Query psy4375
Match_columns 62
No_of_seqs 105 out of 322
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 23:56:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4375.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4375hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1959|consensus 99.9 1.1E-24 2.3E-29 176.0 5.1 57 2-58 103-164 (996)
2 PLN02701 alpha-mannosidase 99.8 1.4E-21 3.1E-26 158.8 5.3 57 2-58 98-157 (1050)
3 KOG1958|consensus 99.8 8.7E-20 1.9E-24 148.8 5.0 58 2-59 221-281 (1129)
4 PF01074 Glyco_hydro_38: Glyco 99.6 2E-15 4.4E-20 104.0 4.9 54 5-58 59-115 (275)
5 PRK09819 alpha-mannosidase; Pr 99.3 2.3E-12 5E-17 102.5 5.2 53 4-58 64-119 (875)
6 PF03065 Glyco_hydro_57: Glyco 96.6 0.0039 8.4E-08 45.2 4.7 50 9-58 113-166 (360)
7 KOG4342|consensus 95.8 0.016 3.4E-07 48.4 4.8 53 6-58 341-396 (1078)
8 PF01522 Polysacc_deac_1: Poly 92.5 0.44 9.6E-06 28.3 4.8 50 8-58 46-98 (123)
9 PF08672 APC2: Anaphase promot 89.6 0.44 9.4E-06 27.7 2.6 24 5-28 35-58 (60)
10 TIGR02764 spore_ybaN_pdaB poly 88.3 1.4 3E-05 28.9 4.6 53 9-62 48-104 (191)
11 PF08220 HTH_DeoR: DeoR-like h 84.1 2.2 4.8E-05 23.7 3.5 29 5-33 28-56 (57)
12 PRK04758 hypothetical protein; 78.5 4.4 9.5E-05 28.0 4.1 59 2-62 118-179 (181)
13 TIGR02884 spore_pdaA delta-lac 78.0 5.9 0.00013 27.1 4.6 54 8-62 78-136 (224)
14 PF08679 DsrD: Dissimilatory s 76.8 4 8.7E-05 24.8 3.1 23 5-27 34-56 (67)
15 PF02082 Rrf2: Transcriptional 69.8 9.5 0.00021 22.2 3.5 31 6-36 40-73 (83)
16 PF00538 Linker_histone: linke 69.5 4.9 0.00011 23.4 2.2 20 6-25 46-65 (77)
17 smart00419 HTH_CRP helix_turn_ 69.5 11 0.00023 18.9 3.3 26 5-30 22-47 (48)
18 PF00374 NiFeSe_Hases: Nickel- 69.3 1.7 3.7E-05 34.0 0.3 38 7-44 112-159 (507)
19 PF10720 DUF2515: Protein of u 68.0 1.8 3.8E-05 32.7 0.1 25 25-49 45-69 (308)
20 smart00526 H15 Domain in histo 67.5 5.4 0.00012 22.5 2.0 20 7-26 47-66 (66)
21 TIGR02873 spore_ylxY probable 65.3 14 0.00031 26.4 4.3 53 9-62 127-183 (268)
22 cd00092 HTH_CRP helix_turn_hel 63.8 14 0.00029 19.8 3.2 26 6-31 40-66 (67)
23 PF06969 HemN_C: HemN C-termin 62.1 16 0.00034 20.0 3.3 28 7-34 37-64 (66)
24 PF12395 DUF3658: Protein of u 59.8 9.4 0.0002 23.9 2.3 22 10-31 86-107 (111)
25 COG0383 AMS1 Alpha-mannosidase 58.6 4.7 0.0001 33.9 1.0 45 14-58 264-311 (943)
26 TIGR03826 YvyF flagellar opero 58.1 8 0.00017 25.8 1.8 18 9-26 60-77 (137)
27 PF04567 RNA_pol_Rpb2_5: RNA p 57.0 13 0.00027 20.4 2.2 15 12-26 1-15 (48)
28 PF06526 DUF1107: Protein of u 56.4 9.6 0.00021 22.8 1.8 28 18-45 29-56 (64)
29 cd00073 H15 linker histone 1 a 55.5 14 0.0003 22.2 2.4 20 7-26 47-66 (88)
30 PRK10170 hydrogenase 1 large s 53.8 11 0.00024 30.5 2.2 39 7-45 165-213 (597)
31 smart00345 HTH_GNTR helix_turn 52.1 27 0.00058 17.9 3.0 22 6-27 35-56 (60)
32 TIGR01764 excise DNA binding d 51.8 19 0.00042 17.8 2.3 26 9-34 15-42 (49)
33 TIGR02944 suf_reg_Xantho FeS a 51.7 34 0.00074 21.1 3.9 41 6-46 40-84 (130)
34 COG3811 Uncharacterized protei 51.1 29 0.00064 21.9 3.4 37 4-40 3-53 (85)
35 PF13812 PPR_3: Pentatricopept 50.8 16 0.00035 16.8 1.8 7 51-57 28-34 (34)
36 PF14394 DUF4423: Domain of un 49.8 25 0.00053 23.7 3.2 31 6-36 56-87 (171)
37 COG3497 Phage tail sheath prot 49.5 10 0.00022 29.6 1.4 47 4-57 322-369 (394)
38 KOG2165|consensus 48.0 19 0.00042 30.3 2.8 22 7-28 740-761 (765)
39 cd07377 WHTH_GntR Winged helix 47.2 35 0.00075 17.8 3.0 24 6-29 40-64 (66)
40 PF11625 DUF3253: Protein of u 46.8 35 0.00075 21.2 3.3 25 6-30 44-68 (83)
41 PF13342 Toprim_Crpt: C-termin 46.2 14 0.00029 21.5 1.3 19 8-26 17-35 (62)
42 PF06819 Arc_PepC: Archaeal Pe 44.9 23 0.0005 23.1 2.4 21 2-22 85-105 (110)
43 PRK08208 coproporphyrinogen II 43.5 49 0.0011 24.8 4.3 41 9-49 379-419 (430)
44 smart00420 HTH_DEOR helix_turn 43.3 42 0.00092 16.6 2.8 25 5-29 28-52 (53)
45 TIGR00738 rrf2_super rrf2 fami 42.7 61 0.0013 19.7 4.0 40 6-45 40-83 (132)
46 COG4707 Uncharacterized protei 42.1 15 0.00032 24.0 1.2 26 18-43 61-91 (107)
47 PRK08898 coproporphyrinogen II 40.2 69 0.0015 23.7 4.6 39 8-46 355-393 (394)
48 PF06677 Auto_anti-p27: Sjogre 40.1 7.7 0.00017 21.1 -0.4 12 26-37 11-22 (41)
49 PF13338 DUF4095: Domain of un 39.4 42 0.00091 19.7 2.8 27 9-35 4-30 (124)
50 PRK08599 coproporphyrinogen II 39.0 69 0.0015 23.3 4.3 39 8-46 336-374 (377)
51 cd00481 Ribosomal_L19e Ribosom 38.4 16 0.00035 24.9 0.9 21 3-23 29-49 (145)
52 PRK15047 N-hydroxyarylamine O- 38.3 25 0.00054 25.5 1.9 32 7-45 52-83 (281)
53 PRK00683 murD UDP-N-acetylmura 38.2 47 0.001 24.4 3.4 39 8-46 267-309 (418)
54 PF13289 SIR2_2: SIR2-like dom 37.9 89 0.0019 18.7 4.1 37 5-46 73-109 (143)
55 PRK08570 rpl19e 50S ribosomal 37.5 17 0.00038 24.9 1.0 21 3-23 32-52 (150)
56 cd00165 S4 S4/Hsp/ tRNA synthe 37.5 42 0.00091 17.1 2.3 22 7-29 14-35 (70)
57 TIGR03212 uraD_N-term-dom puta 37.4 80 0.0017 23.0 4.4 50 8-58 105-157 (297)
58 smart00363 S4 S4 RNA-binding d 37.2 44 0.00096 16.5 2.3 22 7-29 14-35 (60)
59 PRK01379 cyaY frataxin-like pr 36.7 38 0.00082 21.5 2.4 35 19-58 69-103 (103)
60 PF14701 hDGE_amylase: glucano 36.6 19 0.00042 28.0 1.2 21 18-38 324-344 (423)
61 PRK05628 coproporphyrinogen II 36.5 74 0.0016 23.1 4.2 37 9-45 337-373 (375)
62 PF01479 S4: S4 domain; Inter 36.5 46 0.001 17.1 2.4 19 8-27 15-33 (48)
63 KOG0402|consensus 35.8 36 0.00078 21.8 2.1 26 22-47 63-88 (92)
64 cd04415 NDPk7A Nucleoside diph 35.8 70 0.0015 20.6 3.6 38 11-49 18-66 (131)
65 smart00347 HTH_MARR helix_turn 35.5 82 0.0018 17.4 4.1 43 5-47 38-87 (101)
66 PF06044 DRP: Dam-replacing fa 35.3 45 0.00098 24.7 2.9 23 5-27 227-249 (254)
67 cd01418 Ribosomal_L19e_A Ribos 34.9 20 0.00044 24.4 1.0 21 3-23 29-49 (145)
68 KOG2159|consensus 34.7 32 0.00069 27.0 2.1 44 5-49 14-68 (416)
69 PRK13687 hypothetical protein; 34.7 80 0.0017 20.0 3.5 37 4-40 3-53 (85)
70 PF00530 SRCR: Scavenger recep 34.6 17 0.00036 20.8 0.5 14 17-30 7-22 (99)
71 PF09857 DUF2084: Uncharacteri 34.6 91 0.002 19.7 3.8 37 4-40 3-53 (85)
72 PRK10467 hydrogenase 2 large s 34.5 35 0.00076 27.4 2.4 42 6-47 149-200 (567)
73 PRK02166 hypothetical protein; 34.0 90 0.002 21.5 4.1 51 3-57 121-174 (184)
74 PF14177 YkyB: YkyB-like prote 33.1 46 0.001 22.7 2.5 20 8-27 29-48 (140)
75 PRK03902 manganese transport t 33.1 1.1E+02 0.0024 19.2 4.1 38 4-41 35-73 (142)
76 PF14595 Thioredoxin_9: Thiore 32.7 23 0.0005 22.7 0.9 26 5-30 29-54 (129)
77 COG1802 GntR Transcriptional r 32.7 52 0.0011 22.0 2.7 26 7-32 55-81 (230)
78 PRK05799 coproporphyrinogen II 32.5 1.1E+02 0.0024 22.1 4.5 39 8-46 335-373 (374)
79 PF12910 RelB_N: Antitoxin of 32.1 32 0.0007 18.5 1.3 18 32-49 7-24 (46)
80 COG2147 RPL19A Ribosomal prote 32.0 24 0.00052 24.3 0.9 21 3-23 32-52 (150)
81 cd01417 Ribosomal_L19e_E Ribos 31.9 24 0.00051 24.6 0.9 21 3-23 29-49 (164)
82 PF12419 DUF3670: SNF2 Helicas 31.7 60 0.0013 20.9 2.8 28 8-35 85-113 (141)
83 PRK05660 HemN family oxidoredu 31.6 1.2E+02 0.0026 22.3 4.7 39 8-46 338-376 (378)
84 COG1347 NqrD Na+-transporting 31.6 30 0.00064 24.9 1.4 40 10-49 149-198 (208)
85 PF02187 GAS2: Growth-Arrest-S 30.9 18 0.00039 22.1 0.2 14 21-34 49-62 (73)
86 PTZ00097 60S ribosomal protein 30.8 25 0.00054 24.7 0.9 21 3-23 30-50 (175)
87 PF06530 Phage_antitermQ: Phag 30.5 16 0.00036 23.2 -0.0 23 26-49 12-34 (125)
88 PRK10512 selenocysteinyl-tRNA- 29.4 1.2E+02 0.0025 24.4 4.5 43 7-49 522-564 (614)
89 PF04703 FaeA: FaeA-like prote 29.3 86 0.0019 18.1 2.9 21 6-26 30-50 (62)
90 PF14237 DUF4339: Domain of un 28.9 44 0.00096 17.5 1.5 17 6-22 13-29 (45)
91 PF12686 DUF3800: Protein of u 28.6 55 0.0012 20.7 2.2 31 19-49 18-48 (235)
92 PRK13509 transcriptional repre 28.4 77 0.0017 22.1 3.0 25 6-30 34-58 (251)
93 PF06348 DUF1059: Protein of u 28.3 64 0.0014 18.1 2.2 18 1-18 39-56 (57)
94 PRK12569 hypothetical protein; 28.1 74 0.0016 23.2 3.0 27 5-31 191-217 (245)
95 PTZ00436 60S ribosomal protein 27.9 36 0.00077 26.3 1.3 21 3-23 32-52 (357)
96 PF00994 MoCF_biosynth: Probab 27.9 1E+02 0.0022 19.2 3.3 28 5-32 43-70 (144)
97 PRK09802 DNA-binding transcrip 27.6 1E+02 0.0022 21.8 3.6 27 6-32 46-72 (269)
98 PF13545 HTH_Crp_2: Crp-like h 27.5 1.1E+02 0.0025 16.6 3.5 27 7-33 44-70 (76)
99 PLN02578 hydrolase 27.4 1.1E+02 0.0023 21.7 3.7 41 7-47 313-353 (354)
100 PF01280 Ribosomal_L19e: Ribos 27.3 23 0.00049 24.2 0.2 20 4-23 32-51 (148)
101 PF07848 PaaX: PaaX-like prote 27.2 1.1E+02 0.0024 17.9 3.1 29 4-32 36-68 (70)
102 COG1449 Alpha-amylase/alpha-ma 26.9 1.3E+02 0.0027 24.4 4.3 50 8-59 181-239 (615)
103 cd03142 GATase1_ThuA Type 1 gl 26.7 67 0.0014 22.6 2.5 19 1-19 70-88 (215)
104 TIGR02010 IscR iron-sulfur clu 26.6 1.3E+02 0.0028 18.8 3.6 42 7-49 41-86 (135)
105 COG0549 ArcC Carbamate kinase 25.9 67 0.0015 24.5 2.5 19 9-27 174-192 (312)
106 PRK06294 coproporphyrinogen II 25.9 1.4E+02 0.003 22.0 4.1 37 9-45 333-369 (370)
107 PF14417 MEDS: MEDS: MEthanoge 25.7 52 0.0011 21.8 1.7 32 15-46 77-115 (191)
108 PF14059 DUF4251: Domain of un 25.7 90 0.002 20.1 2.8 22 3-24 4-25 (138)
109 PF14503 YhfZ_C: YhfZ C-termin 25.6 1.5E+02 0.0033 21.3 4.2 38 2-49 120-157 (232)
110 PF10925 DUF2680: Protein of u 25.3 73 0.0016 18.3 2.1 16 6-21 18-33 (59)
111 TIGR02277 PaaX_trns_reg phenyl 25.3 1.5E+02 0.0032 21.4 4.1 41 4-44 33-77 (280)
112 PRK06582 coproporphyrinogen II 25.2 1.4E+02 0.0031 22.3 4.1 36 10-46 354-389 (390)
113 TIGR03338 phnR_burk phosphonat 24.9 1.8E+02 0.0039 18.9 4.2 27 6-32 49-76 (212)
114 smart00346 HTH_ICLR helix_turn 24.9 1.3E+02 0.0027 16.9 3.1 34 5-38 34-69 (91)
115 COG1540 Uncharacterized protei 24.9 83 0.0018 23.4 2.8 32 6-37 191-224 (252)
116 PF03536 VRP3: Salmonella viru 24.5 74 0.0016 23.5 2.4 34 28-61 157-197 (240)
117 PRK10513 sugar phosphate phosp 24.4 1E+02 0.0022 20.7 3.0 16 4-19 21-36 (270)
118 PF09935 DUF2167: Protein of u 24.4 78 0.0017 23.0 2.5 29 21-49 63-92 (239)
119 PF13036 DUF3897: Protein of u 24.3 85 0.0018 20.5 2.5 21 8-28 84-104 (180)
120 PF14805 THDPS_N_2: Tetrahydro 24.2 97 0.0021 18.4 2.5 28 5-32 23-57 (70)
121 PF13174 TPR_6: Tetratricopept 24.2 35 0.00076 15.3 0.5 15 30-44 15-29 (33)
122 PRK09897 hypothetical protein; 24.0 1E+02 0.0022 24.3 3.3 24 5-28 391-414 (534)
123 PF06353 DUF1062: Protein of u 23.9 77 0.0017 21.2 2.3 19 9-27 117-135 (142)
124 TIGR02075 pyrH_bact uridylate 23.7 94 0.002 21.3 2.7 30 9-38 111-144 (233)
125 PF13604 AAA_30: AAA domain; P 23.6 1.2E+02 0.0026 20.1 3.2 24 4-27 2-26 (196)
126 cd01389 MATA_HMG-box MATA_HMG- 23.4 66 0.0014 18.2 1.7 36 26-61 38-77 (77)
127 PF08721 Tn7_Tnp_TnsA_C: TnsA 23.3 80 0.0017 17.4 2.0 16 8-23 62-77 (79)
128 cd00758 MoCF_BD MoCF_BD: molyb 23.2 1.1E+02 0.0024 19.0 2.8 27 5-31 45-71 (133)
129 PF13086 AAA_11: AAA domain; P 23.1 73 0.0016 20.0 2.0 24 4-27 2-25 (236)
130 PRK10530 pyridoxal phosphate ( 22.6 1.2E+02 0.0026 20.2 3.0 16 4-19 21-36 (272)
131 cd05398 NT_ClassII-CCAase Nucl 22.5 1.2E+02 0.0025 19.5 2.8 24 6-29 2-26 (139)
132 PRK13347 coproporphyrinogen II 22.5 2E+02 0.0044 21.7 4.5 37 9-45 402-438 (453)
133 PRK08628 short chain dehydroge 22.5 54 0.0012 21.5 1.3 19 18-36 240-258 (258)
134 PRK09058 coproporphyrinogen II 22.4 2.6E+02 0.0056 21.2 5.1 39 9-47 399-437 (449)
135 COG1959 Predicted transcriptio 22.3 1.6E+02 0.0035 19.2 3.6 42 8-49 42-86 (150)
136 PRK13774 formimidoylglutamase; 22.1 1.2E+02 0.0026 22.0 3.1 23 6-28 107-129 (311)
137 PRK11534 DNA-binding transcrip 22.0 2.3E+02 0.005 18.7 4.3 27 6-32 45-72 (224)
138 PF00392 GntR: Bacterial regul 21.9 1.5E+02 0.0033 16.1 3.0 23 6-28 39-62 (64)
139 PF09106 SelB-wing_2: Elongati 21.8 1.4E+02 0.0031 16.3 2.8 20 9-29 38-57 (59)
140 PRK10976 putative hydrolase; P 21.7 1.3E+02 0.0028 20.2 3.1 16 4-19 20-35 (266)
141 PF14627 DUF4453: Domain of un 21.6 34 0.00075 22.4 0.2 22 17-38 81-105 (107)
142 PRK13276 cell wall biosynthesi 21.6 53 0.0011 23.5 1.2 26 20-45 176-201 (224)
143 PF01293 PEPCK_ATP: Phosphoeno 21.6 1.2E+02 0.0026 23.9 3.2 40 10-49 392-439 (466)
144 TIGR02903 spore_lon_C ATP-depe 21.5 1.3E+02 0.0029 24.0 3.5 37 2-38 275-311 (615)
145 cd04762 HTH_MerR-trunc Helix-T 21.5 71 0.0015 15.4 1.4 23 9-31 14-39 (49)
