253 (256)
T ss_pred CCHHHHHHHHHHHHhcCCceEEeecCCEEEEEeCCCCCHHHHHHHHHHHHHcCCCCeEEec
Confidence 55666666666655444 2234423 47899999999998887 444433
No 63
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=44.48 E-value=7.9 Score=27.34 Aligned_cols=66 Identities=8% Similarity=-0.009 Sum_probs=60.9
Q ss_pred CCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhh
Q 034596 10 GDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVR 76 (90)
Q Consensus 10 ~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~ 76 (90)
.-.|-|.++|=|+..-.-|...|..++ |.....|.+|...+.-...+.++.-+.+..+.....|..
T Consensus 10 ~~~~mvrI~~~~l~~~K~v~~aLt~I~-GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 10 DFQHILRILNTNVDGKRKVPYALTAIK-GIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred hhhhhhhccCccCCCCCEEEEeecccc-cccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhc
Confidence 456888899999999999999999999 999999999999999999999999999999999998875
No 64
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=43.82 E-value=25 Score=30.56 Aligned_cols=30 Identities=20% Similarity=0.319 Sum_probs=27.5
Q ss_pred hCCcEEEEeeeHHHHHHHHHHHhhcCCeeE
Q 034596 53 EHGMAIVIVTVKEHAEFYAQMMVRGGLRST 82 (90)
Q Consensus 53 ~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ 82 (90)
..|+.||++|++-.+...+..|.+.||++.
T Consensus 439 ~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~ 468 (830)
T COG1202 439 YRGQTIVFTYSRRRCHELADALTGKGLKAA 468 (830)
T ss_pred cCCceEEEecchhhHHHHHHHhhcCCcccc
Confidence 579999999999999999999998898775
No 65
>PHA01813 hypothetical protein
Probab=43.59 E-value=23 Score=21.04 Aligned_cols=23 Identities=17% Similarity=0.089 Sum_probs=18.5
Q ss_pred EEEEEcCCCC-CHHHHHHHHHHhC
Q 034596 14 RVLLIDDTRH-SEKLVAKVLPQVV 36 (90)
Q Consensus 14 ~ViL~NDd~~-t~e~Vi~~L~~v~ 36 (90)
.|+|+||.++ +|++=|..+.++-
T Consensus 7 ~vlly~~~i~~~~~h~i~~fe~~~ 30 (58)
T PHA01813 7 TVLLYCDEIKGHFPHQISMFEDLY 30 (58)
T ss_pred EEEEEehhhcccChhHHHHHHhhh
Confidence 4889999987 7888888887754
No 66
>PRK05385 phosphoribosylaminoimidazole synthetase; Provisional
Probab=43.02 E-value=1.5e+02 Score=22.51 Aligned_cols=63 Identities=13% Similarity=0.189 Sum_probs=45.5
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 15 VLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
+.+.-|.+..-+-+ ..+++.+ +++.++.+.+ -..|-+++.+.+.+.++...+.++++|+.+++
T Consensus 261 ~~Id~~~iP~~~~~-~~~~~~~-~~~~~~~~~~----~~~G~~Ll~tv~~~~~~~l~~~l~~~g~~~~~ 323 (327)
T PRK05385 261 AEIDKGSWPVPPIF-KWLQKLG-NVEEEEMYRT----FNMGIGMVLIVPPEDADAALALLEAAGEDAWV 323 (327)
T ss_pred EEEecCCCCCCHHH-HHHHHcC-CCCHHHHHHH----HhcCCcEEEEECHHHHHHHHHHHHhcCCCceE
Confidence 44555665444434 7788888 8888765443 33576799999999999999999999987664
No 67
>PF03395 Pox_P4A: Poxvirus P4A protein; InterPro: IPR005058 P4A is one of the most abundant structural proteins in the Vaccinia virion.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=41.72 E-value=27 Score=31.05 Aligned_cols=51 Identities=16% Similarity=0.228 Sum_probs=46.0
Q ss_pred CCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHH
Q 034596 20 DTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQ 72 (90)
Q Consensus 20 Dd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~ 72 (90)
++--|-.|.+.+|+|.+ +|.++|++||-.+|..=.=.|..+....++.|..
T Consensus 547 rprVtk~~i~~~L~K~s--csk~eaeKlisaa~dLL~fmlS~~~~~~yq~Y~~ 597 (888)
T PF03395_consen 547 RPRVTKQYIINMLSKAS--CSKDEAEKLISAAHDLLSFMLSAGDYRNYQSYRQ 597 (888)
T ss_pred CchhhHHHHHHHHHhhc--CCHHHHHHHHHHHHHHHHHHHhcccchhhHHHHH
Confidence 55678899999999997 9999999999999999888899888888888884
No 68
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their li
Probab=41.54 E-value=1.2e+02 Score=23.62 Aligned_cols=49 Identities=20% Similarity=0.347 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhC-CcEEEE-e---------eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAIVI-V---------TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~v~-~---------~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |.-+-. . ...+.|+.++++|++.|+.+++++.
T Consensus 316 ~~d~~~A~~lL~~aG~~~g~~l~i~~~~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 375 (482)
T cd08493 316 EYDPEKAKALLAEAGYPDGFELTLWYPPVSRPYNPNPKKMAELIQADLAKVGIKVEIVTY 375 (482)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEEeCCcccCCCcHHHHHHHHHHHHHHhCCEEEEEEe
Confidence 46899999998777543 443322 1 2357899999999999999988763
No 69
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=41.12 E-value=11 Score=26.34 Aligned_cols=66 Identities=15% Similarity=0.047 Sum_probs=58.5
Q ss_pred CCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhh
Q 034596 10 GDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVR 76 (90)
Q Consensus 10 ~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~ 76 (90)
...|.|.++|=|+..-.-|...|..++ |.....|.+|...+--....-++.-+.+..+.....|.+
T Consensus 5 ~~~~m~rI~~~~i~~~k~i~~aLt~Iy-GIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 70 (149)
T PRK04053 5 EFKYIVRIAGTDLDGTKPVEYALTGIK-GIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70 (149)
T ss_pred hhhhhHhhcCccCCCCCEEeeeccccc-cccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHh
Confidence 345677788888888888899999999 999999999999999999999999999999988888853
No 70
>cd08510 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in sev
Probab=41.02 E-value=1.1e+02 Score=24.31 Aligned_cols=48 Identities=27% Similarity=0.459 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhh------------CCcEEEE--e------eeHHHHHHHHHHHhhcCCeeEEEe
Q 034596 38 SVTPDDARKLFHESRE------------HGMAIVI--V------TVKEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~------------~G~a~v~--~------~~~e~AE~~~~~l~~~gL~~~iep 85 (90)
..+.++|.++..++-. .|+-+.. . ...+.|+.++++|++.|+.+.+.+
T Consensus 340 ~~d~~~Ak~lL~eaG~~~~~~dg~~~~~~G~~l~i~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~~ 407 (516)
T cd08510 340 TYDPEKAKKLLDEAGYKDVDGDGFREDPDGKPLTINFAAMSGSETAEPIAQYYIQQWKKIGLNVELTD 407 (516)
T ss_pred CCCHHHHHHHHHHcCCEEcCCCeeEECCCCcEEEEEEEecCCCccHHHHHHHHHHHHHHcCceEEecc
Confidence 4789999999999865 3544322 1 125679999999999999999964
No 71
>PF08812 YtxC: YtxC-like family; InterPro: IPR014199 This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtilis [].
Probab=41.00 E-value=33 Score=25.14 Aligned_cols=27 Identities=11% Similarity=0.204 Sum_probs=23.0
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCC
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVP 37 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p 37 (90)
.|-++++|+++-....-+++.|+.||.
T Consensus 190 aP~~Ivih~~~~~~~~~~i~TI~~VF~ 216 (221)
T PF08812_consen 190 APKKIVIHTREPDHNKEVIQTIKNVFE 216 (221)
T ss_pred CCCeEEEecCCCccchHHHHHHHHHhh
Confidence 467899999988887799999999994
No 72
>PF04989 CmcI: Cephalosporin hydroxylase; InterPro: IPR007072 This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) []. Members of this family are about 220 amino acids long. It also includes the CmcI protein O85726 from SWISSPROT, which is presumed to represent the cephalosporin-7--hydroxylase []. However this has not been experimentally verified.; GO: 0008168 methyltransferase activity, 0008610 lipid biosynthetic process; PDB: 2BR4_B 2BR3_E 2BR5_E 2BM8_J 2BM9_E.
Probab=40.86 E-value=10 Score=27.87 Aligned_cols=30 Identities=30% Similarity=0.352 Sum_probs=19.5
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCC
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVT 40 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s 40 (90)
++-+|++..|--||.++|...|..++|..+
T Consensus 109 ~~~~vlVilDs~H~~~hvl~eL~~y~plv~ 138 (206)
T PF04989_consen 109 PPHPVLVILDSSHTHEHVLAELEAYAPLVS 138 (206)
T ss_dssp --SSEEEEESS----SSHHHHHHHHHHT--
T ss_pred cCCceEEEECCCccHHHHHHHHHHhCccCC
Confidence 355688899999999999999999887554
No 73
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=40.85 E-value=1.1e+02 Score=24.36 Aligned_cols=46 Identities=11% Similarity=0.113 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhCCcEEEE----eeeH-HHHHHHHHHHhhcCCeeEEEeCC
Q 034596 42 DDARKLFHESREHGMAIVI----VTVK-EHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a~v~----~~~~-e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
-.|..+...+|.+|+-++- +-|+ +=+...+..|.+.|+.+++.+|+
T Consensus 178 gTal~vi~~A~~~gk~~~V~v~EtRP~~qG~rlta~eL~~~GI~vtlI~Ds 228 (356)
T PRK08334 178 GTVGAVLRVMHKDGTLKLLWVDETRPVLQGARLSAWEYHYDGIPLKLISDN 228 (356)
T ss_pred chHHHHHHHHHHcCCeEEEEECCCCchhhHHHHHHHHHHHCCCCEEEEehh
Confidence 4578888999999996552 3333 34566678999999999999986
No 74
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=40.72 E-value=45 Score=18.15 Aligned_cols=26 Identities=12% Similarity=0.213 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHHHHhCCCCCHHHHHH
Q 034596 20 DTRHSEKLVAKVLPQVVPSVTPDDARK 46 (90)
Q Consensus 20 Dd~~t~e~Vi~~L~~v~p~~s~~~A~~ 46 (90)
.+++++.|..++|.++- .++.++=.+
T Consensus 9 ngv~P~~yL~~vL~~i~-~~~~~~~~~ 34 (39)
T PF13817_consen 9 NGVNPYAYLTDVLERIP-NHPANDIDE 34 (39)
T ss_pred cCCCHHHHHHHHHHHHc-cCCHHHHHH
Confidence 36899999999999987 766655443
No 75
>cd08500 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=40.65 E-value=1.2e+02 Score=24.02 Aligned_cols=49 Identities=22% Similarity=0.388 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhC------------Cc--EEEEe------eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH------------GM--AIVIV------TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~------------G~--a~v~~------~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+ .+-.. ...+.|+.++++|++.|+.+++.+.
T Consensus 312 ~~d~e~Ak~lL~~aG~~~~~~dG~~~~~~G~~l~l~i~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 380 (499)
T cd08500 312 EYDPDKANKLLDEAGLKKKDADGFRLDPDGKPVEFTLITNAGNSIREDIAELIKDDWRKIGIKVNLQPI 380 (499)
T ss_pred CCCHHHHHHHHHHcCCcccCCCCcEECCCCcEEEEEEEECCCCchHHHHHHHHHHHHHHhCCceEEEec
Confidence 46789999999888643 54 22211 1257899999999999999999864
No 76
>cd04443 DEP_GPR155 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown.
Probab=40.41 E-value=87 Score=19.60 Aligned_cols=45 Identities=9% Similarity=-0.071 Sum_probs=27.3
Q ss_pred CCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 5 RGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 5 ~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
++.-....|+...+.+-++=.|.|-..+. .-.-.|+++|.+++..
T Consensus 14 ~~~ikdR~~~~~~y~~cF~GselVdWL~~-~~~~~sR~eAv~lg~~ 58 (83)
T cd04443 14 QDIVKDRRCGLRTYKGVFCGCDLVSWLIE-VGLAQDRGEAVLYGRR 58 (83)
T ss_pred chhhccceecceeccccccHHHHHHHHHH-cCCCCCHHHHHHHHHH
Confidence 34556677888888888877777776554 2212455555554443
No 77
>PF08014 DUF1704: Domain of unknown function (DUF1704); InterPro: IPR012548 This family contains many hypothetical proteins.
Probab=40.15 E-value=84 Score=24.73 Aligned_cols=34 Identities=18% Similarity=0.071 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCc
Q 034596 22 RHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGM 56 (90)
Q Consensus 22 ~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~ 56 (90)
..+|--+-..|.+.. +.+.++|+.++..|++-|.
T Consensus 237 ga~F~e~F~~l~~~y-~~~~~~af~~~~Rv~RGg~ 270 (349)
T PF08014_consen 237 GASFSETFRYLREFY-GQDPEDAFTITVRVFRGGG 270 (349)
T ss_pred CCCHHHHHHHHHHHh-CCCHHHHHHHHHHHHhcCC
Confidence 346677778888888 8999999999999999988
No 78
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=40.05 E-value=1.4e+02 Score=23.00 Aligned_cols=49 Identities=16% Similarity=0.227 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHhhCC----------cE--EEE---ee---eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG----------MA--IVI---VT---VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G----------~a--~v~---~~---~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-..+ +. +-. .. ....|+.++++|++.|+.+.+++-
T Consensus 291 ~~d~~~A~~lL~~aG~~~~~~~~~~~~G~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 357 (470)
T cd08490 291 EYDPEKAKELLAEAGWTDGDGDGIEKDGEPLELTLLTYTSRPELPPIAEAIQAQLKKIGIDVEIRVV 357 (470)
T ss_pred CCCHHHHHHHHHHcCCCCCCCcccccCCceEEEEEEecCCCCchHHHHHHHHHHHHHcCceEEEEEe
Confidence 468899999999886542 22 211 11 256799999999999999999863
No 79
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=39.60 E-value=82 Score=18.68 Aligned_cols=18 Identities=17% Similarity=0.117 Sum_probs=8.0
Q ss_pred HHHHHHHHHhhcCCeeEE
Q 034596 66 HAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 66 ~AE~~~~~l~~~gL~~~i 83 (90)
.|...+..|+..|+++.+
T Consensus 19 ~a~~la~~Lr~~g~~v~~ 36 (94)
T cd00861 19 LAEKLYAELQAAGVDVLL 36 (94)
T ss_pred HHHHHHHHHHHCCCEEEE
Confidence 333444444444444444
No 80
>cd08509 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. L
Probab=38.83 E-value=1.2e+02 Score=23.90 Aligned_cols=49 Identities=22% Similarity=0.345 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhC-----------Cc--EEEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GM--AIVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~--a~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+ .+...+ ....|+.++++|++.|+.+.+++.
T Consensus 321 ~~d~~~A~~lL~~aG~~~~~~G~~~~~~g~~l~l~l~~~~~~~~~~~~a~~lq~~l~~iGi~v~i~~~ 388 (509)
T cd08509 321 KYDPDKAKKLLESAGFKKDKDGKWYTPDGTPLKFTIIVPSGWTDWMAAAQIIAEQLKEFGIDVTVKTP 388 (509)
T ss_pred cCCHHHHHHHHHHcCCeECCCCeEECCCCceEEEEEEccCCchHHHHHHHHHHHHHHhcCeEEEEecC
Confidence 57999999999887432 44 332221 256899999999999999999864
No 81
>PF04412 DUF521: Protein of unknown function (DUF521); InterPro: IPR007506 This is a group of hypothetical proteins.
