Query gi|254780834|ref|YP_003065247.1| DNA primase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 648
No_of_seqs 198 out of 1905
Neff 7.9
Searched_HMMs 39220
Date Mon May 30 01:38:42 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780834.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05667 dnaG DNA primase; Val 100.0 0 0 1218.7 59.9 592 1-632 2-598 (600)
2 COG0358 DnaG DNA primase (bact 100.0 0 0 939.4 45.6 413 2-442 1-415 (568)
3 TIGR01391 dnaG DNA primase; In 100.0 0 0 702.8 35.5 413 2-431 1-423 (424)
4 pfam08275 Toprim_N DNA primase 100.0 1.5E-31 3.8E-36 309.8 8.5 128 127-255 1-128 (128)
5 PRK08624 hypothetical protein; 100.0 3.7E-29 9.4E-34 287.8 18.0 273 9-324 5-300 (373)
6 pfam01807 zf-CHC2 CHC2 zinc fi 100.0 2.5E-28 6.4E-33 280.1 11.9 96 3-103 1-96 (98)
7 smart00400 ZnF_CHCC zinc finge 99.8 1.3E-18 3.3E-23 190.8 6.3 55 39-93 1-55 (55)
8 cd03364 TOPRIM_DnaG_primases T 99.7 5E-17 1.3E-21 176.2 7.6 78 273-353 2-79 (79)
9 PHA02415 DNA primase domain-co 99.7 8.7E-14 2.2E-18 146.4 22.4 314 6-381 2-354 (930)
10 cd01029 TOPRIM_primases TOPRIM 99.3 6.8E-12 1.7E-16 129.0 7.4 77 273-352 2-78 (79)
11 PHA02031 putative DnaG-like pr 99.1 4.5E-10 1.2E-14 112.2 9.4 165 166-377 93-266 (274)
12 TIGR02760 TraI_TIGR conjugativ 98.9 2.3E-07 5.8E-12 87.4 14.9 303 45-385 1759-2113(2193)
13 pfam01751 Toprim Toprim domain 98.8 1E-08 2.5E-13 99.9 6.8 79 273-354 2-89 (89)
14 smart00493 TOPRIM topoisomeras 98.8 2.1E-08 5.3E-13 96.9 6.2 68 273-340 2-73 (76)
15 PRK04031 DNA primase; Provisio 98.4 1.8E-06 4.6E-11 79.1 8.8 102 270-385 167-269 (420)
16 TIGR00646 MG010 DNA primase ho 98.4 1E-06 2.6E-11 81.4 7.5 197 124-375 11-212 (218)
17 COG4643 Uncharacterized protei 98.3 4E-05 1E-09 66.7 13.5 266 42-375 34-310 (366)
18 cd00188 TOPRIM Topoisomerase-p 97.9 3.4E-05 8.8E-10 67.4 6.8 67 273-339 2-72 (83)
19 cd01027 TOPRIM_RNase_M5_like T 97.8 4.3E-05 1.1E-09 66.5 5.9 66 272-337 2-68 (81)
20 pfam10410 DnaB_bind DnaB-helic 97.8 3.9E-05 9.9E-10 66.9 5.5 56 381-436 1-56 (59)
21 PRK06904 replicative DNA helic 97.5 0.022 5.5E-07 41.6 15.3 48 214-288 220-267 (472)
22 LOAD_Toprim consensus 97.4 0.00077 2E-08 55.0 7.4 66 273-338 2-70 (98)
23 PRK08760 replicative DNA helic 97.3 0.036 9.1E-07 39.6 15.2 48 214-288 228-275 (476)
24 TIGR03600 phage_DnaB phage rep 97.3 0.032 8.1E-07 40.1 14.3 47 214-287 193-239 (421)
25 PRK08006 replicative DNA helic 97.1 0.05 1.3E-06 38.3 15.2 48 214-288 223-270 (471)
26 PRK07004 replicative DNA helic 97.1 0.051 1.3E-06 38.2 13.9 48 214-288 212-259 (460)
27 PRK05748 replicative DNA helic 97.0 0.067 1.7E-06 37.1 14.1 48 214-288 202-249 (448)