146 PRK08629 coproporphyrinogen II 21.3 2.6E+02 0.0056 21.3 4.9 42 8-49 376-417 (433)
147 smart00243 GAS2 Growth-Arrest- 21.3 22 0.00048 21.8 -0.7 19 15-33 43-61 (73)
148 PF14202 TnpW: Transposon-enco 20.9 90 0.0019 16.4 1.7 17 2-18 20-36 (37)
149 TIGR02147 Fsuc_second hypothet 20.9 1.3E+02 0.0028 21.9 3.1 32 6-37 154-186 (271)
150 smart00550 Zalpha Z-DNA-bindin 20.8 1.7E+02 0.0038 16.4 3.1 28 6-33 37-67 (68)
151 KOG1055|consensus 20.7 1.1E+02 0.0023 26.4 2.9 47 10-57 382-428 (865)
152 COG0617 PcnB tRNA nucleotidylt 20.5 86 0.0019 23.2 2.2 26 3-29 6-32 (412)
153 PF01706 FliG_C: FliG C-termin 20.5 68 0.0015 19.6 1.4 14 10-23 96-109 (110)
154 KOG1515|consensus 20.5 1.1E+02 0.0025 22.8 2.8 26 21-46 94-119 (336)
155 PRK11508 sulfur transfer prote 20.4 51 0.0011 21.2 0.9 26 35-61 40-65 (109)
156 KOG3360|consensus 20.4 42 0.00091 21.7 0.4 6 27-32 38-43 (98)
157 KOG4603|consensus 20.4 70 0.0015 23.0 1.6 20 37-56 174-200 (201)
158 TIGR02988 YaaA_near_RecF S4 do 20.2 1.2E+02 0.0027 16.3 2.3 21 8-29 23-43 (59)
159 smart00529 HTH_DTXR Helix-turn 20.2 1.9E+02 0.004 16.5 4.5 41 5-45 13-54 (96)
160 PF14217 DUF4327: Domain of un 20.1 1E+02 0.0022 18.6 2.1 16 7-22 6-21 (68)
161 PF06908 DUF1273: Protein of u 20.1 1.2E+02 0.0025 20.7 2.6 22 6-27 29-50 (177)
No 1
>KOG1959|consensus
Probab=99.90 E-value=1.1e-24 Score=175.98 Aligned_cols=57 Identities=40% Similarity=0.625 Sum_probs=54.5
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcc--cccC
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFS--VQSS 58 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fg--v~p~ 58 (62)
++|++++|.+||+||++||||||||||||||||++||.|||||+|.|| .+||| .+||
T Consensus 103 ~~qS~~~k~~Vk~LV~~GrLEFi~Ggw~MnDEA~~hY~dvIDQ~TlGlrfL~~tFG~cgrPr 164 (996)
T KOG1959|consen 103 NEQSETQKEQVKKLVNEGRLEFIGGGWSMNDEATTHYQDVIDQFTLGLRFLKDTFGECGRPR 164 (996)
T ss_pred HhcCHHHHHHHHHHHhcCCEEEecCeeeecchhhhhHHHHHHHHHHHHHHHHHHhcccCCcc
Confidence 479999999999999999999999999999999999999999999999 99999 6665
No 2
>PLN02701 alpha-mannosidase
Probab=99.84 E-value=1.4e-21 Score=158.76 Aligned_cols=57 Identities=42% Similarity=0.750 Sum_probs=54.7
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
++++++.|++||+||++||||||+|||||+|||++||++||+||++|| .++||+.|+
T Consensus 98 ~~~~pe~~~~vk~LV~~GrLE~vgGgwvm~DEa~~~~esiI~Ql~~G~~~l~~~fG~~P~ 157 (1050)
T PLN02701 98 RDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIGVAPK 157 (1050)
T ss_pred HhcCHHHHHHHHHHHHcCCEEEECCceecccccccCHHHHHHHHHhhhHHHHhhcCCCCC
Confidence 578999999999999999999999999999999999999999999999 599999985
No 3
>KOG1958|consensus
Probab=99.79 E-value=8.7e-20 Score=148.75 Aligned_cols=58 Identities=53% Similarity=0.867 Sum_probs=54.4
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccCC
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSSK 59 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~~ 59 (62)
+++++++|++||+||++||||||+|||||+|||++||.++|+|+++|| ..+.||.|+.
T Consensus 221 ~~~~~~kk~a~k~lv~~GqlEIvtGGWVMpDEAn~Hy~~~i~qliEGh~Wl~~~igv~P~s 281 (1129)
T KOG1958|consen 221 DDASPTKKNAVKRLVKNGQLEIVTGGWVMPDEANSHYFAMIDQLIEGHQWLKNNIGVTPQS 281 (1129)
T ss_pred hhcChHHHHHHHHHHhcCcEEEEeCccccCcccchhHHHHHHHHhhhhhHHhccCCCCCCc
Confidence 578999999999999999999999999999999999999999999999 7778888864
No 4
>PF01074 Glyco_hydro_38: Glycosyl hydrolases family 38 N-terminal domain; InterPro: IPR000602 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. Glycoside hydrolase family 38 GH38 from CAZY comprises enzymes with only one known activity; alpha-mannosidase (3.2.1.24 from EC) (3.2.1.114 from EC). Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyses the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides, and can cleave all known types of alpha-mannosidic linkages. Defects in the gene cause lysosomal alpha-mannosidosis (AM), a lysosomal storage disease characterised by the accumulation of unbranched oligo-saccharide chains.; GO: 0004559 alpha-mannosidase activity, 0005975 carbohydrate metabolic process; PDB: 2WYI_A 2WYH_A 1O7D_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A ....
Probab=99.58 E-value=2e-15 Score=104.04 Aligned_cols=54 Identities=31% Similarity=0.465 Sum_probs=44.4
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
.++.++.+++||++||||||+|+|||+||++++.+++|+||+.|| .++||++|+
T Consensus 59 ~p~~~~~~~~lv~~Gri~~vgg~~~~~D~~l~~~Eslirql~~G~~~~~~~fg~~~~ 115 (275)
T PF01074_consen 59 APEEFKRIKKLVKEGRIEIVGGWYVQPDENLPSGESLIRQLLYGHKYLRKEFGVRPK 115 (275)
T ss_dssp SGHHHHHHHHHHHTTSEEESSSBSS-B-SSSS-HHHHHHHHHHHHHHHHHHHTG--S
T ss_pred CCHHHHHHHHHHHhceeEEeCceeeeccccCCCHHHHHHHHhhhHHHHHHhcCCCCC
Confidence 455566669999999999999999999999999999999999999 689998875
No 5
>PRK09819 alpha-mannosidase; Provisional
Probab=99.31 E-value=2.3e-12 Score=102.48 Aligned_cols=53 Identities=28% Similarity=0.473 Sum_probs=48.9
Q ss_pred CChHHHHHHHHHHHcCceeEEecce-eecccccccHHHHHHHHhhhh--hhhcccccC
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVTGGW-VMTDEATSHIFAMVDQLIEET--FSTFSVQSS 58 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~GGW-vm~DEA~~~y~~~Idq~t~Gh--~~~Fgv~p~ 58 (62)
..++.+++||+||++||| +.||| ||+||++++++|+|+||+.|| +++||+.|+
T Consensus 64 ~~Pe~~~~ik~lV~~Grl--~~G~W~v~~D~~l~sgEsliRqll~G~~~~~~fG~~~~ 119 (875)
T PRK09819 64 VKPEDKERVKKLVQAGKL--IIGPWYTQTDQLVVSGESIVRNLLYGIRDCREFGEPMK 119 (875)
T ss_pred hChHHHHHHHHHHHcCCE--eECcEEeecccccCCHHHHHHHHHHHHHHHHHcCCCCc
Confidence 468899999999999999 56999 899999999999999999999 899998874
No 6
>PF03065 Glyco_hydro_57: Glycosyl hydrolase family 57; InterPro: IPR004300 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. Glycoside hydrolase family 57 GH57 from CAZY comprises enzymes with two known activities; alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1 from EC).; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1K1X_B 1K1W_A 1K1Y_A 3N98_A 3N8T_A 3N92_A 1UFA_A 3P0B_A.
Probab=96.64 E-value=0.0039 Score=45.18 Aligned_cols=50 Identities=12% Similarity=0.086 Sum_probs=35.3
Q ss_pred HHHHHHHHHcCceeEEecceeeccccccc-HHHHHHHHhhhh---hhhcccccC
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSH-IFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~-y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
=+.+|+|+++|++|++++++.-+==..-. ..++..|+..|. .+.||++|+
T Consensus 113 i~~~~~l~~~G~iEll~~~~~h~ilpl~~~~~d~~~Qi~~~~~~~~~~FG~~P~ 166 (360)
T PF03065_consen 113 IEAFRELAERGQIELLTSPYYHPILPLLPDPEDFRAQIEMGREYFKKHFGRRPR 166 (360)
T ss_dssp HHHHHHHHHTTSEEEEEE-TT-B-GGGSSHHHHHHHHHHHHHHHHHHHHSS--S
T ss_pred HHHHHHHHHCCCEEEEeCchHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 46789999999999999998653222222 366889998888 888999986
No 7
>KOG4342|consensus
Probab=95.83 E-value=0.016 Score=48.38 Aligned_cols=53 Identities=21% Similarity=0.356 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
+.-=+.++..+..||+-=|+|-||-+|--.|+=++++.|+..|. ..+||++-+
T Consensus 341 P~~f~kl~e~~~q~qF~pvGGtWVE~DtNiPsGEslvRQFl~GQ~FFlkeFG~~c~ 396 (1078)
T KOG4342|consen 341 PGLFSKLQEFACQGQFVPVGGTWVEMDTNIPSGESLVRQFLQGQNFFLKEFGKMCS 396 (1078)
T ss_pred hhHHHHHHHHHhcCceeeccceEEecCCCCCChHHHHHHHHhhhhHHHHHhhhhhc
Confidence 33445688899999999999999999999999999999999999 788888754
No 8
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=92.48 E-value=0.44 Score=28.27 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=38.4
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
..+.++.|.++| .||-+-||.-.+-......++.++|.... .+.+|..|+
T Consensus 46 ~~~~l~~l~~~G-~ei~~H~~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g~~~~ 98 (123)
T PF01522_consen 46 YPDQLRELAAAG-HEIGNHGWSHPNLSTLSPEELRREIERSREILEEITGRPPK 98 (123)
T ss_dssp HHHHHHHHHHTT--EEEEE-SSSSCGGGS-HHHHHHHHHHHHHHHHHHHSSEES
T ss_pred ccccchhHHHHH-HHHHhcCCcccccccCCHHHHHHHHHHHHHHHHHHhCCCCc
Confidence 357899999999 99999999988888888888899988887 444666543
No 9
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=89.55 E-value=0.44 Score=27.67 Aligned_cols=24 Identities=25% Similarity=0.549 Sum_probs=17.9
Q ss_pred ChHHHHHHHHHHHcCceeEEecce
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGW 28 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGW 28 (62)
.++-+.-+.+||++|+||+++|-|
T Consensus 35 ~~eL~~fL~~lv~e~~L~~~~G~Y 58 (60)
T PF08672_consen 35 LEELQEFLDRLVEEGKLECSGGSY 58 (60)
T ss_dssp HHHHHHHHHHHHHTTSEE--TTEE
T ss_pred HHHHHHHHHHHHHCCcEEecCCEE
Confidence 456677899999999999997755
No 10
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=88.26 E-value=1.4 Score=28.86 Aligned_cols=53 Identities=17% Similarity=0.316 Sum_probs=40.2
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccCC-CCC
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSSK-RPP 62 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~~-~~~ 62 (62)
.+.+++++++|. ||-+-+|.-.+-..-....+..+|..+. .+..|..|+- |||
T Consensus 48 ~~~~~~i~~~Gh-eig~Ht~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g~~~~~fr~P 104 (191)
T TIGR02764 48 PELVKEIVKDGH-EIGSHGYRHKNYTTLEDEKIKKDILRAQEIIEKLTGKKPTLFRPP 104 (191)
T ss_pred HHHHHHHHhCCC-EEEECCcCCCCcccCCHHHHHHHHHHHHHHHHHHhCCCCCEEECC
Confidence 468999999995 9999999877665566677888888877 4556776642 555
No 11
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=84.08 E-value=2.2 Score=23.72 Aligned_cols=29 Identities=31% Similarity=0.410 Sum_probs=25.9
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeeccc
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTDE 33 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~DE 33 (62)
..+.|..+..|.+.|.+.-+-||++..++
T Consensus 28 ~~TiRRDl~~L~~~g~i~r~~GG~~~~~~ 56 (57)
T PF08220_consen 28 EMTIRRDLNKLEKQGLIKRTHGGAVLNDS 56 (57)
T ss_pred HHHHHHHHHHHHHCCCEEEEcCEEEeCCC
Confidence 46778899999999999999999998775
No 12
>PRK04758 hypothetical protein; Validated
Probab=78.54 E-value=4.4 Score=27.99 Aligned_cols=59 Identities=5% Similarity=0.031 Sum_probs=48.2
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccCCCCC
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSSKRPP 62 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~~~~~ 62 (62)
...+++.|+.++.|.+..|+.+-- =--.+|....|..+|+-+.-+- +.+|+.-|+.+|+
T Consensus 118 ~~~s~e~~E~L~Dl~~Iaql~~d~--~ed~ee~E~al~El~EyvRvaall~~~e~~~~~~~~~~ 179 (181)
T PRK04758 118 PALSEEGEEALQDLARLAQASSDD--FDAAEEDDTALAEIEEFVRVAVLLLHGDCVMGPRFRQR 179 (181)
T ss_pred ccCCHHHHHHHHHHHHHHccCCCc--ccCchHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Confidence 356889999999999999999741 0235677788999999998888 9999999998875
No 13
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production.
Probab=77.95 E-value=5.9 Score=27.08 Aligned_cols=54 Identities=13% Similarity=0.150 Sum_probs=39.5
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccc-cC-CCCC
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQ-SS-KRPP 62 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~-p~-~~~~ 62 (62)
..+.+++++++| .||-|-+|.-.+=..-....+.++|.... .+..|.. |+ -|||
T Consensus 78 ~p~~ir~i~~~G-heIgnHt~~H~~~~~ls~~~~~~ei~~~~~~i~~~~G~~~~~~fR~P 136 (224)
T TIGR02884 78 QPDLIKRMVDEG-HIVGNHSVHHPSLTAVNDEKFKEELTGVEEEFKKVTGQKEMKYFRPP 136 (224)
T ss_pred CHHHHHHHHHcC-CEeeecCccCcCcccCCHHHHHHHHHHHHHHHHHHhCCCCCCEEeCC
Confidence 356899999999 58999999755544455677788888877 4556776 44 4776
No 14
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=76.84 E-value=4 Score=24.75 Aligned_cols=23 Identities=35% Similarity=0.611 Sum_probs=18.6
Q ss_pred ChHHHHHHHHHHHcCceeEEecc
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GG 27 (62)
..+.|+.+..||++|.||+-+-|
T Consensus 34 ~R~vKKi~~~LV~Eg~l~yWSSG 56 (67)
T PF08679_consen 34 PREVKKIVNELVNEGKLEYWSSG 56 (67)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHHHhhCeEEEEcCC
Confidence 45678889999999999996443
No 15
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=69.78 E-value=9.5 Score=22.18 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHcCceeEE---ecceeecccccc
Q psy4375 6 PTKRNIVKKLIAEGRLEMV---TGGWVMTDEATS 36 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv---~GGWvm~DEA~~ 36 (62)
...++.+++|.+.|=++-. +|||....++-.