Probab=38.32 E-value=1.3e+02 Score=24.33 Aligned_cols=45 Identities=20% Similarity=0.314 Sum_probs=33.9
Q ss_pred CCCCCHHHHHHHHHHHhhCC---cEEEEe-e---eHHHHHH--HHHHHhhcCCe
Q 034596 36 VPSVTPDDARKLFHESREHG---MAIVIV-T---VKEHAEF--YAQMMVRGGLR 80 (90)
Q Consensus 36 ~p~~s~~~A~~i~~~vH~~G---~a~v~~-~---~~e~AE~--~~~~l~~~gL~ 80 (90)
||++|.++-.+|+..+..++ ..-+++ . .++.|+. |.+.|.+.|..
T Consensus 297 cPH~S~~El~~ia~ll~gr~~~~~~~~~i~t~~~v~~~a~~~G~~~~le~~G~~ 350 (400)
T PF04412_consen 297 CPHLSLEELREIAELLEGRKVHPNVPLWITTSRAVYELAERMGYVERLEKAGVQ 350 (400)
T ss_pred CCCCCHHHHHHHHHHHhCCCCCCCceEEEECCHHHHHHHHhCCHHHHHHHcCCE
Confidence 89999999999998887766 222332 2 2778888 99999998853
No 82
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=38.16 E-value=85 Score=18.39 Aligned_cols=40 Identities=18% Similarity=0.186 Sum_probs=20.6
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHES 51 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~v 51 (90)
..++...+.+-++--|-|- -|++.++..++++|.+++...
T Consensus 18 ~~~~~~~~~~~F~G~e~v~-WL~~~~~~~~r~ea~~~~~~l 57 (81)
T cd04371 18 RKYHLKTYPNCFTGSELVD-WLLDNLEAITREEAVELGQAL 57 (81)
T ss_pred EEECCEECCceeEcHHHHH-HHHHhCCCCCHHHHHHHHHHH
Confidence 4455666666666555444 444444344555554444443
No 83
>PLN02363 phosphoribosylanthranilate isomerase
Probab=36.98 E-value=71 Score=23.98 Aligned_cols=41 Identities=22% Similarity=0.199 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCC
Q 034596 39 VTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGL 79 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL 79 (90)
.|.++|.+|...+...|...|+++.-+..+...+.++..||
T Consensus 83 Vs~e~a~~I~~~l~~~~~~~VgVfv~~~~~~I~~~~~~~~l 123 (256)
T PLN02363 83 ISLSVAKEISQVAREGGAKPVGVFVDDDANTILRAADSSDL 123 (256)
T ss_pred CCHHHHHHHHHhccccCccEEEEEeCCCHHHHHHHHHhcCC
Confidence 34566666665554444445665555555555555544443
No 84
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=36.97 E-value=77 Score=20.29 Aligned_cols=28 Identities=18% Similarity=0.176 Sum_probs=20.2
Q ss_pred EEEEeee-HHHHHHHHHHHhhcCCeeEEE
Q 034596 57 AIVIVTV-KEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 57 a~v~~~~-~e~AE~~~~~l~~~gL~~~ie 84 (90)
++++.|+ ...|...+++|++.|+.+++-
T Consensus 13 ~iia~G~~~~~al~A~~~L~~~Gi~~~vi 41 (124)
T PF02780_consen 13 TIIAYGSMVEEALEAAEELEEEGIKAGVI 41 (124)
T ss_dssp EEEEETTHHHHHHHHHHHHHHTTCEEEEE
T ss_pred EEEeehHHHHHHHHHHHHHHHcCCceeEE
Confidence 3444444 778888888888888887763
No 85
>cd04442 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=36.88 E-value=76 Score=19.93 Aligned_cols=42 Identities=7% Similarity=0.056 Sum_probs=26.7
Q ss_pred CCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 8 GSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 8 ~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
-.+..|+-..+.+.+.=.|.|-..+.... ..|+++|.++...
T Consensus 15 IkdR~~~~r~y~~cF~GselVdWL~~~~~-~~sR~eAv~lgq~ 56 (82)
T cd04442 15 IKDRRHHLRTYPNCFVGKELIDWLIEHKE-ASDRETAIKIMQK 56 (82)
T ss_pred eeeeEECCEEcCceeEcHHHHHHHHHcCC-CCCHHHHHHHHHH
Confidence 34567888888888888888777665433 3455555554443
No 86
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=36.77 E-value=61 Score=19.60 Aligned_cols=26 Identities=15% Similarity=0.360 Sum_probs=20.0
Q ss_pred HHHHHhCCCCCHHHHHHHHHHHhhCCc
Q 034596 30 KVLPQVVPSVTPDDARKLFHESREHGM 56 (90)
Q Consensus 30 ~~L~~v~p~~s~~~A~~i~~~vH~~G~ 56 (90)
..|++-| +....+|..||.+.-.+|-
T Consensus 24 S~lQR~~-rIGynrAariid~LE~~Gi 49 (65)
T PF09397_consen 24 SLLQRKF-RIGYNRAARIIDQLEEEGI 49 (65)
T ss_dssp HHHHHHH-T--HHHHHHHHHHHHHCTS
T ss_pred HHHHHHh-CCCHHHHHHHHHHHHHCCC
Confidence 4688889 8999999999988888874
No 87
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=36.74 E-value=71 Score=18.69 Aligned_cols=20 Identities=15% Similarity=0.328 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHhhCCcEEEE
Q 034596 41 PDDARKLFHESREHGMAIVI 60 (90)
Q Consensus 41 ~~~A~~i~~~vH~~G~a~v~ 60 (90)
.+.|.++.......|-.+..
T Consensus 14 ~~~a~~~~~~Lr~~g~~v~~ 33 (91)
T cd00860 14 LDYAKEVAKKLSDAGIRVEV 33 (91)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 34555666666666655544
No 88
>PF05822 UMPH-1: Pyrimidine 5'-nucleotidase (UMPH-1); InterPro: IPR006434 This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue []. The structure of mouse sequence has been reported []. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs [] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.; GO: 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0005737 cytoplasm; PDB: 2BDU_B 2G07_A 2G06_A 2G0A_A 2Q4T_A 2G09_A 2G08_A 2VKQ_A 2CN1_A 2JGA_A.
Probab=36.63 E-value=35 Score=25.84 Aligned_cols=24 Identities=21% Similarity=0.612 Sum_probs=17.5
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhC
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVV 36 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~ 36 (90)
..|=++|.||. ||+.|..+|..+|
T Consensus 223 ~~yDIVlv~D~--tm~v~~~il~~I~ 246 (246)
T PF05822_consen 223 EAYDIVLVDDQ--TMDVPNAILQSIL 246 (246)
T ss_dssp CCSSEEEET----B-HHHHHHHHHH-
T ss_pred hcCCEEEECCC--CchHHHHHHHHhC
Confidence 35789999996 9999999999875
No 89
>PF13117 Cag12: Cag pathogenicity island protein Cag12
Probab=36.51 E-value=79 Score=21.19 Aligned_cols=71 Identities=11% Similarity=0.158 Sum_probs=47.3
Q ss_pred CceEEEEEcCCCCCHHHHHHHH--H--HhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVL--P--QVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L--~--~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
..|++|..||+++-+.|+.... - .- ..+.+++..-..-|| +-+.+|.++.......+.+.|+.+|-++-|+
T Consensus 36 ~~~~~V~~s~~~~~~~W~y~~~~~~~~~~--~~~~~~~~~~yalAH-~~~iIv~~~~~~~~~~~K~wL~~nGa~avIe 110 (113)
T PF13117_consen 36 KPNSFVPKSDFVNGQNWTYSIVLPNFKDR--LIDPEQIVVFYALAH-SAKIIVLTGDGNLFFQYKNWLRKNGATAVIE 110 (113)
T ss_pred ccCcCcCCCccccCCCceEEEEecCCccc--ccCchhheEeeeeec-cccEEEEcCCHHHHHHHHHHHHHcCCceeEE
Confidence 3467777777777655532211 1 11 244444444444455 4577899999999999999999999998886
No 90
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 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 entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=36.24 E-value=92 Score=20.25 Aligned_cols=28 Identities=18% Similarity=0.404 Sum_probs=20.5
Q ss_pred eeeHHHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 61 VTVKEHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 61 ~~~~e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
.-.--.|...++-|+..|+.+.|+|+++
T Consensus 7 ~~n~r~AqaF~DYl~sqgI~~~i~~~~~ 34 (101)
T PF12122_consen 7 LNNPRAAQAFIDYLASQGIELQIEPEGQ 34 (101)
T ss_dssp ESSHHHHHHHHHHHHHTT--EEEE-SSS
T ss_pred cCCHHHHHHHHHHHHHCCCeEEEEECCC
Confidence 4446689999999999999999998654
No 91
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=36.04 E-value=87 Score=17.91 Aligned_cols=29 Identities=10% Similarity=0.211 Sum_probs=18.6
Q ss_pred EEEeeeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 58 IVIVTVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 58 ~v~~~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
+....+.-+|+.....|.+.|+.|.+.-+
T Consensus 3 l~~~~~~~ea~~i~~~L~~~gI~~~v~~~ 31 (67)
T PF09413_consen 3 LYTAGDPIEAELIKGLLEENGIPAFVKNE 31 (67)
T ss_dssp EEEE--HHHHHHHHHHHHHTT--EE--S-
T ss_pred EEEcCCHHHHHHHHHHHHhCCCcEEEECC
Confidence 44566678999999999999999988643
No 92
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=35.98 E-value=1.7e+02 Score=22.68 Aligned_cols=49 Identities=18% Similarity=0.266 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhC----------CcE--EEEee------eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH----------GMA--IVIVT------VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~----------G~a--~v~~~------~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+- +-..+ ....|+.++++|++.|+.+.+++.
T Consensus 296 ~~d~~~Ak~lL~eaG~~~~~~g~~~~~g~~l~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~~~ 362 (464)
T cd08518 296 DYDPEKAKKILEEAGWKDGDDGGREKDGQKAEFTLYYPSGDQVRQDLAVAVASQAKKLGIEVKLEGK 362 (464)
T ss_pred CCCHHHHHHHHHHcCCCcCCCCeeccCCcEEEEEEEeCCCCHHHHHHHHHHHHHHHHhCCeEEEEEe
Confidence 57899999999998542 432 21111 246899999999999999999864
No 93
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=35.76 E-value=1e+02 Score=21.24 Aligned_cols=49 Identities=22% Similarity=0.295 Sum_probs=39.8
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeE
Q 034596 26 KLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRST 82 (90)
Q Consensus 26 e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ 82 (90)
.-|++-|.+ | .|.++|..|-.-.-..|. -+.+.|......|...||++-
T Consensus 65 PtViD~lrR-C--~T~EEALEVInylek~GE-----It~e~A~eLr~~L~~kGvr~f 113 (128)
T PF09868_consen 65 PTVIDYLRR-C--KTDEEALEVINYLEKRGE-----ITPEEAKELRSILVKKGVRSF 113 (128)
T ss_pred ChHHHHHHH-h--CcHHHHHHHHHHHHHhCC-----CCHHHHHHHHHHHHHhhHHHh
Confidence 357887776 7 899999999888777774 578999999999988887654
No 94
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=35.09 E-value=1.3e+02 Score=23.44 Aligned_cols=49 Identities=12% Similarity=0.163 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHhh-CCcE--EEE------eeeHHHHHHHHHHHhhcC-CeeEEEeC
Q 034596 38 SVTPDDARKLFHESRE-HGMA--IVI------VTVKEHAEFYAQMMVRGG-LRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~-~G~a--~v~------~~~~e~AE~~~~~l~~~g-L~~~iep~ 86 (90)
..+.++|.++..++=. .|+. +.. ....+.|+.+++++++.| +.+.+.+.
T Consensus 306 ~~d~~kA~~lL~~aG~~~G~~l~l~~~~~~~~~~~~~~a~~i~~~l~~~G~i~v~~~~~ 364 (469)
T cd08519 306 DPNVEKARQLLQQAGYSAENPLKLELWYRSNHPADKLEAATLKAQLEADGLFKVNLKSV 364 (469)
T ss_pred CCCHHHHHHHHHHhCCCCCCCceEEEEecCCCCchhHHHHHHHHHHHhccceEEEEEec
Confidence 4789999999998844 4554 222 233679999999999998 69888764
No 95
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=34.98 E-value=1e+02 Score=21.27 Aligned_cols=40 Identities=10% Similarity=0.232 Sum_probs=31.4
Q ss_pred CCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhC
Q 034596 10 GDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREH 54 (90)
Q Consensus 10 ~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~ 54 (90)
|..++|.|+ -++++=++-+++-. |+|.++|.+++.+....
T Consensus 113 ~~~l~V~i~----A~~~~Rv~ri~~~~-~~s~~~A~~~i~~~D~~ 152 (179)
T PF13189_consen 113 PNVLHVFIY----APLEFRVERIMERE-GISEEEAEKLIKKEDKR 152 (179)
T ss_dssp TTEEEEEEE----E-HHHHHHHHHHHH-T--HHHHHHHHHHHHHH
T ss_pred CCeEEEEEE----CCHHHHHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 467888888 56899999999999 99999999999887653
No 96
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=34.97 E-value=76 Score=18.50 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=21.5
Q ss_pred EEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 57 AIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 57 a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
-.+.+.+++.++.++..|.+.|+.+++.
T Consensus 24 i~~~~~s~~ll~~v~~lL~~lGi~~~i~ 51 (77)
T PF14528_consen 24 ISISSKSKELLEDVQKLLLRLGIKASIY 51 (77)
T ss_dssp EEEEES-HHHHHHHHHHHHHTT--EEEE
T ss_pred EEEEECCHHHHHHHHHHHHHCCCeeEEE
Confidence 3445778999999999999999999987
No 97
>KOG3261 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.91 E-value=22 Score=26.05 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=22.0
Q ss_pred CCCCCC--CCCCCceEEEEEcC-CCCCHHHHH
Q 034596 1 MKDKRG--TGSGDSYRVLLIDD-TRHSEKLVA 29 (90)
Q Consensus 1 ~~~~~~--~~~~~~y~ViL~ND-d~~t~e~Vi 29 (90)
||++.+ +++||+|-.|.--| ..|.+||..
T Consensus 145 Mk~~~G~w~~pPPpyp~I~~~d~~~NL~e~I~ 176 (202)
T KOG3261|consen 145 MKEPDGSWTAPPPPYPPIVAQDILHNLSEYIA 176 (202)
T ss_pred hcCCCCCccCCCCCCCccccccchhhHHHHhh
Confidence 566555 68899999999988 777777653
No 98
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=34.82 E-value=77 Score=18.57 Aligned_cols=51 Identities=18% Similarity=0.221 Sum_probs=35.0
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEEe
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~iep 85 (90)
..|....+.+-++-.|.|-. |+..+ . +.++++|..+++.|.++|+-.-+-+
T Consensus 10 ~~~~~~~~~~~F~G~e~v~w-L~~~~-~----------------------~~~r~eA~~l~~~ll~~g~i~~v~~ 60 (77)
T smart00049 10 RKYFLKTYPNCFTGSELVDW-LMDNL-E----------------------IIDREEAVHLGQLLLDEGLIHHVNG 60 (77)
T ss_pred EEECCEECcceeEcHHHHHH-HHHcC-C----------------------cCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 55777788888887777664 44444 1 4567777888888888887666653
No 99
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=34.63 E-value=1.1e+02 Score=23.35 Aligned_cols=47 Identities=19% Similarity=0.249 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhhCCcEEE----EeeeHHHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 42 DDARKLFHESREHGMAIV----IVTVKEHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a~v----~~~~~e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
..+......+|.+|+-+- -+.|+-.-...+..|.+.|+.+++.+|+.
