Query psy4260
Match_columns 129
No_of_seqs 125 out of 460
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 20:52:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4260.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4260hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00601 rad23 UV excision re 99.9 2.3E-26 5.1E-31 196.6 8.0 92 31-122 146-281 (378)
2 KOG0011|consensus 99.9 2.8E-24 6.1E-29 182.1 6.5 96 28-123 122-250 (340)
3 PF00627 UBA: UBA/TS-N domain; 99.5 8E-14 1.7E-18 83.4 5.1 36 41-76 2-37 (37)
4 cd00194 UBA Ubiquitin Associat 99.4 6.7E-13 1.5E-17 78.7 5.3 37 42-78 2-38 (38)
5 smart00165 UBA Ubiquitin assoc 99.4 7E-13 1.5E-17 78.4 4.9 37 41-77 1-37 (37)
6 KOG0944|consensus 98.6 3.7E-08 8E-13 90.8 4.8 43 39-81 633-675 (763)
7 TIGR00601 rad23 UV excision re 98.2 1.3E-06 2.8E-11 75.5 4.9 42 38-79 334-375 (378)
8 KOG0418|consensus 98.0 1.1E-05 2.4E-10 65.0 4.7 45 35-79 156-200 (200)
9 PF02845 CUE: CUE domain; Int 97.9 2.3E-05 4.9E-10 47.8 4.5 38 42-79 2-41 (42)
10 KOG0011|consensus 97.8 3.1E-05 6.7E-10 66.7 4.8 43 38-80 295-337 (340)
11 PF14555 UBA_4: UBA-like domai 97.7 0.00012 2.6E-09 44.9 5.4 38 42-79 1-39 (43)
12 COG5207 UBP14 Isopeptidase T [ 97.7 6.4E-05 1.4E-09 68.8 5.1 41 42-82 559-600 (749)
13 smart00546 CUE Domain that may 97.6 0.00025 5.4E-09 43.2 5.2 38 42-79 3-42 (43)
14 KOG0944|consensus 97.5 0.00015 3.3E-09 67.5 5.5 43 40-82 570-613 (763)
15 KOG2561|consensus 97.4 0.00017 3.7E-09 64.9 4.2 39 41-79 303-341 (568)
16 COG5207 UBP14 Isopeptidase T [ 97.4 8.1E-05 1.7E-09 68.2 1.8 41 39-79 619-659 (749)
17 PF09288 UBA_3: Fungal ubiquit 97.0 0.00067 1.4E-08 45.0 3.1 27 41-67 9-35 (55)
18 KOG2561|consensus 96.8 0.0018 4E-08 58.5 4.7 46 40-85 428-473 (568)
19 PRK06369 nac nascent polypepti 96.4 0.009 2E-07 44.7 5.3 40 39-78 74-114 (115)
20 KOG0010|consensus 96.4 0.0061 1.3E-07 55.0 5.2 39 40-78 453-492 (493)
21 PF09280 XPC-binding: XPC-bind 96.0 0.00072 1.6E-08 44.9 -1.8 26 96-121 2-33 (59)
22 TIGR00264 alpha-NAC-related pr 95.9 0.016 3.6E-07 43.5 4.9 39 39-77 76-115 (116)
23 TIGR00116 tsf translation elon 95.9 0.013 2.9E-07 49.4 4.8 72 41-112 4-96 (290)
24 PF07223 DUF1421: Protein of u 95.8 0.017 3.6E-07 50.3 5.3 32 33-64 313-344 (358)
25 PRK12332 tsf elongation factor 95.8 0.016 3.5E-07 46.4 4.8 37 42-78 5-42 (198)
26 PF11626 Rap1_C: TRF2-interact 95.8 0.017 3.7E-07 40.1 4.3 35 45-79 1-35 (87)
27 PRK09377 tsf elongation factor 95.8 0.017 3.6E-07 48.8 4.8 77 41-117 5-102 (290)
28 CHL00098 tsf elongation factor 95.6 0.021 4.6E-07 45.9 4.8 36 43-78 3-39 (200)
29 KOG2689|consensus 95.5 0.022 4.8E-07 48.5 4.6 38 45-82 4-43 (290)
30 COG1308 EGD2 Transcription fac 95.2 0.045 9.7E-07 41.5 5.1 39 39-77 82-121 (122)
31 PF07499 RuvA_C: RuvA, C-termi 93.3 0.081 1.8E-06 32.9 2.4 26 41-66 3-28 (47)
32 COG0264 Tsf Translation elonga 93.0 0.18 3.8E-06 43.2 4.8 37 42-78 6-43 (296)
33 PF06972 DUF1296: Protein of u 92.3 0.48 1E-05 32.1 5.2 38 42-79 6-45 (60)
34 PF08938 HBS1_N: HBS1 N-termin 90.8 0.13 2.9E-06 35.2 1.3 26 54-79 45-70 (79)
35 PF11547 E3_UbLigase_EDD: E3 u 90.7 0.87 1.9E-05 30.0 5.0 41 39-79 7-49 (53)
36 KOG1071|consensus 89.2 0.93 2E-05 39.5 5.5 40 40-79 45-85 (340)
37 smart00804 TAP_C C-terminal do 89.0 1.8 3.8E-05 29.0 5.6 36 39-74 10-46 (63)
38 PF02954 HTH_8: Bacterial regu 88.6 0.43 9.3E-06 28.8 2.3 24 53-76 5-28 (42)
39 PF03943 TAP_C: TAP C-terminal 87.5 0.82 1.8E-05 29.2 3.2 33 43-75 2-35 (51)
40 TIGR00084 ruvA Holliday juncti 85.1 1.6 3.6E-05 34.4 4.4 27 40-66 146-172 (191)
41 PF03474 DMA: DMRTA motif; In 82.4 1.9 4.1E-05 26.8 2.9 25 53-77 15-39 (39)
42 COG4008 Predicted metal-bindin 81.6 4.1 8.9E-05 31.8 5.2 41 37-78 110-150 (153)
43 PF11372 DUF3173: Domain of un 79.3 2.3 5E-05 28.5 2.8 20 46-65 7-26 (59)
44 PRK14602 ruvA Holliday junctio 79.2 6.1 0.00013 31.5 5.7 27 39-65 153-179 (203)
45 PRK14603 ruvA Holliday junctio 79.0 6.4 0.00014 31.3 5.7 26 40-65 151-176 (197)
46 PRK14606 ruvA Holliday junctio 79.0 5.6 0.00012 31.5 5.4 27 40-66 142-168 (188)
47 PRK13901 ruvA Holliday junctio 78.2 3 6.4E-05 33.6 3.6 27 41-67 144-170 (196)
48 PRK14600 ruvA Holliday junctio 78.1 5.7 0.00012 31.4 5.2 28 40-67 144-171 (186)
49 PRK14601 ruvA Holliday junctio 76.1 3.5 7.5E-05 32.7 3.4 26 41-66 142-167 (183)
50 PRK14604 ruvA Holliday junctio 76.0 7.6 0.00017 30.9 5.4 25 41-65 149-173 (195)
51 PRK08769 DNA polymerase III su 74.9 7.9 0.00017 32.9 5.5 44 36-79 169-212 (319)
52 PRK07993 DNA polymerase III su 74.5 8.6 0.00019 32.6 5.7 41 38-78 166-207 (334)
53 PF08587 UBA_2: Ubiquitin asso 74.1 1 2.2E-05 28.9 0.0 26 42-67 3-29 (46)
54 COG0632 RuvA Holliday junction 69.4 6.2 0.00013 31.9 3.5 28 40-67 155-182 (201)
55 KOG2239|consensus 67.4 8.6 0.00019 31.6 3.9 35 42-76 172-207 (209)
56 PF05861 PhnI: Bacterial phosp 67.2 8.9 0.00019 33.8 4.2 33 44-76 44-78 (358)
57 PRK14605 ruvA Holliday junctio 65.1 19 0.0004 28.5 5.4 26 41-66 148-173 (194)
58 PF10440 WIYLD: Ubiquitin-bind 63.0 12 0.00027 25.4 3.5 25 40-64 10-34 (65)
59 PF10152 DUF2360: Predicted co 61.5 67 0.0015 24.3 7.7 27 44-70 118-144 (148)
60 PRK05441 murQ N-acetylmuramic 58.9 25 0.00054 29.4 5.3 38 44-81 238-276 (299)
61 PRK07634 pyrroline-5-carboxyla 57.6 28 0.0006 26.9 5.1 34 42-78 186-219 (245)
62 PRK00116 ruvA Holliday junctio 56.2 33 0.00072 26.8 5.3 27 41-67 149-175 (192)
63 PRK01905 DNA-binding protein F 51.1 16 0.00035 24.6 2.5 24 53-76 37-60 (77)
64 PRK00430 fis global DNA-bindin 50.7 30 0.00064 24.5 3.9 24 53-76 55-78 (95)
65 PF07553 Lipoprotein_Ltp: Host 50.2 26 0.00056 22.3 3.2 24 40-63 20-46 (48)
66 TIGR01981 sufD FeS assembly pr 49.5 27 0.0006 29.7 4.2 47 31-83 314-360 (366)
67 PF08784 RPA_C: Replication pr 49.3 9.7 0.00021 26.3 1.2 28 52-79 65-92 (102)
68 PF02536 mTERF: mTERF; InterP 48.8 20 0.00043 29.2 3.1 40 41-80 243-289 (345)
69 TIGR00274 N-acetylmuramic acid 48.6 46 0.00099 27.8 5.3 40 42-81 231-271 (291)
70 PRK06090 DNA polymerase III su 48.4 43 0.00092 28.5 5.2 42 36-79 164-205 (319)
71 KOG3763|consensus 48.2 74 0.0016 29.9 7.0 33 42-74 536-569 (585)
72 KOG0943|consensus 47.9 53 0.0011 34.6 6.3 43 37-79 185-229 (3015)
73 PF04695 Pex14_N: Peroxisomal 47.7 35 0.00075 25.4 4.1 33 38-70 20-52 (136)
74 COG2103 Predicted sugar phosph 46.6 46 0.001 28.8 5.1 40 42-81 234-274 (298)
75 PF03765 CRAL_TRIO_N: CRAL/TRI 46.5 36 0.00078 20.9 3.4 29 49-77 25-53 (55)
76 PF04361 DUF494: Protein of un 46.1 29 0.00063 26.8 3.5 24 40-63 22-45 (155)
77 PRK12570 N-acetylmuramic acid- 45.6 52 0.0011 27.5 5.2 40 42-81 232-272 (296)
78 KOG3837|consensus 44.6 56 0.0012 30.1 5.5 14 63-76 222-235 (523)
79 PRK15115 response regulator Gl 44.3 20 0.00043 30.3 2.5 24 53-76 398-421 (444)
80 PRK10923 glnG nitrogen regulat 44.0 20 0.00043 30.6 2.5 24 53-76 429-452 (469)
81 TIGR01817 nifA Nif-specific re 43.5 20 0.00043 31.7 2.5 24 53-76 490-513 (534)
82 PRK00912 ribonuclease P protei 43.4 51 0.0011 26.0 4.6 36 40-78 184-219 (237)
83 PF14748 P5CR_dimer: Pyrroline 43.1 73 0.0016 22.6 5.0 36 41-79 24-59 (107)
84 PRK05022 anaerobic nitric oxid 42.5 21 0.00045 31.6 2.5 24 53-76 468-491 (509)
85 PF12244 DUF3606: Protein of u 41.8 49 0.0011 21.4 3.6 32 45-76 23-55 (57)
86 TIGR01818 ntrC nitrogen regula 41.5 23 0.00049 30.0 2.5 24 53-76 426-449 (463)
87 PF01988 VIT1: VIT family; In 41.5 47 0.001 26.1 4.2 37 42-79 83-119 (213)
88 PRK11608 pspF phage shock prot 41.4 23 0.0005 29.5 2.5 24 53-76 286-309 (326)
89 TIGR02974 phageshock_pspF psp 40.8 24 0.00052 29.7 2.5 24 53-76 292-315 (329)
90 TIGR01980 sufB FeS assembly pr 39.3 45 0.00098 29.5 4.1 46 32-83 394-439 (448)
91 PF15652 Tox-SHH: HNH/Endo VII 38.9 42 0.00091 24.8 3.2 25 42-66 72-96 (100)
92 PF09722 DUF2384: Protein of u 38.6 26 0.00056 21.7 1.8 20 60-79 2-21 (54)
93 PRK07940 DNA polymerase III su 38.1 78 0.0017 27.6 5.3 38 40-77 177-215 (394)
94 PF14848 HU-DNA_bdg: DNA-bindi 37.0 1E+02 0.0022 22.4 5.1 36 41-79 31-68 (124)
95 PRK11361 acetoacetate metaboli 36.4 31 0.00067 29.1 2.5 24 53-76 417-440 (457)
96 TIGR00678 holB DNA polymerase 36.4 58 0.0013 24.2 3.8 33 40-72 156-188 (188)
97 cd05007 SIS_Etherase N-acetylm 36.2 31 0.00068 28.0 2.4 32 42-73 223-255 (257)
98 COG3626 PhnI Uncharacterized e 35.3 52 0.0011 28.9 3.7 33 44-77 44-78 (367)
99 TIGR02915 PEP_resp_reg putativ 34.9 34 0.00073 28.9 2.5 24 53-76 405-428 (445)
100 PRK10365 transcriptional regul 34.6 34 0.00074 28.6 2.5 27 48-76 402-428 (441)
101 TIGR00274 N-acetylmuramic acid 34.2 54 0.0012 27.4 3.6 23 52-74 269-291 (291)
102 PRK03430 hypothetical protein; 33.4 56 0.0012 25.6 3.3 23 40-62 22-44 (157)
103 PRK11814 cysteine desulfurase 33.1 62 0.0014 29.1 4.0 47 31-83 422-468 (486)
104 PF13411 MerR_1: MerR HTH fami 32.9 46 0.001 20.8 2.4 21 44-64 48-68 (69)
105 smart00422 HTH_MERR helix_turn 32.5 66 0.0014 20.0 3.1 20 44-63 49-68 (70)
106 PRK05707 DNA polymerase III su 32.5 1.2E+02 0.0025 25.7 5.4 40 38-77 164-205 (328)
107 PF10607 CLTH: CTLH/CRA C-term 32.3 52 0.0011 23.5 2.8 25 55-81 5-29 (145)
108 PF01458 UPF0051: Uncharacteri 32.2 33 0.00072 27.0 1.9 31 35-65 198-228 (229)
109 PRK06871 DNA polymerase III su 31.7 1.3E+02 0.0028 25.7 5.5 42 38-79 165-207 (325)
110 CHL00085 ycf24 putative ABC tr 31.4 62 0.0013 29.1 3.7 46 31-82 421-466 (485)
111 cd02433 Nodulin-21_like_2 Nodu 31.0 81 0.0018 25.7 4.0 37 42-78 101-137 (234)
112 PHA01732 proline-rich protein 30.8 1.5E+02 0.0032 21.7 4.9 17 1-17 3-19 (94)
113 PRK10948 cysteine desulfurase 30.8 77 0.0017 28.0 4.1 36 31-66 359-394 (424)
114 smart00668 CTLH C-terminal to 30.7 71 0.0015 19.1 2.9 23 55-79 5-27 (58)
115 PF08671 SinI: Anti-repressor 29.8 90 0.002 18.2 3.0 22 43-64 7-28 (30)
116 PRK05441 murQ N-acetylmuramic 29.4 73 0.0016 26.6 3.6 32 45-76 266-298 (299)
117 PF07506 RepB: RepB plasmid pa 29.3 54 0.0012 25.2 2.6 26 44-69 13-38 (185)
118 PRK05564 DNA polymerase III su 28.0 1.7E+02 0.0036 23.9 5.4 38 41-78 154-193 (313)
119 COG4545 Glutaredoxin-related p 27.7 18 0.00039 25.9 -0.2 25 100-124 50-77 (85)
120 PF02631 RecX: RecX family; I 27.2 65 0.0014 22.8 2.6 24 41-64 95-118 (121)
121 smart00646 Ami_3 Ami_3. 27.1 18 0.00039 25.0 -0.3 35 46-80 79-113 (113)
122 cd00474 SUI1_eIF1 The SUI1/eIF 27.1 53 0.0011 22.5 2.0 24 35-58 51-74 (77)