T Consensus 40 ~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~ 73 (83)
T PF02082_consen 40 SYLRKILQKLKKAGLIESSRGRGGGYRLARPPEE 73 (83)
T ss_dssp HHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCG
T ss_pred HHHHHHHHHHhhCCeeEecCCCCCceeecCCHHH
Confidence 3457789999999999998 789998877643
No 16
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=69.55 E-value=4.9 Score=23.42 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHcCceeEEe
Q psy4375 6 PTKRNIVKKLIAEGRLEMVT 25 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~ 25 (62)
...+..++++|++|.|+.+.
T Consensus 46 ~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 46 SRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHHHHHHHHCCcEEeec
Confidence 45788899999999999998
No 17
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=69.51 E-value=11 Score=18.92 Aligned_cols=26 Identities=27% Similarity=0.322 Sum_probs=21.0
Q ss_pred ChHHHHHHHHHHHcCceeEEecceee
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVM 30 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm 30 (62)
.+...+.+++|.+.|-++...|.|+.
T Consensus 22 ~~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 22 RETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 35567789999999999998877654
No 18
>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium (the [NiFe] and [NiFeSe] hydrogenases) and those lacking nickel (the [Fe] hydrogenases). The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit that contains a signal peptide and a large subunit. All the known large subunits seem to be evolutionary related []; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel []. In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand [].; GO: 0016151 nickel ion binding; PDB: 1E3D_D 3USC_M 3USE_L 3UQY_M 3RGW_L 1CC1_L 1YQ9_I 2FRV_D 1FRV_B 3MYR_F ....
Probab=69.30 E-value=1.7 Score=33.97 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHcCceeEEecceee----------cccccccHHHHHHH
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVM----------TDEATSHIFAMVDQ 44 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm----------~DEA~~~y~~~Idq 44 (62)
..|+.|++||++|||-+.+.||=- |.-|.+||...++-
T Consensus 112 ~vq~kl~~~v~~g~lg~f~~~y~~h~~y~l~pe~nl~~v~hYleAL~~ 159 (507)
T PF00374_consen 112 AVQDKLKKFVESGQLGPFANGYWGHPDYKLPPEVNLIAVAHYLEALEI 159 (507)
T ss_dssp HHHHHHHHHHHTTHHGGGTTHTTT-TT--S-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCCCccCCCCCCCccccCChhHhHHHHHHHHHHHHH
Confidence 478899999999999999888855 34567888777654
No 19
>PF10720 DUF2515: Protein of unknown function (DUF2515); InterPro: IPR019658 This family is conserved in Firmicutes. Several members are annotated as YppC. The function is not known.
Probab=68.03 E-value=1.8 Score=32.70 Aligned_cols=25 Identities=24% Similarity=0.339 Sum_probs=21.0
Q ss_pred ecceeecccccccHHHHHHHHhhhh
Q psy4375 25 TGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 25 ~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
||||-|+|=....|..++..-..-+
T Consensus 45 N~GWnMTDL~g~~~~~lL~~~~~~~ 69 (308)
T PF10720_consen 45 NAGWNMTDLKGELLPRLLSEEEREW 69 (308)
T ss_pred cCCccchhcCcchhhhhcCHHHHHH
Confidence 9999999999999998887655444
No 20
>smart00526 H15 Domain in histone families 1 and 5.
Probab=67.48 E-value=5.4 Score=22.45 Aligned_cols=20 Identities=40% Similarity=0.566 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHcCceeEEec
Q psy4375 7 TKRNIVKKLIAEGRLEMVTG 26 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~G 26 (62)
.-+..++++|++|.|+.+.|
T Consensus 47 ~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 47 LLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred HHHHHHHHHHhcCceeecCC
Confidence 35677999999999998765
No 21
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family. Members of this protein family are most closely related to TIGR02764, a subset of polysaccharide deacetylase family proteins found in a species if and only if the species forms endospores like those of Bacillus subtilis or Clostridium tetani. This family is likewise restricted to spore-formers, but is not universal among them in having sequences with full-length matches to the model.
Probab=65.27 E-value=14 Score=26.36 Aligned_cols=53 Identities=23% Similarity=0.298 Sum_probs=39.7
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC-CCCC
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS-KRPP 62 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~-~~~~ 62 (62)
.+.+++++++| .||-|=+|.-.+-..-....+.++|.... .+..|..|+ -|||
T Consensus 127 p~l~k~i~~~G-heIGnHT~sH~~l~~ls~~~~~~Ei~~~~~~i~~~~G~~p~~fRpP 183 (268)
T TIGR02873 127 SQLAKMIVEQG-HEIGNHAYNHPDMATLSKEEIYDQINQTNEIIEATIGVTPKWFAPP 183 (268)
T ss_pred HHHHHHHHHCC-CEEEecCCcCCCcccCCHHHHHHHHHHHHHHHHHHhCCCCCEEECC
Confidence 45789999999 49999999876666556778888888888 556677665 3554
No 22
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=63.75 E-value=14 Score=19.76 Aligned_cols=26 Identities=23% Similarity=0.299 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHcCceeEEe-cceeec
Q psy4375 6 PTKRNIVKKLIAEGRLEMVT-GGWVMT 31 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~-GGWvm~ 31 (62)
+.....+++|.+.|-++... |.|+..
T Consensus 40 ~tv~r~l~~L~~~g~i~~~~~~~~~l~ 66 (67)
T cd00092 40 ETVSRTLKELEEEGLISRRGRGKYRVN 66 (67)
T ss_pred HHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 45677899999999999988 888754
No 23
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=62.11 E-value=16 Score=20.04 Aligned_cols=28 Identities=21% Similarity=0.338 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHcCceeEEecceeecccc
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVMTDEA 34 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm~DEA 34 (62)
...+.++.|++.|-+++-++.++.+++.
T Consensus 37 ~~~~~l~~l~~~Gll~~~~~~l~lT~~G 64 (66)
T PF06969_consen 37 EFQKELEELQEDGLLEIDGGRLRLTEKG 64 (66)
T ss_dssp H-HHHHHHHHHTTSEEE-SSEEEE-TTT
T ss_pred HHHHHHHHHHHCCCEEEeCCEEEECccc
Confidence 3367799999999999999999988765
No 24
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=59.77 E-value=9.4 Score=23.89 Aligned_cols=22 Identities=27% Similarity=0.336 Sum_probs=17.1
Q ss_pred HHHHHHHHcCceeEEecceeec
Q psy4375 10 NIVKKLIAEGRLEMVTGGWVMT 31 (62)
Q Consensus 10 ~~vk~LV~~GqlEfv~GGWvm~ 31 (62)
-.++.||++|+||+.+----|.
T Consensus 86 ~Ri~~Li~~G~le~~g~~~~mr 107 (111)
T PF12395_consen 86 YRIRELISQGVLEIKGDPKDMR 107 (111)
T ss_pred HHHHHHHHCCCEEEecCCCccc
Confidence 3689999999999987554443
No 25
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=58.62 E-value=4.7 Score=33.92 Aligned_cols=45 Identities=22% Similarity=0.259 Sum_probs=38.0
Q ss_pred HHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 14 KLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 14 ~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
.+|+.++.+.+.|.||-+|=..+.=++...|+..|. ...||..+|
T Consensus 264 ~~v~~~~~~~~~g~~ve~d~n~~sGEslsrq~~~gq~~~~~~f~~ssr 311 (943)
T COG0383 264 PAVEFEQWEIVGGMWVEEDLNTPSGESLSRQFLYGQRFFTEKFGASSR 311 (943)
T ss_pred ccccccceEEeecccccccCCccccchhhhhhhccceeeecccCccce
Confidence 678899999999999999977788889999999988 666666544
No 26
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=58.12 E-value=8 Score=25.80 Aligned_cols=18 Identities=33% Similarity=0.552 Sum_probs=15.4
Q ss_pred HHHHHHHHHcCceeEEec
Q psy4375 9 RNIVKKLIAEGRLEMVTG 26 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~G 26 (62)
-..+.++|++|||++...
T Consensus 60 ~~~I~~~IreGRL~~~~~ 77 (137)
T TIGR03826 60 EKLILKFIREGRLQLKHF 77 (137)
T ss_pred HHHHHHHHHcCCeeccCC
Confidence 457899999999999864
No 27
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=57.03 E-value=13 Score=20.36 Aligned_cols=15 Identities=27% Similarity=0.485 Sum_probs=12.5
Q ss_pred HHHHHHcCceeEEec
Q psy4375 12 VKKLIAEGRLEMVTG 26 (62)
Q Consensus 12 vk~LV~~GqlEfv~G 26 (62)
+..||++|-+|+|+-
T Consensus 1 w~~ll~~G~vE~id~ 15 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDA 15 (48)
T ss_dssp HHHHHHTTSEEEEET
T ss_pred ChhHhhCCCEEEecc
Confidence 357999999999964
No 28
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2JRO_A.
Probab=56.42 E-value=9.6 Score=22.78 Aligned_cols=28 Identities=14% Similarity=0.363 Sum_probs=19.6
Q ss_pred cCceeEEecceeecccccccHHHHHHHH
Q psy4375 18 EGRLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 18 ~GqlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
-|.+||-+|=-++++.++.-..+++.++
T Consensus 29 ~G~feFd~Gkillp~~~~~~~~~~~~Ei 56 (64)
T PF06526_consen 29 IGAFEFDNGKILLPKKADKRHLSVMSEI 56 (64)
T ss_dssp TEEEEEETTEE---SS--HHHHHHHHHH
T ss_pred cccEEEcCCEEeCCccccHHHHHHHHHH
Confidence 4889999999999999999888877665
No 29
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=55.48 E-value=14 Score=22.17 Aligned_cols=20 Identities=35% Similarity=0.443 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHcCceeEEec
Q psy4375 7 TKRNIVKKLIAEGRLEMVTG 26 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~G 26 (62)
-.+..++++|++|.|+.+.|
T Consensus 47 ~l~~aLkk~v~~G~l~~~kG 66 (88)
T cd00073 47 LLKLALKKGVAKGKLVQVKG 66 (88)
T ss_pred HHHHHHHHHHHCCCeEeecC
Confidence 34678999999999999984
No 30
>PRK10170 hydrogenase 1 large subunit; Provisional
Probab=53.80 E-value=11 Score=30.50 Aligned_cols=39 Identities=21% Similarity=0.364 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHcCceeEEecce------ee----cccccccHHHHHHHH
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGW------VM----TDEATSHIFAMVDQL 45 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGW------vm----~DEA~~~y~~~Idq~ 45 (62)
+.++.|+.+|++|||-+...|| .. |..|..||...|+--
T Consensus 165 ~v~~r~~~~v~~g~lgif~~~ywg~~~y~l~~e~n~~~~~hYl~Al~~q 213 (597)
T PRK10170 165 DVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQ 213 (597)
T ss_pred HHHHHHHHHhhccccccccCcCCCCccccCChhHhHHHHHHHHHHHHHH
Confidence 5688999999999999998877 22 455677887776643
No 31
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=52.09 E-value=27 Score=17.89 Aligned_cols=22 Identities=32% Similarity=0.439 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHHcCceeEEecc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GG 27 (62)
+..++.+++|.+.|-++.+.|+
T Consensus 35 ~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 35 TTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred HHHHHHHHHHHHCCCEEEecCC
Confidence 5678889999999999887553
No 32
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=51.82 E-value=19 Score=17.78 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=18.6
Q ss_pred HHHHHHHHHcCceeEE--ecceeecccc
Q psy4375 9 RNIVKKLIAEGRLEMV--TGGWVMTDEA 34 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv--~GGWvm~DEA 34 (62)
+..+++|+++|.|..+ ++.|.-+-+.
T Consensus 15 ~~ti~~~~~~g~i~~~~~g~~~~~~~~~ 42 (49)
T TIGR01764 15 KDTVYRLIHEGELPAYRVGRHYRIPRED 42 (49)
T ss_pred HHHHHHHHHcCCCCeEEeCCeEEEeHHH
Confidence 5679999999998864 5556554443
No 33
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=51.68 E-value=34 Score=21.13 Aligned_cols=41 Identities=22% Similarity=0.388 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHcCceeEE---ecceeecccc-cccHHHHHHHHh
Q psy4375 6 PTKRNIVKKLIAEGRLEMV---TGGWVMTDEA-TSHIFAMVDQLI 46 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv---~GGWvm~DEA-~~~y~~~Idq~t 46 (62)
+..++.++.|.+.|=++-. +|||...... ...+.++++.+-
T Consensus 40 ~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l~ 84 (130)
T TIGR02944 40 PTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAVE 84 (130)
T ss_pred HHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHHc
Confidence 4567789999999999875 7999988777 556888888774
No 34
>COG3811 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.05 E-value=29 Score=21.86 Aligned_cols=37 Identities=19% Similarity=0.453 Sum_probs=27.5
Q ss_pred CChHHHHHHHHHHHcCceeEEe--------------cceeecccccccHHH
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVT--------------GGWVMTDEATSHIFA 40 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~--------------GGWvm~DEA~~~y~~ 40 (62)
++...+..++.|-+-|++||.- -||+-.|=-...|..
T Consensus 3 iSk~eQRtLH~LAqGGrIe~~rd~~grI~~v~C~tRdGw~l~dctlavF~k 53 (85)
T COG3811 3 ISKPEQRTLHALAQGGRIEIERDASGRITSVECYTRDGWLLPDCTLAVFRK 53 (85)
T ss_pred cchHHHHHHHHHhcCCeEEEEecCCCcEEEEEEecccccccCCccHHHHHH
Confidence 3445566899999999999974 288888866665554
No 35
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=50.83 E-value=16 Score=16.77 Aligned_cols=7 Identities=14% Similarity=0.150 Sum_probs=3.3
Q ss_pred hhccccc
Q psy4375 51 STFSVQS 57 (62)
Q Consensus 51 ~~Fgv~p 57 (62)
...||+|
T Consensus 28 ~~~gv~P 34 (34)
T PF13812_consen 28 KEQGVKP 34 (34)
T ss_pred HHhCCCC
Confidence 3445554
No 36
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=49.76 E-value=25 Score=23.66 Aligned_cols=31 Identities=19% Similarity=0.204 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHcCceeEEec-ceeecccccc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTG-GWVMTDEATS 36 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~G-GWvm~DEA~~ 36 (62)
++.++.+..|++.|-|+--++ .|+.++...+
T Consensus 56 ~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~ 87 (171)
T PF14394_consen 56 EEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLT 87 (171)
T ss_pred HHHHHHHHHHHHCCCeEECCCCcEEEecceee
Confidence 567889999999999999866 8999998775
No 37
>COG3497 Phage tail sheath protein FI [General function prediction only]
Probab=49.46 E-value=10 Score=29.58 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=37.9
Q ss_pred CChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh-hhhccccc
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET-FSTFSVQS 57 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh-~~~Fgv~p 57 (62)
..+..+..+++|++.|-| .||.|+-|+.. .--+||..|| +=++++-|
T Consensus 322 v~e~i~~~lr~l~r~Gal---~Gf~~~~d~~~----ns~~~l~~G~l~~~~~~tP 369 (394)
T COG3497 322 VTEGIRAFLRRLWRAGAL---IGFECWYDPEL----NSADQLLAGRLIIDYRFTP 369 (394)
T ss_pred HHHHHHHHHHHHHhccce---eceEEEeCccc----CcHhHHhCCcEEEEeeeec
Confidence 456678889999999986 68999999998 4578999999 66666664
No 38
>KOG2165|consensus
Probab=47.98 E-value=19 Score=30.30 Aligned_cols=22 Identities=23% Similarity=0.667 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHcCceeEEecce
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGW 28 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGW 28 (62)
+-+.-+.++|++|+|+|++|.+
T Consensus 740 eL~~fLq~kV~e~kL~f~~G~Y 761 (765)
T KOG2165|consen 740 ELQGFLQRKVREGKLEFIAGSY 761 (765)
T ss_pred HHHHHHHHHhhccceEEeccee
Confidence 4566688999999999999875
No 39
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=47.21 E-value=35 Score=17.79 Aligned_cols=24 Identities=38% Similarity=0.483 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHcCceeEEec-cee
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTG-GWV 29 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~G-GWv 29 (62)
+..++.+++|.+.|=++...| ||.