T Consensus 131 ~tv~~~l~~A~~~~k~~~V~v~EsrP~~~G~~~a~~L~~~GI~vtlI~Dsa 181 (310)
T PRK08535 131 SAALSVIKTAHEQGKDIEVIATETRPRNQGHITAKELAEYGIPVTLIVDSA 181 (310)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCCchhhHHHHHHHHHHCCCCEEEEehhH
Confidence 456666778888887432 24445455678888999999999999863
No 100
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=34.31 E-value=79 Score=18.00 Aligned_cols=18 Identities=28% Similarity=0.416 Sum_probs=10.7
Q ss_pred HHHHHHHHHhhCCcEEEE
Q 034596 43 DARKLFHESREHGMAIVI 60 (90)
Q Consensus 43 ~A~~i~~~vH~~G~a~v~ 60 (90)
.|.+++...+..|..+..
T Consensus 16 ~a~~i~~~Lr~~g~~v~~ 33 (91)
T cd00859 16 EALELAEQLRDAGIKAEI 33 (91)
T ss_pred HHHHHHHHHHHCCCEEEE
Confidence 466666666666664443
No 101
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=34.20 E-value=1.1e+02 Score=19.50 Aligned_cols=56 Identities=18% Similarity=0.274 Sum_probs=35.4
Q ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeH
Q 034596 7 TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVK 64 (90)
Q Consensus 7 ~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~ 64 (90)
.+.+.--|--|.|+...+|++....++++||++.. +...|-| ...+|--+..+..-
T Consensus 11 ~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~-~~ftlky-~DeeGDlvtIssde 66 (87)
T cd06402 11 DANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLRG-KNFQLFW-KDEEGDLVAFSSDE 66 (87)
T ss_pred CCccceEEEEecCCCCcCHHHHHHHHHHHccccCC-CcEEEEE-ECCCCCEEeecCHH
Confidence 33444556667888888999999999999976543 3333332 34455544444443
No 102
>PF09759 Atx10homo_assoc: Spinocerebellar ataxia type 10 protein domain; InterPro: IPR019156 This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region [].
Probab=34.13 E-value=1.1e+02 Score=20.04 Aligned_cols=55 Identities=11% Similarity=0.171 Sum_probs=35.1
Q ss_pred CCCCCH--HHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 20 DTRHSE--KLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 20 Dd~~t~--e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
||.||| ||.+.+++-.+ .- -+++.++-...-..|. .-...|++.|+.+.+.+++.
T Consensus 40 D~~nP~irEwai~aiRnL~-e~-n~eNQ~~I~~L~~~~~------------~~~~~L~~~G~~v~~d~~Gk 96 (102)
T PF09759_consen 40 DDHNPFIREWAIFAIRNLC-EG-NPENQEFIAQLEPQGV------------ADNEELEELGLEVEIDKDGK 96 (102)
T ss_pred CcccHHHHHHHHHHHHHHH-hC-CHHHHHHHHhccccCC------------cchHHHHHcCCeEEEcCCCe
Confidence 777775 89999999999 33 3334443333333333 22356788999999877653
No 103
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=33.38 E-value=1.6e+02 Score=22.90 Aligned_cols=49 Identities=22% Similarity=0.337 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhC-----------CcEE-E-E---e---eeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-----------GMAI-V-I---V---TVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-----------G~a~-v-~---~---~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++-.. |+.+ + . . .....|+.+++++++.|+.+++.+-
T Consensus 303 ~~d~~~A~~lL~~aG~~~~~~~g~~~~~g~~~~~~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~ 370 (488)
T cd08489 303 SYDPEKANALLDEAGWTLNEGDGIREKDGKPLSLELVYQTDNALQKSIAEYLQSELKKIGIDLNIIGE 370 (488)
T ss_pred CCCHHHHHHHHHHcCCCcCCCCceEccCCceEEEEEEecCCCchHHHHHHHHHHHHHHcCcEEEEeec
Confidence 46789999999988753 3322 2 1 1 2257889999999999999998763
No 104
>PF11110 Phage_hub_GP28: Baseplate hub distal subunit; InterPro: IPR024342 Gp28 is a structural component of the central part of the bacteriophage T4 baseplate. The membrane-bound protein forms a complex with an another baseplate structural component, Gp27 []. This complex may function as an initiator of the central hub assembly.
Probab=33.19 E-value=69 Score=22.73 Aligned_cols=36 Identities=14% Similarity=0.237 Sum_probs=30.1
Q ss_pred EcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhh
Q 034596 18 IDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESRE 53 (90)
Q Consensus 18 ~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~ 53 (90)
+-|.-.+++-....+..++|++|.+++.-+++..+.
T Consensus 12 iKd~k~~~~~l~~LidSI~p~LtaAE~D~V~LHLl~ 47 (151)
T PF11110_consen 12 IKDMKDPDENLKILIDSIKPGLTAAERDFVSLHLLE 47 (151)
T ss_pred HhccCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 345666788888899999999999999999988775
No 105
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=32.91 E-value=36 Score=22.95 Aligned_cols=60 Identities=8% Similarity=0.053 Sum_probs=50.8
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 15 VLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
|.++|=++..-.-|...|..++ |.....|.+|...+--....-++..+.+.-+.....+.
T Consensus 2 vrI~~~~i~~~k~v~~aLt~i~-GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 61 (122)
T CHL00137 2 VRIAGVDLPRNKRIEYALTYIY-GIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIE 61 (122)
T ss_pred ceEcCccCCCCCEeeeeecccc-cccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHH
Confidence 3455666666666778899999 99999999999999999999999999888888888775
No 106
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=32.64 E-value=1.4e+02 Score=24.08 Aligned_cols=49 Identities=12% Similarity=0.036 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhC-CcEE-E---E-ee--eHHHHHHHHHHHhh-cCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-GMAI-V---I-VT--VKEHAEFYAQMMVR-GGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-G~a~-v---~-~~--~~e~AE~~~~~l~~-~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+.+ + . .+ ..+.|+..++++++ .|+.+.|++.
T Consensus 356 ~~d~~kAk~LL~eAG~~~g~~~~l~l~~~~~~~~~~~a~~iq~~l~~~iGI~v~i~~~ 413 (535)
T PRK09755 356 SERVAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQVTLRTM 413 (535)
T ss_pred ccCHHHHHHHHHHcCCcCCCCceEEEEeCCCchHHHHHHHHHHHHHHHhCCeeEEEec
Confidence 57899999999987553 3221 1 1 12 36899999999999 8999999874
No 107
>KOG2599 consensus Pyridoxal/pyridoxine/pyridoxamine kinase [Coenzyme transport and metabolism]
Probab=32.63 E-value=40 Score=26.41 Aligned_cols=49 Identities=20% Similarity=0.329 Sum_probs=41.5
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHH
Q 034596 19 DDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAE 68 (90)
Q Consensus 19 NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE 68 (90)
-|=.||-.|=++.|...- =.|.++|.+.+...|+.|-..|-+.+.+.-+
T Consensus 145 adiiTPNqFE~EiLtg~~-I~t~eda~~a~~~lhq~~v~~vVITS~~~~~ 193 (308)
T KOG2599|consen 145 ADIITPNQFEAEILTGME-IRTEEDAKRAVEKLHQKGVKTVVITSFDLGE 193 (308)
T ss_pred hhhcCCcchhhhhhcCCe-eccHHHHHHHHHHHHHhCCCEEEEEeeeeCC
Confidence 488899999999998876 7999999999999999998777777766443
No 108
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=32.60 E-value=1.7e+02 Score=20.30 Aligned_cols=62 Identities=10% Similarity=0.187 Sum_probs=47.0
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhC-CC------CCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHH
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVV-PS------VTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQ 72 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~-p~------~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~ 72 (90)
+.=++++-||..-.-++--.+|.-.. |. +|.++|.+.-.......+.++.+.+-+.|....+
T Consensus 29 ~~~~IiVvdD~vA~D~~~k~~lkma~~P~gvk~~i~sv~~a~~~l~~~~~~~~vlvl~~~~~da~~l~~ 97 (158)
T PRK09756 29 GANLLVVVDDVVANDDIQQKLMGITAETYGFGIRFFTIEKTINVIGKAAPHQKIFLICRTPQTVRKLVE 97 (158)
T ss_pred CCCEEEEEcchhcCCHHHHHHHHhcCCCCCCEEEEEEHHHHHHHHHhccCCceEEEEECCHHHHHHHHH
Confidence 34478999999999998888888656 65 7899998887764455567777777777766655
No 109
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=32.50 E-value=95 Score=20.44 Aligned_cols=41 Identities=12% Similarity=0.106 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHhCCCCCHHHHHHHH------HHHhhCCcEEEEe
Q 034596 20 DTRHSEKLVAKVLPQVVPSVTPDDARKLF------HESREHGMAIVIV 61 (90)
Q Consensus 20 Dd~~t~e~Vi~~L~~v~p~~s~~~A~~i~------~~vH~~G~a~v~~ 61 (90)
++...|-|=+.-|.++| |+|...|.+|- -.+-+.|+-+|.-
T Consensus 39 ~~~~~yvyG~~GlAklf-gcSv~Ta~RiK~sG~id~AI~Q~Gr~IivD 85 (96)
T PF12964_consen 39 KDEKKYVYGLKGLAKLF-GCSVPTANRIKKSGKIDPAITQIGRKIIVD 85 (96)
T ss_pred CcccceeehHHHHHHHh-CCCchhHHHHHhcCCccHHHHHcCCEEEEe
Confidence 34455667788999999 99999999988 5778888888753
No 110
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=32.48 E-value=2.1e+02 Score=23.05 Aligned_cols=49 Identities=16% Similarity=0.244 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhC-------CcE--EEEee-----eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREH-------GMA--IVIVT-----VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~-------G~a--~v~~~-----~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++..++=.. |+. +.... ....|+.++++|++.|+.+.|++.
T Consensus 354 ~~d~~kA~~lL~~AG~~~~~~g~~G~~l~i~~~~~~~~~~~~~a~~iq~~l~~iGI~v~i~~~ 416 (528)
T cd08505 354 RYDLELAKALLAEAGYPDGRDGPTGKPLVLNYDTQATPDDKQRLEWWRKQFAKLGIQLNVRAT 416 (528)
T ss_pred CCCHHHHHHHHHHcCCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHHHHcCceEEEEec
Confidence 57899999999997543 332 22211 257899999999999999999874
No 111
>PRK11633 cell division protein DedD; Provisional
Probab=32.38 E-value=67 Score=23.93 Aligned_cols=24 Identities=13% Similarity=0.122 Sum_probs=21.4
Q ss_pred eHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 63 VKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 63 ~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.|+..+.+|+..|+.+.++|.
T Consensus 159 n~~~A~~l~~kL~~~G~~Ay~~~~ 182 (226)
T PRK11633 159 NADKVNEIVAKLRLSGYRVYTVPS 182 (226)
T ss_pred CHHHHHHHHHHHHHCCCeeEEEee
Confidence 378999999999999999999874
No 112
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=32.29 E-value=73 Score=18.69 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=13.2
Q ss_pred HHHHHHHHHHhhCCcEEEEee
Q 034596 42 DDARKLFHESREHGMAIVIVT 62 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a~v~~~ 62 (90)
+.|.+++.+.+..|-.+....
T Consensus 18 ~~a~~~~~~Lr~~g~~v~~~~ 38 (94)
T cd00738 18 EYAQKLLNALLANGIRVLYDD 38 (94)
T ss_pred HHHHHHHHHHHHCCCEEEecC
Confidence 456667777777776555433
No 113
>cd04437 DEP_Epac DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion. Epac-like proteins share a common domain architecture, containing RasGEF, DEP and CAP-effector (cAMP binding) domains. The DEP domain is involved in membrane localization.
Probab=32.14 E-value=1.3e+02 Score=20.32 Aligned_cols=52 Identities=19% Similarity=0.192 Sum_probs=37.6
Q ss_pred CCCCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCC-CCHHHHHHHHHHHhhCC
Q 034596 3 DKRGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPS-VTPDDARKLFHESREHG 55 (90)
Q Consensus 3 ~~~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~-~s~~~A~~i~~~vH~~G 55 (90)
+.+..-.+..|+-..+.+.+.-.|.|-..+.. ++. .|+++|..+....=.+|
T Consensus 12 ~~~~~ikdR~~~~~~y~~cF~GsElVdWLl~~-~~~v~sR~eAv~lgq~Ll~~g 64 (125)
T cd04437 12 DAPHLIRDRKYHLRTYRQCCVGTELVDWLLQQ-SPCVQSRSQAVGMWQVLLEEG 64 (125)
T ss_pred cCcccceeeeECCEECCcccccHHHHHHHHHc-CCCCCCHHHHHHHHHHHHhCC
Confidence 44555667889999999999999988776655 433 47888888777654444
No 114
>COG0309 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.09 E-value=1.7e+02 Score=23.31 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=48.4
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCC-eeEE
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGL-RSTI 83 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL-~~~i 83 (90)
..+.+.+.-|.+--.+.| +.+++.| |+++= ++=++|+-++. -+++.|+...+.|+++|+ .+++
T Consensus 241 Sgvgi~I~ee~Ipv~~eV-r~vce~l-GiDPl-------~~anEG~lv~~-V~~~~a~~~l~~L~~~~~~~A~i 304 (339)
T COG0309 241 SGVGISIEEEKIPVREEV-RGVCELL-GLDPL-------ELANEGKLVIA-VPPEHAEEVLEALRSHGLKDAAI 304 (339)
T ss_pred cCCeEEEeeccccccHHH-HHHHHHh-CCCHH-------HhhcCceEEEE-ECHHHHHHHHHHHHhcCCcccee
Confidence 456677888888777776 6788999 99974 45568886665 478999999999999994 5444
No 115
>cd02144 iodotyrosine_dehalogenase Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
Probab=31.85 E-value=61 Score=21.92 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=23.4
Q ss_pred HHHHHHHHhhCCcEEEEeeeHHHHHHHHHHH
Q 034596 44 ARKLFHESREHGMAIVIVTVKEHAEFYAQMM 74 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l 74 (90)
|..+|+.++..|-+.|+.+.++..+...+.|
T Consensus 129 ~~~l~LaA~~~Glgs~~~~~~~~~~~v~~~l 159 (193)
T cd02144 129 CGLLLAALQNAGLGTVTTTPLNMGPFLRRLL 159 (193)
T ss_pred HHHHHHHHHHCCCceeecCCcchhHHHHHHh
Confidence 5569999999999999877776545454444
No 116
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.65 E-value=1.3e+02 Score=18.48 Aligned_cols=61 Identities=5% Similarity=-0.084 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh-hcCCeeEE
Q 034596 21 TRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV-RGGLRSTI 83 (90)
Q Consensus 21 d~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~-~~gL~~~i 83 (90)
..=+.+-+..+|.. . |.+.++..+++..+..++.+.+..-.+-.+-....+.+ ++.|..++
T Consensus 25 G~Is~~el~~~l~~-~-~~~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~~~g~~~~~~~ 86 (96)
T smart00027 25 GTVTGAQAKPILLK-S-GLPQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRKLNGYPIPASL 86 (96)
T ss_pred CeEeHHHHHHHHHH-c-CCCHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHcCCCCCccC
Confidence 34567778888887 6 89999999999999988888776544444433333333 33444443
No 117
>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=31.59 E-value=1.8e+02 Score=24.48 Aligned_cols=69 Identities=14% Similarity=0.202 Sum_probs=53.2
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHH---HHHh--hCCcEEEEeeeHHHHHHHHHHHhhcCCee
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLF---HESR--EHGMAIVIVTVKEHAEFYAQMMVRGGLRS 81 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~---~~vH--~~G~a~v~~~~~e~AE~~~~~l~~~gL~~ 81 (90)
.+.+|.+-|.+...-...|..+..+| . ..++...|+ ..++ ..|+.||+.-.+..|+.....++..|+.|
T Consensus 295 ~~~~i~ig~~~~~~a~~~i~qive~~-~-~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a 368 (519)
T KOG0331|consen 295 NPIQINVGNKKELKANHNIRQIVEVC-D-ETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPA 368 (519)
T ss_pred CceEEEecchhhhhhhcchhhhhhhc-C-HHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcce
Confidence 45678888887778888899999999 4 555555444 3343 67899999999999999999999876544
No 118
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=31.25 E-value=83 Score=26.77 Aligned_cols=34 Identities=12% Similarity=0.188 Sum_probs=26.9
Q ss_pred HhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 51 SREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 51 vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
-|..|.+|+...++..+|..+++|+..|+.+..-
T Consensus 227 ~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~Y 260 (590)
T COG0514 227 PQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAY 260 (590)
T ss_pred cccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEe
Confidence 3445558889999999999999999888777653
No 119
>cd02149 NfsB_like_nitroreductase NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs.