28 PRK08082 consensus 96.9 0.052 1.3E-06 38.1 12.6 48 214-288 202-249 (453)
29 PRK08694 consensus 96.9 0.074 1.9E-06 36.7 14.5 49 213-288 216-264 (468)
30 smart00766 DnaG_DnaB_bind DNA 96.9 0.033 8.5E-07 39.9 11.4 109 484-603 1-109 (125)
31 COG1658 Small primase-like pro 96.9 0.0019 4.8E-08 51.4 4.8 63 271-333 9-74 (127)
32 PRK08840 replicative DNA helic 96.8 0.085 2.2E-06 36.2 14.1 47 214-287 216-262 (464)
33 PRK04017 hypothetical protein; 96.8 0.0099 2.5E-07 44.7 8.2 82 270-366 21-103 (132)
34 PRK07263 consensus 96.7 0.099 2.5E-06 35.5 13.9 70 214-311 202-277 (453)
35 PRK07773 replicative DNA helic 96.7 0.1 2.5E-06 35.5 13.5 23 231-253 421-444 (868)
36 PRK06321 replicative DNA helic 96.7 0.1 2.6E-06 35.4 14.1 71 214-312 225-301 (472)
37 PRK05636 replicative DNA helic 96.6 0.11 2.9E-06 35.1 14.9 10 156-165 8-17 (507)
38 PRK08506 replicative DNA helic 96.6 0.12 3.1E-06 34.7 12.8 69 214-311 192-266 (473)
39 PRK05595 replicative DNA helic 96.5 0.13 3.3E-06 34.4 13.9 69 214-310 200-274 (444)
40 pfam08278 DnaG_DnaB_bind DNA p 96.4 0.16 4E-06 33.7 14.0 109 484-603 2-110 (126)
41 PRK09165 replicative DNA helic 96.2 0.18 4.6E-06 33.1 14.7 48 52-99 41-95 (484)
42 COG3593 Predicted ATP-dependen 96.1 0.086 2.2E-06 36.1 9.5 85 243-337 378-471 (581)
43 COG0305 DnaB Replicative DNA h 96.0 0.23 5.8E-06 32.2 15.2 49 52-100 35-90 (435)
44 pfam00772 DnaB DnaB-like helic 95.9 0.069 1.8E-06 37.0 8.3 65 482-546 7-71 (103)
45 PRK06749 replicative DNA helic 95.4 0.36 9.2E-06 30.4 12.8 47 214-288 185-231 (428)
46 TIGR00334 primaseG_like primas 90.8 0.52 1.3E-05 28.9 4.8 65 272-336 3-69 (176)
47 PRK05301 pyrroloquinoline quin 90.6 1.6 4.2E-05 24.3 7.3 85 270-357 70-169 (375)
48 pfam08273 Prim_Zn_Ribbon Zinc- 89.8 0.27 6.9E-06 31.5 2.7 33 40-73 3-38 (39)
49 cd01026 TOPRIM_OLD TOPRIM_OLD: 89.1 0.79 2E-05 27.3 4.6 55 272-328 4-69 (97)
50 PRK13758 anaerobic sulfatase-m 89.0 1.2 3.2E-05 25.5 5.5 72 290-364 92-179 (370)
51 KOG2373 consensus 86.2 2.9 7.3E-05 22.1 7.4 133 230-383 94-229 (514)
52 COG0641 AslB Arylsulfatase reg 85.7 3 7.7E-05 21.9 6.7 131 289-433 89-241 (378)
53 PRK09897 hypothetical protein; 85.3 2.1 5.5E-05 23.3 5.1 191 142-398 79-297 (535)
54 PRK13745 anaerobic sulfatase-m 81.1 3.7 9.5E-05 21.1 4.9 70 291-363 102-187 (412)
55 TIGR03470 HpnH hopanoid biosyn 80.3 4.6 0.00012 20.3 7.9 89 271-363 80-181 (318)
56 pfam03291 Pox_MCEL mRNA cappin 80.3 0.71 1.8E-05 27.7 1.0 75 12-100 5-94 (327)
57 PRK12383 putative mutase; Prov 79.3 4.9 0.00012 20.0 6.5 140 213-360 178-344 (406)
58 TIGR00678 holB DNA polymerase 76.1 5.2 0.00013 19.7 4.4 67 294-363 68-165 (216)
59 smart00778 Prim_Zn_Ribbon Zinc 74.4 2.4 6E-05 22.9 2.3 30 40-70 3-34 (37)