123 PRK09112 DNA polymerase III su 26.6 1.7E+02 0.0037 25.0 5.5 42 38-79 199-244 (351)
124 PRK02264 N(5),N(10)-methenylte 26.2 38 0.00081 29.5 1.4 38 26-63 169-206 (317)
125 PF13331 DUF4093: Domain of un 26.1 60 0.0013 22.8 2.2 20 44-63 68-87 (87)
126 TIGR03120 one_C_mch methenylte 25.9 39 0.00085 29.4 1.4 39 26-64 168-206 (312)
127 smart00299 CLH Clathrin heavy 25.6 1.3E+02 0.0029 21.0 4.0 35 42-77 86-120 (140)
128 cd00545 MCH Methenyltetrahydro 25.2 41 0.00088 29.3 1.4 39 26-64 168-206 (312)
129 PRK12570 N-acetylmuramic acid- 25.1 92 0.002 26.1 3.5 31 44-74 261-292 (296)
130 TIGR02329 propionate_PrpR prop 25.1 59 0.0013 29.5 2.5 24 53-76 490-513 (526)
131 COG2766 PrkA Putative Ser prot 24.3 67 0.0014 30.5 2.7 29 39-67 616-644 (649)
132 PRK06964 DNA polymerase III su 24.1 1.7E+02 0.0038 25.1 5.0 40 36-77 188-227 (342)
133 COG4770 Acetyl/propionyl-CoA c 23.9 45 0.00098 31.6 1.5 27 39-65 380-406 (645)
134 PRK06476 pyrroline-5-carboxyla 23.8 1.1E+02 0.0023 24.2 3.5 34 40-76 171-204 (258)
135 cd04773 HTH_TioE_rpt2 Second H 23.8 2.2E+02 0.0048 20.0 4.8 33 44-76 49-83 (108)
136 PF11329 DUF3131: Protein of u 23.8 30 0.00065 30.5 0.3 56 51-119 165-227 (367)
137 smart00733 Mterf Mitochondrial 23.6 73 0.0016 16.0 1.8 14 41-54 18-31 (31)
138 PRK10144 formate-dependent nit 23.5 96 0.0021 23.6 3.0 38 31-68 52-89 (126)
139 PF03333 PapB: Adhesin biosynt 23.3 1E+02 0.0023 22.1 3.0 32 33-64 16-48 (91)
140 TIGR03147 cyt_nit_nrfF cytochr 23.0 99 0.0021 23.5 3.0 37 32-68 53-89 (126)
141 PF14490 HHH_4: Helix-hairpin- 22.9 2.3E+02 0.005 19.4 4.7 37 40-79 7-43 (94)
142 KOG1364|consensus 22.8 1.7E+02 0.0037 26.0 4.8 38 42-79 7-46 (356)
143 PF14433 SUKH-3: SUKH-3 immuni 22.8 31 0.00067 25.2 0.2 17 56-72 2-18 (142)
144 PF07798 DUF1640: Protein of u 22.6 1.1E+02 0.0025 23.4 3.3 22 43-64 6-27 (177)
145 PF09784 L31: Mitochondrial ri 22.6 1.1E+02 0.0024 22.7 3.1 25 60-85 40-64 (103)
146 PRK11388 DNA-binding transcrip 22.4 74 0.0016 28.8 2.6 24 53-76 591-614 (638)
147 PF07848 PaaX: PaaX-like prote 22.4 75 0.0016 21.4 2.0 25 41-65 23-47 (70)
148 COG5457 Uncharacterized conser 22.0 1.1E+02 0.0025 20.6 2.8 23 46-68 41-63 (63)
149 PF03918 CcmH: Cytochrome C bi 21.9 60 0.0013 24.8 1.7 29 40-68 61-89 (148)
150 KOG4044|consensus 21.7 68 0.0015 26.2 2.0 59 48-111 124-186 (201)
151 PF15187 Augurin: Oesophageal 21.5 71 0.0015 24.0 1.9 20 42-61 51-70 (114)
152 KOG3450|consensus 21.5 1E+02 0.0022 23.4 2.7 34 45-78 84-118 (119)
153 PRK15424 propionate catabolism 21.4 76 0.0016 29.0 2.4 24 53-76 497-520 (538)
154 PTZ00431 pyrroline carboxylate 21.3 2.4E+02 0.0052 22.5 5.1 34 42-78 177-210 (260)
155 TIGR00112 proC pyrroline-5-car 21.1 2.4E+02 0.0052 22.4 5.0 33 42-77 164-196 (245)
156 PRK00117 recX recombination re 21.0 1.4E+02 0.0031 21.9 3.5 27 42-68 130-156 (157)
157 PF03701 UPF0181: Uncharacteri 20.9 1.1E+02 0.0025 20.0 2.5 19 42-60 17-35 (51)
158 PRK12491 pyrroline-5-carboxyla 20.6 2.4E+02 0.0051 23.0 5.0 33 42-77 184-216 (272)
159 PF10905 DUF2695: Protein of u 20.4 1.8E+02 0.0038 19.0 3.4 26 42-67 19-44 (53)
160 COG1918 FeoA Fe2+ transport sy 20.4 73 0.0016 21.9 1.7 21 43-63 22-42 (75)
161 TIGR00465 ilvC ketol-acid redu 20.3 1.9E+02 0.0041 24.4 4.5 31 44-78 196-227 (314)
162 PF06135 DUF965: Bacterial pro 20.2 1.1E+02 0.0023 21.8 2.5 33 41-79 13-46 (79)
No 1
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=2.3e-26 Score=196.63 Aligned_cols=92 Identities=42% Similarity=0.642 Sum_probs=77.0
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcCCCC----C----------C-c----
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEE----A----------P-V---- 91 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~~~~----~----------~-~---- 91 (129)
+.|++++|+.+|+.|++||+|||+|++|++|||++|||+|||||||++|||+..+..+ + + .
T Consensus 146 ~~s~l~~g~~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 225 (378)
T TIGR00601 146 AASTLVVGSERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPVQQTAASTAAATTETPQHGSV 225 (378)
T ss_pred cccccccchHHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhCCCccccccccCCCcccccccccCCCCCCcch
Confidence 5678999999999999999999999999999999999999999999999997632100 0 0 0
Q ss_pred -------------------cCCCCCCCCCCCccchhhhh------hhhhhhcCCce
Q psy4260 92 -------------------AANEPQGNNIKQFSSVKEIE------IPNLMQGDNKV 122 (129)
Q Consensus 92 -------------------a~~~~~~~n~PqF~~~r~~~------lp~llq~~~~~ 122 (129)
...+.+||++|+|.+||++| |+.|||++++-
T Consensus 226 f~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~ 281 (378)
T TIGR00601 226 FEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQE 281 (378)
T ss_pred hhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhh
Confidence 01236689999999999999 99999998764
No 2
>KOG0011|consensus
Probab=99.90 E-value=2.8e-24 Score=182.07 Aligned_cols=96 Identities=41% Similarity=0.589 Sum_probs=81.3
Q ss_pred CCCCcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcCCCC---------C-----Cc--
Q psy4260 28 PGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVVGEE---------A-----PV-- 91 (129)
Q Consensus 28 ~~~~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~~~~---------~-----~~-- 91 (129)
.+.+.++++.|+.++..|.+||+|||+|++|++|||++|||+|||||||++|||++...+. . ++
T Consensus 122 ~~~aas~Lv~G~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~~~~~p~~~~p~~ 201 (340)
T KOG0011|consen 122 YEIAASTLVVGSEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAAAAELPANAQPLD 201 (340)
T ss_pred hhhhhhhhhccchhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCcccCCCCCCCCChhh
Confidence 3446788999999999999999999999999999999999999999999999999633211 1 11
Q ss_pred ---------cCC--CCCCCCCCCccchhhhh------hhhhhhcCCceE
Q psy4260 92 ---------AAN--EPQGNNIKQFSSVKEIE------IPNLMQGDNKVY 123 (129)
Q Consensus 92 ---------a~~--~~~~~n~PqF~~~r~~~------lp~llq~~~~~~ 123 (129)
..+ ..++||.|||.+||++| |..|||++||.+
T Consensus 202 ~~~~~~~~~~~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqqlg~~n 250 (340)
T KOG0011|consen 202 LFPQGAVEASGGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQLGKQN 250 (340)
T ss_pred cCCccchhhhcCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHHhhhC
Confidence 022 56789999999999999 999999999875
No 3
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=99.47 E-value=8e-14 Score=83.38 Aligned_cols=36 Identities=42% Similarity=0.654 Sum_probs=33.9
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L 76 (129)
+++.|++|++|||++++|++||++++||+++|++||
T Consensus 2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 678999999999999999999999999999999998
No 4
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=99.40 E-value=6.7e-13 Score=78.68 Aligned_cols=37 Identities=38% Similarity=0.696 Sum_probs=35.3
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
++.|++|++|||++++|++||++++||+++|++||++
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 6789999999999999999999999999999999984
No 5
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=99.38 E-value=7e-13 Score=78.35 Aligned_cols=37 Identities=35% Similarity=0.636 Sum_probs=35.1
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
+++.|++|++|||++++|++||++++||+++|++|||
T Consensus 1 ~~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 3678999999999999999999999999999999996
No 6
>KOG0944|consensus
Probab=98.62 E-value=3.7e-08 Score=90.78 Aligned_cols=43 Identities=33% Similarity=0.558 Sum_probs=41.0
Q ss_pred CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP 81 (129)
+..++.+..|++|||++.||++||++.+||+|||+||+|+++.
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWif~h~d 675 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWIFSHMD 675 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence 5789999999999999999999999999999999999999965
No 7
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.24 E-value=1.3e-06 Score=75.48 Aligned_cols=42 Identities=24% Similarity=0.408 Sum_probs=39.3
Q ss_pred CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
..+..+.|++|++|||+|+.|+.|-.+|+-|.|.|++|||++
T Consensus 334 T~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~ 375 (378)
T TIGR00601 334 TPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQ 375 (378)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence 556778999999999999999999999999999999999976
No 8
>KOG0418|consensus
Probab=97.95 E-value=1.1e-05 Score=65.01 Aligned_cols=45 Identities=24% Similarity=0.260 Sum_probs=41.5
Q ss_pred ccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 35 LLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 35 ~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
...+..+..+|+.|.+|||+|+.++.+|+..+||.++|.+.|++|
T Consensus 156 ~~~~~~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 156 LPDDPWDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred CCCCchhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence 456677889999999999999999999999999999999999875
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=97.92 E-value=2.3e-05 Score=47.79 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=34.6
Q ss_pred HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
++.|++|.+| .++++.++.+|++++||+|+|++.|+.+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 6789999999 8999999999999999999999999864
No 10
>KOG0011|consensus
Probab=97.78 E-value=3.1e-05 Score=66.69 Aligned_cols=43 Identities=23% Similarity=0.347 Sum_probs=39.5
Q ss_pred CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260 38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80 (129)
Q Consensus 38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi 80 (129)
..+..+.|++|++|||+|.-|+.|.=+|+-|.|.|++|||++.
T Consensus 295 tpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 295 TPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHS 337 (340)
T ss_pred CHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhc
Confidence 4456778999999999999999999999999999999999884
No 11
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=97.71 E-value=0.00012 Score=44.91 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=32.5
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
+++|.++++. |.+++.|+.-|++++||+++||+..|..