Probab=30.62 E-value=37 Score=22.62 Aligned_cols=23 Identities=4% Similarity=0.042 Sum_probs=19.5
Q ss_pred HHHHHHHHhhCCcEEEEeeeHHH
Q 034596 44 ARKLFHESREHGMAIVIVTVKEH 66 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~~e~ 66 (90)
+.++|+.+|..|-+.|+.+.++.
T Consensus 94 ~~~l~LaA~~lGlgs~~i~~~~~ 116 (157)
T cd02149 94 LGNMLLAAASLGIDSCPIEGFDP 116 (157)
T ss_pred HHHHHHHHHHcCCCcCcccCcCH
Confidence 56889999999999999876653
No 120
>TIGR00963 secA preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.
Probab=30.22 E-value=1.4e+02 Score=26.26 Aligned_cols=35 Identities=14% Similarity=0.300 Sum_probs=29.0
Q ss_pred HhhCCcEEE-EeeeHHHHHHHHHHHhhcCCeeEEEe
Q 034596 51 SREHGMAIV-IVTVKEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 51 vH~~G~a~v-~~~~~e~AE~~~~~l~~~gL~~~iep 85 (90)
.|.+|+.+. ++-+.+.+|..+..|...|+.+.+--
T Consensus 401 ~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Ln 436 (745)
T TIGR00963 401 RHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLN 436 (745)
T ss_pred HHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEee
Confidence 489998766 67779999999999999998876543
No 121
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=29.84 E-value=92 Score=22.53 Aligned_cols=31 Identities=16% Similarity=0.237 Sum_probs=25.7
Q ss_pred CCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 54 HGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 54 ~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
.|+-++.+-|.+.++..+.+|++.|..+..-
T Consensus 2 ~g~~vlvTRp~~~~~~l~~~l~~~G~~~~~~ 32 (255)
T PRK05752 2 SGWRLLLTRPAEECAALAASLAEAGIFSSSL 32 (255)
T ss_pred CCCEEEECCcHHHHHHHHHHHHHcCCCEEEc
Confidence 4788889999999999999999998555543
No 122
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.77 E-value=1.7e+02 Score=23.26 Aligned_cols=30 Identities=10% Similarity=0.133 Sum_probs=24.0
Q ss_pred CCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 54 HGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 54 ~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
..+++|...+++.|+..+..|++.|+.+..
T Consensus 226 ~~~~IIF~~s~~~~e~la~~L~~~g~~~~~ 255 (470)
T TIGR00614 226 GKSGIIYCPSRKKSEQVTASLQNLGIAAGA 255 (470)
T ss_pred CCceEEEECcHHHHHHHHHHHHhcCCCeeE
Confidence 334588899999999999999988876654
No 123
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=29.50 E-value=1.2e+02 Score=19.27 Aligned_cols=45 Identities=9% Similarity=0.006 Sum_probs=22.3
Q ss_pred CCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 5 RGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 5 ~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
++.-..+.+.-..+...+.-.|.|-..+... +-.|+++|.++...
T Consensus 16 ~~~ik~R~~~~~~y~~cF~GsElVdWL~~~~-~~~sR~eAv~lgq~ 60 (85)
T cd04441 16 NSILQVREEEGVKYERTFVGSEFIDWLLQEG-EAESRREAVQLCRR 60 (85)
T ss_pred CCceeeeEeCCEEcCCEeEchHHHHHHHHcC-CCCCHHHHHHHHHH
Confidence 3333444555556666666666665544432 13344444444433
No 124
>TIGR00512 salvage_mtnA S-methyl-5-thioribose-1-phosphate isomerase. The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
Probab=29.20 E-value=2e+02 Score=22.52 Aligned_cols=45 Identities=22% Similarity=0.258 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhCCcEEE-E---eeeH-HHHHHHHHHHhhcCCeeEEEeCC
Q 034596 43 DARKLFHESREHGMAIV-I---VTVK-EHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 43 ~A~~i~~~vH~~G~a~v-~---~~~~-e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.|..+...+|.+|+-+. . +-|+ +=++..+..|.+.|+.|++.+|+
T Consensus 166 tal~~l~~A~~~g~~~~V~v~EsrP~~qG~rlta~~L~~~GI~vtlI~Ds 215 (331)
T TIGR00512 166 TALGVIRSAHEKGRLEHVYADETRPRLQGARLTAWELVQEGIPATLITDS 215 (331)
T ss_pred hHHHHHHHHHHcCCceEEEECCCCchhhHHHHHHHHHHHCCCCEEEEccc
Confidence 57778888999997432 2 2333 23446688899999999999985
No 125
>PRK15320 transcriptional activator SprB; Provisional
Probab=28.42 E-value=1.3e+02 Score=22.81 Aligned_cols=59 Identities=12% Similarity=0.086 Sum_probs=45.3
Q ss_pred EEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCC---cEEE--EeeeHHHHHHHHH
Q 034596 14 RVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHG---MAIV--IVTVKEHAEFYAQ 72 (90)
Q Consensus 14 ~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G---~a~v--~~~~~e~AE~~~~ 72 (90)
.||++-|.++.-=-|..++.+..|++.-+.|+.+.--.|+-. .|+. .--|+|+-=....
T Consensus 3 ~viiyg~~w~~~~a~~~~~~~~~p~~~~~t~~~l~~ll~~l~~~p~a~lil~l~p~eh~~lf~~ 66 (251)
T PRK15320 3 NVIIYGINWTNCYALQSIFKQKYPEKCVKTCNSLTALLHSLSDMPDAGLILALNPHEHVYLFHA 66 (251)
T ss_pred cEEEEeccchHHHHHHHHHHHHCCccchhhhhhHHHHHHHHhhCCCceEEEeeCchhHHHHHHH
Confidence 689999999888778888999999999999999998888643 2333 3556776654433
No 126
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=28.22 E-value=1.8e+02 Score=22.78 Aligned_cols=33 Identities=12% Similarity=0.187 Sum_probs=26.3
Q ss_pred HhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 51 SREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 51 vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
.+..++++|..-.++.|+..+..|...|+.+..
T Consensus 239 ~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~ 271 (460)
T PRK11776 239 HHQPESCVVFCNTKKECQEVADALNAQGFSALA 271 (460)
T ss_pred hcCCCceEEEECCHHHHHHHHHHHHhCCCcEEE
Confidence 445678889999999999999999888876543
No 127
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=28.22 E-value=92 Score=15.80 Aligned_cols=40 Identities=10% Similarity=0.147 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEE
Q 034596 21 TRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVI 60 (90)
Q Consensus 21 d~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~ 60 (90)
..-+++.+..+|....+..+.+.+..++.....++.+.+.
T Consensus 15 g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 54 (63)
T cd00051 15 GTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKID 54 (63)
T ss_pred CcCcHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCCeEe
Confidence 3457778888898887788999999999988877766554
No 128
>PRK08335 translation initiation factor IF-2B subunit alpha; Validated
Probab=27.94 E-value=1.7e+02 Score=22.40 Aligned_cols=46 Identities=13% Similarity=0.207 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhCCcE---EEE-eeeH-HHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 42 DDARKLFHESREHGMA---IVI-VTVK-EHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a---~v~-~~~~-e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
..+..+...+|.+|+- +|. +-|+ +=+.. +.+|.+.|+.+++.+|+.
T Consensus 120 ~tv~~~l~~A~~~gk~~~V~v~EsrP~~qG~~l-a~eL~~~GI~vtlI~Dsa 170 (275)
T PRK08335 120 SAVLEILKTAKRKGKRFKVILTESAPDYEGLAL-ANELEFLGIEFEVITDAQ 170 (275)
T ss_pred HHHHHHHHHHHHcCCceEEEEecCCCchhHHHH-HHHHHHCCCCEEEEeccH
Confidence 4677788889999973 332 3343 34555 999999999999999863
No 129
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=27.82 E-value=1.5e+02 Score=22.59 Aligned_cols=46 Identities=20% Similarity=0.232 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhCCcEEE---E-eeeHHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 42 DDARKLFHESREHGMAIV---I-VTVKEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a~v---~-~~~~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
..+..+...+|.+|+-+- . +.|.-.-...+..|.+.|+.+++.+|+
T Consensus 126 ~tv~~~l~~a~~~~~~f~V~v~EsrP~~~G~~~a~~L~~~gI~vtlI~Ds 175 (301)
T TIGR00511 126 EAALSVIKTAFEQGKDIEVIATETRPRKQGHITAKELRDYGIPVTLIVDS 175 (301)
T ss_pred HHHHHHHHHHHHcCCcEEEEEecCCCcchHHHHHHHHHHCCCCEEEEehh
Confidence 346677788888877332 2 333434456788889999999999885
No 130
>cd02150 NADPH_oxidoreductase_1 NAD(P)H:flavin oxidoreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=27.76 E-value=98 Score=20.64 Aligned_cols=23 Identities=13% Similarity=0.251 Sum_probs=19.4
Q ss_pred HHHHHHHHhhCCcEEEEeeeHHH
Q 034596 44 ARKLFHESREHGMAIVIVTVKEH 66 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~~e~ 66 (90)
+.++++.++..|-+.|+.+.++.
T Consensus 96 ~~nl~Laa~~~Glgt~~~~~~~~ 118 (166)
T cd02150 96 VQNILLAAHALGLGAVWLGVYPF 118 (166)
T ss_pred HHHHHHHHHHcCCceEEEecccc
Confidence 55789999999999999877663
No 131
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=27.54 E-value=1.5e+02 Score=26.66 Aligned_cols=35 Identities=14% Similarity=0.259 Sum_probs=29.8
Q ss_pred HHhhCCcEEE-EeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 50 ESREHGMAIV-IVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 50 ~vH~~G~a~v-~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
+.|..|+.+. ++.+.+.+|.++..|...|+.+.+-
T Consensus 439 ~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vL 474 (896)
T PRK13104 439 ECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVL 474 (896)
T ss_pred HHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEee
Confidence 4599999765 7888999999999999999887764
No 132
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=27.32 E-value=1.1e+02 Score=17.68 Aligned_cols=24 Identities=17% Similarity=0.152 Sum_probs=17.6
Q ss_pred CcEEEEee-eHHHHHHHHHHHhhcC
Q 034596 55 GMAIVIVT-VKEHAEFYAQMMVRGG 78 (90)
Q Consensus 55 G~a~v~~~-~~e~AE~~~~~l~~~g 78 (90)
|-++.+.+ +.+.|+...+++++.+
T Consensus 59 G~~v~~l~~~~~~~~~v~~~l~~~~ 83 (85)
T PF08544_consen 59 GPTVFALCKDEDDAERVAEALREHY 83 (85)
T ss_dssp SSEEEEEESSHHHHHHHHHHHHHHT
T ss_pred CCeEEEEECCHHHHHHHHHHHHHhC
Confidence 44555666 7889999999887653
No 133
>cd04439 DEP_1_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and by the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=27.14 E-value=1.5e+02 Score=18.42 Aligned_cols=46 Identities=9% Similarity=0.006 Sum_probs=26.5
Q ss_pred CCCCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q 034596 5 RGTGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHES 51 (90)
Q Consensus 5 ~~~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~v 51 (90)
...-....|....+-.-++=.|.|-..+.. ..--++++|..+....
T Consensus 12 ~~~ikdr~~~~~~~~~cF~GselVdWL~~~-~~~~~r~eAv~lg~~L 57 (81)
T cd04439 12 GSLIKDRRRKLSTFPKCFLGNEFVSWLLEI-GEISKPEEGVNLGQAL 57 (81)
T ss_pred CCceEeeEECcEEcCceeEhHHHHHHHHHc-CCCCCHHHHHHHHHHH
Confidence 334445677777777777777777665533 3133445555554433
No 134
>PRK05443 polyphosphate kinase; Provisional
Probab=27.06 E-value=4.2e+02 Score=22.97 Aligned_cols=65 Identities=17% Similarity=0.242 Sum_probs=45.9
Q ss_pred EEEcCCCCCHHHHHHHHHHhCCC-------------C-CHHHHHHHHHHHhhCCcEEEEeee------HHHHHHHHHHHh
Q 034596 16 LLIDDTRHSEKLVAKVLPQVVPS-------------V-TPDDARKLFHESREHGMAIVIVTV------KEHAEFYAQMMV 75 (90)
Q Consensus 16 iL~NDd~~t~e~Vi~~L~~v~p~-------------~-s~~~A~~i~~~vH~~G~a~v~~~~------~e~AE~~~~~l~ 75 (90)
||+.=|+++|+.|++.|.+.- . . +...-.+--..+..+|+-+-..-+ .+....++.+|+
T Consensus 341 iLLh~PY~SF~~~~~~i~~Aa-~DP~V~~Ik~tlYr~~~~s~iv~aL~~Aa~~Gk~V~vlve~karfde~~n~~~~~~L~ 419 (691)
T PRK05443 341 ILLHHPYESFDPVVEFLRQAA-ADPDVLAIKQTLYRTSKDSPIVDALIEAAENGKQVTVLVELKARFDEEANIRWARRLE 419 (691)
T ss_pred EEEECCccCchHHHHHHHHhc-cCCCeeEEEEEEEEecCCHHHHHHHHHHHHcCCEEEEEEccCccccHHHHHHHHHHHH
Confidence 478889999999999998865 2 0 123333444567778887665333 455668888999
Q ss_pred hcCCee
Q 034596 76 RGGLRS 81 (90)
Q Consensus 76 ~~gL~~ 81 (90)
+.|.++
T Consensus 420 ~aGv~V 425 (691)
T PRK05443 420 EAGVHV 425 (691)
T ss_pred HcCCEE
Confidence 999776
No 135
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=26.78 E-value=1e+02 Score=23.69 Aligned_cols=46 Identities=22% Similarity=0.292 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhhCCcEEE-E---eeeHH-HHHHHHHHHhhcCCeeEEEeCC
Q 034596 42 DDARKLFHESREHGMAIV-I---VTVKE-HAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 42 ~~A~~i~~~vH~~G~a~v-~---~~~~e-~AE~~~~~l~~~gL~~~iep~~ 87 (90)
..+..+...+|.+|+-.- . +-|+- -+...+..|.+.|+.|++.+|+
T Consensus 137 ~tv~~~l~~A~~~g~~~~V~v~EsrP~~~G~~~~a~~L~~~gI~vtlI~Ds 187 (303)
T TIGR00524 137 GTALGVIRSAWEDGKRIRVIACETRPRNQGSRLTAWELMQDGIDVTLITDS 187 (303)
T ss_pred chHHHHHHHHHHcCCceEEEECCCCCccchHHHHHHHHHHCCCCEEEEChh
Confidence 346667778888887432 2 23332 3577889999999999999875
No 136
>PF05614 DUF782: Circovirus protein of unknown function (DUF782); InterPro: IPR008500 This family consists of porcine and bovine circovirus ORF3 proteins of unknown function.