T Consensus 40 ~~v~~~l~~L~~~G~i~~~~~~~~~ 64 (66)
T cd07377 40 TTVREALRELEAEGLVERRPGRGTF 64 (66)
T ss_pred HHHHHHHHHHHHCCCEEecCCCeEE
Confidence 455778999999999887754 665
No 40
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=46.80 E-value=35 Score=21.20 Aligned_cols=25 Identities=28% Similarity=0.530 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHcCceeEEecceee
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVM 30 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm 30 (62)
+..|.....|...|+++|.-+|=+-
T Consensus 44 ~~vR~~A~~L~~~G~i~I~qkG~~V 68 (83)
T PF11625_consen 44 PPVRAAARRLARAGRIEITQKGKPV 68 (83)
T ss_dssp HHHHHHHHHHHHTTSEEEEETTEE-
T ss_pred HHHHHHHHHHHHCCcEEEEECCEec
Confidence 4678889999999999999888754
No 41
>PF13342 Toprim_Crpt: C-terminal repeat of topoisomerase
Probab=46.19 E-value=14 Score=21.47 Aligned_cols=19 Identities=26% Similarity=0.590 Sum_probs=15.8
Q ss_pred HHHHHHHHHHcCceeEEec
Q psy4375 8 KRNIVKKLIAEGRLEMVTG 26 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~G 26 (62)
..++++.|+++|+-..+.|
T Consensus 17 t~~~~~~Ll~~gkT~~ikG 35 (62)
T PF13342_consen 17 TDEEVKELLEKGKTGLIKG 35 (62)
T ss_pred CHHHHHHHHHcCCccCccC
Confidence 3568999999999997765
No 42
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=44.94 E-value=23 Score=23.14 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=17.5
Q ss_pred CcCChHHHHHHHHHHHcCcee
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLE 22 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlE 22 (62)
+..+.++=+.+|+|+++|.||
T Consensus 85 EGLs~E~IE~Lk~Lv~eGKi~ 105 (110)
T PF06819_consen 85 EGLSKEDIEKLKKLVEEGKIE 105 (110)
T ss_pred cCCCHHHHHHHHHHHHcCCCc
Confidence 456778888999999999986
No 43
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=43.52 E-value=49 Score=24.79 Aligned_cols=41 Identities=24% Similarity=0.182 Sum_probs=36.7
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
...+..|++.|-|+.-++.+..+++..-...+++.++..++
T Consensus 379 ~~~l~~l~~~gll~~~~~~l~lT~~G~~~~d~i~~~~~~~~ 419 (430)
T PRK08208 379 FPELELLIDRGWLEQNGGRLRLTEEGLALSDAIGPVFISPE 419 (430)
T ss_pred HHHHHHHHHCCCEEEECCEEEECcchhhHHHHHHHHHcCHH
Confidence 45788999999999989999999999999999999997665
No 44
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=43.29 E-value=42 Score=16.63 Aligned_cols=25 Identities=40% Similarity=0.416 Sum_probs=19.9
Q ss_pred ChHHHHHHHHHHHcCceeEEeccee
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWV 29 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWv 29 (62)
....+..++.|.+.|-++...||-+
T Consensus 28 ~~tv~~~l~~L~~~g~i~~~~~~~~ 52 (53)
T smart00420 28 EMTIRRDLNKLEEQGLLTRVHGGAV 52 (53)
T ss_pred HHHHHHHHHHHHHCCCEEEeecCcc
Confidence 3456778999999999998887754
No 45
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=42.71 E-value=61 Score=19.72 Aligned_cols=40 Identities=20% Similarity=0.317 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHcCceeEE---ecceeeccccccc-HHHHHHHH
Q psy4375 6 PTKRNIVKKLIAEGRLEMV---TGGWVMTDEATSH-IFAMVDQL 45 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv---~GGWvm~DEA~~~-y~~~Idq~ 45 (62)
...++.++.|++.|=++.. +|||.....+... ..++++.+
T Consensus 40 ~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~itl~~I~~~~ 83 (132)
T TIGR00738 40 SYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEITVGDVVRAV 83 (132)
T ss_pred HHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHCCHHHHHHHH
Confidence 4567889999999998875 4699997776644 66777765
No 46
>COG4707 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.05 E-value=15 Score=24.05 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=17.6
Q ss_pred cCceeEEecceeecccccc-----cHHHHHH
Q psy4375 18 EGRLEMVTGGWVMTDEATS-----HIFAMVD 43 (62)
Q Consensus 18 ~GqlEfv~GGWvm~DEA~~-----~y~~~Id 43 (62)
...|.+=|||||--.|-.- ++.+|.+
T Consensus 61 ~k~L~iengG~VyYP~~kg~rW~F~ak~M~e 91 (107)
T COG4707 61 KKMLSIENGGWVYYPEKKGERWSFIAKEMME 91 (107)
T ss_pred hhheeeecCcEEEccccCCceeeEeHHHHHH
Confidence 4678889999998665433 4555544
No 47
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=40.25 E-value=69 Score=23.73 Aligned_cols=39 Identities=10% Similarity=-0.020 Sum_probs=32.1
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
....+++|++.|-++.-++.|..+++..-...++..++.
T Consensus 355 ~~~~l~~l~~~gll~~~~~~~~LT~~G~~~~d~i~~~~~ 393 (394)
T PRK08898 355 IEPQLAAAEQRGLLERDHTRIRPTPLGQRFLNDLQELFL 393 (394)
T ss_pred HHHHHHHHHHCCCEEEECCEEEEChhHhHHHHHHHHHHh
Confidence 345788999999999878889999999888888877654
No 48
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=40.11 E-value=7.7 Score=21.07 Aligned_cols=12 Identities=42% Similarity=0.850 Sum_probs=10.3
Q ss_pred cceeeccccccc
Q psy4375 26 GGWVMTDEATSH 37 (62)
Q Consensus 26 GGWvm~DEA~~~ 37 (62)
=||.|.+|-|+.
T Consensus 11 ~G~~ML~~~Cp~ 22 (41)
T PF06677_consen 11 QGWTMLDEHCPD 22 (41)
T ss_pred HhHhHhcCccCC
Confidence 499999999974
No 49
>PF13338 DUF4095: Domain of unknown function (DUF4095)
Probab=39.36 E-value=42 Score=19.75 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=19.9
Q ss_pred HHHHHHHHHcCceeEEecceeeccccc
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEAT 35 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~ 35 (62)
+..+++|+++|.|+-+.-|+=...+.-
T Consensus 4 r~~l~~~~~~G~l~rl~rGvY~~~~~~ 30 (124)
T PF13338_consen 4 RRALRRLVRRGELIRLRRGVYASPEYP 30 (124)
T ss_pred HHHHHHHHHCCCEEEeeCCEEEcCCCC
Confidence 578999999999999865554444333
No 50
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=38.97 E-value=69 Score=23.28 Aligned_cols=39 Identities=13% Similarity=0.097 Sum_probs=33.6
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
-+..+..|++.|-+++-++.+..+++..-.+.+++..+.
T Consensus 336 ~~~~~~~l~~~gl~~~~~~~~~lt~~G~~~~~~i~~~~~ 374 (377)
T PRK08599 336 FGETIQELQEQGLLEEDDDHVRLTKKGKFLGNEVFEAFL 374 (377)
T ss_pred HHHHHHHHHHCCCEEEECCEEEECccHhHHHHHHHHHHh
Confidence 355788999999999988999999999998888887764
No 51
>cd00481 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=38.37 E-value=16 Score=24.89 Aligned_cols=21 Identities=29% Similarity=0.483 Sum_probs=17.5
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.|++||++|-+..
T Consensus 29 I~~A~tR~dIR~LIkdG~I~~ 49 (145)
T cd00481 29 IANANTREDIRKLIKDGLIIK 49 (145)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 456788999999999998754
No 52
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=38.29 E-value=25 Score=25.47 Aligned_cols=32 Identities=22% Similarity=0.468 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHH
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
+-...+.|||.++| ||||+ |-+..|..++.++
T Consensus 52 d~~~l~~KlV~~~R-----GGyCf--E~N~Lf~~~L~~L 83 (281)
T PRK15047 52 DDQSLEEKLVIARR-----GGYCF--EQNGLFERVLREL 83 (281)
T ss_pred CHHHHHHHHhcCCC-----CEEcH--hHHHHHHHHHHHc
Confidence 34567899999885 99998 6666677777665
No 53
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=38.21 E-value=47 Score=24.41 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=28.0
Q ss_pred HHHHHHHH-HHcCceeEE---ecceeecccccccHHHHHHHHh
Q psy4375 8 KRNIVKKL-IAEGRLEMV---TGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 8 ~k~~vk~L-V~~GqlEfv---~GGWvm~DEA~~~y~~~Idq~t 46 (62)
.++.+..+ --.||+|++ +|..+.+|..+++..+++.-+.
T Consensus 267 i~~~l~~~~~~~~R~e~v~~~~g~~~i~Ds~~t~~~s~~~al~ 309 (418)
T PRK00683 267 FLEAVATFEKPPHRMEYLGEKDGVHYINDSKATTVSAVEKALL 309 (418)
T ss_pred HHHHHHhCCCCCCceEEEeecCCeEEEEcCCCCCHHHHHHHHH
Confidence 34444443 245999998 4667889988899999887764
No 54
>PF13289 SIR2_2: SIR2-like domain
Probab=37.90 E-value=89 Score=18.65 Aligned_cols=37 Identities=19% Similarity=0.403 Sum_probs=26.9
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
.+..++.++.+..+.-+=|| |+-+.|+ +...++.++.
T Consensus 73 ~~~~~~~l~~~l~~~~~lfi--Gys~~D~---~i~~~l~~~~ 109 (143)
T PF13289_consen 73 NPWFPNFLRSLLRSKTLLFI--GYSFNDP---DIRQLLRSAL 109 (143)
T ss_pred HHHHHHHHHHHHcCCCEEEE--EECCCCH---HHHHHHHHHH
Confidence 35567788899989999999 8889998 4444554443
No 55
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=37.50 E-value=17 Score=24.87 Aligned_cols=21 Identities=24% Similarity=0.498 Sum_probs=17.4
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.|++||++|-+..
T Consensus 32 I~~A~tR~dIR~LI~~G~I~~ 52 (150)
T PRK08570 32 VAEAITREDIRELIKEGVIKA 52 (150)
T ss_pred HHHHhhHHHHHHHHHCCCeee
Confidence 456788999999999998754
No 56
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=37.49 E-value=42 Score=17.06 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHcCceeEEeccee
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWV 29 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWv 29 (62)
..+..++++++.|++. |||--+
T Consensus 14 ~sr~~~~~~i~~g~V~-vn~~~~ 35 (70)
T cd00165 14 PSRSEARQLIKHGHVL-VNGKVV 35 (70)
T ss_pred cCHHHHHHHHHcCCEE-ECCEEc
Confidence 3578899999999876 677655
No 57
>TIGR03212 uraD_N-term-dom putative urate catabolism protein. This model represents a protein that is predominantly found just upstream of the UraD protein (OHCU decarboxylase) and in a number of instances as a N-terminal fusion with it. UraD itself catalyzes the last step in the catabolism of urate to allantoate. The function of this protein is presently unknown. It shows homology with the pfam01522 polysaccharide deacetylase domain family.
Probab=37.36 E-value=80 Score=22.95 Aligned_cols=50 Identities=12% Similarity=0.085 Sum_probs=37.0
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhcccccC
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQSS 58 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~ 58 (62)
.-+.++.+++.| -||.+=||.-.+-..-......++|.... .+..|.+|+
T Consensus 105 ~P~~v~~i~~~G-HEIg~Hg~~H~~~~~ls~~~e~~~i~~s~~~i~~~tG~~P~ 157 (297)
T TIGR03212 105 NPEAVAAMKEAG-WEIASHGLRWIDYQDMDEAQEREHIAEAIRLHTEVTGERPL 157 (297)
T ss_pred CHHHHHHHHHcC-CEEeeccccCcccccCCHHHHHHHHHHHHHHHHHHhCCCCc
Confidence 346789999999 99999999876555555666777777777 444677775
No 58
>smart00363 S4 S4 RNA-binding domain.
Probab=37.16 E-value=44 Score=16.48 Aligned_cols=22 Identities=41% Similarity=0.655 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHcCceeEEeccee
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWV 29 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWv 29 (62)
..+..++++++.|++. |||--+
T Consensus 14 ~s~~~~~~~i~~g~i~-vng~~~ 35 (60)
T smart00363 14 PSRSQARKLIEQGRVK-VNGKKV 35 (60)
T ss_pred cCHHHHHHHHHcCCEE-ECCEEe
Confidence 3578899999999876 677655
No 59
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=36.72 E-value=38 Score=21.54 Aligned_cols=35 Identities=11% Similarity=0.243 Sum_probs=20.3
Q ss_pred CceeEEecceeecccccccHHHHHHHHhhhhhhhcccccC
Q psy4375 19 GRLEMVTGGWVMTDEATSHIFAMVDQLIEETFSTFSVQSS 58 (62)
Q Consensus 19 GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh~~~Fgv~p~ 58 (62)
-++.+.+|-|+ +......+.-+-..+. ..||+||+
T Consensus 69 ~hF~y~~g~W~-~r~g~el~~~L~~e~~----~~~~~~~~ 103 (103)
T PRK01379 69 YHFFYEQGKWK-NRAGLELMAILTEELN----IKFDTRPT 103 (103)
T ss_pred cceecCCCeeE-ECCCchHHHHHHHHHH----HHhCcCcC
Confidence 36777899999 5554443333333332 23777774
No 60
>PF14701 hDGE_amylase: glucanotransferase domain of human glycogen debranching enzyme
Probab=36.60 E-value=19 Score=28.05 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=16.7
Q ss_pred cCceeEEecceeecccccccH
Q psy4375 18 EGRLEMVTGGWVMTDEATSHI 38 (62)
Q Consensus 18 ~GqlEfv~GGWvm~DEA~~~y 38 (62)
.+.+-.+|-||||++.+..+|
T Consensus 324 ~~~~~lAnNGWV~~~dpl~dF 344 (423)
T PF14701_consen 324 GKKLALANNGWVWNADPLVDF 344 (423)
T ss_pred CceEEEEeCCceeCCchhhhh
Confidence 346777899999999887655
No 61
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=36.52 E-value=74 Score=23.14 Aligned_cols=37 Identities=27% Similarity=0.291 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHH
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
+..++.|++.|-+.+-++.|..+++..-...+++..+
T Consensus 337 ~~~l~~l~~~gl~~~~~~~~~lT~~G~~~~~~i~~~~ 373 (375)
T PRK05628 337 RARAARVVADGLLAAEGGRLVLTLRGRLLADAVVRDL 373 (375)
T ss_pred HHHHHHHHHCCCEEEECCEEEEChhhhHHHHHHHHHH
Confidence 4678899999999988888999999888888877655
No 62
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=36.51 E-value=46 Score=17.09 Aligned_cols=19 Identities=37% Similarity=0.728 Sum_probs=14.8
Q ss_pred HHHHHHHHHHcCceeEEecc
Q psy4375 8 KRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GG 27 (62)
.|..+++||++|++. |||-
T Consensus 15 sr~~a~~~I~~g~V~-VNg~ 33 (48)
T PF01479_consen 15 SRSEARRLIKQGRVK-VNGK 33 (48)
T ss_dssp SHHHHHHHHHTTTEE-ETTE
T ss_pred CHHHHHHhcCCCEEE-ECCE
Confidence 478899999999985 4543
No 63
>KOG0402|consensus
Probab=35.82 E-value=36 Score=21.76 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=22.3
Q ss_pred eEEecceeecccccccHHHHHHHHhh
Q psy4375 22 EMVTGGWVMTDEATSHIFAMVDQLIE 47 (62)
Q Consensus 22 Efv~GGWvm~DEA~~~y~~~Idq~t~ 47 (62)
-+.+|.|+++--|.....++|.++-+
T Consensus 63 v~agga~~~~t~aa~t~rs~irrlre 88 (92)
T KOG0402|consen 63 VVAGGAYTVTTAAAATVRSTIRRLRE 88 (92)
T ss_pred eeccceEEeccchhHHHHHHHHHHHH
Confidence 35689999999999999999998754
No 64
>cd04415 NDPk7A Nucleoside diphosphate kinase 7 domain A (NDPk7A): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
Probab=35.79 E-value=70 Score=20.56 Aligned_cols=38 Identities=5% Similarity=0.078 Sum_probs=27.2
Q ss_pred HHHHHHHcCceeEEecceeeccccc-----------ccHHHHHHHHhhhh
Q psy4375 11 IVKKLIAEGRLEMVTGGWVMTDEAT-----------SHIFAMVDQLIEET 49 (62)
Q Consensus 11 ~vk~LV~~GqlEfv~GGWvm~DEA~-----------~~y~~~Idq~t~Gh 49 (62)
.+.++.++ -|.|+.--.+.-++.. +.|.++++.|+.|-
T Consensus 18 Il~~i~~~-Gf~I~~~k~~~lt~~~a~~~y~~~~gk~f~~~Lv~~m~sgp 66 (131)
T cd04415 18 IIQIIEDA-GFTITKAKMTKLSRKEAQDFYAEHQSKPFYNELVQFMTSGP 66 (131)
T ss_pred HHHHHHHC-CCEEEEeeeecCCHHHHHHHHHHhCCCCchHHHHHHHhcCC
Confidence 34444444 4999988887777643 57788999998874
No 65
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.54 E-value=82 Score=17.44 Aligned_cols=43 Identities=16% Similarity=0.213 Sum_probs=30.9
Q ss_pred ChHHHHHHHHHHHcCceeEEec-------ceeecccccccHHHHHHHHhh
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTG-------GWVMTDEATSHIFAMVDQLIE 47 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~G-------GWvm~DEA~~~y~~~Idq~t~ 47 (62)
.+.....+++|++.|-++..-. .+..++++...+..+...+..
T Consensus 38 ~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~~~ 87 (101)
T smart00347 38 PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEARHE 87 (101)
T ss_pred chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHHHH
Confidence 4566788999999999987644 466677777766666655543
No 66
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=35.30 E-value=45 Score=24.73 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=19.2
Q ss_pred ChHHHHHHHHHHHcCceeEEecc
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GG 27 (62)
.+..|++++.|-..|-+||++-|
T Consensus 227 k~KIRQqLQ~LRD~g~IeFl~rG 249 (254)
T PF06044_consen 227 KAKIRQQLQILRDKGIIEFLGRG 249 (254)
T ss_dssp HHHHHHHHHHHHHTTSEEE-STT
T ss_pred hHHHHHHHHHHhhCCceEEecCC
Confidence 46789999999999999999766
No 67
>cd01418 Ribosomal_L19e_A Ribosomal protein L19e, archaeal. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=34.87 E-value=20 Score=24.45 Aligned_cols=21 Identities=24% Similarity=0.493 Sum_probs=17.3
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.|++||++|-+..