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 5788998887 9999999999999999999999987764
No 12
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=6.4e-05 Score=68.82 Aligned_cols=41 Identities=22% Similarity=0.477 Sum_probs=37.8
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHHcCCCC
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFN-NPDRAVEYLITGIPA 82 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~-n~erAvE~L~~giP~ 82 (129)
+..|.||++|||..+.+.|||-..+| |.|-|.+|||.|+.+
T Consensus 559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdD 600 (749)
T COG5207 559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDD 600 (749)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccC
Confidence 56899999999999999999999988 999999999999654
No 13
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=97.56 E-value=0.00025 Score=43.17 Aligned_cols=38 Identities=18% Similarity=0.420 Sum_probs=34.9
Q ss_pred HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
++.|+.|.+| .++++.+++.|++++||+|+|++-|+.+
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 5679999999 6889999999999999999999999875
No 14
>KOG0944|consensus
Probab=97.51 E-value=0.00015 Score=67.46 Aligned_cols=43 Identities=19% Similarity=0.363 Sum_probs=39.2
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHHHcCCCC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRAS-FNNPDRAVEYLITGIPA 82 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras-~~n~erAvE~L~~giP~ 82 (129)
.++..|.+|++|||..+.++|||-.+ |.+.|.|.+||+.||.|
T Consensus 570 ~d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~HMdD 613 (763)
T KOG0944|consen 570 ADRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEHMDD 613 (763)
T ss_pred hhHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHhccC
Confidence 56778999999999999999999999 66999999999999765
No 15
>KOG2561|consensus
Probab=97.39 E-value=0.00017 Score=64.93 Aligned_cols=39 Identities=31% Similarity=0.476 Sum_probs=35.3
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
.++....+|+|||.+.+++.|||.|+||+|+||.|+.+.
T Consensus 303 ~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI~er 341 (568)
T KOG2561|consen 303 NDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFIIER 341 (568)
T ss_pred cchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHHHHH
Confidence 356778899999999999999999999999999999764
No 16
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=8.1e-05 Score=68.17 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=39.1
Q ss_pred CchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 39 DEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 39 ~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
+.+|++++.|++|||...++|+||...++|.+|+|+|.+++
T Consensus 619 eVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~~N~ 659 (749)
T COG5207 619 EVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVWCIND 659 (749)
T ss_pred cccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEEEEeC
Confidence 45899999999999999999999999999999999999996
No 17
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=97.04 E-value=0.00067 Score=45.02 Aligned_cols=27 Identities=33% Similarity=0.426 Sum_probs=21.2
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
..+.|+++++|||++++|+.|||+-+-
T Consensus 9 ~~~lVd~F~~mGF~~dkVvevlrrlgi 35 (55)
T PF09288_consen 9 DKDLVDQFENMGFERDKVVEVLRRLGI 35 (55)
T ss_dssp SHHHHHHHHHHT--HHHHHHHHHHS--
T ss_pred CHHHHHHHHHcCCcHHHHHHHHHHhCC
Confidence 467899999999999999999998753
No 18
>KOG2561|consensus
Probab=96.77 E-value=0.0018 Score=58.48 Aligned_cols=46 Identities=28% Similarity=0.333 Sum_probs=40.4
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCCcC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAAVV 85 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~~~ 85 (129)
.++.+|.+|+.|||++-.++.||+..+||.+.|...|.-.++.+.+
T Consensus 428 vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L~~s~~n~~~ 473 (568)
T KOG2561|consen 428 VDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLLSASVANEGE 473 (568)
T ss_pred cchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHHHHhCCCCcc
Confidence 3577899999999999999999999999999999999876665533
No 19
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=96.36 E-value=0.009 Score=44.68 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=36.1
Q ss_pred CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
...++.|+.+++- |-+++.|++||+.++||+-.|+-+|.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 4678889999887 999999999999999999999988864
No 20
>KOG0010|consensus
Probab=96.35 E-value=0.0061 Score=55.00 Aligned_cols=39 Identities=36% Similarity=0.551 Sum_probs=34.8
Q ss_pred chHHHHHHHHHcCC-ChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 40 EYGRMVQNIVDMGY-ERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 40 ~~ee~I~~L~eMGF-~reqv~~ALras~~n~erAvE~L~~ 78 (129)
.+....++|-+||| +|+...+||++.+||+++|||-|+.
T Consensus 453 r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 453 RYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 35667899999996 5999999999999999999999985
No 21
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=96.03 E-value=0.00072 Score=44.92 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=22.9
Q ss_pred CCCCCCCCccchhhhh------hhhhhhcCCc
Q psy4260 96 PQGNNIKQFSSVKEIE------IPNLMQGDNK 121 (129)
Q Consensus 96 ~~~~n~PqF~~~r~~~------lp~llq~~~~ 121 (129)
.++||+|+|+.||++| ||.|||+.+.
T Consensus 2 ~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~ 33 (59)
T PF09280_consen 2 EFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQ 33 (59)
T ss_dssp GGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHC
T ss_pred hHHHcChHHHHHHHHHHHCHHHHHHHHHHHhc
Confidence 4689999999999999 9999998754
No 22
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=95.92 E-value=0.016 Score=43.46 Aligned_cols=39 Identities=10% Similarity=0.066 Sum_probs=35.1
Q ss_pred CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~ 77 (129)
...++.|+.+++- |-+|+.|++||++++||+-.|+-||.
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 3678889999887 89999999999999999999998874
No 23
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=95.91 E-value=0.013 Score=49.41 Aligned_cols=72 Identities=15% Similarity=0.152 Sum_probs=50.3
Q ss_pred hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc-CCCCCcC--C-CCCCc----------------cCCCCCCC
Q psy4260 41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT-GIPAAVV--G-EEAPV----------------AANEPQGN 99 (129)
Q Consensus 41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~-giP~~~~--~-~~~~~----------------a~~~~~~~ 99 (129)
.-+.|.+|-++ |..--+|++||..++||.|.|++||-. |+-.... . ..... --.++++-
T Consensus 4 sa~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVA 83 (290)
T TIGR00116 4 TAQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVA 83 (290)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCcccc
Confidence 34568999988 999999999999999999999999974 3211000 0 00000 14457777
Q ss_pred CCCCccchhhhhh
Q psy4260 100 NIKQFSSVKEIEI 112 (129)
Q Consensus 100 n~PqF~~~r~~~l 112 (129)
...+|..|-.-++
T Consensus 84 rne~F~~l~~~ia 96 (290)
T TIGR00116 84 KNAGFKEFANKLL 96 (290)
T ss_pred CChHHHHHHHHHH
Confidence 8889988876663
No 24
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=95.85 E-value=0.017 Score=50.30 Aligned_cols=32 Identities=19% Similarity=0.412 Sum_probs=25.4
Q ss_pred ccccCCCchHHHHHHHHHcCCChHHHHHHHHH
Q psy4260 33 STLLMGDEYGRMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 33 s~~~~g~~~ee~I~~L~eMGF~reqv~~ALra 64 (129)
+.+......++.|++++.|||.||+|+...|+
T Consensus 313 ~~~~~~~p~ddvidKv~~MGf~rDqV~a~v~r 344 (358)
T PF07223_consen 313 PQSGNRHPYDDVIDKVASMGFRRDQVRATVRR 344 (358)
T ss_pred ccccccCcHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 34455566899999999999999999875444
No 25
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=95.84 E-value=0.016 Score=46.41 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=33.6
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
-+.|.+|-++ |..--+|.+||..++||.|.|++||-.
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4568888888 999999999999999999999999974
No 26
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=95.82 E-value=0.017 Score=40.15 Aligned_cols=35 Identities=29% Similarity=0.519 Sum_probs=30.8
Q ss_pred HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 45 I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
|+.+.+.||+++.|..||.++.+|+..|..|++.+
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 56688999999999999999999999999988877
No 27
>PRK09377 tsf elongation factor Ts; Provisional
Probab=95.75 E-value=0.017 Score=48.80 Aligned_cols=77 Identities=14% Similarity=0.166 Sum_probs=53.2
Q ss_pred hHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc-CCCCCc---CCCCCCc----------------cCCCCCCC
Q psy4260 41 YGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT-GIPAAV---VGEEAPV----------------AANEPQGN 99 (129)
Q Consensus 41 ~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~-giP~~~---~~~~~~~----------------a~~~~~~~ 99 (129)
.-..|.+|-++ |..--+|++||..++||.|.|++||-. |+-... .-..... --.++++-
T Consensus 5 s~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVA 84 (290)
T PRK09377 5 TAALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVA 84 (290)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCcccc
Confidence 34678999988 999999999999999999999999974 321100 0000000 14456777
Q ss_pred CCCCccchhhhhhhhhhh
Q psy4260 100 NIKQFSSVKEIEIPNLMQ 117 (129)
Q Consensus 100 n~PqF~~~r~~~lp~llq 117 (129)
....|..|-+-++-++|.
T Consensus 85 rne~F~~l~~~i~~~~l~ 102 (290)
T PRK09377 85 KNEDFQALANEVAEAALA 102 (290)
T ss_pred CChHHHHHHHHHHHHHHh
Confidence 888898887777544444
No 28
>CHL00098 tsf elongation factor Ts
Probab=95.64 E-value=0.021 Score=45.90 Aligned_cols=36 Identities=22% Similarity=0.300 Sum_probs=32.9
Q ss_pred HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
+.|.+|-++ |..--+|++||..++||.|.|++||-.
T Consensus 3 ~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~ 39 (200)
T CHL00098 3 ELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQ 39 (200)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 468888888 899999999999999999999999975
No 29
>KOG2689|consensus
Probab=95.48 E-value=0.022 Score=48.47 Aligned_cols=38 Identities=18% Similarity=0.356 Sum_probs=32.5
Q ss_pred HHHHHHcCCChHHHHHHHHHh-CCCHHHHHHHH-HcCCCC
Q psy4260 45 VQNIVDMGYERSAVTEALRAS-FNNPDRAVEYL-ITGIPA 82 (129)
Q Consensus 45 I~~L~eMGF~reqv~~ALras-~~n~erAvE~L-~~giP~ 82 (129)
++.|++|||++..+.+||--. +-+.+.|++|| +.+..+
T Consensus 4 ~~~l~~mgfps~k~e~al~~~~n~~~e~al~wl~~d~~~d 43 (290)
T KOG2689|consen 4 AQSLEEMGFPSGKAEKALAVYGNRGIEQALDWLEMDHAGD 43 (290)
T ss_pred HHHHHHhcCchhhhhhHhhhhccccHHHHHHHHHhcccCC
Confidence 389999999999999999877 66899999999 666433
No 30
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=95.23 E-value=0.045 Score=41.50 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=34.1
Q ss_pred CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~ 77 (129)
...++-|..+++- |-+|++|++||+.++||+-.|+-.|.
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 4567889988887 99999999999999999999986663
No 31
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=93.25 E-value=0.081 Score=32.95 Aligned_cols=26 Identities=12% Similarity=0.434 Sum_probs=22.4
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
.++.++-|+.+||++.++.+|++...
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 46789999999999999999999884
No 32
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=93.01 E-value=0.18 Score=43.18 Aligned_cols=37 Identities=19% Similarity=0.335 Sum_probs=32.8
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
-..|+.|-++ |-.--+|.+||..++||.|.|+|||-.
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4568888888 888899999999999999999999964
No 33
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=92.30 E-value=0.48 Score=32.07 Aligned_cols=38 Identities=21% Similarity=0.349 Sum_probs=31.8
Q ss_pred HHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
...|+.|-|. +++++++-..|+.|+.|+|.|++-|++-
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 4456776666 3699999999999999999999999863
No 34
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=90.75 E-value=0.13 Score=35.17 Aligned_cols=26 Identities=23% Similarity=0.495 Sum_probs=23.0
Q ss_pred ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 54 ERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 54 ~reqv~~ALras~~n~erAvE~L~~g 79 (129)
++.+++.||-.+++|+++||+||++.
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 88999999999999999999999987
No 35
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=90.72 E-value=0.87 Score=29.96 Aligned_cols=41 Identities=15% Similarity=0.185 Sum_probs=32.4
Q ss_pred CchHHHHHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 39 DEYGRMVQNIVD--MGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 39 ~~~ee~I~~L~e--MGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
...|+.|.+... -|-+|+-+++-|+.++-|++.||+-|++.
T Consensus 7 ~vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR 49 (53)
T PF11547_consen 7 QVPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR 49 (53)
T ss_dssp GS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence 446788877544 49999999999999999999999999876
No 36
>KOG1071|consensus
Probab=89.19 E-value=0.93 Score=39.54 Aligned_cols=40 Identities=15% Similarity=0.122 Sum_probs=35.2
Q ss_pred chHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 40 EYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 40 ~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
..-+.|.+|-+- |++-..|++||..++||...|.+||..-
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~ 85 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKK 85 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 456778888776 9999999999999999999999999754
No 37
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=88.98 E-value=1.8 Score=29.02 Aligned_cols=36 Identities=22% Similarity=0.204 Sum_probs=30.5
Q ss_pred CchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260 39 DEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVE 74 (129)
Q Consensus 39 ~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE 74 (129)
...++.|.++... |-..+=++++|..++||.++|+.
T Consensus 10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~ 46 (63)
T smart00804 10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALK 46 (63)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH
Confidence 3456677777666 99999999999999999999995
No 38
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=88.64 E-value=0.43 Score=28.79 Aligned_cols=24 Identities=25% Similarity=0.398 Sum_probs=21.0
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+++-++.||+.++||..+|.+.|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 678889999999999999999877
No 39
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=87.55 E-value=0.82 Score=29.20 Aligned_cols=33 Identities=21% Similarity=0.238 Sum_probs=25.8
Q ss_pred HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHH
Q psy4260 43 RMVQNIVDM-GYERSAVTEALRASFNNPDRAVEY 75 (129)
Q Consensus 43 e~I~~L~eM-GF~reqv~~ALras~~n~erAvE~ 75 (129)
+.|.++... |-..+-+.+.|..++||.++|+.-
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~ 35 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQN 35 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHH
Confidence 456666655 889999999999999999999963
No 40
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=85.10 E-value=1.6 Score=34.40 Aligned_cols=27 Identities=19% Similarity=0.443 Sum_probs=23.9
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
..++.++.|..+||++.+|.+|+++..