Probab=26.74 E-value=56 Score=21.14 Aligned_cols=18 Identities=33% Similarity=0.453 Sum_probs=14.6
Q ss_pred CCCCCceEEEEEcCCCCC
Q 034596 7 TGSGDSYRVLLIDDTRHS 24 (90)
Q Consensus 7 ~~~~~~y~ViL~NDd~~t 24 (90)
.-.+++|||+|-|-..++
T Consensus 61 eisdkryrvllcnghqtp 78 (104)
T PF05614_consen 61 EISDKRYRVLLCNGHQTP 78 (104)
T ss_pred hhccceEEEEEECCCCCh
Confidence 345689999999988776
No 137
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=26.72 E-value=1.1e+02 Score=23.79 Aligned_cols=31 Identities=23% Similarity=0.303 Sum_probs=26.7
Q ss_pred hCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 53 EHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 53 ~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
..++++|..-.++.|+..+..|+..|+.+..
T Consensus 244 ~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~ 274 (434)
T PRK11192 244 EVTRSIVFVRTRERVHELAGWLRKAGINCCY 274 (434)
T ss_pred CCCeEEEEeCChHHHHHHHHHHHhCCCCEEE
Confidence 4588999999999999999999988887654
No 138
>TIGR02421 QEGLA conserved hypothetical protein. Members of this family include a possible metal-binding motif HEXXXH and, nearby, a perfectly conserved motif QEGLA. All members belong to the Proteobacteria, including Agrobacterium tumefaciens and several species of Vibrio and Pseudomonas, and are found in only one copy per chromosome (Vibrio vulnificus, with two chromosomes, has two). The function is unknown.
Probab=26.71 E-value=1.4e+02 Score=23.89 Aligned_cols=34 Identities=12% Similarity=-0.019 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCc
Q 034596 22 RHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGM 56 (90)
Q Consensus 22 ~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~ 56 (90)
.-+|--|-..|.+-. +.+.++|+.++..|++-|-
T Consensus 260 ga~F~e~f~~l~~~y-~~~~~~af~~t~RV~RGGG 293 (366)
T TIGR02421 260 GADFIQVFRYLTEQY-GFDAAQAFSITQRVFRGGG 293 (366)
T ss_pred CCCHHHHHHHHHHHc-CCCHHHHHHHHHHHhccCC
Confidence 346667778888888 8999999999999999854
No 139
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=26.67 E-value=87 Score=17.43 Aligned_cols=27 Identities=11% Similarity=0.379 Sum_probs=15.7
Q ss_pred CCCCCHHHHHHHHHHhCCCCCHHHHHHH
Q 034596 20 DTRHSEKLVAKVLPQVVPSVTPDDARKL 47 (90)
Q Consensus 20 Dd~~t~e~Vi~~L~~v~p~~s~~~A~~i 47 (90)
++.+..+..+.+|..++ +.|.++...|
T Consensus 19 ~~~~~~~~llpvi~tlL-~fs~~e~~~i 45 (46)
T PF01465_consen 19 REPSEREQLLPVIATLL-KFSPEEKQKI 45 (46)
T ss_dssp SS---HHHHHHHHHHHT-T--HHHHHHH
T ss_pred CchhhHHHHHHHHHHHH-CCCHHHHHhh
Confidence 33456677778888888 8888776654
No 140
>PF13166 AAA_13: AAA domain
Probab=26.53 E-value=34 Score=28.38 Aligned_cols=18 Identities=22% Similarity=0.270 Sum_probs=15.0
Q ss_pred ceEEEEEcCCCCCHHHHH
Q 034596 12 SYRVLLIDDTRHSEKLVA 29 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi 29 (90)
.=++|++|||++++|+-.
T Consensus 527 ~~~iiViDDPISSLD~~~ 544 (712)
T PF13166_consen 527 KKKIIVIDDPISSLDHNR 544 (712)
T ss_pred cCceEEECCCCCCCCHHH
Confidence 457999999999998743
No 141
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=26.49 E-value=94 Score=18.89 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=14.7
Q ss_pred HHHHHHhCCCCCHHHHHHHH
Q 034596 29 AKVLPQVVPSVTPDDARKLF 48 (90)
Q Consensus 29 i~~L~~v~p~~s~~~A~~i~ 48 (90)
++-|++-| |+|..+|+-++
T Consensus 47 ~~el~~~C-gL~~aEAeLl~ 65 (70)
T PF10975_consen 47 VEELMEEC-GLSRAEAELLL 65 (70)
T ss_pred HHHHHHHc-CCCHHHHHHHH
Confidence 35578889 99999997554
No 142
>PF15517 TBPIP_N: TBP-interacting protein N-terminus; PDB: 2CZR_A.
Probab=26.39 E-value=54 Score=21.63 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=19.7
Q ss_pred eeeHHHHHHHHHHHhhcCCeeEEEeCCCC
Q 034596 61 VTVKEHAEFYAQMMVRGGLRSTIEPDSST 89 (90)
Q Consensus 61 ~~~~e~AE~~~~~l~~~gL~~~iep~~~~ 89 (90)
..++|+|+..++. ...|+...+.|+.+|
T Consensus 46 a~skE~AdKla~k-~~~gi~iivvP~kgt 73 (99)
T PF15517_consen 46 AESKEEADKLAEK-EEVGIDIIVVPGKGT 73 (99)
T ss_dssp -SSHHHHHHHSS----SSEEEEEES-TT-
T ss_pred cCCHHHHHHhhhc-cCCCeEEEEECCCCe
Confidence 5679999999884 778999999998876
No 143
>PRK12757 cell division protein FtsN; Provisional
Probab=26.32 E-value=1.2e+02 Score=23.14 Aligned_cols=33 Identities=21% Similarity=0.106 Sum_probs=25.0
Q ss_pred CcEEE--Eee-eHHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 55 GMAIV--IVT-VKEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 55 G~a~v--~~~-~~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
|.-+| |.+ .++.|+.+..+|...|+.+.|...+
T Consensus 183 ~~~~VQVGAF~~~~nAe~L~arL~~~G~~a~I~~~g 218 (256)
T PRK12757 183 QRWMVQCGSFKGTEQAESVRAQLAFAGIESRITTGG 218 (256)
T ss_pred ccEEEEEeeCCCHHHHHHHHHHHHhcCCceEEeecC
Confidence 44444 433 4899999999999999988887654
No 144
>cd04450 DEP_RGS7-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction.
Probab=26.12 E-value=1.7e+02 Score=18.10 Aligned_cols=39 Identities=10% Similarity=0.118 Sum_probs=20.0
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
.+|+-..+...++-.+-|-..+ +-+.-.++++|.+++..
T Consensus 18 ~r~~~~~~~~~F~G~~~v~WL~-~~~~~~~~~EA~~~~~~ 56 (88)
T cd04450 18 EKSFLTTVPYAFTGKAIVQWLM-DCTDVVDPSEALEIAAL 56 (88)
T ss_pred eEEeeeEcCceeEhHHHHHHHH-HCCCCCCHHHHHHHHHH
Confidence 4566666666666666555543 33312444444444433
No 145
>COG0114 FumC Fumarase [Energy production and conversion]
Probab=25.96 E-value=46 Score=27.46 Aligned_cols=23 Identities=22% Similarity=0.426 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHHHHHhhCCcEE
Q 034596 36 VPSVTPDDARKLFHESREHGMAI 58 (90)
Q Consensus 36 ~p~~s~~~A~~i~~~vH~~G~a~ 58 (90)
=|.+-.++|.+|+..+|.+|+.+
T Consensus 412 np~IGYdkAa~IAK~A~keg~tl 434 (462)
T COG0114 412 NPHIGYDKAAKIAKKAHKEGTTL 434 (462)
T ss_pred ccccchHHHHHHHHHHHHCCCcH
Confidence 36778899999999999999864
No 146
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=25.95 E-value=62 Score=21.37 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEE
Q 034596 24 SEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIV 59 (90)
Q Consensus 24 t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v 59 (90)
+.+|....|+-|+ |+-+-+|..+...+.++|..+-
T Consensus 44 ~~~~~~~~LqfV~-GLGPRKA~~Ll~~l~~~g~~l~ 78 (104)
T PF14635_consen 44 SHPHLANLLQFVC-GLGPRKAQALLKALKQNGGRLE 78 (104)
T ss_dssp T-HHHHGGGGGST-T--HHHHHHHHHHHHHC-S---
T ss_pred cChHHHhhHhHhc-CCChHHHHHHHHHHHHcCCccc
Confidence 4577888888888 9999999999999999886554
No 147
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=25.83 E-value=12 Score=21.82 Aligned_cols=21 Identities=14% Similarity=0.260 Sum_probs=15.9
Q ss_pred CCCHHHHHHHHHHHhhCCcEE
Q 034596 38 SVTPDDARKLFHESREHGMAI 58 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G~a~ 58 (90)
.+..++|.+|+.++..+|+.+
T Consensus 8 ~iGYe~aa~iAk~A~~~g~sv 28 (55)
T PF10415_consen 8 YIGYEKAAEIAKEALAEGRSV 28 (55)
T ss_dssp HHHHHHHHHHHHHHHHHT--H
T ss_pred hhccHHHHHHHHHHHHcCCCH
Confidence 345689999999999999864
No 148
>PF08564 CDC37_C: Cdc37 C terminal domain; InterPro: IPR013873 Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain IPR013874 from INTERPRO and the N-terminal kinase binding domain of Cdc37 IPR013855 from INTERPRO []. ; PDB: 1US7_B.
Probab=25.51 E-value=46 Score=21.84 Aligned_cols=32 Identities=13% Similarity=0.094 Sum_probs=19.5
Q ss_pred HHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEE
Q 034596 29 AKVLPQVVPSVTPDDARKLFHESREHGMAIVI 60 (90)
Q Consensus 29 i~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~ 60 (90)
+..|.+||-.|+.++|..++......|.=.+.
T Consensus 37 ld~vnkVl~~M~veeAE~~v~~~~esGi~~~~ 68 (99)
T PF08564_consen 37 LDEVNKVLGKMPVEEAEYHVERCIESGIWSPE 68 (99)
T ss_dssp ---HHHHHT--SSSHHHHHHHHHHHTTSS--T
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhCCccccc
Confidence 35677888778888888888888877765543
No 149
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=25.48 E-value=1.3e+02 Score=17.46 Aligned_cols=23 Identities=9% Similarity=0.336 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 27 LVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 27 ~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
|.|+.+.+-. |+|.++|.+++-+
T Consensus 6 ~~Ie~~A~~~-~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 6 FCIEEFAKKL-NISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHH-CcCHHHHHHHHHH
Confidence 3555666778 9999999998874
No 150
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=25.35 E-value=1.5e+02 Score=24.67 Aligned_cols=33 Identities=12% Similarity=0.163 Sum_probs=27.9
Q ss_pred HhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 51 SREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 51 vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
.+..++++|...+++.|+..+..|++.|+.+..
T Consensus 233 ~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~ 265 (607)
T PRK11057 233 EQRGKSGIIYCNSRAKVEDTAARLQSRGISAAA 265 (607)
T ss_pred hcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEE
Confidence 356678899999999999999999998877654
No 151
>PF12367 PFO_beta_C: Pyruvate ferredoxin oxidoreductase beta subunit C terminal
Probab=25.28 E-value=78 Score=19.22 Aligned_cols=54 Identities=4% Similarity=-0.017 Sum_probs=35.6
Q ss_pred EcCCCCCHHHHHHHHHHhCCCC---CHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 18 IDDTRHSEKLVAKVLPQVVPSV---TPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 18 ~NDd~~t~e~Vi~~L~~v~p~~---s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
+|. +||++|==+-+-++=.++ +.++|.+++++ .++-.+|+.-++...++-+++.
T Consensus 4 FNk-~nT~~wY~~rvy~l~e~~Dp~d~~~A~~~a~e---~d~iplGIfY~~~~ptfee~~~ 60 (67)
T PF12367_consen 4 FNK-INTYDWYKERVYKLDEDHDPSDREAAMEKARE---GDKIPLGIFYRNERPTFEERLP 60 (67)
T ss_pred ccc-cchHHHHHHheEECCCCCCchhHHHHHHHHHh---cCCceEEEEEeCCCCCHHHHhh
Confidence 344 788888777666662244 45567766666 6677778776666777777765
No 152
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=25.06 E-value=85 Score=19.48 Aligned_cols=41 Identities=20% Similarity=0.314 Sum_probs=25.9
Q ss_pred HHHHHhCCCCCHHHHHHHHH---------HHhhCCcEEEEeeeHHHHHHH
Q 034596 30 KVLPQVVPSVTPDDARKLFH---------ESREHGMAIVIVTVKEHAEFY 70 (90)
Q Consensus 30 ~~L~~v~p~~s~~~A~~i~~---------~vH~~G~a~v~~~~~e~AE~~ 70 (90)
.+..++|||+|.+.|.+-+. ..+..-||.=++.-.+.|.-.