T Consensus 29 I~~A~tR~dIR~LI~~G~I~~ 49 (145)
T cd01418 29 VAEAITRDDIRALIKEGVIKA 49 (145)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 456788999999999997754
No 68
>KOG2159|consensus
Probab=34.75 E-value=32 Score=27.03 Aligned_cols=44 Identities=27% Similarity=0.561 Sum_probs=30.1
Q ss_pred ChHHHHHHHHHHHcCceeE-Eecceee----------cccccccHHHHHHHHhhhh
Q psy4375 5 HPTKRNIVKKLIAEGRLEM-VTGGWVM----------TDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEf-v~GGWvm----------~DEA~~~y~~~Idq~t~Gh 49 (62)
++..+....++.+.| +|. +-||||= -|=|++.-...+-++..++
T Consensus 14 ~~~~~~v~~~~~~~~-~elRiaGGwVRD~LLg~~p~DiDiatta~~g~~~e~f~~~ 68 (416)
T KOG2159|consen 14 TDSTRLVLSKLKKKG-YELRLAGGWVRDLLLGREPKDIDIATTAMSGQMKEMFQSA 68 (416)
T ss_pred cHHHHHHHHHhhcCC-CeeEEecccHHHHHcCCCCcccceeeccccHHHHHHHHHH
Confidence 455666667777777 776 8999993 3556666555566776666
No 69
>PRK13687 hypothetical protein; Provisional
Probab=34.68 E-value=80 Score=19.95 Aligned_cols=37 Identities=22% Similarity=0.466 Sum_probs=26.3
Q ss_pred CChHHHHHHHHHHHcCceeEEe---c-----------ceeecccccccHHH
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVT---G-----------GWVMTDEATSHIFA 40 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~---G-----------GWvm~DEA~~~y~~ 40 (62)
.+...+..++-|-+-|++++.- | ||+.+|=....|..
T Consensus 3 ISk~EQRvLHvLAqGGrI~~~rd~~gri~~v~C~TReG~~l~dctl~vF~k 53 (85)
T PRK13687 3 ISRQEQRTLHVLAQGGRIEHERDDSGRITAVECYTREGWLLADCTLAVFKK 53 (85)
T ss_pred ccHHHHHHHHHHhcCCeEEEEECCCCcEEEEEEEccCCcccCCCCHHHHHH
Confidence 3455566788898889999874 3 88888866655543
No 70
>PF00530 SRCR: Scavenger receptor cysteine-rich domain; InterPro: IPR001190 The egg peptide speract receptor is a transmembrane glycoprotein []. Other members of this family include the macrophage scavenger receptor type I (a membrane glycoprotein implicated in the pathologic deposition of cholesterol in arterial walls during artherogenesis), an enteropeptidase and T-cell surface glycoprotein CD5 (may act as a receptor in regulating T-cell proliferation).; GO: 0005044 scavenger receptor activity, 0016020 membrane; PDB: 2XRC_D 2JP0_A 2JOP_A 2OYA_A 2OY3_A 1BY2_A 2OTT_Y 2JA4_A.
Probab=34.60 E-value=17 Score=20.79 Aligned_cols=14 Identities=43% Similarity=0.959 Sum_probs=10.8
Q ss_pred HcCceeE-E-ecceee
Q psy4375 17 AEGRLEM-V-TGGWVM 30 (62)
Q Consensus 17 ~~GqlEf-v-~GGWvm 30 (62)
.+|+||+ . +|.|--
T Consensus 7 ~~G~vev~~~~~~W~~ 22 (99)
T PF00530_consen 7 CEGRVEVCFYNGSWGT 22 (99)
T ss_dssp TEEEEEEEEETTEEEE
T ss_pred eeEEEEEEEECCEEEe
Confidence 3699999 6 888853
No 71
>PF09857 DUF2084: Uncharacterized protein conserved in bacteria (DUF2084); InterPro: IPR018654 This domain is found in various hypothetical bacterial proteins that have no known function.
Probab=34.60 E-value=91 Score=19.68 Aligned_cols=37 Identities=16% Similarity=0.424 Sum_probs=26.7
Q ss_pred CChHHHHHHHHHHHcCceeEEec--------------ceeecccccccHHH
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVTG--------------GWVMTDEATSHIFA 40 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~G--------------GWvm~DEA~~~y~~ 40 (62)
.+...+..++-|-+-|+++++-. ||+.+|=....|..
T Consensus 3 ISk~EQR~LHvLAqGG~I~~~rd~~gri~~v~C~TReG~~l~dctl~vF~k 53 (85)
T PF09857_consen 3 ISKQEQRVLHVLAQGGRIRHERDDSGRITAVECYTREGWLLSDCTLAVFRK 53 (85)
T ss_pred ccHHHHHHHHHHhcCCeEEEEECCCCCEEEEEEEccCCeeeCCCCHHHHHH
Confidence 34555667888998899988743 89888866665543
No 72
>PRK10467 hydrogenase 2 large subunit; Provisional
Probab=34.53 E-value=35 Score=27.44 Aligned_cols=42 Identities=21% Similarity=0.336 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHcCceeEEecceee----------cccccccHHHHHHHHhh
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVM----------TDEATSHIFAMVDQLIE 47 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm----------~DEA~~~y~~~Idq~t~ 47 (62)
.+.++.++.+++.|||-+...||== |..|..||...++--.+
T Consensus 149 ~~v~~~~~~~~~~g~l~~f~~~y~g~~~y~l~~e~n~~~~~hYl~Al~~~r~ 200 (567)
T PRK10467 149 TKVQNKIKDLVASGQLGIFANGYWGHPAMKLPPEVNLIAVAHYLQALECQRD 200 (567)
T ss_pred HHHHHHHHHHHhccccCcccCCCCCCccccCChhHhHHHHHHHHHHHHHHHH
Confidence 3578899999999999988877622 45677888877764433
No 73
>PRK02166 hypothetical protein; Reviewed
Probab=34.03 E-value=90 Score=21.51 Aligned_cols=51 Identities=10% Similarity=0.263 Sum_probs=41.5
Q ss_pred cCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh---hhhccccc
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET---FSTFSVQS 57 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p 57 (62)
..+++.|+.++.|.+..|+.+=-- -.+|....|..+|+-..-+- +.+|+ +|
T Consensus 121 ~~s~e~~E~l~Dl~~Iaql~~d~d---d~ee~E~al~Ei~EyvRvaall~~~e~~-~~ 174 (184)
T PRK02166 121 DLSGEAKEVLQDLAAISQVQDALE---ESEDGETDYMEVMEYLRVAPLLLFTEFA-KP 174 (184)
T ss_pred CCCHHHHHHHHHHHHHHccCCCCC---CCchHHHHHHHHHHHHHHHHHHHHHHhC-CC
Confidence 467899999999999999996321 35777778999999988888 99997 44
No 74
>PF14177 YkyB: YkyB-like protein
Probab=33.12 E-value=46 Score=22.72 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=17.1
Q ss_pred HHHHHHHHHHcCceeEEecc
Q psy4375 8 KRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GG 27 (62)
++..+.+||++|+.+.|+=-
T Consensus 29 Kk~aL~Kll~E~kA~kiGlH 48 (140)
T PF14177_consen 29 KKKALQKLLEEGKAKKIGLH 48 (140)
T ss_pred HHHHHHHHHHcCcceEEEEe
Confidence 57789999999999999644
No 75
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=33.05 E-value=1.1e+02 Score=19.19 Aligned_cols=38 Identities=18% Similarity=0.112 Sum_probs=29.3
Q ss_pred CChHHHHHHHHHHHcCceeEE-ecceeecccccccHHHH
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMV-TGGWVMTDEATSHIFAM 41 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv-~GGWvm~DEA~~~y~~~ 41 (62)
..++....+++|.+.|-++.. .+|+..++.+...+..+
T Consensus 35 s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 35 HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 356777889999999999864 58899998886655443
No 76
>PF14595 Thioredoxin_9: Thioredoxin; PDB: 1Z6N_A.
Probab=32.73 E-value=23 Score=22.67 Aligned_cols=26 Identities=12% Similarity=0.188 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHHcCceeEEecceee
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVM 30 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm 30 (62)
+++..+.++.+-+..++-+++|.||=
T Consensus 29 ~~~~~~~l~~~~~~~~ilvi~e~WCg 54 (129)
T PF14595_consen 29 SEEQIEKLKSIQKPYNILVITETWCG 54 (129)
T ss_dssp -HHHHHHHHT--S-EEEEEE--TT-H
T ss_pred CHHHHHHHHhcCCCcEEEEEECCCch
Confidence 55666778888888889999999993
No 77
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=32.67 E-value=52 Score=22.05 Aligned_cols=26 Identities=27% Similarity=0.414 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHcCceeEE-ecceeecc
Q psy4375 7 TKRNIVKKLIAEGRLEMV-TGGWVMTD 32 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv-~GGWvm~D 32 (62)
-.|+.+.+|.++|-+++. +.||+..+
T Consensus 55 PVReAL~rL~~eGlv~~~p~rG~~V~~ 81 (230)
T COG1802 55 PVREALRRLEAEGLVEIEPNRGAFVAP 81 (230)
T ss_pred cHHHHHHHHHHCCCeEecCCCCCeeCC
Confidence 468999999999999998 88998765
No 78
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=32.45 E-value=1.1e+02 Score=22.10 Aligned_cols=39 Identities=13% Similarity=0.219 Sum_probs=32.2
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
-+..+..|++.|-+++-++-+..+++......+++..+.
T Consensus 335 ~~~~l~~l~~~gl~~~~~~~~~lT~~G~~~~~~i~~~~~ 373 (374)
T PRK05799 335 YGEVINKYIKLGLLIEKEGRIYLSERGIEVSNSIMSDFL 373 (374)
T ss_pred HHHHHHHHHHCCCEEEECCEEEEChhHHHHHHHHHHHHh
Confidence 345688999999999888889999999988888877653
No 79
>PF12910 RelB_N: Antitoxin of toxin-antitoxin stability system N-terminal; PDB: 3K6Q_C.
Probab=32.10 E-value=32 Score=18.46 Aligned_cols=18 Identities=17% Similarity=0.464 Sum_probs=15.3
Q ss_pred ccccccHHHHHHHHhhhh
Q psy4375 32 DEATSHIFAMVDQLIEET 49 (62)
Q Consensus 32 DEA~~~y~~~Idq~t~Gh 49 (62)
-||-+++.++||+-..||
T Consensus 7 ~eAR~~ls~l~d~v~~~~ 24 (46)
T PF12910_consen 7 SEARNNLSKLIDRVVNGE 24 (46)
T ss_dssp HHHHHTHHHHHHHHHHT-
T ss_pred HHHHHhHHHHHHHHHcCC
Confidence 478899999999999998
No 80
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=32.00 E-value=24 Score=24.34 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=17.0
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.++.||++|-+-.
T Consensus 32 i~~A~TR~dIr~LIk~g~I~~ 52 (150)
T COG2147 32 IASAITREDIRALIKDGVIKA 52 (150)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 356788999999999997743
No 81
>cd01417 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=31.87 E-value=24 Score=24.57 Aligned_cols=21 Identities=29% Similarity=0.494 Sum_probs=17.4
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.|++||++|-+..
T Consensus 29 I~~A~tR~dIR~LIkdG~I~~ 49 (164)
T cd01417 29 ISNANSRQSIRKLIKDGLIIK 49 (164)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 456788999999999998754
No 82
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=31.72 E-value=60 Score=20.94 Aligned_cols=28 Identities=21% Similarity=0.391 Sum_probs=22.3
Q ss_pred HHHHHHHHHHc-CceeEEecceeeccccc
Q psy4375 8 KRNIVKKLIAE-GRLEMVTGGWVMTDEAT 35 (62)
Q Consensus 8 ~k~~vk~LV~~-GqlEfv~GGWvm~DEA~ 35 (62)
+.+.|.+|+++ ..|-.++|=||.-|...
T Consensus 85 s~eEf~~L~~~~~~LV~~rg~WV~ld~~~ 113 (141)
T PF12419_consen 85 SEEEFEQLVEQKRPLVRFRGRWVELDPEE 113 (141)
T ss_pred CHHHHHHHHHcCCCeEEECCEEEEECHHH
Confidence 45678899988 56888999999998653
No 83
>PRK05660 HemN family oxidoreductase; Provisional
Probab=31.58 E-value=1.2e+02 Score=22.32 Aligned_cols=39 Identities=15% Similarity=0.378 Sum_probs=32.1
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
....++.|++.|-+++-++-+..+++..-...++...+.
T Consensus 338 ~~~~l~~l~~~gl~~~~~~~~~lt~~G~~~~d~i~~~~~ 376 (378)
T PRK05660 338 IRPQLDEALAQGYLTETADHWQITEHGKLFLNDLLELFL 376 (378)
T ss_pred HHHHHHHHHHCCCEEEeCCEEEECcchhHHHHHHHHHHh
Confidence 456789999999999877778899999888888877664
No 84
>COG1347 NqrD Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD [Energy production and conversion]
Probab=31.56 E-value=30 Score=24.88 Aligned_cols=40 Identities=23% Similarity=0.523 Sum_probs=28.8
Q ss_pred HHHHHHHHcCce-------eEEecceeecccc---cccHHHHHHHHhhhh
Q psy4375 10 NIVKKLIAEGRL-------EMVTGGWVMTDEA---TSHIFAMVDQLIEET 49 (62)
Q Consensus 10 ~~vk~LV~~Gql-------Efv~GGWvm~DEA---~~~y~~~Idq~t~Gh 49 (62)
.-+|+|+-.|.| ++.+|||-++|-. .|.-+=+|-=|++|.
T Consensus 149 ~~iREL~G~Gkl~G~~v~~~i~~ggwy~pnGL~lLaPSAFFliG~~IW~~ 198 (208)
T COG1347 149 GFVRELFGSGKLFGFTVFPTIQDGGWYQPNGLFLLAPSAFFLIGFMIWGL 198 (208)
T ss_pred HHHHHHhccCceeeEEeeeeeccCcccCCCceEEeCchHHHHHHHHHHHH
Confidence 357899999987 6789999999863 344445566666654
No 85
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=30.93 E-value=18 Score=22.08 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=10.0
Q ss_pred eeEEecceeecccc
Q psy4375 21 LEMVTGGWVMTDEA 34 (62)
Q Consensus 21 lEfv~GGWvm~DEA 34 (62)
+--|+|||.--+|-
T Consensus 49 MVRVGGGW~tL~~~ 62 (73)
T PF02187_consen 49 MVRVGGGWDTLEEY 62 (73)
T ss_dssp EEEETTEEEEHHHH
T ss_pred EEEeCCcHHHHHHH
Confidence 45589999876653
No 86
>PTZ00097 60S ribosomal protein L19; Provisional
Probab=30.84 E-value=25 Score=24.69 Aligned_cols=21 Identities=29% Similarity=0.381 Sum_probs=17.4
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
.++..+|+.|++||++|-+..
T Consensus 30 I~~A~tR~dIR~LIkdG~I~~ 50 (175)
T PTZ00097 30 ISLANSRFSIRKLIKDGLIIR 50 (175)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 456788999999999998754
No 87
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=30.45 E-value=16 Score=23.22 Aligned_cols=23 Identities=13% Similarity=0.362 Sum_probs=18.3
Q ss_pred cceeecccccccHHHHHHHHhhhh
Q psy4375 26 GGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 26 GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
|+|+.++.....|.+++.-+ .|.
T Consensus 12 G~W~~~~~~~~~~s~i~a~f-~~~ 34 (125)
T PF06530_consen 12 GAWVRSGRSGVDYSPIAAGF-KGV 34 (125)
T ss_pred hHHHhCCCCCCCcccHHHHH-hcC
Confidence 89999988888888887776 443
No 88
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=29.36 E-value=1.2e+02 Score=24.38 Aligned_cols=43 Identities=12% Similarity=0.212 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
..++.++.|+++|.+--++.+.+++.+|...+.+.+.++..-+
T Consensus 522 ~~~~~l~~l~~~g~lv~l~~~~~~~~~~~~~~~~~~~~~~~~~ 564 (614)
T PRK10512 522 AMRLTLRQAAQQGIITAIVKDRYYRNDRIVQFANMIRELDQEC 564 (614)
T ss_pred HHHHHHHHHHHCCCEEEecCCEEECHHHHHHHHHHHHHHHhhC
Confidence 3478899999999999999999999999998888888876543
No 89
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=29.30 E-value=86 Score=18.11 Aligned_cols=21 Identities=29% Similarity=0.297 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHcCceeEEec
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTG 26 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~G 26 (62)
-+.|..+..|.++|+++.+..
T Consensus 30 ~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 30 YQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp HHHHHHHHHHHHCTSEEEES-
T ss_pred HHHHHHHHHHHHCCCEEEecC
Confidence 356788999999999998764
No 90
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=28.89 E-value=44 Score=17.46 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=13.3
Q ss_pred hHHHHHHHHHHHcCcee
Q psy4375 6 PTKRNIVKKLIAEGRLE 22 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlE 22 (62)
|-..+.+++|+++|+|.