T Consensus 146 ~~~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 146 ARDELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 357889999999999999999999874
No 41
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=82.35 E-value=1.9 Score=26.84 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=21.1
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L~ 77 (129)
-.|......|+.|+||+-+|+|.++
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHhC
Confidence 3467778899999999999999763
No 42
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=81.63 E-value=4.1 Score=31.76 Aligned_cols=41 Identities=17% Similarity=0.060 Sum_probs=35.7
Q ss_pred CCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 37 MGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 37 ~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
......+.|.-+.+-|.+.+.|++||..++ |+-+|++.|..
T Consensus 110 ~s~~~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l~~ 150 (153)
T COG4008 110 HSEPPVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKILRM 150 (153)
T ss_pred cCCCcHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHHHH
Confidence 345567889999999999999999999998 99999998754
No 43
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=79.28 E-value=2.3 Score=28.51 Aligned_cols=20 Identities=15% Similarity=0.674 Sum_probs=18.3
Q ss_pred HHHHHcCCChHHHHHHHHHh
Q psy4260 46 QNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 46 ~~L~eMGF~reqv~~ALras 65 (129)
+.|++|||...+|++-+|.+
T Consensus 7 ~dLi~lGf~~~tA~~IIrqA 26 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQA 26 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHH
Confidence 56999999999999999887
No 44
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.22 E-value=6.1 Score=31.51 Aligned_cols=27 Identities=11% Similarity=0.384 Sum_probs=24.2
Q ss_pred CchHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 39 DEYGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 39 ~~~ee~I~~L~eMGF~reqv~~ALras 65 (129)
...++.++-|+.+||++.++.+|+++.
T Consensus 153 ~~~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 153 SVFRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 345789999999999999999999987
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.04 E-value=6.4 Score=31.33 Aligned_cols=26 Identities=12% Similarity=0.266 Sum_probs=23.6
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras 65 (129)
..++.+.-|+.+||++.++.+|+++.
T Consensus 151 ~~~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 151 AAEDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 45789999999999999999999986
No 46
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.98 E-value=5.6 Score=31.47 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=24.1
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
..++.++-|+.+||++.++.+|++...
T Consensus 142 ~~~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 142 IYHESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 357889999999999999999999884
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.21 E-value=3 Score=33.59 Aligned_cols=27 Identities=30% Similarity=0.613 Sum_probs=24.0
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
.++.++-|+.+||.+.++.+|++....
T Consensus 144 ~~ea~~AL~~LGy~~~ea~~al~~v~~ 170 (196)
T PRK13901 144 FKELEQSIVNMGFDRKLVNSAIKEIML 170 (196)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 578999999999999999999987644
No 48
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.14 E-value=5.7 Score=31.43 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=24.5
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
..++.+..|+.+||++.++.+||++...
T Consensus 144 ~~~e~~~aL~~LGy~~~ea~~al~~v~~ 171 (186)
T PRK14600 144 INDDALAALISLGYEKTKAFNAIQKIKP 171 (186)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 3578899999999999999999998753
No 49
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.12 E-value=3.5 Score=32.67 Aligned_cols=26 Identities=8% Similarity=0.344 Sum_probs=23.6
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
.++.++-|+.+||++.+|.+|++...
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~ 167 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQ 167 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcc
Confidence 57889999999999999999999873
No 50
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.96 E-value=7.6 Score=30.88 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=23.0
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras 65 (129)
.++.+.-|+.+||.+.++.+|++..
T Consensus 149 ~~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 149 DRELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4788999999999999999999887
No 51
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=74.88 E-value=7.9 Score=32.87 Aligned_cols=44 Identities=20% Similarity=0.212 Sum_probs=36.7
Q ss_pred cCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 36 LMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 36 ~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
+.....++.++-|.+-|.+.+++..+++.++|++.+|++|+-.+
T Consensus 169 ~~~~~~~~~~~~L~~~~~~~~~a~~~~~l~~G~p~~A~~~~~~~ 212 (319)
T PRK08769 169 FKLPPAHEALAWLLAQGVSERAAQEALDAARGHPGLAAQWLRED 212 (319)
T ss_pred CCCcCHHHHHHHHHHcCCChHHHHHHHHHcCCCHHHHHHHhcCc
Confidence 34455677788898899999999999999999999999987543
No 52
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=74.53 E-value=8.6 Score=32.60 Aligned_cols=41 Identities=20% Similarity=0.131 Sum_probs=32.0
Q ss_pred CCchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 38 GDEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 38 g~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
....++..+-|.+- |.+.+++..+++.++|++.+|++|+-+
T Consensus 166 ~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~~~ 207 (334)
T PRK07993 166 PPPEQYALTWLSREVTMSQDALLAALRLSAGAPGAALALLQP 207 (334)
T ss_pred CCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 33345555567665 899999999999999999999988743
No 53
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=74.08 E-value=1 Score=28.94 Aligned_cols=26 Identities=31% Similarity=0.523 Sum_probs=15.9
Q ss_pred HHHHHHH-HHcCCChHHHHHHHHHhCC
Q psy4260 42 GRMVQNI-VDMGYERSAVTEALRASFN 67 (129)
Q Consensus 42 ee~I~~L-~eMGF~reqv~~ALras~~ 67 (129)
++.|..| ..|||+|+++..||++...
T Consensus 3 e~vv~~Ls~tMGY~kdeI~eaL~~~~~ 29 (46)
T PF08587_consen 3 EDVVSKLSKTMGYDKDEIYEALESSEP 29 (46)
T ss_dssp HCCHHHHHCTT---HHHHHHHCCSSS-
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHcCCC
Confidence 3445554 3699999999999998543
No 54
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=69.40 E-value=6.2 Score=31.88 Aligned_cols=28 Identities=18% Similarity=0.491 Sum_probs=23.6
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
..++.|..|+.+||.+.++.+|+++..-
T Consensus 155 ~~~~~v~AL~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 155 ALEEAVEALVALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred hhhHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 3445599999999999999999988764
No 55
>KOG2239|consensus
Probab=67.37 E-value=8.6 Score=31.65 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=27.7
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L 76 (129)
++-|+.+|.. +-+|.++++||+.++||+=-|+=-|
T Consensus 172 ~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 172 AKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMEL 207 (209)
T ss_pred hhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHh
Confidence 3347776655 8999999999999999998887433
No 56
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=67.16 E-value=8.9 Score=33.84 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=28.5
Q ss_pred HHHHHHHcC--CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 44 MVQNIVDMG--YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 44 ~I~~L~eMG--F~reqv~~ALras~~n~erAvE~L 76 (129)
.|+++|.=| |+++-|..|||.+.||...|+=+|
T Consensus 44 avdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 44 AVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 467777777 999999999999999999999433
No 57
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.07 E-value=19 Score=28.52 Aligned_cols=26 Identities=15% Similarity=0.333 Sum_probs=23.7
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
.++.+..|..+||++.+|.+|++...
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 57889999999999999999999884
No 58
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=62.96 E-value=12 Score=25.44 Aligned_cols=25 Identities=12% Similarity=0.385 Sum_probs=20.4
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHH
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALra 64 (129)
.-+..++.+..|||++++|+..|+.
T Consensus 10 R~daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 10 RIDAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3466788899999999999887664
No 59
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=61.54 E-value=67 Score=24.34 Aligned_cols=27 Identities=26% Similarity=0.383 Sum_probs=22.7
Q ss_pred HHHHHHHcCCChHHHHHHHHHhCCCHH
Q psy4260 44 MVQNIVDMGYERSAVTEALRASFNNPD 70 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALras~~n~e 70 (129)
+-=+|+.||..+..|+.-|++-+-|++
T Consensus 118 kYfKMl~~GvP~~aVk~KM~~eGlDp~ 144 (148)
T PF10152_consen 118 KYFKMLKMGVPREAVKQKMQAEGLDPS 144 (148)
T ss_pred HHHHHHHcCCCHHHHHHHHHHcCCCHH
Confidence 344566999999999999999988875
No 60
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=58.88 E-value=25 Score=29.39 Aligned_cols=38 Identities=24% Similarity=0.374 Sum_probs=30.3
Q ss_pred HHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 44 MVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 44 ~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~giP 81 (129)
.+..+++. |-++++|.++|.+++|++-.|+-.++.++.
T Consensus 238 a~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~~ 276 (299)
T PRK05441 238 AVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGLD 276 (299)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCCC
Confidence 34444443 899999999999999999999987777743
No 61
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=57.62 E-value=28 Score=26.89 Aligned_cols=34 Identities=6% Similarity=0.103 Sum_probs=26.8
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
+..++.++++||+++++++.+... ...+++.|.+
T Consensus 186 ~a~~~~~~~~Gl~~~~a~~~~~~~---~~g~~~~~~~ 219 (245)
T PRK07634 186 ESLIEATKSYGVDEETAKHLVIQM---ISGSASMLEQ 219 (245)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHhC
Confidence 667788999999999999988776 5556666654
No 62
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=56.15 E-value=33 Score=26.81 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=24.5
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
.++.+..|..+||++.++.++++....
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 578899999999999999999998864
No 63
>PRK01905 DNA-binding protein Fis; Provisional
Probab=51.14 E-value=16 Score=24.56 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=21.9
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+++-++++|+.++||..+|.+.|
T Consensus 37 ~E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 37 VEKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 678899999999999999999866
No 64
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=50.66 E-value=30 Score=24.52 Aligned_cols=24 Identities=21% Similarity=0.191 Sum_probs=22.2
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|++.-++.+|+.++||..+|.++|
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 788899999999999999999877
No 65
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=50.21 E-value=26 Score=22.34 Aligned_cols=24 Identities=8% Similarity=0.199 Sum_probs=19.3
Q ss_pred chHHHHHHHHHc---CCChHHHHHHHH
Q psy4260 40 EYGRMVQNIVDM---GYERSAVTEALR 63 (129)
Q Consensus 40 ~~ee~I~~L~eM---GF~reqv~~ALr 63 (129)
..+..+++|+.- ||+.++|..|+.
T Consensus 20 Sk~~l~~QL~se~ge~Ft~e~A~YAv~ 46 (48)
T PF07553_consen 20 SKQGLYDQLTSEYGEGFTEEEAQYAVD 46 (48)
T ss_pred CHHHHHHHHHhhcccCCCHHHHHHHHH
Confidence 456778899886 899999988864
No 66
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=49.49 E-value=27 Score=29.73 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=36.9
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCC
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~ 83 (129)
|+.+-..|..+++.+=-|+..|+++++|++-|...| ++-++..||++
T Consensus 314 ~sHgATvG~ldee~LFYL~SRGi~~~eA~~llv~gF------~~~vi~~i~~e 360 (366)
T TIGR01981 314 ASHGATVGQIDDEQLFYLRSRGIDEEEARRLLIRGF------LGEIIEEIPDE 360 (366)
T ss_pred EecceeecCCCHHHHHHHHHcCCCHHHHHHHHHHHH------HHHHHHhCCCH
Confidence 344555688899999999999999999999998886 44456666653
No 67
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=49.26 E-value=9.7 Score=26.31 Aligned_cols=28 Identities=21% Similarity=0.351 Sum_probs=19.5
Q ss_pred CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 52 GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 52 GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
|-..+++.+-|...-.++..|+++|.+.
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 6777777777766666777788888754
No 68
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=48.77 E-value=20 Score=29.21 Aligned_cols=40 Identities=10% Similarity=0.292 Sum_probs=28.7
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhC----CCHH---HHHHHHHcCC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASF----NNPD---RAVEYLITGI 80 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~----~n~e---rAvE~L~~gi 80 (129)
-+.+|+-|.++||+++++.+.++++- .+.| +=++||.+.+
T Consensus 243 l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m 289 (345)
T PF02536_consen 243 LKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEM 289 (345)
T ss_dssp HHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHh
Confidence 46688999999999999999998863 2444 4558998763
No 69
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=48.55 E-value=46 Score=27.84 Aligned_cols=40 Identities=15% Similarity=0.226 Sum_probs=31.7
Q ss_pred HHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 42 GRMVQNIVD-MGYERSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 42 ee~I~~L~e-MGF~reqv~~ALras~~n~erAvE~L~~giP 81 (129)
++.+..+++ .|-++++|.++|.+++|++-.|+=-++.++.
T Consensus 231 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~~~ 271 (291)
T TIGR00274 231 ARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILSTLS 271 (291)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhCCC
Confidence 445555554 3899999999999999999999977777743
No 70
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=48.40 E-value=43 Score=28.52 Aligned_cols=42 Identities=14% Similarity=0.230 Sum_probs=32.9
Q ss_pred cCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 36 LMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 36 ~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
+.....++.++-|.+.|.+ .+..+|+.++|++-+|++++-++
T Consensus 164 ~~~~~~~~~~~~L~~~~~~--~~~~~l~l~~G~p~~A~~~~~~~ 205 (319)
T PRK06090 164 VTPPSTAQAMQWLKGQGIT--VPAYALKLNMGSPLKTLAMMKEG 205 (319)
T ss_pred CCCCCHHHHHHHHHHcCCc--hHHHHHHHcCCCHHHHHHHhCCC
Confidence 3445567777889999987 45688999999999999987544
No 71
>KOG3763|consensus
Probab=48.18 E-value=74 Score=29.92 Aligned_cols=33 Identities=15% Similarity=0.149 Sum_probs=29.7
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVE 74 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE 74 (129)
++++..+++- |-..+=+...|..++||.|+|+.
T Consensus 536 ~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k 569 (585)
T KOG3763|consen 536 DEKLLKFQEETGLNSEWSTMCLEQNNWDYERALK 569 (585)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHH
Confidence 7778877766 99999999999999999999995
No 72
>KOG0943|consensus
Probab=47.88 E-value=53 Score=34.62 Aligned_cols=43 Identities=19% Similarity=0.229 Sum_probs=36.4
Q ss_pred CCCchHHHHHH--HHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 37 MGDEYGRMVQN--IVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 37 ~g~~~ee~I~~--L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
.....|+.|++ .+=-|-+|+-+++-|+..+-|++.||+-|++.