T Consensus 19 ~v~~~yf~~lt~~~a~rk~~~g~lplPv~rl~~SqKs~~~V~v~dLA~yi 68 (76)
T PF11112_consen 19 EVCEDYFPHLTPKTAKRKANAGELPLPVFRLDDSQKSPKFVHVQDLAAYI 68 (76)
T ss_pred HHHHHHHccCCHHHHHHHHHCCCCCCceeecCCcccCCceeeHHHHHHHH
Confidence 56678999999999988553 233344455555555555533
No 153
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=24.89 E-value=2e+02 Score=18.61 Aligned_cols=47 Identities=15% Similarity=0.091 Sum_probs=30.9
Q ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHh-----C-C-CCCHHHHHHHHHHHhhCC
Q 034596 9 SGDSYRVLLIDDTRHSEKLVAKVLPQV-----V-P-SVTPDDARKLFHESREHG 55 (90)
Q Consensus 9 ~~~~y~ViL~NDd~~t~e~Vi~~L~~v-----~-p-~~s~~~A~~i~~~vH~~G 55 (90)
...+|+.-+|+|.+.-.|-|-.++.-. | | ..|+++|.+++...=.+|
T Consensus 15 kdRr~~lk~y~~CF~GsEaVDwL~~~l~~n~~f~~~~~tR~~Av~l~q~Ll~~g 68 (95)
T cd04446 15 KKRRHNLKSYHDCFLGSEAVDVVLAHLMQNKYFGDVDVPRAKAVRLCQALMDCR 68 (95)
T ss_pred cceeeeceecccccchHHHHHHHHHHHhhccccCcccCCHHHHHHHHHHHHHcC
Confidence 357899999999999888776554433 2 0 236666666666554444
No 154
>PRK12326 preprotein translocase subunit SecA; Reviewed
Probab=24.85 E-value=1.2e+02 Score=26.66 Aligned_cols=35 Identities=17% Similarity=0.203 Sum_probs=30.5
Q ss_pred HHhhCCcEEE-EeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 50 ESREHGMAIV-IVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 50 ~vH~~G~a~v-~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
+.|.+|+.+. |+.+-+..|.++..|.+.|+...+-
T Consensus 422 ~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vL 457 (764)
T PRK12326 422 EVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVL 457 (764)
T ss_pred HHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceee
Confidence 5799999876 7888999999999999999887764
No 155
>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=24.83 E-value=1.9e+02 Score=22.58 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=34.7
Q ss_pred HHHHHHHHHhhCCc---EEEE-eeeHHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 43 DARKLFHESREHGM---AIVI-VTVKEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 43 ~A~~i~~~vH~~G~---a~v~-~~~~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.+.++...+...|+ .+|. +-|.-+.-..+.+|.+.|+.+++.+|+
T Consensus 131 ~v~~~l~~A~~~~k~~~V~VtESRP~~eG~~~ak~L~~~gI~~~~I~Ds 179 (301)
T COG1184 131 TVLEVLKTAADRGKRFKVIVTESRPRGEGRIMAKELRQSGIPVTVIVDS 179 (301)
T ss_pred HHHHHHHHhhhcCCceEEEEEcCCCcchHHHHHHHHHHcCCceEEEech
Confidence 35667777888884 5554 455666788899999999999999986
No 156
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=24.61 E-value=2.2e+02 Score=19.54 Aligned_cols=68 Identities=18% Similarity=0.222 Sum_probs=52.0
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
..|-|+|-.. --.-=-||...+.+. |+..-+|..+-..+ .+.+----++|.||....+|...|-.+++
T Consensus 56 tefdVvL~~~-g~kKI~VIK~vR~it-GLGLKEAKdlVe~a---P~~~KE~v~k~eAe~~kkkleeaGa~V~~ 123 (124)
T COG0222 56 TEFDVVLKSA-GGKKIAVIKVVRELT-GLGLKEAKDLVEGA---PKVLKEGVSKEEAEEIKKKLEEAGAKVEL 123 (124)
T ss_pred ceeEEEeccc-CCcchhHHHHHHHHh-cccHHHHHHHHHhC---cHHHHccCCHHHHHHHHHHHHHcCCeEee
Confidence 3477887766 555567999999999 99999999975433 33333445799999999999999977665
No 157
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=24.42 E-value=1.3e+02 Score=16.14 Aligned_cols=33 Identities=15% Similarity=0.387 Sum_probs=24.8
Q ss_pred HHHHHHHHh-CCC-CCHHHHHHHHHHHhhCCcEEEE
Q 034596 27 LVAKVLPQV-VPS-VTPDDARKLFHESREHGMAIVI 60 (90)
Q Consensus 27 ~Vi~~L~~v-~p~-~s~~~A~~i~~~vH~~G~a~v~ 60 (90)
-...+|..+ . . +|.+++..|+..+..+|.+.|.
T Consensus 9 ~~~~~l~~~g~-~~~s~~e~~~l~~~~D~~~~G~I~ 43 (54)
T PF13833_consen 9 EFRRALSKLGI-KDLSEEEVDRLFREFDTDGDGYIS 43 (54)
T ss_dssp HHHHHHHHTTS-SSSCHHHHHHHHHHHTTSSSSSEE
T ss_pred HHHHHHHHhCC-CCCCHHHHHHHHHhcccCCCCCCC
Confidence 344555332 2 3 8899999999999999998874
No 158
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=24.13 E-value=2.3e+02 Score=19.03 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=26.0
Q ss_pred HhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 51 SREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 51 vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
....|+.++.......+......|++.|...++....+
T Consensus 130 Lk~gG~~~~~~~~~~~~~~~~~~l~~~gf~~~~~~~~~ 167 (179)
T TIGR00537 130 LKEGGRVQLIQSSLNGEPDTFDKLDERGFRYEIVAERG 167 (179)
T ss_pred hCCCCEEEEEEeccCChHHHHHHHHhCCCeEEEEEEee
Confidence 34556655555555547778888889998888876544
No 159
>PF15574 Imm28: Immunity protein 28
Probab=24.07 E-value=1.3e+02 Score=20.61 Aligned_cols=23 Identities=9% Similarity=0.203 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHH
Q 034596 28 VAKVLPQVVPSVTPDDARKLFHES 51 (90)
Q Consensus 28 Vi~~L~~v~p~~s~~~A~~i~~~v 51 (90)
.|++|.+-| |.|.+.|.+.+..+
T Consensus 55 mI~ili~~l-~ys~~~A~~~~qf~ 77 (123)
T PF15574_consen 55 MIRILIEKL-GYSTEAAAQFCQFV 77 (123)
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHH
Confidence 578888999 99999999887654
No 160
>KOG3052 consensus Cytochrome c1 [Energy production and conversion]
Probab=23.93 E-value=74 Score=24.82 Aligned_cols=29 Identities=31% Similarity=0.316 Sum_probs=22.2
Q ss_pred CCCHHHHHH-HHHHhCCCCCHHHHHHHHHHHh
Q 034596 22 RHSEKLVAK-VLPQVVPSVTPDDARKLFHESR 52 (90)
Q Consensus 22 ~~t~e~Vi~-~L~~v~p~~s~~~A~~i~~~vH 52 (90)
.|+|+|+.+ -|.-|+ +|+++|.+.+-++-
T Consensus 109 CHSm~~iayR~lVgv~--~Te~EaKa~A~eie 138 (311)
T KOG3052|consen 109 CHSMDLIAYRHLVGVC--YTEEEAKAMAAEIE 138 (311)
T ss_pred hhhhHHHHHHhhhhhh--ccHHHHHHhhhhee
Confidence 478888875 577777 89999988887763
No 161
>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=23.80 E-value=3.1e+02 Score=20.59 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=35.1
Q ss_pred ceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHH-HHHHHHHHHh
Q 034596 12 SYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKE-HAEFYAQMMV 75 (90)
Q Consensus 12 ~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e-~AE~~~~~l~ 75 (90)
.|-++|+|.+--+.| -.+.+--.++-.++...|-|++|++.-| .-|..++++.
T Consensus 170 d~pILLLDEPTasLD-----------a~Nr~vVveli~e~Ka~GaAlvGIFHDeevre~vadR~~ 223 (235)
T COG4778 170 DYPILLLDEPTASLD-----------ATNRAVVVELIREAKARGAALVGIFHDEEVREAVADRLL 223 (235)
T ss_pred cCceEEecCCccccc-----------ccchHHHHHHHHHHHhcCceEEEeeccHHHHHHHhhhee
Confidence 477888887765544 2333334456667788999999999854 4456666654
No 162
>cd02143 NADH_nitroreductase Nitroreductase family. Members of this family utilize FMN as a cofactor. This family is involved in the reduction of flavin or nitroaromatic compounds by using NAD(P)H as electron donor in a obligatory two-electron transfer. Nitrogenase is homodimer. Each subunit contains one FMN molecule. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.74 E-value=1.1e+02 Score=20.20 Aligned_cols=24 Identities=4% Similarity=-0.035 Sum_probs=19.9
Q ss_pred HHHHHHHHHhhCCcEEEEeeeHHH
Q 034596 43 DARKLFHESREHGMAIVIVTVKEH 66 (90)
Q Consensus 43 ~A~~i~~~vH~~G~a~v~~~~~e~ 66 (90)
-+.++|+.++..|-+.|+.+-+..
T Consensus 82 a~~~l~LaA~~lGlgs~~~~~~~~ 105 (147)
T cd02143 82 ALTYFELAAQALGLGTCWAGFFQA 105 (147)
T ss_pred HHHHHHHHHHHcCCCEehhhhHHH
Confidence 367899999999999999876554
No 163
>PRK14129 heat shock protein HspQ; Provisional
Probab=23.66 E-value=32 Score=23.06 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=19.8
Q ss_pred CCCCCCceEEEEEcCCCCCH-HHHHHH
Q 034596 6 GTGSGDSYRVLLIDDTRHSE-KLVAKV 31 (90)
Q Consensus 6 ~~~~~~~y~ViL~NDd~~t~-e~Vi~~ 31 (90)
..+..|-|.|+..||+-... -||.+.
T Consensus 45 p~kdqPwYHvl~en~~~~~v~tYVaE~ 71 (105)
T PRK14129 45 ELRAAPWYHVVMEDDDGQPVHTYLAEA 71 (105)
T ss_pred CccCCCceEEEEEcCCCceEEEEeeec
Confidence 34566889999999998876 677653
No 164
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=23.64 E-value=2.6e+02 Score=21.90 Aligned_cols=49 Identities=22% Similarity=0.384 Sum_probs=34.7
Q ss_pred EEEEcCCCCCHHHHH-HHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeee-HHHHHHHHHHHh
Q 034596 15 VLLIDDTRHSEKLVA-KVLPQVVPSVTPDDARKLFHESREHGMAIVIVTV-KEHAEFYAQMMV 75 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi-~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~-~e~AE~~~~~l~ 75 (90)
.+++|-+|.-.|=|- +.|.+. -.+...+|.+++.+.. .|.+|..|+.+.
T Consensus 151 LlILDEPFSGLDPVN~elLk~~------------I~~lk~~GatIifSsH~Me~vEeLCD~ll 201 (300)
T COG4152 151 LLILDEPFSGLDPVNVELLKDA------------IFELKEEGATIIFSSHRMEHVEELCDRLL 201 (300)
T ss_pred EEEecCCccCCChhhHHHHHHH------------HHHHHhcCCEEEEecchHHHHHHHhhhhh
Confidence 466676666655552 333333 3567789999999777 899999999884
No 165
>PHA02593 62 clamp loader small subunit; Provisional
Probab=23.61 E-value=1.4e+02 Score=22.04 Aligned_cols=44 Identities=30% Similarity=0.399 Sum_probs=32.2
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
++|..-.==|+...+-.++++|++.. +.|.++|.+-....-.+|
T Consensus 110 KRy~~WAKl~ed~e~~~~i~ll~~~Y-~vn~~kA~eyl~iltk~~ 153 (191)
T PHA02593 110 KRYGKWAKLTEDSEEKLIIKLLAKAY-SVNTDDAREYLDILKKKG 153 (191)
T ss_pred ccCchhhccCcchHHHHHHHHHHHHh-CCCHHHHHHHHHHhcccc
Confidence 33333333456667778999999999 999999998766665565
No 166
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=23.61 E-value=1.9e+02 Score=17.82 Aligned_cols=39 Identities=18% Similarity=0.128 Sum_probs=23.2
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
..|+...+.+.+.=.|.|-..+..-. ..|+++|..+...
T Consensus 18 rr~~~~~y~~cF~GselVdWL~~~~~-~~~R~eAv~~gq~ 56 (81)
T cd04448 18 HRYRLRTYTNCILGKELVNWLIRQGK-AATRVQAIAIGQA 56 (81)
T ss_pred EEECCEEcCcccChHHHHHHHHHcCC-CCCHHHHHHHHHH
Confidence 46677777777777777766665432 3555555544443
No 167
>cd02139 Nitroreductase_3 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.50 E-value=1e+02 Score=20.41 Aligned_cols=23 Identities=9% Similarity=0.211 Sum_probs=19.9
Q ss_pred HHHHHHHHhhCCcEEEEeeeHHH
Q 034596 44 ARKLFHESREHGMAIVIVTVKEH 66 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~~e~ 66 (90)
+..+++.++..|-+.|+.+.++.
T Consensus 101 ~~~l~l~A~~~Glgt~~~~~~~~ 123 (164)
T cd02139 101 MEHMMLAAAELGLGTCWIGAFDE 123 (164)
T ss_pred HHHHHHHHHHcCCceeeeeccCH
Confidence 67899999999999999877664
No 168
>cd02135 Arsenite_oxidase Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-proteobacterial strain is able to oxidize arsenite to arsenate.
Probab=23.47 E-value=78 Score=20.62 Aligned_cols=20 Identities=20% Similarity=0.204 Sum_probs=17.2
Q ss_pred HHHHHHHHhhCCcEEEEeee
Q 034596 44 ARKLFHESREHGMAIVIVTV 63 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~ 63 (90)
+.++++.++..|-+.|+.+.
T Consensus 113 ~~nl~LaA~~~Glgs~~~~~ 132 (160)
T cd02135 113 IQNLLLAAHALGFGAVWRTG 132 (160)
T ss_pred HHHHHHHHHHCCCCeEeecC
Confidence 56699999999999999753
No 169
>COG0458 CarB Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=23.05 E-value=3.8e+02 Score=21.85 Aligned_cols=71 Identities=23% Similarity=0.390 Sum_probs=51.1
Q ss_pred CceEEEEEcCCCC-----------------CHHHHHHHHHH-----hCCCCCHHHHHHHHHHHhhCC------cEEEEee
Q 034596 11 DSYRVLLIDDTRH-----------------SEKLVAKVLPQ-----VVPSVTPDDARKLFHESREHG------MAIVIVT 62 (90)
Q Consensus 11 ~~y~ViL~NDd~~-----------------t~e~Vi~~L~~-----v~p~~s~~~A~~i~~~vH~~G------~a~v~~~ 62 (90)
..|+|+|.|.+-. ++|+|..++.+ ++|.+.-+.|..+....+.+| --++++.