T Consensus 13 P~s~~el~~l~~~g~i~ 29 (45)
T PF14237_consen 13 PFSLEELRQLISSGEID 29 (45)
T ss_pred CcCHHHHHHHHHcCCCC
Confidence 33457899999999875
No 91
>PF12686 DUF3800: Protein of unknown function (DUF3800); InterPro: IPR024524 This family of proteins is functionally uncharacterised. Some family members possess a DE motif at their N terminus and a QXXD motif at their C terminus that may be functionally important.
Probab=28.58 E-value=55 Score=20.69 Aligned_cols=31 Identities=23% Similarity=0.306 Sum_probs=26.1
Q ss_pred CceeEEecceeecccccccHHHHHHHHhhhh
Q psy4375 19 GRLEMVTGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 19 GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
++=-||-||++.+++........+..+.+-|
T Consensus 18 ~~~~fvl~gv~i~~~~~~~~~~~~~~~~~~~ 48 (235)
T PF12686_consen 18 NSPYFVLGGVIIEDEDWKKIINEIRSLKKKY 48 (235)
T ss_pred CCCEEEEEEEEEcHHHHHHHHHHHHHHHHHh
Confidence 5667999999999999888888888887666
No 92
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=28.35 E-value=77 Score=22.11 Aligned_cols=25 Identities=32% Similarity=0.377 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHcCceeEEecceee
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVM 30 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm 30 (62)
.+.|..++.|-+.|.++.+-||=+.
T Consensus 34 ~TirRdL~~Le~~g~i~r~~gga~~ 58 (251)
T PRK13509 34 ATARRDINKLDESGKLKKVRNGAEA 58 (251)
T ss_pred HHHHHHHHHHHHCCCEEEecCCccc
Confidence 5678889999999999999999764
No 93
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=28.27 E-value=64 Score=18.14 Aligned_cols=18 Identities=17% Similarity=0.285 Sum_probs=14.2
Q ss_pred CCcCChHHHHHHHHHHHc
Q psy4375 1 MEIVHPTKRNIVKKLIAE 18 (62)
Q Consensus 1 ~d~~~~~~k~~vk~LV~~ 18 (62)
|++.+++.++.||++|++
T Consensus 39 ~~~~~~el~~~ir~~I~~ 56 (57)
T PF06348_consen 39 MTEIPEELREKIRSAIKD 56 (57)
T ss_pred CccCCHHHHHHHHHHhhc
Confidence 456778899999998875
No 94
>PRK12569 hypothetical protein; Provisional
Probab=28.13 E-value=74 Score=23.24 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=23.0
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeec
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMT 31 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~ 31 (62)
.++..+++.+|+++|++.-++|.|+--
T Consensus 191 ~~~~~~~~~~m~~~g~v~t~~G~~i~~ 217 (245)
T PRK12569 191 PQQVAAKVLRACREGKVRTVDGKDIDI 217 (245)
T ss_pred HHHHHHHHHHHHHcCCEEecCCCEEEe
Confidence 355678899999999999999999754
No 95
>PTZ00436 60S ribosomal protein L19-like protein; Provisional
Probab=27.90 E-value=36 Score=26.35 Aligned_cols=21 Identities=33% Similarity=0.496 Sum_probs=17.3
Q ss_pred cCChHHHHHHHHHHHcCceeE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf 23 (62)
..+..+|+.|++||++|-|..
T Consensus 32 Ia~AiTReDIRkLIkdGlIik 52 (357)
T PTZ00436 32 ISNANSRKSVRKLIKDGLIIR 52 (357)
T ss_pred HHHhhhHHHHHHHHHCCCeee
Confidence 345678999999999998765
No 96
>PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F ....
Probab=27.85 E-value=1e+02 Score=19.23 Aligned_cols=28 Identities=14% Similarity=0.215 Sum_probs=22.3
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeecc
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMTD 32 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~D 32 (62)
.+..++.++.++++..+-+++||=-..+
T Consensus 43 ~~~i~~~l~~~~~~~D~VittGG~g~~~ 70 (144)
T PF00994_consen 43 PDAIKEALRRALDRADLVITTGGTGPGP 70 (144)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSSSSST
T ss_pred HHHHHHHHHhhhccCCEEEEcCCcCccc
Confidence 3567788899999999999999865543
No 97
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=27.60 E-value=1e+02 Score=21.83 Aligned_cols=27 Identities=30% Similarity=0.245 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHcCceeEEecceeecc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVMTD 32 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm~D 32 (62)
.+.|..+..|-+.|.+..+-||++..+
T Consensus 46 ~TIRRDL~~Le~~G~l~r~~GGa~~~~ 72 (269)
T PRK09802 46 VTIRNDLAFLEKQGIAVRAYGGALICD 72 (269)
T ss_pred HHHHHHHHHHHhCCCeEEEeCCEEecC
Confidence 567889999999999999999998654
No 98
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=27.53 E-value=1.1e+02 Score=16.60 Aligned_cols=27 Identities=33% Similarity=0.498 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHcCceeEEecceeeccc
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVMTDE 33 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm~DE 33 (62)
..-+.+++|.++|-++.-.|.|+-.|-
T Consensus 44 tv~r~l~~l~~~g~I~~~~~~i~I~d~ 70 (76)
T PF13545_consen 44 TVSRILKRLKDEGIIEVKRGKIIILDP 70 (76)
T ss_dssp HHHHHHHHHHHTTSEEEETTEEEESSH
T ss_pred HHHHHHHHHHHCCCEEEcCCEEEECCH
Confidence 345679999999999988888888774
No 99
>PLN02578 hydrolase
Probab=27.40 E-value=1.1e+02 Score=21.73 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhh
Q psy4375 7 TKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~ 47 (62)
..-..+++++.+.++..+++|=+.+.|.-.-+.+.|.+...
T Consensus 313 ~~~~~l~~~~p~a~l~~i~~GH~~~~e~p~~~~~~I~~fl~ 353 (354)
T PLN02578 313 AKAEKIKAFYPDTTLVNLQAGHCPHDEVPEQVNKALLEWLS 353 (354)
T ss_pred HHHHHHHHhCCCCEEEEeCCCCCccccCHHHHHHHHHHHHh
Confidence 34445788888999998999999999988888888887764
No 100
>PF01280 Ribosomal_L19e: Ribosomal protein L19e; InterPro: IPR000196 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 structural domain of the ribosomal protein L19 from eukaryotes, as well as L19e from archaea []. L19/L19e is absent in bacteria. L19/L19e is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species []. L19/L19e is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_T 3O58_S 3O5H_S 3IZS_T 2WWA_J 1S1I_P 2WW9_J 2ZKR_7 4A1A_O 4A1C_O ....
Probab=27.28 E-value=23 Score=24.18 Aligned_cols=20 Identities=25% Similarity=0.423 Sum_probs=15.3
Q ss_pred CChHHHHHHHHHHHcCceeE
Q psy4375 4 VHPTKRNIVKKLIAEGRLEM 23 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEf 23 (62)
+++.+|+.+++||++|-+..
T Consensus 32 ~~A~tR~~IR~LIk~G~I~~ 51 (148)
T PF01280_consen 32 ANAITREDIRKLIKDGLIIK 51 (148)
T ss_dssp HH--SHHHHHHHHHTTSEEE
T ss_pred HhhhhHHHHHHHHHCCCeEe
Confidence 45678999999999998864
No 101
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=27.21 E-value=1.1e+02 Score=17.89 Aligned_cols=29 Identities=24% Similarity=0.454 Sum_probs=22.3
Q ss_pred CChHHHHHHHHHHHcCceeEEecc----eeecc
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVTGG----WVMTD 32 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~GG----Wvm~D 32 (62)
.....|..+.+|+++|-||-..-| |-.+|
T Consensus 36 ~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~ 68 (70)
T PF07848_consen 36 SESAVRTALSRLVRRGWLESERRGRRSYYRLTE 68 (70)
T ss_dssp -HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-H
T ss_pred ChHHHHHHHHHHHHcCceeeeecCccceEeeCC
Confidence 456789999999999999988766 65554
No 102
>COG1449 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=26.93 E-value=1.3e+02 Score=24.44 Aligned_cols=50 Identities=16% Similarity=0.300 Sum_probs=34.9
Q ss_pred HHHHHHHHHHcCceeEEecce------eecccccccHHHHHHHHhhhh---hhhcccccCC
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGW------VMTDEATSHIFAMVDQLIEET---FSTFSVQSSK 59 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGW------vm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~~ 59 (62)
.=..+++|.++|+.|++.==+ .-+|.- .|.++++|+..+- .+.||+-|+.
T Consensus 181 vl~~~r~l~e~g~~e~~~~pyyHsl~pl~~d~g--w~~d~~~qv~~~~~~~~elfG~~p~~ 239 (615)
T COG1449 181 VLEAFRELAESGKVELTASPYYHSLIPLLADDG--WYEDFKEQVMMSRELYKELFGVWPSG 239 (615)
T ss_pred hHHHHHHHHhcCceEEEecccccccchhcccCC--chHHHHHHHHHHHHHHHHHhCCCCcc
Confidence 445789999999999984321 111111 4557778887777 8999999875
No 103
>cd03142 GATase1_ThuA Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). This group includes proteins similar to SmThuA which plays a role in a major pathway for trehalose catabolism. SmThuA is induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. Proteins in this group lack the catalytic triad of typical GATase1 domains: a His replaces the reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. S. meliloti Rm1021 thuA mutants are impaired in competitive colonization of Medicago sativa roots but are more competitive than the wild-type Rml021 in infecting alfalfa roots and forming nitrogen-fixing nodules.
Probab=26.74 E-value=67 Score=22.55 Aligned_cols=19 Identities=16% Similarity=0.212 Sum_probs=17.2
Q ss_pred CCcCChHHHHHHHHHHHcC
Q psy4375 1 MEIVHPTKRNIVKKLIAEG 19 (62)
Q Consensus 1 ~d~~~~~~k~~vk~LV~~G 19 (62)
|+..++++++.|.+.|++|
T Consensus 70 ~~~l~~eq~~~l~~~V~~G 88 (215)
T cd03142 70 HDEVKDEIVERVHRRVLDG 88 (215)
T ss_pred cCcCCHHHHHHHHHHHHcC
Confidence 5778999999999999997
No 104
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=26.55 E-value=1.3e+02 Score=18.84 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHcCceeEE---ecceeeccccc-ccHHHHHHHHhhhh
Q psy4375 7 TKRNIVKKLIAEGRLEMV---TGGWVMTDEAT-SHIFAMVDQLIEET 49 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlEfv---~GGWvm~DEA~-~~y~~~Idq~t~Gh 49 (62)
-.++.+.+|.+.|=++-+ +|||.-...+. -...++++.+ +|.
T Consensus 41 ~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~~~Itl~dv~~a~-eg~ 86 (135)
T TIGR02010 41 YLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAEDISVADIIDAV-DES 86 (135)
T ss_pred HHHHHHHHHHHCCceEEEeCCCCCEeccCCHHHCcHHHHHHHh-CCC
Confidence 456789999999998876 57999888665 4466666655 454
No 105
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=25.92 E-value=67 Score=24.51 Aligned_cols=19 Identities=26% Similarity=0.630 Sum_probs=16.4
Q ss_pred HHHHHHHHHcCceeEEecc
Q psy4375 9 RNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GG 27 (62)
.+.+|.|+++|.+-+..||
T Consensus 174 ~~~Ik~L~~~g~vVI~~GG 192 (312)
T COG0549 174 AEAIKALLESGHVVIAAGG 192 (312)
T ss_pred HHHHHHHHhCCCEEEEeCC
Confidence 4679999999999998765
No 106
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=25.88 E-value=1.4e+02 Score=21.97 Aligned_cols=37 Identities=3% Similarity=0.077 Sum_probs=29.7
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHH
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
...+++|++.|-++.-++.+..+++......+++..+
T Consensus 333 ~~~l~~~~~~gll~~~~~~i~lT~~G~~~~~~i~~~~ 369 (370)
T PRK06294 333 SELIMHPIIQELFTKNDQALSLNKKGRLFHDTIAEEI 369 (370)
T ss_pred HHHHHHHHHCCCEEEECCEEEECcchhhHHHHHHHHh
Confidence 3568899999999988888999999887777776544
No 107
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=25.71 E-value=52 Score=21.76 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=25.4
Q ss_pred HHHcCceeEEec-------ceeecccccccHHHHHHHHh
Q psy4375 15 LIAEGRLEMVTG-------GWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 15 LV~~GqlEfv~G-------GWvm~DEA~~~y~~~Idq~t 46 (62)
.+..|||+|++. |+--.+.+...|.+.+++-.
T Consensus 77 ~~~~gqL~~~~~~~~Y~~~g~f~~~~~i~~~~~~~~~a~ 115 (191)
T PF14417_consen 77 YLDSGQLELLDAEEWYLPDGRFDPARMIAFWRAALEQAL 115 (191)
T ss_pred cccCCCEEEecchhhhccCCCcCHHHHHHHHHHHHHHHH
Confidence 478899999975 77777788888888777665
No 108
>PF14059 DUF4251: Domain of unknown function (DUF4251); PDB: 3FYF_B.
Probab=25.71 E-value=90 Score=20.07 Aligned_cols=22 Identities=14% Similarity=0.108 Sum_probs=15.2
Q ss_pred cCChHHHHHHHHHHHcCceeEE
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEMV 24 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEfv 24 (62)
+..++..+.+++||+++++.|.
T Consensus 4 ~~~~~~~~~~~~~l~~~~f~i~ 25 (138)
T PF14059_consen 4 EKKAQKFAQVKEALESRNFKIE 25 (138)
T ss_dssp ----HHHHHHHHHHHTT-EEEE
T ss_pred hhhHHHHHHHHHHHHcCCeEEE
Confidence 3456677889999999999986
No 109
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=25.61 E-value=1.5e+02 Score=21.30 Aligned_cols=38 Identities=8% Similarity=0.072 Sum_probs=29.1
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
|..|.+++-..+..++....||| ...|..++..+..|.
T Consensus 120 D~~S~Dq~~LT~~~~~gk~Ve~V----------ei~Y~q~~~~l~~g~ 157 (232)
T PF14503_consen 120 DPSSIDQKILTEAEFEGKNVEFV----------EIPYNQLLELLRSGE 157 (232)
T ss_dssp -TT-HHHHHHHHHHHTTS--EEE----------E--HHHHHHHHHHTS
T ss_pred CCCCccHHHHHHHHhCCCceEEE----------EecHHHHHHHHHCCC
Confidence 66788899999999999999999 467999999999998
No 110
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=25.28 E-value=73 Score=18.30 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHcCce
Q psy4375 6 PTKRNIVKKLIAEGRL 21 (62)
Q Consensus 6 ~~~k~~vk~LV~~Gql 21 (62)
+.+|+.|.+.|+.|.|
T Consensus 18 e~kK~~idk~Ve~G~i 33 (59)
T PF10925_consen 18 ELKKQIIDKYVEAGVI 33 (59)
T ss_pred HHHHHHHHHHHHcCCC
Confidence 4577889999999976
No 111
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=25.26 E-value=1.5e+02 Score=21.35 Aligned_cols=41 Identities=22% Similarity=0.298 Sum_probs=32.2
Q ss_pred CChHHHHHHHHHHHcCceeEEe----cceeecccccccHHHHHHH
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVT----GGWVMTDEATSHIFAMVDQ 44 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~----GGWvm~DEA~~~y~~~Idq 44 (62)
.....+..+.+|+++|.||-.. +.+-.++++...+...-.-
T Consensus 33 ~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~r 77 (280)
T TIGR02277 33 NERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQR 77 (280)
T ss_pred CcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhh
Confidence 3456788999999999999975 5788888888777664433
No 112
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=25.22 E-value=1.4e+02 Score=22.25 Aligned_cols=36 Identities=22% Similarity=0.183 Sum_probs=30.7
Q ss_pred HHHHHHHHcCceeEEecceeecccccccHHHHHHHHh
Q psy4375 10 NIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 10 ~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
+.+++|++.|-++. ++.+..+++......+++..+.
T Consensus 354 ~~l~~l~~~gll~~-~~~l~lT~~G~~~~d~i~~~~~ 389 (390)
T PRK06582 354 NNLKHYQALDLIRL-DENIYLTDKGLMLHSYIVPRLI 389 (390)
T ss_pred HHHHHHHHCCCEEE-CCEEEECcchhHHHHHHHHHHh
Confidence 56889999999998 7889999999888888877664
No 113
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=24.93 E-value=1.8e+02 Score=18.92 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHcCceeEE-ecceeecc
Q psy4375 6 PTKRNIVKKLIAEGRLEMV-TGGWVMTD 32 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv-~GGWvm~D 32 (62)
...|+.++.|...|=++.. +.||+-..