T Consensus 185 AsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 185 ASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred cccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 34456888765 34569999999999999999999999999987
No 73
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=47.73 E-value=35 Score=25.40 Aligned_cols=33 Identities=15% Similarity=0.229 Sum_probs=24.8
Q ss_pred CCchHHHHHHHHHcCCChHHHHHHHHHhCCCHH
Q psy4260 38 GDEYGRMVQNIVDMGYERSAVTEALRASFNNPD 70 (129)
Q Consensus 38 g~~~ee~I~~L~eMGF~reqv~~ALras~~n~e 70 (129)
....+++|+=|..-|.+.+++.+||+.+.++..
T Consensus 20 ~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~~ 52 (136)
T PF04695_consen 20 NSPLEKKIAFLESKGLTEEEIDEALGRAGSPPA 52 (136)
T ss_dssp CS-HHHHHHHHHHCT--HHHHHHHHHHHT--S-
T ss_pred cCCHHHHHHHHHcCCCCHHHHHHHHHhcCCccc
Confidence 455789999999999999999999999988773
No 74
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=46.62 E-value=46 Score=28.78 Aligned_cols=40 Identities=23% Similarity=0.344 Sum_probs=33.2
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~giP 81 (129)
++.+..+++. |-+++++.++|+.+++++-.|+=.++.|+.
T Consensus 234 dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~~~~~~ 274 (298)
T COG2103 234 DRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVMLLTGLS 274 (298)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHHHhCCC
Confidence 4456666665 899999999999999999999987777754
No 75
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=46.51 E-value=36 Score=20.95 Aligned_cols=29 Identities=17% Similarity=0.115 Sum_probs=22.7
Q ss_pred HHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 49 VDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 49 ~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
.....+..-..|=||+-.||++.|.+-|.
T Consensus 25 ~~~~~~d~~llRFLRARkf~v~~A~~mL~ 53 (55)
T PF03765_consen 25 EKEDHDDNFLLRFLRARKFDVEKAFKMLK 53 (55)
T ss_dssp HTSS-SHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHccCCHHHHHHHHH
Confidence 34467888899999999999999998764
No 76
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=46.11 E-value=29 Score=26.76 Aligned_cols=24 Identities=17% Similarity=0.458 Sum_probs=18.7
Q ss_pred chHHHHHHHHHcCCChHHHHHHHH
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALR 63 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALr 63 (129)
..++...+|.+.||+.+++.+||.
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~Al~ 45 (155)
T PF04361_consen 22 DQDDLTRELSAAGFEDEEINKALD 45 (155)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHH
Confidence 356667889999999998877653
No 77
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=45.56 E-value=52 Score=27.52 Aligned_cols=40 Identities=25% Similarity=0.395 Sum_probs=31.0
Q ss_pred HHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 42 GRMVQNIVD-MGYERSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 42 ee~I~~L~e-MGF~reqv~~ALras~~n~erAvE~L~~giP 81 (129)
++.+..+++ .|-+++.|.++|.++.|++-.|+=-++.|++
T Consensus 232 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~~~ 272 (296)
T PRK12570 232 ARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILTGMD 272 (296)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhCCC
Confidence 444444444 3899999999999999999999976776643
No 78
>KOG3837|consensus
Probab=44.55 E-value=56 Score=30.11 Aligned_cols=14 Identities=29% Similarity=0.359 Sum_probs=11.8
Q ss_pred HHhCCCHHHHHHHH
Q psy4260 63 RASFNNPDRAVEYL 76 (129)
Q Consensus 63 ras~~n~erAvE~L 76 (129)
-++.||.|.|=.||
T Consensus 222 AKs~gD~eqAK~yl 235 (523)
T KOG3837|consen 222 AKSKGDQEQAKMYL 235 (523)
T ss_pred hhhhccHHHHHHHH
Confidence 46789999999987
No 79
>PRK15115 response regulator GlrR; Provisional
Probab=44.33 E-value=20 Score=30.27 Aligned_cols=24 Identities=17% Similarity=0.199 Sum_probs=22.5
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|.+.|
T Consensus 398 ~E~~~i~~al~~~~gn~~~aA~~L 421 (444)
T PRK15115 398 FELNYLRKLLQITKGNVTHAARMA 421 (444)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 789999999999999999999977
No 80
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=43.97 E-value=20 Score=30.58 Aligned_cols=24 Identities=33% Similarity=0.434 Sum_probs=22.6
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|.+.|
T Consensus 429 ~E~~~i~~aL~~~~gn~~~aA~~L 452 (469)
T PRK10923 429 LERTLLTTALRHTQGHKQEAARLL 452 (469)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 789999999999999999999977
No 81
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=43.50 E-value=20 Score=31.68 Aligned_cols=24 Identities=25% Similarity=0.183 Sum_probs=22.8
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|...|
T Consensus 490 ~Er~~i~~aL~~~~gn~~~aA~~L 513 (534)
T TIGR01817 490 SERERLIAALEQAGWVQAKAARLL 513 (534)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 899999999999999999999876
No 82
>PRK00912 ribonuclease P protein component 3; Provisional
Probab=43.42 E-value=51 Score=26.01 Aligned_cols=36 Identities=17% Similarity=0.143 Sum_probs=29.5
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
..++.+..+..+||++++++.+|... +++-++|+..
T Consensus 184 ~~~~~~~l~~~~Gl~~~~~~~~~~~~---~~~i~~~~~~ 219 (237)
T PRK00912 184 SPREMIALAELFGMEEDEALKALSYY---PESIIKKNRN 219 (237)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHh---HHHHHHhhcc
Confidence 56788999999999999999998875 6777777643
No 83
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=43.06 E-value=73 Score=22.55 Aligned_cols=36 Identities=14% Similarity=0.121 Sum_probs=26.5
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
-+..++-.+.+|++++++++....+ ..-++++|..+
T Consensus 24 ~eal~~a~v~~Gl~~~~A~~lv~~t---~~G~a~ll~~~ 59 (107)
T PF14748_consen 24 IEALADAAVAQGLPREEARKLVAQT---FIGAAKLLEES 59 (107)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHH---HHHHHHHHHHC
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHcc
Confidence 3677888899999999999977766 56677777654
No 84
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=42.50 E-value=21 Score=31.63 Aligned_cols=24 Identities=25% Similarity=0.292 Sum_probs=22.8
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|.+.|
T Consensus 468 ~Er~~I~~aL~~~~gn~~~aA~~L 491 (509)
T PRK05022 468 FQRQLIRQALAQHQGNWAAAARAL 491 (509)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 889999999999999999999876
No 85
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=41.77 E-value=49 Score=21.38 Aligned_cols=32 Identities=28% Similarity=0.316 Sum_probs=26.2
Q ss_pred HHHH-HHcCCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 45 VQNI-VDMGYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 45 I~~L-~eMGF~reqv~~ALras~~n~erAvE~L 76 (129)
|.-. -.+|-++++.+.|.++.+++...--.||
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~vG~~~~~V~~~L 55 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRAVGNSRAAVRAYL 55 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHCcCHHHHHHHH
Confidence 4443 4569999999999999999988777777
No 86
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=41.53 E-value=23 Score=30.03 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=22.5
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+...+||+.++||..+|.+.|
T Consensus 426 ~E~~~i~~al~~~~gn~~~aA~~L 449 (463)
T TIGR01818 426 FERPLLEAALQHTRGHKQEAAALL 449 (463)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 789999999999999999999976
No 87
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=41.51 E-value=47 Score=26.09 Aligned_cols=37 Identities=11% Similarity=0.226 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
+|.++.+.+.||+++++.+..+.-.-|.|. ++..+..
T Consensus 83 ~el~~iy~~~Gl~~~~a~~i~~~l~~~~~~-~~~m~~e 119 (213)
T PF01988_consen 83 EELVEIYRAKGLSEEDAEEIAEELSKDKDA-LDFMMRE 119 (213)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHhCchH-HHHHHhh
Confidence 456678889999999999999999899999 9887744
No 88
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=41.42 E-value=23 Score=29.53 Aligned_cols=24 Identities=29% Similarity=0.360 Sum_probs=22.7
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|.+.|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~L 309 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELL 309 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 889999999999999999999876
No 89
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=40.84 E-value=24 Score=29.67 Aligned_cols=24 Identities=33% Similarity=0.401 Sum_probs=22.8
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+++...+||+.++||..+|.+.|
T Consensus 292 ~E~~~I~~aL~~~~gn~~~aA~~L 315 (329)
T TIGR02974 292 YEIELLQQALAEAQFNQRKAAELL 315 (329)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 899999999999999999999876
No 90
>TIGR01980 sufB FeS assembly protein SufB. This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=39.28 E-value=45 Score=29.51 Aligned_cols=46 Identities=13% Similarity=0.200 Sum_probs=36.3
Q ss_pred cccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCC
Q psy4260 32 ESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83 (129)
Q Consensus 32 ~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~ 83 (129)
+..-..|..+++.+=-|+..|+++++|++-|...| ++-++.+||.+
T Consensus 394 sHgAtvG~ideeqLFYL~SRGi~~~eA~~Lii~gF------~~evi~~ip~e 439 (448)
T TIGR01980 394 EHEATVSKISEEQLFYLMSRGLSEEDARAMIVRGF------VEPITKELPME 439 (448)
T ss_pred EeeeeccCCCHHHHHHHHHcCCCHHHHHHHHHHHh------HHHHHHhCChH
Confidence 34455688899999999999999999999998885 44456666654
No 91
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=38.86 E-value=42 Score=24.77 Aligned_cols=25 Identities=20% Similarity=0.433 Sum_probs=20.0
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
....+.|.+-||+++.++++|++.+
T Consensus 72 ~~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 72 NNSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3346667778999999999999864
No 92
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=38.61 E-value=26 Score=21.70 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=15.8
Q ss_pred HHHHHhCCCHHHHHHHHHcC
Q psy4260 60 EALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 60 ~ALras~~n~erAvE~L~~g 79 (129)
+.+..-+||.++|..||.+.
T Consensus 2 ~~a~~vfgd~~~a~~Wl~~p 21 (54)
T PF09722_consen 2 KQAEEVFGDEDKARRWLRTP 21 (54)
T ss_pred hHHHHHHCCHHHHHHHHHCh
Confidence 34566679999999999754
No 93
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=38.15 E-value=78 Score=27.60 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=29.7
Q ss_pred chHHHHHHHH-HcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 40 EYGRMVQNIV-DMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 40 ~~ee~I~~L~-eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
..++.++.|. ..|.+.+.+..+++.++|++.+|++|+.
T Consensus 177 ~~~~i~~~L~~~~~~~~~~a~~la~~s~G~~~~A~~l~~ 215 (394)
T PRK07940 177 SVEAVAEVLVRRDGVDPETARRAARASQGHIGRARRLAT 215 (394)
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence 3455555665 4599999999999999999999987753
No 94
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=37.01 E-value=1e+02 Score=22.40 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=29.2
Q ss_pred hHHHHHHHHH--cCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 41 YGRMVQNIVD--MGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 41 ~ee~I~~L~e--MGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
.++.++.+.. .+|.+++++.+|... .+...++|++|
T Consensus 31 l~~Ia~~i~~~~s~~t~~di~~vl~~~---~~~~~~~l~~G 68 (124)
T PF14848_consen 31 LEDIAEEIAKEGSTLTRADIEAVLNAL---KDEMIEALMNG 68 (124)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHH---HHHHHHHHhCC
Confidence 3555677764 689999999999998 57788899988
No 95
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=36.42 E-value=31 Score=29.09 Aligned_cols=24 Identities=25% Similarity=0.288 Sum_probs=22.3
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|.+.|
T Consensus 417 ~E~~~i~~al~~~~gn~~~aA~~L 440 (457)
T PRK11361 417 VEKRIIMEVLEQQEGNRTRTALML 440 (457)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 689999999999999999999876
No 96
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=36.35 E-value=58 Score=24.24 Aligned_cols=33 Identities=18% Similarity=0.188 Sum_probs=24.3
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHH
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRA 72 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erA 72 (129)
..++..+-|...|++++++...++.++||+-+|
T Consensus 156 ~~~~~~~~l~~~gi~~~~~~~i~~~~~g~~r~~ 188 (188)
T TIGR00678 156 SEEALLQWLIRQGISEEAAELLLALAGGSPGAA 188 (188)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHcCCCcccC
Confidence 345556667777888888888888888887654
No 97
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=36.18 E-value=31 Score=28.05 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=24.6
Q ss_pred HHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHH
Q psy4260 42 GRMVQNIVDM-GYERSAVTEALRASFNNPDRAV 73 (129)
Q Consensus 42 ee~I~~L~eM-GF~reqv~~ALras~~n~erAv 73 (129)
++.+..+++. |-++++|.++|.+++|++-.|+
T Consensus 223 ~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 223 ERAIRIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 3444445544 8999999999999999988775
No 98
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=35.27 E-value=52 Score=28.87 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=27.3
Q ss_pred HHHHHHHcC--CChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 44 MVQNIVDMG--YERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 44 ~I~~L~eMG--F~reqv~~ALras~~n~erAvE~L~ 77 (129)
.|+..|.-| |+|+.+.-|||.+.||.-.|+ ||+
T Consensus 44 aVdRVM~EgslyDreLAALAikQa~GD~~EAI-FLl 78 (367)
T COG3626 44 AVDRVMTEGSLYDRELAALALKQASGDLVEAI-FLL 78 (367)
T ss_pred HHHHHhhccchhHHHHHHHHHHHhcchHHHHH-HHH
Confidence 356666666 999999999999999999999 553
No 99
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=34.93 E-value=34 Score=28.88 Aligned_cols=24 Identities=42% Similarity=0.386 Sum_probs=22.3
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
++|+...+||+.++||..+|++.|
T Consensus 405 ~E~~~i~~al~~~~gn~~~aA~~L 428 (445)
T TIGR02915 405 AEREAVRKAIARVDGNIARAAELL 428 (445)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 688999999999999999999877
No 100
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=34.65 E-value=34 Score=28.60 Aligned_cols=27 Identities=26% Similarity=0.348 Sum_probs=23.8
Q ss_pred HHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 48 IVDMGYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 48 L~eMGF~reqv~~ALras~~n~erAvE~L 76 (129)
|.+ ++|+..++||+.++||..+|++.|
T Consensus 402 l~~--~e~~~i~~~l~~~~gn~~~aa~~L 428 (441)
T PRK10365 402 LVE--VEKEVILAALEKTGGNKTEAARQL 428 (441)
T ss_pred HHH--HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 444 689999999999999999999876
No 101
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=34.22 E-value=54 Score=27.40 Aligned_cols=23 Identities=13% Similarity=-0.018 Sum_probs=21.4
Q ss_pred CCChHHHHHHHHHhCCCHHHHHH
Q psy4260 52 GYERSAVTEALRASFNNPDRAVE 74 (129)
Q Consensus 52 GF~reqv~~ALras~~n~erAvE 74 (129)
|++.++|++.|.+++|++-+|++
T Consensus 269 ~~~~~~a~~~l~~~~g~~~~~l~ 291 (291)
T TIGR00274 269 TLSASEAKVLLDRHGGFLRQALD 291 (291)
T ss_pred CCCHHHHHHHHHHcCCcHHHhhC
Confidence 79999999999999999999874
No 102
>PRK03430 hypothetical protein; Validated
Probab=33.43 E-value=56 Score=25.58 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=18.9
Q ss_pred chHHHHHHHHHcCCChHHHHHHH
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEAL 62 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~AL 62 (129)
..++...+|.+-||+++.+.+||
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~AL 44 (157)
T PRK03430 22 DQDKLEDDLTDAGFHREDIYNAL 44 (157)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHH
Confidence 45677889999999999887765
No 103
>PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional
Probab=33.13 E-value=62 Score=29.08 Aligned_cols=47 Identities=9% Similarity=0.091 Sum_probs=36.1
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCCC
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPAA 83 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~~ 83 (129)
++..-..|..+++.+--|+..|+++++|++-|...| ++-++..||.+
T Consensus 422 ~sHgATvG~ideeqLFYL~SRGi~e~eA~~Llv~gF------~~evi~~ip~e 468 (486)
T PRK11814 422 VEHEATTSKISEDQLFYCRQRGISEEDAVSMIVNGF------CKEVFQELPME 468 (486)
T ss_pred EEeeeecCCCCHHHHHHHHHcCCCHHHHHHHHHHHH------HHHHHHHCCcH
Confidence 334455688899999999999999999999998886 34455556543
No 104
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=32.94 E-value=46 Score=20.78 Aligned_cols=21 Identities=10% Similarity=0.289 Sum_probs=16.1
Q ss_pred HHHHHHHcCCChHHHHHHHHH
Q psy4260 44 MVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALra 64 (129)
.|..|.+.||+-+++++.|+.