T Consensus 28 eg~~vvlvnsnpAti~td~e~AD~~y~eP~~~E~v~~Ii~~E~~Dailp~~ggqt~Ln~~~~l~e~g~l~~~gV~vvgs~ 107 (400)
T COG0458 28 EGYGVVLVNSNPATIMTDPELADKVYIEPITKEPVEKIIEKERPDAILPTLGGQTALNAALELKEKGVLEKYGVEVVGSD 107 (400)
T ss_pred cCCeEEEEcCCCccccCCchhcceeeeecCcHHHHHHHHHhcCcceeecccCCcchhhHHHHHHHhcchhhcCCEEEecC
Confidence 5688888888755 47888888876 577889999999999999994 4457765
Q ss_pred e--HHHHH---HHHHHHhhcCCee
Q 034596 63 V--KEHAE---FYAQMMVRGGLRS 81 (90)
Q Consensus 63 ~--~e~AE---~~~~~l~~~gL~~ 81 (90)
. -++|+ ...+.+++.|+.+
T Consensus 108 ~eaI~iaeDr~~fke~m~eigi~~ 131 (400)
T COG0458 108 PEAIEIAEDKKLFKEAMREIGIPV 131 (400)
T ss_pred HHHhhhhhhHHHHHHHHHHcCCCC
Confidence 5 44555 3444556666543
No 170
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=23.04 E-value=1.6e+02 Score=16.99 Aligned_cols=33 Identities=15% Similarity=0.143 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 21 TRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 21 d~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
|+||-..- .|..++||++...|.+|...--..|
T Consensus 9 nvNta~~~--~L~~~ipgig~~~a~~Il~~R~~~g 41 (69)
T TIGR00426 9 NINTATAE--ELQRAMNGVGLKKAEAIVSYREEYG 41 (69)
T ss_pred ECcCCCHH--HHHhHCCCCCHHHHHHHHHHHHHcC
Confidence 45554432 6777788999999999988765555
No 171
>PRK12928 lipoyl synthase; Provisional
Probab=22.96 E-value=3.4e+02 Score=20.55 Aligned_cols=28 Identities=14% Similarity=0.184 Sum_probs=24.9
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 28 VAKVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 28 Vi~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
+=+++.++.|+.|.++..+++..+|..|
T Consensus 174 ~~~vl~~m~r~~t~e~~le~l~~ak~~g 201 (290)
T PRK12928 174 VPRLQKAVRRGADYQRSLDLLARAKELA 201 (290)
T ss_pred cHHHHHHhCCCCCHHHHHHHHHHHHHhC
Confidence 3567778889999999999999999999
No 172
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=22.89 E-value=1.8e+02 Score=18.09 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=25.6
Q ss_pred hhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 52 REHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 52 H~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
+-+|+-++.+|.=+.|..++..|.+.|-..++-
T Consensus 4 ~l~~~~vlVvGgG~va~~k~~~Ll~~gA~v~vi 36 (103)
T PF13241_consen 4 DLKGKRVLVVGGGPVAARKARLLLEAGAKVTVI 36 (103)
T ss_dssp --TT-EEEEEEESHHHHHHHHHHCCCTBEEEEE
T ss_pred EcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEE
Confidence 457888888999999999999999999666653
No 173
>COG1587 HemD Uroporphyrinogen-III synthase [Coenzyme metabolism]
Probab=22.68 E-value=1.5e+02 Score=21.39 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=24.6
Q ss_pred CcEEEEeeeHHHHHHHHHHHhhcCCeeEEEe
Q 034596 55 GMAIVIVTVKEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 55 G~a~v~~~~~e~AE~~~~~l~~~gL~~~iep 85 (90)
|+-++.+-+++.|+.+++.++..|..+..-|
T Consensus 1 ~~~vlvtR~~~~~~~~~~~l~~~G~~~~~~P 31 (248)
T COG1587 1 GMRVLVTRPREQAEELAALLRKAGAEPLELP 31 (248)
T ss_pred CcEEEEeCchhhhHHHHHHHHhCCCcceeec
Confidence 5667778888999999999999987655544
No 174
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=22.67 E-value=1.1e+02 Score=19.50 Aligned_cols=22 Identities=32% Similarity=0.375 Sum_probs=17.6
Q ss_pred HHHHHHHHHhhcCCeeEEEeCC
Q 034596 66 HAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 66 ~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.++..++.++..||.+.+||+.
T Consensus 30 ~~~EI~~a~~~Lgl~~~~E~~K 51 (95)
T PF01922_consen 30 TLEEIADACKKLGLPCVVEPDK 51 (95)
T ss_dssp -HHHHHHHHHHTTSEEEEETTE
T ss_pred CHHHHHHHHHHcCCCEEEcccc
Confidence 4667778889999999999763
No 175
>COG0747 DdpA ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]
Probab=22.64 E-value=2.1e+02 Score=22.22 Aligned_cols=49 Identities=14% Similarity=0.289 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHhhCC------cEEE--E------eeeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG------MAIV--I------VTVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G------~a~v--~------~~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
..+.++|.++.-++=..+ ...- . ....+.|+..+++|+..|+.+.+++.
T Consensus 363 ~~d~~~Ak~lL~eaG~~~~~g~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~iGI~v~~~~~ 425 (556)
T COG0747 363 AYDPEKAKALLDEAGYKDNDGFGGGPLTLTLESAGYNPGARAIAELIQAQLAKIGIKVELQTL 425 (556)
T ss_pred CCCHHHHHHHHHHcCCCCCCCCcceeEEEecccCCCCcchHHHHHHHHHHHHHcCCeeEEEEe
Confidence 478999999999987776 1111 1 13468999999999999999999874
No 176
>TIGR03714 secA2 accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.
Probab=22.57 E-value=3.1e+02 Score=24.17 Aligned_cols=35 Identities=26% Similarity=0.523 Sum_probs=28.2
Q ss_pred HHhhCCc-EEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 50 ESREHGM-AIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 50 ~vH~~G~-a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
+.|..|+ ++|++-+.+.++.++..|...|+.+.+-
T Consensus 419 ~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L 454 (762)
T TIGR03714 419 EYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLL 454 (762)
T ss_pred HHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEe
Confidence 4566676 5567888999999999999999887754
No 177
>PRK08811 uroporphyrinogen-III synthase; Validated
Probab=22.43 E-value=1.6e+02 Score=21.78 Aligned_cols=30 Identities=10% Similarity=0.110 Sum_probs=24.9
Q ss_pred hCCcEEEEeeeHHHHHHHHHHHhhcCCeeE
Q 034596 53 EHGMAIVIVTVKEHAEFYAQMMVRGGLRST 82 (90)
Q Consensus 53 ~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ 82 (90)
-.|+-|+.+-+.+.++..+.+|++.|-.+.
T Consensus 16 l~g~~IlvTRp~~q~~~l~~~L~~~G~~~~ 45 (266)
T PRK08811 16 DAAWTLISLRPSGEHAPLRRAVARHGGRLL 45 (266)
T ss_pred CCCCEEEEeCCHHHHHHHHHHHHHCCCcEE
Confidence 368889999999999999999998884443
No 178
>PRK06371 translation initiation factor IF-2B subunit alpha; Provisional
Probab=22.33 E-value=3.3e+02 Score=21.44 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhCCcEEEE----eeeH-HHHHHHHHHHhhcCCeeEEEeCC
Q 034596 43 DARKLFHESREHGMAIVI----VTVK-EHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 43 ~A~~i~~~vH~~G~a~v~----~~~~-e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.|..+...+|.+|+-+.- +-|+ +=++..+..|.+.|+.+++.+|+
T Consensus 156 Tal~~l~~A~~~gk~f~V~v~EsRP~~qG~rlta~eL~~~GI~vtlI~Ds 205 (329)
T PRK06371 156 TALAPIRIAHRNGKNIFVFVDETRPRLQGARLTAWELAQEGIDHAIIADN 205 (329)
T ss_pred hHHHHHHHHHHcCCeeEEEECCCCCcchHHHHHHHHHHHCCCCEEEEccc
Confidence 356788889999885432 2232 23556788999999999998875
No 179
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=22.23 E-value=1.4e+02 Score=18.04 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=19.6
Q ss_pred HHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 30 KVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 30 ~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
..|++-| .....+|..|+.+.-.+|
T Consensus 23 S~lQR~~-~IGynrAariid~lE~~G 47 (63)
T smart00843 23 SLLQRRL-RIGYNRAARLIDQLEEEG 47 (63)
T ss_pred HHHHHHH-hcchhHHHHHHHHHHHCc
Confidence 4577788 888888888888877776
No 180
>PF07775 PaRep2b: PaRep2b protein; InterPro: IPR011689 This is a group of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional [].
Probab=22.21 E-value=1.5e+02 Score=24.93 Aligned_cols=35 Identities=17% Similarity=0.206 Sum_probs=27.7
Q ss_pred CCcEEE--EeeeHHHHHHHHHHHhhcCCeeEEEeCCC
Q 034596 54 HGMAIV--IVTVKEHAEFYAQMMVRGGLRSTIEPDSS 88 (90)
Q Consensus 54 ~G~a~v--~~~~~e~AE~~~~~l~~~gL~~~iep~~~ 88 (90)
.|+.+. +.+++|.||..+..|+.-|-.+.+.|-++
T Consensus 104 ~g~~L~a~F~gsRE~AErlAsILrAlG~~aEvk~~g~ 140 (512)
T PF07775_consen 104 DGNSLRAQFGGSREKAERLASILRALGAEAEVKKYGG 140 (512)
T ss_pred eccEEEEEecccHHHHHHHHHHHHhcCCeeEEEEcCC
Confidence 466655 46789999999999999998888877543
No 181
>KOG1438 consensus Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=22.08 E-value=81 Score=25.07 Aligned_cols=25 Identities=28% Similarity=0.190 Sum_probs=21.8
Q ss_pred CcEEEEeeeHHHHHHHHHHHhhcCC
Q 034596 55 GMAIVIVTVKEHAEFYAQMMVRGGL 79 (90)
Q Consensus 55 G~a~v~~~~~e~AE~~~~~l~~~gL 79 (90)
-..|+|+|.+|.++.++..+++.|.
T Consensus 218 ~~rivGVy~k~L~~~~AKal~~~g~ 242 (373)
T KOG1438|consen 218 SYRIVGVYHKDLVVKMAKALQRFGM 242 (373)
T ss_pred hhheeeeeHHHHHHHHHHHHHHhCC
Confidence 4679999999999999999987663
No 182
>PRK00076 recR recombination protein RecR; Reviewed
Probab=22.08 E-value=1.3e+02 Score=21.97 Aligned_cols=44 Identities=18% Similarity=0.244 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 23 HSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 23 ~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
.+++-.|+.|.+ +||.....|.++++.+=. .+.+.++..++.|.
T Consensus 4 ~~~~~Li~~l~~-LPGIG~KsA~Rla~~ll~--------~~~~~~~~la~~i~ 47 (196)
T PRK00076 4 PPIEKLIEALRK-LPGIGPKSAQRLAFHLLQ--------RDREDVLRLAQALE 47 (196)
T ss_pred HHHHHHHHHHHH-CCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHH
Confidence 458889999999 579999999999998744 35667777777664
No 183
>PF11097 DUF2883: Protein of unknown function (DUF2883); InterPro: IPR020112 This group of proteins currently have no known function and are found primarily in the T4-like bacteriophages.
Probab=22.06 E-value=1e+02 Score=19.14 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHHHHHhhCCcEEEEeeeH
Q 034596 36 VPSVTPDDARKLFHESREHGMAIVIVTVK 64 (90)
Q Consensus 36 ~p~~s~~~A~~i~~~vH~~G~a~v~~~~~ 64 (90)
|||++..+-+.+|++..+-|.+.=..+.+
T Consensus 11 ~pg~p~nKle~LMlELRTV~~~sGlefrf 39 (75)
T PF11097_consen 11 YPGLPPNKLEGLMLELRTVGRSSGLEFRF 39 (75)
T ss_pred CCCCChHHHHHHHHHHHhccccCCceeec
Confidence 68999999999999999988876655554
No 184
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=22.03 E-value=81 Score=21.60 Aligned_cols=60 Identities=12% Similarity=0.026 Sum_probs=51.1
Q ss_pred EEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 15 VLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 15 ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
|.+.|=|+..-..|...|..++ |.....|.+|...+--.-...++.-+-|+.+...+.+.
T Consensus 2 aRIagvdip~~K~v~iALt~Iy-GIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~ 61 (121)
T COG0099 2 ARIAGVDIPGNKRVVIALTYIY-GIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61 (121)
T ss_pred ceecccCCCCCceEeehhhhhc-cccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence 3455666667777888999999 99999999999999988889999999888888888776
No 185
>cd02148 Nitroreductase_5 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=22.01 E-value=59 Score=22.32 Aligned_cols=28 Identities=7% Similarity=-0.005 Sum_probs=20.8
Q ss_pred HHHHHHhhCCcEEEEeeeHHHHHHHHHHH
Q 034596 46 KLFHESREHGMAIVIVTVKEHAEFYAQMM 74 (90)
Q Consensus 46 ~i~~~vH~~G~a~v~~~~~e~AE~~~~~l 74 (90)
++|+.+|..|-+.|+.+.++. +.+.+.|
T Consensus 123 ~l~LaA~~lGlgs~~~~g~d~-~~~~~~L 150 (185)
T cd02148 123 YFILAARALGLDAGPMSGFDA-AAVDAEF 150 (185)
T ss_pred HHHHHHHHcCCCcCCCcccCH-HHHHHHh
Confidence 399999999999998776665 3334444
No 186
>PRK13844 recombination protein RecR; Provisional
Probab=21.95 E-value=1.5e+02 Score=21.81 Aligned_cols=43 Identities=16% Similarity=0.177 Sum_probs=34.9
Q ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 24 SEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 24 t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
+++-.|..|.+ +||.....|.++++.+=. .+.+.|+..++.|.
T Consensus 9 ~~~~LI~~l~~-LPGIG~KsA~Rla~~lL~--------~~~~~~~~la~~i~ 51 (200)
T PRK13844 9 KISAVIESLRK-LPTIGKKSSQRLALYLLD--------KSPETAIAIANSLL 51 (200)
T ss_pred HHHHHHHHHHH-CCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHH
Confidence 68899999999 569999999999998744 45677777777764
No 187
>PRK08445 hypothetical protein; Provisional
Probab=21.92 E-value=1.6e+02 Score=22.90 Aligned_cols=33 Identities=15% Similarity=0.226 Sum_probs=27.4
Q ss_pred HHHHHhCC-CCCHHHHHHHHHHHhhCCcEEEEee
Q 034596 30 KVLPQVVP-SVTPDDARKLFHESREHGMAIVIVT 62 (90)
Q Consensus 30 ~~L~~v~p-~~s~~~A~~i~~~vH~~G~a~v~~~ 62 (90)
+++..+|| +.|.++-.+....+|..|.-++...
T Consensus 169 ~v~~~~~pk~~t~~~~i~~i~~a~~~Gi~~~sg~ 202 (348)
T PRK08445 169 RVRDIIAPKKLDSDRWLEVHRQAHLIGMKSTATM 202 (348)
T ss_pred HHHHhhCCCCCCHHHHHHHHHHHHHcCCeeeeEE
Confidence 46777877 7888888999999999999888643
No 188
>PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.90 E-value=2.5e+02 Score=22.54 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhhCC-----cEEEE-------------eeeHHHHHHHHHHHhhcCCeeEEEeC
Q 034596 38 SVTPDDARKLFHESREHG-----MAIVI-------------VTVKEHAEFYAQMMVRGGLRSTIEPD 86 (90)
Q Consensus 38 ~~s~~~A~~i~~~vH~~G-----~a~v~-------------~~~~e~AE~~~~~l~~~gL~~~iep~ 86 (90)
+-|.++|.+++..+...+ .+.|= .-+.+..+...+.|+.+|+.|+++..
T Consensus 283 NDs~e~A~~L~~llk~~~~~~~l~~~VNLIp~Np~~~~~~~~ps~~~i~~F~~~L~~~gi~vtiR~s 349 (371)
T PRK14461 283 NDHPEQAAALARLLRGEAPPGPLLVHVNLIPWNPVPGTPLGRSERERVTTFQRILTDYGIPCTVRVE 349 (371)
T ss_pred CCCHHHHHHHHHHHcCCccccCCceEEEEecCCCCCCCCCCCCCHHHHHHHHHHHHHCCceEEEeCC
Confidence 567899999999887542 23331 12366788899999999999999865
No 189
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=21.62 E-value=3.3e+02 Score=22.32 Aligned_cols=31 Identities=13% Similarity=0.203 Sum_probs=24.1
Q ss_pred hCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 53 EHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 53 ~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
..++++|...++..|+..++.|...|+.+..
T Consensus 223 ~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~ 253 (591)
T TIGR01389 223 RGQSGIIYASSRKKVEELAERLESQGISALA 253 (591)
T ss_pred CCCCEEEEECcHHHHHHHHHHHHhCCCCEEE
Confidence 3567888888888888888888887766543
No 190
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.61 E-value=1.5e+02 Score=21.65 Aligned_cols=43 Identities=16% Similarity=0.216 Sum_probs=34.4
Q ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 24 SEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 24 t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
+++-.|+.|.+ +||.....|.++++.+=. .+.+.++..++.|.