T Consensus 49 tpVReAL~~L~~eGlv~~~~~~G~~V~~ 76 (212)
T TIGR03338 49 GPVREAFRALEEAGLVRNEKNRGVFVRE 76 (212)
T ss_pred HHHHHHHHHHHHCCCEEEecCCCeEEec
Confidence 4578999999999999998 55888765
No 114
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=24.90 E-value=1.3e+02 Score=16.90 Aligned_cols=34 Identities=15% Similarity=0.179 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHHHcCceeEE--ecceeecccccccH
Q psy4375 5 HPTKRNIVKKLIAEGRLEMV--TGGWVMTDEATSHI 38 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv--~GGWvm~DEA~~~y 38 (62)
.......++.|++.|-++.. +|.|.....+...-
T Consensus 34 ~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~~~~ 69 (91)
T smart00346 34 KSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELG 69 (91)
T ss_pred HHHHHHHHHHHHHCCCeeecCCCCceeecHHHHHHH
Confidence 34567789999999999886 45577666554433
No 115
>COG1540 Uncharacterized proteins, homologs of lactam utilization protein B [General function prediction only]
Probab=24.88 E-value=83 Score=23.36 Aligned_cols=32 Identities=25% Similarity=0.538 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHcCceeEEecceee--ccccccc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGWVM--TDEATSH 37 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGWvm--~DEA~~~ 37 (62)
++.-++|.++++.|++.-++|-|+- .|.-|.|
T Consensus 191 ~~a~~qvl~m~~~g~v~a~dG~~v~v~adsiCvH 224 (252)
T COG1540 191 EEALAQVLQMVREGKVTAIDGEWVAVEADSICVH 224 (252)
T ss_pred HHHHHHHHHHHhcCceEeeCCcEEeeecceEEEc
Confidence 4556789999999999999999974 3444443
No 116
>PF03536 VRP3: Salmonella virulence-associated 28kDa protein; InterPro: IPR003519 Salmonella typhimurium contains a 90kb plasmid that is associated with virulence. This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the 70kDa mkaA protein [], a recognised virulence factor. Deletion studies into the virulence plasmid have shown that an open reading frame encoding a 28kDa protein was needed for successful invasion of the host. This protein, designated mkfA [], VRP4 [] or VirA [] by different groups, is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.; PDB: 2Z8P_A 2Z8O_B 2Z8M_B 2Z8N_A 2P1W_A 2Q8Y_A 3I0U_B 3BO6_B.
Probab=24.54 E-value=74 Score=23.45 Aligned_cols=34 Identities=32% Similarity=0.447 Sum_probs=16.7
Q ss_pred eeecccccccHHHH----HHHHhhhh---hhhcccccCCCC
Q psy4375 28 WVMTDEATSHIFAM----VDQLIEET---FSTFSVQSSKRP 61 (62)
Q Consensus 28 Wvm~DEA~~~y~~~----Idq~t~Gh---~~~Fgv~p~~~~ 61 (62)
++-+|.+++.|.+- +.++++-. +.+=||.|..||
T Consensus 157 Y~kpd~eds~Ys~~~l~k~r~fi~~iE~~L~~agi~pg~~P 197 (240)
T PF03536_consen 157 YVKPDREDSQYSAEYLHKTRQFIESIESELSEAGIQPGERP 197 (240)
T ss_dssp EEE-SSTTS---HHHHHHHHHHHHHHHHHHHHTT--B----
T ss_pred EecCccccccCCHHHHHHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 68899999999876 23343333 888899999998
No 117
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=24.43 E-value=1e+02 Score=20.65 Aligned_cols=16 Identities=19% Similarity=0.436 Sum_probs=10.7
Q ss_pred CChHHHHHHHHHHHcC
Q psy4375 4 VHPTKRNIVKKLIAEG 19 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~G 19 (62)
.++..++.+++|.+.|
T Consensus 21 i~~~~~~ai~~l~~~G 36 (270)
T PRK10513 21 ISPAVKQAIAAARAKG 36 (270)
T ss_pred cCHHHHHHHHHHHHCC
Confidence 4566677777776665
No 118
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=24.38 E-value=78 Score=23.00 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=24.7
Q ss_pred eeEEecceeeccc-ccccHHHHHHHHhhhh
Q psy4375 21 LEMVTGGWVMTDE-ATSHIFAMVDQLIEET 49 (62)
Q Consensus 21 lEfv~GGWvm~DE-A~~~y~~~Idq~t~Gh 49 (62)
+++..-|+|.-|| +.-+|++++.+|.+|.
T Consensus 63 ~~y~~~GyVkDdda~~id~d~LL~~~k~~t 92 (239)
T PF09935_consen 63 FEYEDSGYVKDDDAKNIDYDELLKSMKEGT 92 (239)
T ss_pred EEEcCCCceecchhhhCCHHHHHHHHHHhH
Confidence 4666678999898 5789999999999998
No 119
>PF13036 DUF3897: Protein of unknown function (DUF3897)
Probab=24.30 E-value=85 Score=20.53 Aligned_cols=21 Identities=29% Similarity=0.608 Sum_probs=16.5
Q ss_pred HHHHHHHHHHcCceeEEecce
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGW 28 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGW 28 (62)
++.....|+++|++.|+.++-
T Consensus 84 t~~I~~~L~~sgk~~~v~~~~ 104 (180)
T PF13036_consen 84 TNKIRTALLNSGKFRFVSGGQ 104 (180)
T ss_pred HHHHHHHHHHCCCEEEEchHH
Confidence 455678899999999987654
No 120
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=24.22 E-value=97 Score=18.42 Aligned_cols=28 Identities=36% Similarity=0.710 Sum_probs=17.9
Q ss_pred ChHHHHHH---HHHHHcCce---eEE-ecceeecc
Q psy4375 5 HPTKRNIV---KKLIAEGRL---EMV-TGGWVMTD 32 (62)
Q Consensus 5 ~~~~k~~v---k~LV~~Gql---Efv-~GGWvm~D 32 (62)
+++.|+.| ..|+.+|.+ |-. +|+|+-|.
T Consensus 23 ~~~~~~av~~~i~~Ld~G~lRvAek~~~g~W~vne 57 (70)
T PF14805_consen 23 DPELRDAVEEVIELLDSGELRVAEKDADGEWVVNE 57 (70)
T ss_dssp -HHHHHHHHHHHHHHHTTSS-SEEEETTTEEEE-H
T ss_pred CHHHHHHHHHHHHHhcCCCeEEEeecCCCCEEeeH
Confidence 45555554 456778987 445 89999774
No 121
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=24.16 E-value=35 Score=15.35 Aligned_cols=15 Identities=20% Similarity=0.200 Sum_probs=10.9
Q ss_pred ecccccccHHHHHHH
Q psy4375 30 MTDEATSHIFAMVDQ 44 (62)
Q Consensus 30 m~DEA~~~y~~~Idq 44 (62)
..|+|...|..+|++
T Consensus 15 ~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 15 DYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHH
Confidence 457788888877765
No 122
>PRK09897 hypothetical protein; Provisional
Probab=23.99 E-value=1e+02 Score=24.33 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=19.6
Q ss_pred ChHHHHHHHHHHHcCceeEEecce
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGW 28 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGW 28 (62)
.++.=..+..|+++|+|+++.||=
T Consensus 391 P~~sa~~l~~l~~aG~L~v~~~~~ 414 (534)
T PRK09897 391 PSESIRRLLALREAGIIHILALGE 414 (534)
T ss_pred ChHHHHHHHHHHHcCCEEEEecCc
Confidence 345556789999999999998875
No 123
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.87 E-value=77 Score=21.18 Aligned_cols=19 Identities=26% Similarity=0.405 Sum_probs=16.6
Q ss_pred HHHHHHHHHcCceeEEecc
Q psy4375 9 RNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GG 27 (62)
|..|++|++.|.|....+.
T Consensus 117 rs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 117 RSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred HHHHHHHHHCCCEEecCcc
Confidence 6789999999999988765
No 124
>TIGR02075 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076.
Probab=23.72 E-value=94 Score=21.27 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=22.2
Q ss_pred HHHHHHHHHcCceeEEecc----eeecccccccH
Q psy4375 9 RNIVKKLIAEGRLEMVTGG----WVMTDEATSHI 38 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GG----Wvm~DEA~~~y 38 (62)
++.+++|+++|.+-+++|+ |+-+|...+..
T Consensus 111 ~~~i~~ll~~g~VpV~~g~~g~~~~s~D~~a~~l 144 (233)
T TIGR02075 111 RRKAIKHLEKGKVVIFSGGTGNPFFTTDTAAALR 144 (233)
T ss_pred HHHHHHHHHCCCEEEEECCCCCCCCCchHHHHHH
Confidence 5788899999999888776 56665555443
No 125
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=23.61 E-value=1.2e+02 Score=20.13 Aligned_cols=24 Identities=21% Similarity=0.591 Sum_probs=18.8
Q ss_pred CChHHHHHHHHHHHcC-ceeEEecc
Q psy4375 4 VHPTKRNIVKKLIAEG-RLEMVTGG 27 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~G-qlEfv~GG 27 (62)
.++++++.++.++.++ ++-+|.|.
T Consensus 2 L~~~Q~~a~~~~l~~~~~~~~l~G~ 26 (196)
T PF13604_consen 2 LNEEQREAVRAILTSGDRVSVLQGP 26 (196)
T ss_dssp S-HHHHHHHHHHHHCTCSEEEEEES
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEEC
Confidence 4788999999998876 78888774
No 126
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=23.39 E-value=66 Score=18.21 Aligned_cols=36 Identities=11% Similarity=0.238 Sum_probs=28.2
Q ss_pred cce-eecccccccHHHHHHHHhhhh---hhhcccccCCCC
Q psy4375 26 GGW-VMTDEATSHIFAMVDQLIEET---FSTFSVQSSKRP 61 (62)
Q Consensus 26 GGW-vm~DEA~~~y~~~Idq~t~Gh---~~~Fgv~p~~~~ 61 (62)
--| .|++|.-..|.++-....+-| +.++-.+|++++
T Consensus 38 ~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p~~~~ 77 (77)
T cd01389 38 RMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTPRKSS 77 (77)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccCCCCC
Confidence 345 356777788889999999999 888888898764
No 127
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=23.28 E-value=80 Score=17.36 Aligned_cols=16 Identities=25% Similarity=0.499 Sum_probs=12.0
Q ss_pred HHHHHHHHHHcCceeE
Q psy4375 8 KRNIVKKLIAEGRLEM 23 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEf 23 (62)
--..+++||.++++.|
T Consensus 62 ~L~~l~~LiA~k~i~~ 77 (79)
T PF08721_consen 62 ALPLLRHLIATKRIKV 77 (79)
T ss_dssp HHHHHHHHHHTTSEE-
T ss_pred hHHHHHHHHhCChhcc
Confidence 3457899999998875
No 128
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=23.16 E-value=1.1e+02 Score=18.99 Aligned_cols=27 Identities=22% Similarity=0.211 Sum_probs=21.2
Q ss_pred ChHHHHHHHHHHHcCceeEEecceeec
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVTGGWVMT 31 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~GGWvm~ 31 (62)
.+..++.+.+++++-.+-|++||=.+.
T Consensus 45 ~~~i~~~i~~~~~~~DlvittGG~g~g 71 (133)
T cd00758 45 ADSIRAALIEASREADLVLTTGGTGVG 71 (133)
T ss_pred HHHHHHHHHHHHhcCCEEEECCCCCCC
Confidence 355678889999888999999995443
No 129
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=23.12 E-value=73 Score=20.01 Aligned_cols=24 Identities=8% Similarity=0.430 Sum_probs=16.6
Q ss_pred CChHHHHHHHHHHHcCceeEEecc
Q psy4375 4 VHPTKRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~GqlEfv~GG 27 (62)
.|+.+++.|+.++++..+-+|.|.
T Consensus 2 ln~~Q~~Ai~~~~~~~~~~~i~Gp 25 (236)
T PF13086_consen 2 LNESQREAIQSALSSNGITLIQGP 25 (236)
T ss_dssp --HHHHHHHHHHCTSSE-EEEE-S
T ss_pred CCHHHHHHHHHHHcCCCCEEEECC
Confidence 467888888888888887888774
No 130
>PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional
Probab=22.56 E-value=1.2e+02 Score=20.17 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=11.0
Q ss_pred CChHHHHHHHHHHHcC
Q psy4375 4 VHPTKRNIVKKLIAEG 19 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~G 19 (62)
.++..++.+++|.+.|
T Consensus 21 i~~~~~~ai~~~~~~G 36 (272)
T PRK10530 21 ILPESLEALARAREAG 36 (272)
T ss_pred cCHHHHHHHHHHHHCC
Confidence 4566677777777765
No 131
>cd05398 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal io
Probab=22.51 E-value=1.2e+02 Score=19.49 Aligned_cols=24 Identities=25% Similarity=0.426 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHc-CceeEEeccee
Q psy4375 6 PTKRNIVKKLIAE-GRLEMVTGGWV 29 (62)
Q Consensus 6 ~~~k~~vk~LV~~-GqlEfv~GGWv 29 (62)
+..+..++.|-+. |-=-++-||||
T Consensus 2 ~~~~~il~~l~~~~g~~~ylVGG~V 26 (139)
T cd05398 2 PELLKLLRELKKALGYEAYLVGGAV 26 (139)
T ss_pred HHHHHHHHHHHhccCceEEEECChH
Confidence 3456778888887 65556778888
No 132
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=22.49 E-value=2e+02 Score=21.70 Aligned_cols=37 Identities=24% Similarity=0.290 Sum_probs=30.6
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHH
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
...++.|++.|-+++-++.|..+++.......+...+
T Consensus 402 ~~~l~~l~~~gl~~~~~~~~~lT~~G~~~~~~i~~~f 438 (453)
T PRK13347 402 LARLEPLAADGLVTIDGGGIRVTPEGRPLIRAVAAAF 438 (453)
T ss_pred HHHHHHHHHCCCEEEECCEEEECcchhHHHHHHHHHH
Confidence 4578899999999998888999999888777766555
No 133
>PRK08628 short chain dehydrogenase; Provisional
Probab=22.47 E-value=54 Score=21.49 Aligned_cols=19 Identities=37% Similarity=0.620 Sum_probs=15.7
Q ss_pred cCceeEEecceeecccccc
Q psy4375 18 EGRLEMVTGGWVMTDEATS 36 (62)
Q Consensus 18 ~GqlEfv~GGWvm~DEA~~ 36 (62)
+|+.=.+.|||...+|+|+
T Consensus 240 ~g~~~~~~gg~~~~~~~~~ 258 (258)
T PRK08628 240 TGQWLFVDGGYVHLDRALT 258 (258)
T ss_pred cCceEEecCCccccccccC
Confidence 4677788999999999984
No 134
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=22.41 E-value=2.6e+02 Score=21.21 Aligned_cols=39 Identities=15% Similarity=0.183 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhh
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIE 47 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~ 47 (62)
...+.+|++.|-+++-++.+..+++..-...++...+..
T Consensus 399 ~~~l~~~~~~Gll~~~~~~l~lT~~G~~~~~~i~~~~~~ 437 (449)
T PRK09058 399 APLLAQWQQAGLVELSSDCLRLTLAGRFWAVNLTQGLIE 437 (449)
T ss_pred HHHHHHHHHCCCEEEECCEEEECCCcccHHHHHHHHHHH
Confidence 457889999999998888899999888877777665543
No 135
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=22.28 E-value=1.6e+02 Score=19.17 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=31.6
Q ss_pred HHHHHHHHHHcCceeEE---ecceeecccccccHHHHHHHHhhhh
Q psy4375 8 KRNIVKKLIAEGRLEMV---TGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv---~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
-.+.+.+|.+.|=++-+ +|||.-..+|..---.-|-.-++|-
T Consensus 42 L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~Isl~dVv~ave~~ 86 (150)
T COG1959 42 LEKILSKLRKAGLVKSVRGKGGGYRLARPPEEITLGDVVRALEGP 86 (150)
T ss_pred HHHHHHHHHHcCCEEeecCCCCCccCCCChHHCcHHHHHHHhcCC
Confidence 35678999999999997 7799999888765544444555554
No 136
>PRK13774 formimidoylglutamase; Provisional
Probab=22.07 E-value=1.2e+02 Score=21.96 Aligned_cols=23 Identities=26% Similarity=0.248 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHHcCceeEEecce
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGGW 28 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GGW 28 (62)
...++.|.+++++|.+=|+-||=
T Consensus 107 ~~i~~~v~~i~~~g~~pivlGGd 129 (311)
T PRK13774 107 KEFAMLAAKSIANHRQTFLLGGG 129 (311)
T ss_pred HHHHHHHHHHHHCCCeEEEEcCc
Confidence 45577899999999999988773
No 137
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=21.97 E-value=2.3e+02 Score=18.70 Aligned_cols=27 Identities=22% Similarity=0.390 Sum_probs=21.7
Q ss_pred hHHHHHHHHHHHcCceeEE-ecceeecc
Q psy4375 6 PTKRNIVKKLIAEGRLEMV-TGGWVMTD 32 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv-~GGWvm~D 32 (62)
...|+.++.|...|=++++ +.||.-..