T Consensus 48 ~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 48 EIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHTTTHHHHHHHHH--
T ss_pred HHHHHHHCcCCHHHHHHHHcc
Confidence 467788889999999988864
No 105
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=32.55 E-value=66 Score=19.97 Aligned_cols=20 Identities=15% Similarity=0.551 Sum_probs=16.3
Q ss_pred HHHHHHHcCCChHHHHHHHH
Q psy4260 44 MVQNIVDMGYERSAVTEALR 63 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALr 63 (129)
.|..|.++||+-+++++.|.
T Consensus 49 ~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 49 FIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHcCCCHHHHHHHHh
Confidence 46778888999999888875
No 106
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=32.47 E-value=1.2e+02 Score=25.73 Aligned_cols=40 Identities=15% Similarity=0.033 Sum_probs=30.9
Q ss_pred CCchHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 38 GDEYGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 38 g~~~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~ 77 (129)
....++..+-|.+- ++..+++..+|+.++|.+.+|++|+-
T Consensus 164 ~~~~~~~~~~L~~~~~~~~~~~~~~~l~la~Gsp~~A~~l~~ 205 (328)
T PRK05707 164 LPSNEESLQWLQQALPESDERERIELLTLAGGSPLRALQLHE 205 (328)
T ss_pred CcCHHHHHHHHHHhcccCChHHHHHHHHHcCCCHHHHHHHHC
Confidence 34455666666664 57888899999999999999998754
No 107
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=32.28 E-value=52 Score=23.51 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=19.7
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHcCCC
Q psy4260 55 RSAVTEALRASFNNPDRAVEYLITGIP 81 (129)
Q Consensus 55 reqv~~ALras~~n~erAvE~L~~giP 81 (129)
|.+++.++ -.||.+.|++|+-.+-|
T Consensus 5 r~~I~~~I--~~g~i~~Ai~w~~~~~~ 29 (145)
T PF10607_consen 5 RKKIRQAI--LNGDIDPAIEWLNENFP 29 (145)
T ss_pred HHHHHHHH--HcCCHHHHHHHHHHcCH
Confidence 56777787 67899999999977644
No 108
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=32.18 E-value=33 Score=26.97 Aligned_cols=31 Identities=6% Similarity=0.097 Sum_probs=23.4
Q ss_pred ccCCCchHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 35 LLMGDEYGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 35 ~~~g~~~ee~I~~L~eMGF~reqv~~ALras 65 (129)
...|..+++.+=-|+..|+++++|++-|-..
T Consensus 198 AtvG~idee~LFYL~SRGl~~~eA~~Liv~g 228 (229)
T PF01458_consen 198 ATVGQIDEEQLFYLMSRGLSEEEARKLIVKG 228 (229)
T ss_dssp EEEEES-HHHHHHHHCTT--HHHHHHHHHHH
T ss_pred eEeecCCHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 3457788999999999999999999977654
No 109
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=31.72 E-value=1.3e+02 Score=25.72 Aligned_cols=42 Identities=24% Similarity=0.290 Sum_probs=30.9
Q ss_pred CCchHHHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 38 GDEYGRMVQNIVDM-GYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 38 g~~~ee~I~~L~eM-GF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
....++.++-|.+. +.+.+++..+++.++|.+.+|++++-++
T Consensus 165 ~~~~~~~~~~L~~~~~~~~~~~~~~~~l~~g~p~~A~~~~~~~ 207 (325)
T PRK06871 165 PPEEQQALDWLQAQSSAEISEILTALRINYGRPLLALTFLEQG 207 (325)
T ss_pred CCCHHHHHHHHHHHhccChHHHHHHHHHcCCCHHHHHHHhhCC
Confidence 34455556667665 4555678889999999999999987544
No 110
>CHL00085 ycf24 putative ABC transporter
Probab=31.37 E-value=62 Score=29.05 Aligned_cols=46 Identities=11% Similarity=0.110 Sum_probs=35.8
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCCCC
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGIPA 82 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~giP~ 82 (129)
++..-..|..+++.+--|+..|+++++|++-|...| ++-++.+||.
T Consensus 421 ~sHgAtvG~ideeqLFYL~SRGi~e~eA~~Llv~gF------~~evi~~ip~ 466 (485)
T CHL00085 421 IEHEASTSKIGEEQLFYFLQRGINLEEAISLLISGF------CKDVFNKLPM 466 (485)
T ss_pred EEEeeccCCCCHHHHHHHHHcCCCHHHHHHHHHHHH------HHHHHHhCCH
Confidence 344455688899999999999999999999998886 3345555554
No 111
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=30.96 E-value=81 Score=25.71 Aligned_cols=37 Identities=14% Similarity=0.266 Sum_probs=30.6
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
+|.++.+.+.||++++++...+.-.-|.+..++..+.
T Consensus 101 ~el~~iy~~~G~~~~~a~~~~~~l~~~~~~~~~~~~~ 137 (234)
T cd02433 101 AELALIYRAKGLDEEEAKRVASQLMNDPEQALDTLAR 137 (234)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhCcchhHHHHHH
Confidence 4456677788999999999988888889998887664
No 112
>PHA01732 proline-rich protein
Probab=30.82 E-value=1.5e+02 Score=21.70 Aligned_cols=17 Identities=18% Similarity=0.382 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCCCCC
Q psy4260 1 MIGAPAAATSTPSTPVS 17 (129)
Q Consensus 1 ~~~~p~a~tstp~~p~~ 17 (129)
|+|||.++..-+.-+..
T Consensus 3 ~fgAP~~p~ppPpPpP~ 19 (94)
T PHA01732 3 IFRAPKPPEPPAPLPPA 19 (94)
T ss_pred ccCCCCCCCCCCCCCCC
Confidence 57999887766644433
No 113
>PRK10948 cysteine desulfurase activator complex subunit SufD; Provisional
Probab=30.76 E-value=77 Score=28.00 Aligned_cols=36 Identities=8% Similarity=0.111 Sum_probs=31.0
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhC
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASF 66 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~ 66 (129)
|+.+-..|..+|+.+=-|+..|+++++|++-|...|
T Consensus 359 ~sHgATvG~ldee~LFYL~SRGi~~~~A~~Llv~gF 394 (424)
T PRK10948 359 CSHGATVGRIDDEQLFYLRSRGINQQDAQQMIIYAF 394 (424)
T ss_pred EEeeeecCCCCHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 444555788899999999999999999999998886
No 114
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=30.71 E-value=71 Score=19.13 Aligned_cols=23 Identities=26% Similarity=0.302 Sum_probs=17.4
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 55 RSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 55 reqv~~ALras~~n~erAvE~L~~g 79 (129)
+.+.+.++. .||.+.|++|+-..
T Consensus 5 ~~~i~~~i~--~g~~~~a~~~~~~~ 27 (58)
T smart00668 5 RKRIRELIL--KGDWDEALEWLSSL 27 (58)
T ss_pred HHHHHHHHH--cCCHHHHHHHHHHc
Confidence 456666665 68999999999655
No 115
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=29.80 E-value=90 Score=18.16 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=16.4
Q ss_pred HHHHHHHHcCCChHHHHHHHHH
Q psy4260 43 RMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 43 e~I~~L~eMGF~reqv~~ALra 64 (129)
+.|..-++||.+.+++++=|+.
T Consensus 7 ~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 7 ELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHh
Confidence 4678889999999999987754
No 116
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=29.40 E-value=73 Score=26.59 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=25.5
Q ss_pred HHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 45 VQNIVDM-GYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 45 I~~L~eM-GF~reqv~~ALras~~n~erAvE~L 76 (129)
+.-||-. |++.+++++.|.+++|++.+|++.+
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence 3344433 6999999999999999999999643
No 117
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=29.29 E-value=54 Score=25.19 Aligned_cols=26 Identities=15% Similarity=0.321 Sum_probs=21.4
Q ss_pred HHHHHHHcCCChHHHHHHHHHhCCCH
Q psy4260 44 MVQNIVDMGYERSAVTEALRASFNNP 69 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALras~~n~ 69 (129)
-+.+|.+.||+++.+..||-.....+
T Consensus 13 fa~~l~~~G~~~~~I~~aL~id~~~l 38 (185)
T PF07506_consen 13 FARRLEERGFSREEIAAALGIDKSYL 38 (185)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence 47899999999999999987664444
No 118
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=27.99 E-value=1.7e+02 Score=23.93 Aligned_cols=38 Identities=11% Similarity=0.070 Sum_probs=29.1
Q ss_pred hHHHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 41 YGRMVQNIVDM--GYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 41 ~ee~I~~L~eM--GF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
.++.++-|..- |.+++.+.+++..++|++.+|.+|+..
T Consensus 154 ~~~~~~~l~~~~~~~~~~~~~~l~~~~~g~~~~a~~~~~~ 193 (313)
T PRK05564 154 KEEIEKFISYKYNDIKEEEKKSAIAFSDGIPGKVEKFIED 193 (313)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHhcc
Confidence 44445555544 788999999999999999999987643
No 119
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.71 E-value=18 Score=25.95 Aligned_cols=25 Identities=36% Similarity=0.507 Sum_probs=19.1
Q ss_pred CCCCccchhhhh---hhhhhhcCCceEE
Q psy4260 100 NIKQFSSVKEIE---IPNLMQGDNKVYT 124 (129)
Q Consensus 100 n~PqF~~~r~~~---lp~llq~~~~~~~ 124 (129)
-.|+|++.|..- +|+||--+|+|.-
T Consensus 50 s~~~Fd~vk~~gyiGIPall~~d~~vVl 77 (85)
T COG4545 50 SRPEFDEVKSNGYIGIPALLTDDGKVVL 77 (85)
T ss_pred cchhHHhhhhcCcccceEEEeCCCcEEE
Confidence 456666666544 9999999999865
No 120
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=27.15 E-value=65 Score=22.75 Aligned_cols=24 Identities=4% Similarity=0.321 Sum_probs=18.4
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHH
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALra 64 (129)
....+..|+--||+.+.+.++|+.
T Consensus 95 ~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 95 KQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHhh
Confidence 345678899999999999999886
No 121
>smart00646 Ami_3 Ami_3.