T Consensus 5 ~~~~Li~~l~~-LPGIG~KsA~RlA~~ll~--------~~~~~~~~la~ai~ 47 (195)
T TIGR00615 5 PISKLIESLKK-LPGIGPKSAQRLAFHLLK--------RDPSEVLRLAQALL 47 (195)
T ss_pred HHHHHHHHHHH-CCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHH
Confidence 58899999999 579999999999988744 45667777777664
No 191
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=21.51 E-value=2.3e+02 Score=17.93 Aligned_cols=12 Identities=25% Similarity=0.409 Sum_probs=7.4
Q ss_pred hcCCeeEEEeCC
Q 034596 76 RGGLRSTIEPDS 87 (90)
Q Consensus 76 ~~gL~~~iep~~ 87 (90)
++|-.+.+.|.+
T Consensus 66 ~~gy~~~iv~~g 77 (86)
T PF11360_consen 66 SAGYEYEIVPPG 77 (86)
T ss_pred HCCceEEEECCC
Confidence 456666666655
No 192
>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=21.45 E-value=1.6e+02 Score=20.83 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=20.3
Q ss_pred HHHHHHHHHhC----------CCCCHHHHHHHHHHH
Q 034596 26 KLVAKVLPQVV----------PSVTPDDARKLFHES 51 (90)
Q Consensus 26 e~Vi~~L~~v~----------p~~s~~~A~~i~~~v 51 (90)
.++...|.+.+ |.+|.++|.+++.++
T Consensus 142 ~~~~~~Le~~~~~~~~~~~~~~~ms~eea~~l~~~~ 177 (212)
T cd03757 142 SLIQPLLDNQVGRKNQNNVERTPLSLEEAVSLVKDA 177 (212)
T ss_pred HHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHH
Confidence 45677787775 789999999987663
No 193
>PRK05720 mtnA methylthioribose-1-phosphate isomerase; Reviewed
Probab=21.26 E-value=3.5e+02 Score=21.24 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhCCcEEE-E---eeeH-HHHHHHHHHHhhcCCeeEEEeCC
Q 034596 43 DARKLFHESREHGMAIV-I---VTVK-EHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 43 ~A~~i~~~vH~~G~a~v-~---~~~~-e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
.|..+...+|.+|+-+- . +-|+ +=+...+..|.+.|+.+++.+|+
T Consensus 166 Tal~~i~~A~~~gk~~~V~v~EsRP~~qG~~lta~eL~~~GI~vtlI~Ds 215 (344)
T PRK05720 166 TALAPIYAAKEKGIDIHVYADETRPRLQGARLTAWELYQAGIDVTVITDN 215 (344)
T ss_pred HHHHHHHHHHHcCCceEEEEcCCCChhhhHHHHHHHHHHCCCCEEEEccc
Confidence 46667888999888542 2 2332 33456688999999999999985
No 194
>COG0337 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]
Probab=21.15 E-value=77 Score=25.35 Aligned_cols=63 Identities=14% Similarity=0.006 Sum_probs=48.3
Q ss_pred CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEEe
Q 034596 22 RHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIEP 85 (90)
Q Consensus 22 ~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~iep 85 (90)
-||+-|.++.+..+= ..+.-+|..+-+..-.+=....|..+.+.++.....|.++||-.++.+
T Consensus 244 GHT~GHAiE~~~~y~-~~~HGeAVaiGmv~aa~ls~~lG~~~~~~~~r~~~~L~~~gLP~~~~~ 306 (360)
T COG0337 244 GHTFGHAIEALTGYG-KWLHGEAVAIGMVMAARLSERLGLLDKADAERILNLLKRYGLPTSLPD 306 (360)
T ss_pred chHHHHHHHHHhCCC-ccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCccCCC
Confidence 488999999998863 477778777765554444455667788889999999999999887754
No 195
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=20.81 E-value=1.4e+02 Score=24.14 Aligned_cols=47 Identities=26% Similarity=0.296 Sum_probs=35.4
Q ss_pred CHHHHHHHHHHHhhCCcEEEEeeeHHHHH--HHHHHHh---hcCCeeEEEeC
Q 034596 40 TPDDARKLFHESREHGMAIVIVTVKEHAE--FYAQMMV---RGGLRSTIEPD 86 (90)
Q Consensus 40 s~~~A~~i~~~vH~~G~a~v~~~~~e~AE--~~~~~l~---~~gL~~~iep~ 86 (90)
+.++-..+.-.+|.+|+.+|.++.+-..+ ..-..|+ +.||.+.|+|-
T Consensus 193 ~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~P 244 (408)
T COG0593 193 TQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPP 244 (408)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCC
Confidence 37778899999999999999887554444 2335564 56899999974
No 196
>TIGR02223 ftsN cell division protein FtsN. FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by Pfam model pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis.
Probab=20.79 E-value=3.4e+02 Score=20.95 Aligned_cols=45 Identities=18% Similarity=0.148 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhCCc------------EEEEeee---HHHHHHHHHHHhhcCCeeEE
Q 034596 39 VTPDDARKLFHESREHGM------------AIVIVTV---KEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 39 ~s~~~A~~i~~~vH~~G~------------a~v~~~~---~e~AE~~~~~l~~~gL~~~i 83 (90)
.+.+.|..+...+...|. --|.+|+ ++.|+...++|+..|+...|
T Consensus 236 ~~~~~Ae~l~akL~~~G~~~~i~~~~g~~~yRV~vGPf~sr~~A~~~~~~Lk~~Gi~~~i 295 (298)
T TIGR02223 236 ANKEQAESVRAKLAFLGISSKITTTDGGKWYRVVSGPYKNKDDAEKDLNKLKVAGVAGCI 295 (298)
T ss_pred CCHHHHHHHHHHHHhcCCceEEEecCCceEEEEEeCCCCCHHHHHHHHHHHHHcCCCCeE
Confidence 567777777777776662 2243444 58899999999988865544
No 197
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=20.76 E-value=2.7e+02 Score=23.55 Aligned_cols=33 Identities=15% Similarity=0.110 Sum_probs=27.6
Q ss_pred hhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEEE
Q 034596 52 REHGMAIVIVTVKEHAEFYAQMMVRGGLRSTIE 84 (90)
Q Consensus 52 H~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~ie 84 (90)
....+++|.+.+++.|+..++.|...|+.+..-
T Consensus 444 ~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~ 476 (652)
T PRK05298 444 AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYL 476 (652)
T ss_pred hCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEE
Confidence 345567888999999999999999999887664
No 198
>cd02146 NfsA_FRP This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as an electron donor. Oxygen-insensitive nitroreductase, such as NfsA protein in Escherichia coli, catalyzes reduction of nitrocompounds using NADPH as electron donor.
Probab=20.66 E-value=1.3e+02 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.196 Sum_probs=18.4
Q ss_pred HHHHHHHHhhCCcEEEEeeeH
Q 034596 44 ARKLFHESREHGMAIVIVTVK 64 (90)
Q Consensus 44 A~~i~~~vH~~G~a~v~~~~~ 64 (90)
+..+|+.++..|-+.|+.+.+
T Consensus 114 ~~nl~LaA~~lGLgtc~ig~~ 134 (229)
T cd02146 114 AQNAAVAAESLGLGIVYIGGI 134 (229)
T ss_pred HHHHHHHHHHcCCCEEEEccc
Confidence 568999999999999998765
No 199
>PRK08734 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=20.65 E-value=1.6e+02 Score=22.13 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=15.4
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Q 034596 27 LVAKVLPQVVPSVTPDDARKLFHE 50 (90)
Q Consensus 27 ~Vi~~L~~v~p~~s~~~A~~i~~~ 50 (90)
-|..=|..+||++|.++..+|+.+
T Consensus 46 v~~~NL~~~fP~~s~~e~~~i~~~ 69 (305)
T PRK08734 46 VTRRNLELAYPELSPQQRAQLHAQ 69 (305)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Confidence 345566777777777776666543
No 200
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=20.43 E-value=2.7e+02 Score=23.45 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=28.9
Q ss_pred HHHHhhCCcEEEEeeeHHHHHHHHHHHhhcCCeeEE
Q 034596 48 FHESREHGMAIVIVTVKEHAEFYAQMMVRGGLRSTI 83 (90)
Q Consensus 48 ~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~gL~~~i 83 (90)
.+..+...+++|+...+..|+.+++.|...|+.+..
T Consensus 239 ~L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~ 274 (629)
T PRK11634 239 FLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAA 274 (629)
T ss_pred HHHhcCCCCEEEEeccHHHHHHHHHHHHhCCCCEEE
Confidence 344556688999999999999999999988876543
No 201
>PRK10927 essential cell division protein FtsN; Provisional
Probab=20.43 E-value=1.4e+02 Score=23.70 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=25.9
Q ss_pred CCcEEEEeee---HHHHHHHHHHHhhcCCeeEEEeCC
Q 034596 54 HGMAIVIVTV---KEHAEFYAQMMVRGGLRSTIEPDS 87 (90)
Q Consensus 54 ~G~a~v~~~~---~e~AE~~~~~l~~~gL~~~iep~~ 87 (90)
+|+=+|=.|+ .+.||....+|...|+.+.|..++
T Consensus 245 ~~~~~VQvGSF~n~~nAE~LrAkLa~~G~~A~I~~~g 281 (319)
T PRK10927 245 ERRWMVQCGSFRGAEQAETVRAQLAFEGFDSKITTNN 281 (319)
T ss_pred CCcEEEEeCccCCHHHHHHHHHHHHHcCCeeEEccCC
Confidence 3665553333 789999999999999999996543
No 202
>TIGR00036 dapB dihydrodipicolinate reductase.
Probab=20.37 E-value=2.7e+02 Score=20.60 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHH
Q 034596 37 PSVTPDDARKLFHESREHGMAIVIVTVKEHAE 68 (90)
Q Consensus 37 p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE 68 (90)
||.|.+++.+|-..+...|..++....+...-
T Consensus 100 tg~~~e~~~~l~~aA~~~g~~v~~a~NfSlGv 131 (266)
T TIGR00036 100 TGFSEEDKQELADLAEKAGIAAVIAPNFSIGV 131 (266)
T ss_pred CCCCHHHHHHHHHHHhcCCccEEEECcccHHH
Confidence 56777777777777777777777666655443
No 203
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=20.29 E-value=60 Score=21.53 Aligned_cols=54 Identities=15% Similarity=0.077 Sum_probs=45.1
Q ss_pred CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHh
Q 034596 21 TRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMV 75 (90)
Q Consensus 21 d~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~ 75 (90)
|+..-.-|...|.+++ |.....|.+|+..+--.-.+-++..+.+.-+.....|.
T Consensus 6 ~l~~~k~v~~aL~~i~-GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~ 59 (113)
T TIGR03631 6 DIPNNKRVEIALTYIY-GIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIE 59 (113)
T ss_pred cCCCCCEEeeeeeeee-cccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHH
Confidence 3344444567889999 99999999999999999999999999998888888885
No 204
>COG1753 Predicted antotoxin, copG family [Signal transduction mechanisms]
Probab=20.23 E-value=1.8e+02 Score=18.32 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=17.6
Q ss_pred HHHHHHhCCCCCHHHHHHHHHHH
Q 034596 29 AKVLPQVVPSVTPDDARKLFHES 51 (90)
Q Consensus 29 i~~L~~v~p~~s~~~A~~i~~~v 51 (90)
+++|+..|+..|.+++..+-.+.
T Consensus 41 levl~~~~g~~s~eEvek~~~e~ 63 (74)
T COG1753 41 LEVLMRAFGTLSEEEVEKIKKEE 63 (74)
T ss_pred HHHHHHHhCCCcHHHHHHHHHHH
Confidence 46778889888888888876553
No 205
>COG1764 osmC Organic hydroperoxide reductase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=20.23 E-value=1e+02 Score=21.29 Aligned_cols=41 Identities=17% Similarity=0.100 Sum_probs=28.8
Q ss_pred eEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhh
Q 034596 13 YRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESRE 53 (90)
Q Consensus 13 y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~ 53 (90)
-.|-|.+.+--++-+..-.|.-.+||.+.++|.+|+..+|.
T Consensus 84 a~V~l~~~~~g~~~~i~v~l~v~i~g~~~~~a~~L~~~Ah~ 124 (143)
T COG1764 84 ATVGLGKVEDGTIFKIKVRLEVKIPGLDQAKAEALIKKAHE 124 (143)
T ss_pred eeEeccccCCCceEEEEEEEEEEecCCCHHHHHHHHHHHHH
Confidence 34555554433344444456667899999999999999996
No 206
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=20.14 E-value=1.1e+02 Score=16.66 Aligned_cols=20 Identities=20% Similarity=0.250 Sum_probs=14.1
Q ss_pred HHHHHHhCCCCCHHHHHHHHH
Q 034596 29 AKVLPQVVPSVTPDDARKLFH 49 (90)
Q Consensus 29 i~~L~~v~p~~s~~~A~~i~~ 49 (90)
...|..=| |++...|.+|-.
T Consensus 12 ~~~L~~~f-~ip~~vAk~IV~ 31 (40)
T PF02022_consen 12 AKALRHKF-GIPRLVAKQIVN 31 (40)
T ss_dssp HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHH-ccCHHHHHHHHH
Confidence 35678778 999999999854
No 207
>cd04444 DEP_PLEK2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 2-like proteins. Pleckstrin 2 is found in a wide variety of cell types, which suggest a more general role in signaling than pleckstrin 1. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains.
Probab=20.02 E-value=2.1e+02 Score=19.10 Aligned_cols=44 Identities=14% Similarity=0.005 Sum_probs=31.8
Q ss_pred CceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 11 ~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
.+|+--.|++.++=-+.|=..+..-+ -.|+++|.++....=..|
T Consensus 21 ~r~~~k~y~~CF~Gse~VDWLv~~~~-~i~R~EAv~l~q~Lmd~g 64 (109)
T cd04444 21 NMEQGSTYKKTFLGSALVDWLISNSF-AASRLEAVTLASMLMEEN 64 (109)
T ss_pred hhhccccccccccchHHHHHHHHCCC-CCCHHHHHHHHHHHHhCC
Confidence 45666788888888888877776655 667777777776665554
No 208
>PF11256 DUF3055: Protein of unknown function (DUF3055); InterPro: IPR021415 This family of proteins with unknown function appear to be restricted to Firmicutes.
Probab=20.02 E-value=1.4e+02 Score=19.03 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=21.2
Q ss_pred EEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Q 034596 16 LLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESR 52 (90)
Q Consensus 16 iL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH 52 (90)
||=-||.---.| |..+| ++|.++|.++..-.+
T Consensus 48 ilg~dDlee~gy----l~~~f-~l~~eea~eL~~fl~ 79 (81)
T PF11256_consen 48 ILGPDDLEEPGY----LEHAF-GLSEEEAEELREFLY 79 (81)
T ss_pred EEChhhcccccH----HHHHh-CCCHHHHHHHHHHHh
Confidence 333455554444 56788 999999999865443
No 209
>PF13041 PPR_2: PPR repeat family
Probab=20.00 E-value=1.6e+02 Score=15.56 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCC
Q 034596 23 HSEKLVAKVLPQVVPSVTPDDARKLFHESREHG 55 (90)
Q Consensus 23 ~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G 55 (90)
.++.-++..+.+ .-..++|.++..+...+|
T Consensus 4 ~~yn~li~~~~~---~~~~~~a~~l~~~M~~~g 33 (50)
T PF13041_consen 4 VTYNTLISGYCK---AGKFEEALKLFKEMKKRG 33 (50)
T ss_pred HHHHHHHHHHHH---CcCHHHHHHHHHHHHHcC
Confidence 344445555555 234566666665555554
Done!