T Consensus 45 tpVREAL~~L~~eGlv~~~~~~G~~V~~ 72 (224)
T PRK11534 45 GPLREALSQLVAERLVTVVNQKGYRVAS 72 (224)
T ss_pred HHHHHHHHHHHHCCCEEEeCCCceEeCC
Confidence 4578999999999999998 55776543
No 138
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=21.91 E-value=1.5e+02 Score=16.06 Aligned_cols=23 Identities=39% Similarity=0.539 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHcCceeEEec-ce
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTG-GW 28 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~G-GW 28 (62)
...|+.++.|.+.|-++...| ||
T Consensus 39 ~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 39 TTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp HHHHHHHHHHHHTTSEEEETTTEE
T ss_pred cHHHHHHHHHHHCCcEEEECCceE
Confidence 467889999999999998744 54
No 139
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=21.80 E-value=1.4e+02 Score=16.26 Aligned_cols=20 Identities=45% Similarity=1.013 Sum_probs=15.4
Q ss_pred HHHHHHHHHcCceeEEeccee
Q psy4375 9 RNIVKKLIAEGRLEMVTGGWV 29 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv~GGWv 29 (62)
...+..|+++|.+.. .|+||
T Consensus 38 ~~ll~~l~~~g~l~~-~g~~v 57 (59)
T PF09106_consen 38 NALLEALVAEGRLKV-EGDWV 57 (59)
T ss_dssp HHHHHHHHHTTSEEE-ESSEE
T ss_pred HHHHHHHHHCCCeee-ECCEe
Confidence 456889999999975 56676
No 140
>PRK10976 putative hydrolase; Provisional
Probab=21.71 E-value=1.3e+02 Score=20.17 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=10.6
Q ss_pred CChHHHHHHHHHHHcC
Q psy4375 4 VHPTKRNIVKKLIAEG 19 (62)
Q Consensus 4 ~~~~~k~~vk~LV~~G 19 (62)
.++..++.+++|.+.|
T Consensus 20 is~~~~~ai~~l~~~G 35 (266)
T PRK10976 20 LSPYAKETLKLLTARG 35 (266)
T ss_pred CCHHHHHHHHHHHHCC
Confidence 4566677777776665
No 141
>PF14627 DUF4453: Domain of unknown function (DUF4453)
Probab=21.60 E-value=34 Score=22.37 Aligned_cols=22 Identities=14% Similarity=0.380 Sum_probs=15.2
Q ss_pred HcCceeEEecceeecc---cccccH
Q psy4375 17 AEGRLEMVTGGWVMTD---EATSHI 38 (62)
Q Consensus 17 ~~GqlEfv~GGWvm~D---EA~~~y 38 (62)
.++-..++++||.-.+ |+|+.|
T Consensus 81 ~~~dW~~k~~GW~~~~~~pe~C~~F 105 (107)
T PF14627_consen 81 HDPDWQVKSAGWYDGSAYPEHCTQF 105 (107)
T ss_pred ecCCcceecccceEcccchhHHHhh
Confidence 3556677899998765 666654
No 142
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=21.58 E-value=53 Score=23.48 Aligned_cols=26 Identities=15% Similarity=0.146 Sum_probs=22.0
Q ss_pred ceeEEecceeecccccccHHHHHHHH
Q psy4375 20 RLEMVTGGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 20 qlEfv~GGWvm~DEA~~~y~~~Idq~ 45 (62)
+|.-++.+++-+++||.+|..+-..|
T Consensus 176 ~i~~lTn~yt~P~~AC~t~r~ly~~L 201 (224)
T PRK13276 176 KMSELTSSYEPPIEACGTWRLVYQRL 201 (224)
T ss_pred HHHHHhCCCCCCcchhHHHHHHHHHH
Confidence 56667999999999999998877665
No 143
>PF01293 PEPCK_ATP: Phosphoenolpyruvate carboxykinase The Prosite pattern is specific to the ATP binding region; InterPro: IPR001272 Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (4.1.1.49 from EC) and GTP-utilising (4.1.1.32 from EC) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria []. Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle. PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding []. With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels []. PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an alpha/beta topology that is partly similar to one another [, ]. Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site []. PCK uses an alpha/beta/alpha motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium. This entry represents ATP-utilising phosphoenolpyruvate carboxykinase enzymes.; GO: 0004612 phosphoenolpyruvate carboxykinase (ATP) activity, 0005524 ATP binding, 0006094 gluconeogenesis; PDB: 2PY7_X 2OLR_A 1AYL_A 1K3D_A 1OEN_A 1AQ2_A 1OS1_A 2OLQ_A 1K3C_A 2PXZ_X ....
Probab=21.57 E-value=1.2e+02 Score=23.87 Aligned_cols=40 Identities=18% Similarity=0.322 Sum_probs=29.2
Q ss_pred HHHHHHHHcCc--eeEEecceeec------ccccccHHHHHHHHhhhh
Q psy4375 10 NIVKKLIAEGR--LEMVTGGWVMT------DEATSHIFAMVDQLIEET 49 (62)
Q Consensus 10 ~~vk~LV~~Gq--lEfv~GGWvm~------DEA~~~y~~~Idq~t~Gh 49 (62)
+.++++++... .-+||=||+.- .=-..+..++|+.+..|.
T Consensus 392 ~~l~~~~~~~~~~~yl~NTG~~gg~~~~g~ri~~~~t~~~i~~il~g~ 439 (466)
T PF01293_consen 392 ELLKEKIKKHGVNCYLVNTGWTGGPYGVGKRIPLEYTRAIIEAILDGT 439 (466)
T ss_dssp HHHHHHHHHHT-EEEEEE-SBETTSCCCSSB--HHHHHHHHHHHHTSG
T ss_pred HHHHHHHHhcCCCEEEEeCCccCCCCCceeECCHHHHHHHHHHHhcCC
Confidence 45777777654 55699999984 556678999999999998
No 144
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=21.51 E-value=1.3e+02 Score=23.96 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=29.0
Q ss_pred CcCChHHHHHHHHHHHcCceeEEecceeecccccccH
Q psy4375 2 EIVHPTKRNIVKKLIAEGRLEMVTGGWVMTDEATSHI 38 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y 38 (62)
+..+...+..+.+++++++..|+++-|--.|+..+.|
T Consensus 275 ~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ 311 (615)
T TIGR02903 275 GELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKY 311 (615)
T ss_pred ccCCHHHHHHHHHHHhhCeEEeecceeccCCcccchh
Confidence 3456778889999999999999988777776655444
No 145
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=21.48 E-value=71 Score=15.41 Aligned_cols=23 Identities=17% Similarity=0.455 Sum_probs=15.7
Q ss_pred HHHHHHHHHcCceeEE---ecceeec
Q psy4375 9 RNIVKKLIAEGRLEMV---TGGWVMT 31 (62)
Q Consensus 9 k~~vk~LV~~GqlEfv---~GGWvm~ 31 (62)
+..+++++++|.+... +|.|.-+
T Consensus 14 ~~tl~~~~~~g~~~~~~~~~~~~~~~ 39 (49)
T cd04762 14 PSTLRRWVKEGKLKAIRTPGGHRRFP 39 (49)
T ss_pred HHHHHHHHHcCCCCceeCCCCceecC
Confidence 5678999999998643 3455433
No 146
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=21.32 E-value=2.6e+02 Score=21.29 Aligned_cols=42 Identities=14% Similarity=0.063 Sum_probs=36.2
Q ss_pred HHHHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhh
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEET 49 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh 49 (62)
-...+..|+..|-++.-++-|..++...-...+++.++..|.
T Consensus 376 ~~~~l~~l~~~Gll~~~~~~l~lT~~G~~~~d~i~~~f~~g~ 417 (433)
T PRK08629 376 LFKEMLLLKLIGAIKNDPGDLIVTDFGKYLGVVMMKEFYTGM 417 (433)
T ss_pred HHHHHHHHHHCCCEEEECCEEEECcchhHHHHHHHHHHHhCh
Confidence 345778999999999877779999999999999999998876
No 147
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=21.32 E-value=22 Score=21.83 Aligned_cols=19 Identities=32% Similarity=0.623 Sum_probs=12.1
Q ss_pred HHHcCceeEEecceeeccc
Q psy4375 15 LIAEGRLEMVTGGWVMTDE 33 (62)
Q Consensus 15 LV~~GqlEfv~GGWvm~DE 33 (62)
++++-=+--|+|||.--+|
T Consensus 43 il~~~VMVRVGGGW~tL~~ 61 (73)
T smart00243 43 ILRSTVMVRVGGGWETLDE 61 (73)
T ss_pred EeCCeEEEEECCcHHHHHH
Confidence 3444445668999975544
No 148
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=20.94 E-value=90 Score=16.37 Aligned_cols=17 Identities=29% Similarity=0.425 Sum_probs=12.5
Q ss_pred CcCChHHHHHHHHHHHc
Q psy4375 2 EIVHPTKRNIVKKLIAE 18 (62)
Q Consensus 2 d~~~~~~k~~vk~LV~~ 18 (62)
+++.+...+.+++|+.+
T Consensus 20 ~~s~et~~DKi~rli~~ 36 (37)
T PF14202_consen 20 ETSKETMQDKIKRLIRR 36 (37)
T ss_pred CCccccHHHHHHHHHhc
Confidence 35667778888888864
No 149
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=20.94 E-value=1.3e+02 Score=21.87 Aligned_cols=32 Identities=22% Similarity=0.188 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHcCceeEEe-cceeeccccccc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVT-GGWVMTDEATSH 37 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~-GGWvm~DEA~~~ 37 (62)
++.++.+.-|++-|-|+-.+ |-|+.+|...+.
T Consensus 154 ~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~ 186 (271)
T TIGR02147 154 EQVKESLDLLERLGLIKKNEDGFYKQTDKAVST 186 (271)
T ss_pred HHHHHHHHHHHHCCCeeECCCCcEEeecceeec
Confidence 45788999999999999864 559999887763
No 150
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=20.79 E-value=1.7e+02 Score=16.43 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHcCceeEEe---cceeeccc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVT---GGWVMTDE 33 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~---GGWvm~DE 33 (62)
...+..+..|.+.|.++..+ +-|....+
T Consensus 37 ~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~~ 67 (68)
T smart00550 37 KEVNRVLYSLEKKGKVCKQGGTPPLWKLTDK 67 (68)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCceEeecC
Confidence 45677889999999999864 56876554
No 151
>KOG1055|consensus
Probab=20.66 E-value=1.1e+02 Score=26.44 Aligned_cols=47 Identities=11% Similarity=0.280 Sum_probs=39.9
Q ss_pred HHHHHHHHcCceeEEecceeecccccccHHHHHHHHhhhhhhhccccc
Q psy4375 10 NIVKKLIAEGRLEMVTGGWVMTDEATSHIFAMVDQLIEETFSTFSVQS 57 (62)
Q Consensus 10 ~~vk~LV~~GqlEfv~GGWvm~DEA~~~y~~~Idq~t~Gh~~~Fgv~p 57 (62)
+.+..-+++-+++=|+|+-+..+ +----...|.||..|-|+.+|+.-
T Consensus 382 d~i~eamn~tsF~GvsG~V~F~~-geR~a~t~ieQ~qdg~y~k~g~Yd 428 (865)
T KOG1055|consen 382 DQIYEAMNSTSFEGVSGHVVFSN-GERMALTLIEQFQDGKYKKIGYYD 428 (865)
T ss_pred HHHHHHhhcccccccccceEecc-hhhHHHHHHHHHhCCceEeecccc
Confidence 45666677889999999999998 888889999999999988888653
No 152
>COG0617 PcnB tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
Probab=20.54 E-value=86 Score=23.23 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=19.4
Q ss_pred cCChHHHHHHHHHHHcCceeE-Eeccee
Q psy4375 3 IVHPTKRNIVKKLIAEGRLEM-VTGGWV 29 (62)
Q Consensus 3 ~~~~~~k~~vk~LV~~GqlEf-v~GGWv 29 (62)
..++.-+..+..|-+.| +|. +-||||
T Consensus 6 ~~~~~~~~v~~~l~~~g-~eaylVGGaV 32 (412)
T COG0617 6 DLSPNALKVLSKLKEAG-YEAYLVGGAV 32 (412)
T ss_pred hhhHHHHHHHHHHHhCC-CeEEEeCcHH
Confidence 45667788889999999 444 667776
No 153
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=20.52 E-value=68 Score=19.60 Aligned_cols=14 Identities=43% Similarity=0.828 Sum_probs=10.7
Q ss_pred HHHHHHHHcCceeE
Q psy4375 10 NIVKKLIAEGRLEM 23 (62)
Q Consensus 10 ~~vk~LV~~GqlEf 23 (62)
..+++|.++|++++
T Consensus 96 ~~~r~l~~~G~I~l 109 (110)
T PF01706_consen 96 EIVRRLEEEGEIEL 109 (110)
T ss_dssp HHHHHHHHTTSS-B
T ss_pred HHHHHHHHCcCEee
Confidence 45899999999875
No 154
>KOG1515|consensus
Probab=20.50 E-value=1.1e+02 Score=22.83 Aligned_cols=26 Identities=12% Similarity=0.253 Sum_probs=21.4
Q ss_pred eeEEecceeecccccccHHHHHHHHh
Q psy4375 21 LEMVTGGWVMTDEATSHIFAMVDQLI 46 (62)
Q Consensus 21 lEfv~GGWvm~DEA~~~y~~~Idq~t 46 (62)
+-|=+||||+---+.+.|......|.
T Consensus 94 vyfHGGGf~~~S~~~~~y~~~~~~~a 119 (336)
T KOG1515|consen 94 VYFHGGGFCLGSANSPAYDSFCTRLA 119 (336)
T ss_pred EEEeCCccEeCCCCCchhHHHHHHHH
Confidence 34559999999989999998888773
No 155
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=20.43 E-value=51 Score=21.20 Aligned_cols=26 Identities=12% Similarity=0.238 Sum_probs=17.0
Q ss_pred cccHHHHHHHHhhhhhhhcccccCCCC
Q psy4375 35 TSHIFAMVDQLIEETFSTFSVQSSKRP 61 (62)
Q Consensus 35 ~~~y~~~Idq~t~Gh~~~Fgv~p~~~~ 61 (62)
+...+.+|+-+.. -|.+||+.|.-|+
T Consensus 40 T~~HW~VI~~lR~-~y~e~~~~P~~R~ 65 (109)
T PRK11508 40 SPEHWEVVRFVRD-FYLEFNTSPAIRM 65 (109)
T ss_pred CHHHHHHHHHHHH-HHHHHCCCCcHHH
Confidence 3445555655544 5889999998764
No 156
>KOG3360|consensus
Probab=20.41 E-value=42 Score=21.65 Aligned_cols=6 Identities=67% Similarity=1.608 Sum_probs=5.1
Q ss_pred ceeecc
Q psy4375 27 GWVMTD 32 (62)
Q Consensus 27 GWvm~D 32 (62)
|||||-
T Consensus 38 GWv~Nt 43 (98)
T KOG3360|consen 38 GWVMNT 43 (98)
T ss_pred EEEEec
Confidence 999984
No 157
>KOG4603|consensus
Probab=20.38 E-value=70 Score=22.97 Aligned_cols=20 Identities=15% Similarity=0.484 Sum_probs=16.2
Q ss_pred cHHHHHHHHhhhh-------hhhcccc
Q psy4375 37 HIFAMVDQLIEET-------FSTFSVQ 56 (62)
Q Consensus 37 ~y~~~Idq~t~Gh-------~~~Fgv~ 56 (62)
-|.++||++++|. +++.||.
T Consensus 174 mf~ei~d~~~e~~pk~ksel~eelGIE 200 (201)
T KOG4603|consen 174 MFREIIDKLLEGLPKKKSELYEELGIE 200 (201)
T ss_pred HHHHHHHHHHcCCcchHHHHHHHhCcC
Confidence 4788999999998 7777764
No 158
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=20.22 E-value=1.2e+02 Score=16.34 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=16.3
Q ss_pred HHHHHHHHHHcCceeEEeccee
Q psy4375 8 KRNIVKKLIAEGRLEMVTGGWV 29 (62)
Q Consensus 8 ~k~~vk~LV~~GqlEfv~GGWv 29 (62)
.|..+++|++.|++- |||.=|
T Consensus 23 SR~~~k~li~~G~V~-VNg~~~ 43 (59)
T TIGR02988 23 SGGQAKWFLQENEVL-VNGELE 43 (59)
T ss_pred CHHHHHHHHHcCCEE-ECCEEc
Confidence 588899999999874 477644
No 159
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=20.17 E-value=1.9e+02 Score=16.45 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=31.5
Q ss_pred ChHHHHHHHHHHHcCceeEEe-cceeecccccccHHHHHHHH
Q psy4375 5 HPTKRNIVKKLIAEGRLEMVT-GGWVMTDEATSHIFAMVDQL 45 (62)
Q Consensus 5 ~~~~k~~vk~LV~~GqlEfv~-GGWvm~DEA~~~y~~~Idq~ 45 (62)
.+.....++.|.+.|=++... +++..++.+...+..+....
T Consensus 13 ~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~~ 54 (96)
T smart00529 13 PPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRKH 54 (96)
T ss_pred hHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHHH
Confidence 456678899999999999987 58888888777666655433
No 160
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=20.14 E-value=1e+02 Score=18.57 Aligned_cols=16 Identities=13% Similarity=0.331 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHcCcee
Q psy4375 7 TKRNIVKKLIAEGRLE 22 (62)
Q Consensus 7 ~~k~~vk~LV~~GqlE 22 (62)
..|+.+++||+.|-+.
T Consensus 6 ~iq~ear~LV~~g~v~ 21 (68)
T PF14217_consen 6 KIQDEARSLVESGVVS 21 (68)
T ss_pred HHHHHHHHHHHcCCCC
Confidence 4678899999999775
No 161
>PF06908 DUF1273: Protein of unknown function (DUF1273); InterPro: IPR024718 This entry represents a functionally uncharacterised domain.; PDB: 2NX2_A.
Probab=20.10 E-value=1.2e+02 Score=20.67 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHHcCceeEEecc
Q psy4375 6 PTKRNIVKKLIAEGRLEMVTGG 27 (62)
Q Consensus 6 ~~~k~~vk~LV~~GqlEfv~GG 27 (62)
...++.+..|+++|---|++||
T Consensus 29 ~~L~~~i~~lie~G~~~fi~Gg 50 (177)
T PF06908_consen 29 KALKKQIIELIEEGVRWFITGG 50 (177)
T ss_dssp HHHHHHHHHHHTTT--EEEE--
T ss_pred HHHHHHHHHHHHCCCCEEEECC
Confidence 3456788999999988888887
Done!