Probab=27.15 E-value=18 Score=25.04 Aligned_cols=35 Identities=14% Similarity=0.234 Sum_probs=21.7
Q ss_pred HHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcCC
Q psy4260 46 QNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80 (129)
Q Consensus 46 ~~L~eMGF~reqv~~ALras~~n~erAvE~L~~gi 80 (129)
.-|+||||=.+...+++-....+.++.++.+..||
T Consensus 79 avlvE~gfisN~~d~~~l~~~~~~~~iA~~I~~gi 113 (113)
T smart00646 79 AVLVELGFITNPSDARKLKSAAYQQKLARAIAKGI 113 (113)
T ss_pred eeeEEecccCCHHHHHHhCCHHHHHHHHHHHHhhC
Confidence 34788998665555554444444566667776653
No 122
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=27.12 E-value=53 Score=22.49 Aligned_cols=24 Identities=21% Similarity=0.567 Sum_probs=18.8
Q ss_pred ccCCCchHHHHHHHHHcCCChHHH
Q psy4260 35 LLMGDEYGRMVQNIVDMGYERSAV 58 (129)
Q Consensus 35 ~~~g~~~ee~I~~L~eMGF~reqv 58 (129)
.+.|+..+...+.|.+|||.++.+
T Consensus 51 ~lQGD~r~~v~~~L~~~g~~~~~i 74 (77)
T cd00474 51 ELQGDQRKKIKEFLIKMGFAKDNI 74 (77)
T ss_pred EEeCcHHHHHHHHHHHcCCCHHHe
Confidence 345777788889999999998653
No 123
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=26.62 E-value=1.7e+02 Score=25.00 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=30.4
Q ss_pred CCchHHHHHHHHHcC----CChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 38 GDEYGRMVQNIVDMG----YERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 38 g~~~ee~I~~L~eMG----F~reqv~~ALras~~n~erAvE~L~~g 79 (129)
....++..+-|...| |+.+.+...++.++|++-+|+++|-.+
T Consensus 199 pl~~~~~~~~L~~~~~~~~~~~~~~~~i~~~s~G~pr~Al~ll~~~ 244 (351)
T PRK09112 199 PLDDDELKKALSHLGSSQGSDGEITEALLQRSKGSVRKALLLLNYG 244 (351)
T ss_pred CCCHHHHHHHHHHhhcccCCCHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 334455555555544 667888889999999999999988544
No 124
>PRK02264 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional
Probab=26.24 E-value=38 Score=29.54 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=30.8
Q ss_pred CCCCCCcccccCCCchHHHHHHHHHcCCChHHHHHHHH
Q psy4260 26 TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALR 63 (129)
Q Consensus 26 ~~~~~~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALr 63 (129)
+|.+.+.|-.+.+..-|-.+-+|.++||+-.+++.|.-
T Consensus 169 pT~SlaGsvqi~aRvvE~a~hKl~elgfd~~~I~~~~G 206 (317)
T PRK02264 169 PTASLAGSVQVSARVVEVALHKLHELGFDLTKIVSAAG 206 (317)
T ss_pred cCCcceeEEEeehhHHHHHHHHHHHcCCCHHHheecee
Confidence 34556677777788889999999999999999987643
No 125
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=26.11 E-value=60 Score=22.81 Aligned_cols=20 Identities=25% Similarity=0.484 Sum_probs=16.4
Q ss_pred HHHHHHHcCCChHHHHHHHH
Q psy4260 44 MVQNIVDMGYERSAVTEALR 63 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALr 63 (129)
..+.|--||+++++..+||+
T Consensus 68 llkrLN~f~it~~e~~~alk 87 (87)
T PF13331_consen 68 LLKRLNMFGITREEFEEALK 87 (87)
T ss_pred HHHHHHHcCCCHHHHHHHhC
Confidence 46778888999999998874
No 126
>TIGR03120 one_C_mch methenyltetrahydromethanopterin cyclohydrolase. Members of this protein family are the enzyme methenyltetrahydromethanopterin cyclohydrolase, a key enzyme for tetrahydromethanopterin (H4MPT)-linked C1 transfer metabolism.
Probab=25.93 E-value=39 Score=29.37 Aligned_cols=39 Identities=10% Similarity=0.210 Sum_probs=30.7
Q ss_pred CCCCCCcccccCCCchHHHHHHHHHcCCChHHHHHHHHH
Q psy4260 26 TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 26 ~~~~~~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALra 64 (129)
+|.+.+.|-.+.+..-|-.+-+|.++||+-.+++.|.-.
T Consensus 168 pT~SlaGsvqi~aRvvE~a~hKl~elgfd~~~I~~~~G~ 206 (312)
T TIGR03120 168 PTASLVGSIQISARVVETALHKLEELGFDVTKIVSAAGT 206 (312)
T ss_pred cCCcceeEEEeehhHHHHHHHHHHHcCCCHHHheeceec
Confidence 345566677777888899999999999999999877433
No 127
>smart00299 CLH Clathrin heavy chain repeat homology.
Probab=25.65 E-value=1.3e+02 Score=21.04 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=16.5
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
++.+--+..||..++-+.-+|+.. +|+++|++|.-
T Consensus 86 ~~~~~l~~k~~~~~~Al~~~l~~~-~d~~~a~~~~~ 120 (140)
T smart00299 86 EEAVELYKKDGNFKDAIVTLIEHL-GNYEKAIEYFV 120 (140)
T ss_pred HHHHHHHHhhcCHHHHHHHHHHcc-cCHHHHHHHHH
Confidence 344444445555444333333322 55666666554
No 128
>cd00545 MCH Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+) from N(5)-formyltetrahydromethanopterin (formyl- H4MPT), in the third step of the reaction to reduce CO2 to CH4. The protein functions as a homodimer or homotrimer, depending on the organism.
Probab=25.22 E-value=41 Score=29.26 Aligned_cols=39 Identities=13% Similarity=0.219 Sum_probs=30.8
Q ss_pred CCCCCCcccccCCCchHHHHHHHHHcCCChHHHHHHHHH
Q psy4260 26 TTPGNAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 26 ~~~~~~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALra 64 (129)
+|.+.+.|-.+.+..-|-.+-+|.++||+-.+++.|.-.
T Consensus 168 pT~SlaGsvqi~aRvvE~a~hKl~elgfd~~~I~~~~G~ 206 (312)
T cd00545 168 PTASLAGSVQIVARVVEVALHKAHELGFDLNKVKDGAGS 206 (312)
T ss_pred cCCcceeEEEeehhHHHHHHHHHHHcCCCHHHheecccc
Confidence 345566677777888899999999999999999877443
No 129
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=25.12 E-value=92 Score=26.06 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=25.5
Q ss_pred HHHHHHHc-CCChHHHHHHHHHhCCCHHHHHH
Q psy4260 44 MVQNIVDM-GYERSAVTEALRASFNNPDRAVE 74 (129)
Q Consensus 44 ~I~~L~eM-GF~reqv~~ALras~~n~erAvE 74 (129)
++.-||.+ |++.+++++.|.+++|+..+|++
T Consensus 261 k~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l~ 292 (296)
T PRK12570 261 KLAILMILTGMDVEQARAALSHADGFLRKAIE 292 (296)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCChHHHHHH
Confidence 34445443 79999999999999999999996
No 130
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=25.06 E-value=59 Score=29.49 Aligned_cols=24 Identities=33% Similarity=0.209 Sum_probs=22.4
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
|+|+..++||+.++||..+|++.|
T Consensus 490 ~Er~~I~~aL~~~~Gn~~~aA~~L 513 (526)
T TIGR02329 490 VEALAVRAALERFGGDRDAAAKAL 513 (526)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 678999999999999999999877
No 131
>COG2766 PrkA Putative Ser protein kinase [Signal transduction mechanisms]
Probab=24.34 E-value=67 Score=30.53 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=23.7
Q ss_pred CchHHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 39 DEYGRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 39 ~~~ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
....+.|+.|++-||++.+|+.+|+-...
T Consensus 616 kk~ne~V~rlverGYt~~~a~~l~~~~~~ 644 (649)
T COG2766 616 KKHNDFVARLVERGYTRKQARLLLEWYGR 644 (649)
T ss_pred HHHHHHHHHHHHcCccHHHHHHHHHHHHH
Confidence 34566799999999999999999886543
No 132
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=24.07 E-value=1.7e+02 Score=25.10 Aligned_cols=40 Identities=10% Similarity=-0.002 Sum_probs=30.6
Q ss_pred cCCCchHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 36 LMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 36 ~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
+.....++.++-|.+.|.+..++ .|..++|++.+|++|+-
T Consensus 188 ~~~~~~~~~~~~L~~~~~~~~~~--~l~~~~Gsp~~Al~~~~ 227 (342)
T PRK06964 188 MTVPAPEAAAAWLAAQGVADADA--LLAEAGGAPLAALALAS 227 (342)
T ss_pred ecCCCHHHHHHHHHHcCCChHHH--HHHHcCCCHHHHHHHHC
Confidence 34455677788898889876554 57889999999998873
No 133
>COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]
Probab=23.93 E-value=45 Score=31.58 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=24.1
Q ss_pred CchHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 39 DEYGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 39 ~~~ee~I~~L~eMGF~reqv~~ALras 65 (129)
..|+-.|.+|+--|-+|++|++.|+.+
T Consensus 380 ~~YDpMiAKLi~~G~dR~eAl~rl~~A 406 (645)
T COG4770 380 PFYDPMIAKLIVHGADREEALDRLRRA 406 (645)
T ss_pred cccchHHHHHhhcCCCHHHHHHHHHHH
Confidence 358999999999999999999998765
No 134
>PRK06476 pyrroline-5-carboxylate reductase; Reviewed
Probab=23.82 E-value=1.1e+02 Score=24.16 Aligned_cols=34 Identities=9% Similarity=-0.022 Sum_probs=26.6
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L 76 (129)
--++.++-...+||+++++++.+... ...+++.|
T Consensus 171 ~~~~~~~~~~~~Gl~~~~a~~~~~~~---~~G~~~l~ 204 (258)
T PRK06476 171 ILETATGWLEEQGLKRQKARAYLAPL---FASLAQDA 204 (258)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHH
Confidence 34677788899999999999988776 56666663
No 135
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=23.78 E-value=2.2e+02 Score=20.00 Aligned_cols=33 Identities=9% Similarity=0.149 Sum_probs=23.7
Q ss_pred HHHHHHHcCCChHHHHHHHHHhC--CCHHHHHHHH
Q psy4260 44 MVQNIVDMGYERSAVTEALRASF--NNPDRAVEYL 76 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~ALras~--~n~erAvE~L 76 (129)
.|..|.++||+-++++..|.... ++.+...+.|
T Consensus 49 ~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l 83 (108)
T cd04773 49 LIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAAL 83 (108)
T ss_pred HHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHH
Confidence 57889999999999999988642 3344444433
No 136
>PF11329 DUF3131: Protein of unknown function (DUF3131); InterPro: IPR021478 This bacterial family of proteins has no known function.
Probab=23.76 E-value=30 Score=30.47 Aligned_cols=56 Identities=16% Similarity=0.189 Sum_probs=39.4
Q ss_pred cCCChHHHHHHHHHhCCCHHHHHHH------HHcCCCCCcCCCCCCccCCCCCCCCCCCccchhhhh-hhhhhhcC
Q psy4260 51 MGYERSAVTEALRASFNNPDRAVEY------LITGIPAAVVGEEAPVAANEPQGNNIKQFSSVKEIE-IPNLMQGD 119 (129)
Q Consensus 51 MGF~reqv~~ALras~~n~erAvE~------L~~giP~~~~~~~~~~a~~~~~~~n~PqF~~~r~~~-lp~llq~~ 119 (129)
+|+ ++=+.++|+.-+-|+.+|+++ -+.|+ ..+...||.+.|.....++ .|+||.|+
T Consensus 165 lGy-e~YAA~~~~lwG~~~~~a~~~~~~~~~~i~Gv------------~vp~d~r~~~~~~~~~~v~sePylL~gl 227 (367)
T PF11329_consen 165 LGY-EEYAARGFQLWGFDVPKAYRPEPYKTVDIYGV------------SVPYDTRDPRFFGAHNYVVSEPYLLDGL 227 (367)
T ss_pred ccH-HHHHHHHHHHcCCCccccccCCCcceeEEece------------EccccCccchhccCCCcccchhHHHHHH
Confidence 456 566778888888888888865 12232 2335577999997777777 99999875
No 137
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=23.58 E-value=73 Score=16.02 Aligned_cols=14 Identities=14% Similarity=0.408 Sum_probs=10.6
Q ss_pred hHHHHHHHHHcCCC
Q psy4260 41 YGRMVQNIVDMGYE 54 (129)
Q Consensus 41 ~ee~I~~L~eMGF~ 54 (129)
-+..++-|.+|||+
T Consensus 18 l~~~~~~l~~~g~~ 31 (31)
T smart00733 18 LKPKVEFLKELGFS 31 (31)
T ss_pred hhHHHHHHHHcCCC
Confidence 35578889999985
No 138
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=23.52 E-value=96 Score=23.56 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=28.8
Q ss_pred CcccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCC
Q psy4260 31 AESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNN 68 (129)
Q Consensus 31 ~~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n 68 (129)
+.|+-.-.......|.+.+.-|-+.++++.-|..-+||
T Consensus 52 adSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~ 89 (126)
T PRK10144 52 LESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGD 89 (126)
T ss_pred hhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 33443334445667888889999999999999999886
No 139
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=23.32 E-value=1e+02 Score=22.08 Aligned_cols=32 Identities=16% Similarity=0.231 Sum_probs=20.7
Q ss_pred ccccCCCchHHHHHHHHHc-CCChHHHHHHHHH
Q psy4260 33 STLLMGDEYGRMVQNIVDM-GYERSAVTEALRA 64 (129)
Q Consensus 33 s~~~~g~~~ee~I~~L~eM-GF~reqv~~ALra 64 (129)
..+..|..+++....|+++ +-.-++++.||+.
T Consensus 16 ~~L~pG~vs~e~F~lLl~ls~IrS~kiI~AL~d 48 (91)
T PF03333_consen 16 GYLIPGKVSEEHFWLLLELSSIRSEKIIAALRD 48 (91)
T ss_dssp C---TT-S-HHHHHHHHHHS----HHHHHHHHH
T ss_pred CccCCCCcCHHHHHHHHHHCCCCcHHHHHHHHH
Confidence 3466799999999999999 6889999999985
No 140
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=23.04 E-value=99 Score=23.45 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=28.2
Q ss_pred cccccCCCchHHHHHHHHHcCCChHHHHHHHHHhCCC
Q psy4260 32 ESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNN 68 (129)
Q Consensus 32 ~s~~~~g~~~ee~I~~L~eMGF~reqv~~ALras~~n 68 (129)
.|+-.-.......|.+.+.-|-+.++++.-|..-+||
T Consensus 53 dS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 53 ESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred hcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 3433333445667888889999999999999999886
No 141
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=22.87 E-value=2.3e+02 Score=19.38 Aligned_cols=37 Identities=11% Similarity=0.142 Sum_probs=25.5
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~g 79 (129)
...+.+..|.++|++...+.+..+..+. .|++-|-.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~---~ai~~l~~n 43 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGD---DAIEILKEN 43 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-T---THHHHHHH-
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhH---HHHHHHHHC
Confidence 4566789999999999999999998765 566666555
No 142
>KOG1364|consensus
Probab=22.81 E-value=1.7e+02 Score=26.01 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCC--ChHHHHHHHHHhCCCHHHHHHHHHcC
Q psy4260 42 GRMVQNIVDMGY--ERSAVTEALRASFNNPDRAVEYLITG 79 (129)
Q Consensus 42 ee~I~~L~eMGF--~reqv~~ALras~~n~erAvE~L~~g 79 (129)
...|++.++.+- .-+.|+.-|.++.||.+.|+..+|.+
T Consensus 7 ~~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~ 46 (356)
T KOG1364|consen 7 RALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEH 46 (356)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHh
Confidence 456788888765 67889999999999999999977754
No 143
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=22.77 E-value=31 Score=25.17 Aligned_cols=17 Identities=35% Similarity=0.216 Sum_probs=9.5
Q ss_pred HHHHHHHHHhCCCHHHH
Q psy4260 56 SAVTEALRASFNNPDRA 72 (129)
Q Consensus 56 eqv~~ALras~~n~erA 72 (129)
++|+.+|++++|-++|-
T Consensus 2 ~~v~~~L~~aGW~~~R~ 18 (142)
T PF14433_consen 2 EKVIELLRAAGWYEGRK 18 (142)
T ss_pred HHHHHHHHHcCCCCCcc
Confidence 45556666666655443
No 144
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=22.60 E-value=1.1e+02 Score=23.39 Aligned_cols=22 Identities=14% Similarity=0.433 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCChHHHHHHHHH
Q psy4260 43 RMVQNIVDMGYERSAVTEALRA 64 (129)
Q Consensus 43 e~I~~L~eMGF~reqv~~ALra 64 (129)
..|++|..-||+++||..-+++
T Consensus 6 ~~v~~Le~~Gft~~QAe~i~~~ 27 (177)
T PF07798_consen 6 KFVKRLEAAGFTEEQAEAIMKA 27 (177)
T ss_pred HHHHHHHHCCCCHHHHHHHHHH
Confidence 3578999999999999876554
No 145
>PF09784 L31: Mitochondrial ribosomal protein L31; InterPro: IPR016340 This group represents a predicted mitochondrial ribosomal protein L31, fungal type [, ].
Probab=22.58 E-value=1.1e+02 Score=22.69 Aligned_cols=25 Identities=28% Similarity=0.309 Sum_probs=18.5
Q ss_pred HHHHHhCCCHHHHHHHHHcCCCCCcC
Q psy4260 60 EALRASFNNPDRAVEYLITGIPAAVV 85 (129)
Q Consensus 60 ~ALras~~n~erAvE~L~~giP~~~~ 85 (129)
.||..- |-.-.++++|+..+|.+.+
T Consensus 40 ~al~~~-~~~~~~~~~~~~~~P~E~e 64 (103)
T PF09784_consen 40 EALKKK-GKQCKALERLKFEFPKESE 64 (103)
T ss_pred HHHHHc-CCcHHHHHHHHHhCCChhh
Confidence 555443 6778899999988887755
No 146
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=22.40 E-value=74 Score=28.77 Aligned_cols=24 Identities=17% Similarity=0.180 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
++|+..++||+.++||..+|.+.|
T Consensus 591 ~E~~~i~~al~~~~gn~~~aA~~L 614 (638)
T PRK11388 591 LEKEAIINAAQVCGGRIQEMAALL 614 (638)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 678999999999999999999876
No 147
>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=22.40 E-value=75 Score=21.36 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=18.7
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHh
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRAS 65 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras 65 (129)
....|.-+.+||+++..+|.||...
T Consensus 23 ~~~Li~ll~~~Gv~e~avR~alsRl 47 (70)
T PF07848_consen 23 VASLIRLLAAFGVSESAVRTALSRL 47 (70)
T ss_dssp HHHHHHHHCCTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHH
Confidence 3556888889999999999998654
No 148
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=22.00 E-value=1.1e+02 Score=20.57 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=19.4
Q ss_pred HHHHHcCCChHHHHHHHHHhCCC
Q psy4260 46 QNIVDMGYERSAVTEALRASFNN 68 (129)
Q Consensus 46 ~~L~eMGF~reqv~~ALras~~n 68 (129)
.+|-|.|.+|.++.+...+.+|+
T Consensus 41 ~~L~DiGisR~d~~~e~~k~fw~ 63 (63)
T COG5457 41 HLLSDIGISRADIEAEAAKPFWR 63 (63)
T ss_pred HHHHHcCCCHHHHHHHHHHhhcC
Confidence 56889999999999988887763
No 149
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=21.89 E-value=60 Score=24.81 Aligned_cols=29 Identities=7% Similarity=0.295 Sum_probs=22.9
Q ss_pred chHHHHHHHHHcCCChHHHHHHHHHhCCC
Q psy4260 40 EYGRMVQNIVDMGYERSAVTEALRASFNN 68 (129)
Q Consensus 40 ~~ee~I~~L~eMGF~reqv~~ALras~~n 68 (129)
...+.|.+++..|-++++++..|..-+|+
T Consensus 61 dmR~~I~~~l~~G~s~~eI~~~~v~rYG~ 89 (148)
T PF03918_consen 61 DMRREIREMLAEGKSDEEIIDYFVERYGE 89 (148)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHhcCc
Confidence 34567888889999999999999999885
No 150
>KOG4044|consensus
Probab=21.72 E-value=68 Score=26.22 Aligned_cols=59 Identities=19% Similarity=0.227 Sum_probs=30.8
Q ss_pred HHHcCCChHHHHHHH-HHhCCCHHHHHHHHHcCCCCCcCCCCCCcc---CCCCCCCCCCCccchhhhh
Q psy4260 48 IVDMGYERSAVTEAL-RASFNNPDRAVEYLITGIPAAVVGEEAPVA---ANEPQGNNIKQFSSVKEIE 111 (129)
Q Consensus 48 L~eMGF~reqv~~AL-ras~~n~erAvE~L~~giP~~~~~~~~~~a---~~~~~~~n~PqF~~~r~~~ 111 (129)
|++-|.+..-|..|- .+++.|-+.|++-+-.. -.. -...+ -++....|+|+|.+++.++
T Consensus 124 Ll~rgl~VhvVaDacSSRs~~DR~~Al~r~rq~-G~~----lstsEsvI~~Lvgd~~~pkFkei~kLi 186 (201)
T KOG4044|consen 124 LLERGLNVHVVADACSSRSNQDRDLALERMRQA-GAN----LSTSESVILNLVGDKNHPKFKEIQKLI 186 (201)
T ss_pred HHhCCceEEEEeehhccccchhHHHHHHHHHhc-CCc----ccchHHHHHHHhcCCCCccHHHHHHHh
Confidence 556666554444432 23455556666655321 000 00000 2333445999999999998
No 151
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=21.51 E-value=71 Score=24.04 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=15.6
Q ss_pred HHHHHHHHHcCCChHHHHHH
Q psy4260 42 GRMVQNIVDMGYERSAVTEA 61 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~A 61 (129)
+.-|++++=|||++.+-..=
T Consensus 51 QQW~qQFlYmGFDEak~E~D 70 (114)
T PF15187_consen 51 QQWYQQFLYMGFDEAKFEDD 70 (114)
T ss_pred HHHHHHHHHhcchHHHhhhh
Confidence 45689999999998775443
No 152
>KOG3450|consensus
Probab=21.49 E-value=1e+02 Score=23.40 Aligned_cols=34 Identities=18% Similarity=0.295 Sum_probs=28.6
Q ss_pred HHHH-HHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 45 VQNI-VDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 45 I~~L-~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
|+.| -+|-.++..|++-||..+||+-.|+.-|++
T Consensus 84 lelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 84 LELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 4443 367789999999999999999999988875
No 153
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=21.36 E-value=76 Score=29.02 Aligned_cols=24 Identities=21% Similarity=0.261 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q psy4260 53 YERSAVTEALRASFNNPDRAVEYL 76 (129)
Q Consensus 53 F~reqv~~ALras~~n~erAvE~L 76 (129)
++++...++|+.++||..+|.+.|
T Consensus 497 ~Er~~I~~~L~~~~Gn~~~aA~~L 520 (538)
T PRK15424 497 LLAATLQQALERFNGDKTAAANYL 520 (538)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 478899999999999999999987
No 154
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=21.26 E-value=2.4e+02 Score=22.50 Aligned_cols=34 Identities=12% Similarity=0.126 Sum_probs=25.2
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHc
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~~ 78 (129)
|..++-.+.+|++|+++++-...+ ..-+++.|..
T Consensus 177 ~al~~~~v~~Gl~~~~a~~l~~~~---~~G~a~ll~~ 210 (260)
T PTZ00431 177 ESLIDAGVKNGLNRDVSKNLVLQT---ILGSVHMVKA 210 (260)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHh
Confidence 667888899999999999965555 4556665543
No 155
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=21.12 E-value=2.4e+02 Score=22.40 Aligned_cols=33 Identities=18% Similarity=0.140 Sum_probs=25.4
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
+..++-.+.+||+++++++....+ ..-++++|.
T Consensus 164 ~al~~~~v~~Gl~~~~A~~lv~~~---~~G~a~l~~ 196 (245)
T TIGR00112 164 EALADAGVKQGLPRELALELAAQT---VKGAAKLLE 196 (245)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHH
Confidence 667788899999999999976655 455666664
No 156
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=20.97 E-value=1.4e+02 Score=21.88 Aligned_cols=27 Identities=15% Similarity=0.482 Sum_probs=20.5
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCC
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNN 68 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n 68 (129)
...++.|+--||+-+.+.++|+...++
T Consensus 130 ~Ki~~~L~rkGF~~~~I~~~l~~~~~~ 156 (157)
T PRK00117 130 AKLVRFLARRGFSMDVIQRVLRNALDD 156 (157)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHhhhcc
Confidence 445677888899999998888876543
No 157
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=20.89 E-value=1.1e+02 Score=20.05 Aligned_cols=19 Identities=11% Similarity=0.204 Sum_probs=16.0
Q ss_pred HHHHHHHHHcCCChHHHHH
Q psy4260 42 GRMVQNIVDMGYERSAVTE 60 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ 60 (129)
-|.|++||+-|.+..+|++
T Consensus 17 vE~Iq~LMaqGmSsgEAI~ 35 (51)
T PF03701_consen 17 VERIQELMAQGMSSGEAIA 35 (51)
T ss_pred HHHHHHHHHhcccHHHHHH
Confidence 3578999999999988876
No 158
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=20.57 E-value=2.4e+02 Score=22.99 Aligned_cols=33 Identities=12% Similarity=0.057 Sum_probs=25.1
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHH
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~n~erAvE~L~ 77 (129)
|..++-.++|||+++++++-.... ..-+++.|.
T Consensus 184 eal~~a~v~~Gl~~~~A~~l~~~t---~~G~a~ll~ 216 (272)
T PRK12491 184 EAMADAAVLGGMPRKQAYKFAAQA---VLGSAKMVL 216 (272)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHH
Confidence 667888899999999999866655 455666654
No 159
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=20.42 E-value=1.8e+02 Score=18.99 Aligned_cols=26 Identities=19% Similarity=0.012 Sum_probs=21.7
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCC
Q psy4260 42 GRMVQNIVDMGYERSAVTEALRASFN 67 (129)
Q Consensus 42 ee~I~~L~eMGF~reqv~~ALras~~ 67 (129)
.-..+-|..|+++.+.+...|++.+|
T Consensus 19 r~t~~fl~~~~~~~~~vl~~l~~nGg 44 (53)
T PF10905_consen 19 RLTRQFLRQRQLDWEDVLEWLRENGG 44 (53)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCC
Confidence 33566788999999999999999877
No 160
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=20.38 E-value=73 Score=21.86 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCChHHHHHHHH
Q psy4260 43 RMVQNIVDMGYERSAVTEALR 63 (129)
Q Consensus 43 e~I~~L~eMGF~reqv~~ALr 63 (129)
...+.|++|||-+...+.-++
T Consensus 22 ~~~~RL~~mG~~~G~~i~vi~ 42 (75)
T COG1918 22 GLRRRLLSMGIVPGASITVVR 42 (75)
T ss_pred HHHHHHHHcCCCCCCEEEEEE
Confidence 667899999998766554433
No 161
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=20.31 E-value=1.9e+02 Score=24.40 Aligned_cols=31 Identities=13% Similarity=0.230 Sum_probs=21.8
Q ss_pred HHHHHHHcCCChHHHHH-HHHHhCCCHHHHHHHHHc
Q psy4260 44 MVQNIVDMGYERSAVTE-ALRASFNNPDRAVEYLIT 78 (129)
Q Consensus 44 ~I~~L~eMGF~reqv~~-ALras~~n~erAvE~L~~ 78 (129)
.++.|+++||+++.|.+ ++... ..+++.+..
T Consensus 196 ~~ealv~~G~~~e~A~~~~~~~~----~g~~~l~~e 227 (314)
T TIGR00465 196 GFDTLVEAGYQPELAYFETVHEL----KLIVDLIYE 227 (314)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHH----HHHHHHHHH
Confidence 56888999999999887 44444 446665543
No 162
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=20.25 E-value=1.1e+02 Score=21.77 Aligned_cols=33 Identities=30% Similarity=0.514 Sum_probs=24.9
Q ss_pred hHHHHHHHHHcCCChHHHHHHHHHhCCCH-HHHHHHHHcC
Q psy4260 41 YGRMVQNIVDMGYERSAVTEALRASFNNP-DRAVEYLITG 79 (129)
Q Consensus 41 ~ee~I~~L~eMGF~reqv~~ALras~~n~-erAvE~L~~g 79 (129)
.+..|..++. +|-+||+.-++|+ ++-|.||++|
T Consensus 13 ~~~~~~~iL~------~Vy~AL~EKGYnPinQivGYllSG 46 (79)
T PF06135_consen 13 KEKEIREILK------QVYAALEEKGYNPINQIVGYLLSG 46 (79)
T ss_pred chhhHHHHHH------HHHHHHHHcCCChHHHHHhheecC
Confidence 3445555543 6889999998875 7888999999
Done!