60 KOG2593 consensus 73.8 2.7 6.8E-05 22.4 2.4 48 43-95 131-182 (436)
61 PRK00133 metG methionyl-tRNA s 73.2 3.4 8.6E-05 21.5 2.8 60 355-414 334-397 (666)
62 TIGR00396 leuS_bact leucyl-tRN 72.1 5.3 0.00013 19.7 3.6 56 354-416 669-725 (916)
63 PRK00076 recR recombination pr 71.1 7.4 0.00019 18.3 7.1 81 271-356 78-172 (197)
64 TIGR03655 anti_R_Lar restricti 71.0 4 0.0001 20.8 2.8 42 42-91 3-48 (53)
65 PRK00390 leuS leucyl-tRNA synt 70.7 7.5 0.00019 18.3 4.8 18 206-223 231-248 (822)
66 TIGR01418 PEP_synth phosphoeno 70.0 7.7 0.0002 18.1 6.5 281 87-435 294-648 (877)
67 TIGR00014 arsC arsenate reduct 70.0 3.8 9.6E-05 21.0 2.5 48 136-186 11-59 (114)
68 TIGR02478 6PF1K_euk 6-phosphof 68.3 6 0.00015 19.2 3.2 15 321-335 582-596 (777)
69 pfam01921 tRNA-synt_1f tRNA sy 68.0 8.2 0.00021 17.9 3.9 25 356-380 286-310 (355)
70 TIGR01059 gyrB DNA gyrase, B s 67.5 8.5 0.00022 17.8 5.8 99 286-396 477-582 (818)
71 COG2604 Uncharacterized protei 66.4 8.2 0.00021 17.9 3.6 55 295-366 229-284 (594)
72 TIGR01430 aden_deam adenosine 66.3 8.1 0.00021 17.9 3.6 68 78-146 8-80 (346)
73 TIGR01696 deoB phosphopentomut 66.1 5.6 0.00014 19.5 2.7 85 277-361 246-352 (404)
74 TIGR02482 PFKA_ATP 6-phosphofr 65.4 7 0.00018 18.5 3.1 29 271-300 92-124 (302)
75 COG2137 OraA Uncharacterized p 64.9 9.4 0.00024 17.4 4.3 45 498-545 54-98 (174)
76 TIGR00600 rad2 DNA excision re 64.6 3.8 9.6E-05 21.0 1.6 22 3-24 265-286 (1127)
77 cd01025 TOPRIM_recR TOPRIM_rec 64.2 9.7 0.00025 17.2 6.6 79 273-356 2-94 (112)
78 COG5440 Uncharacterized conser 64.1 7 0.00018 18.5 2.9 57 294-365 56-113 (161)
79 PRK13738 conjugal transfer pil 63.8 9.8 0.00025 17.2 4.0 82 187-280 75-156 (210)
80 PRK13844 recombination protein 63.5 9.9 0.00025 17.1 7.2 80 271-356 82-175 (200)
81 TIGR00020 prfB peptide chain r 62.2 10 0.00026 17.0 11.2 95 535-633 19-121 (373)
82 pfam04273 DUF442 Putative phos 60.9 11 0.00028 16.8 7.1 84 292-384 6-92 (110)
83 PRK02853 hypothetical protein; 60.9 9.1 0.00023 17.5 3.0 81 203-322 63-145 (161)
84 TIGR01980 sufB FeS assembly pr 60.1 5.3 0.00013 19.7 1.7 34 299-339 18-51 (469)
85 pfam06840 DUF1241 Protein of u 58.3 10 0.00027 16.9 3.0 28 514-541 31-58 (154)
86 KOG3578 consensus 57.2 3.3 8.5E-05 21.5 0.3 35 68-102 79-125 (1058)
87 pfam00133 tRNA-synt_1 tRNA syn 56.9 7.9 0.0002 18.0 2.1 19 205-223 189-208 (606)
88 TIGR00658 orni_carb_tr ornithi 56.8 12 0.0003 16.5 3.0 70 305-380 147-222 (341)
89 pfam01113 DapB_N Dihydrodipico 56.7 7.4 0.00019 18.3 2.0 42 278-321 76-118 (122)
90 pfam01458 UPF0051 Uncharacteri 56.6 6.9 0.00018 18.6 1.8 12 357-368 204-217 (230)
91 TIGR01981 sufD FeS assembly pr 56.0 6.3 0.00016 19.0 1.5 69 345-422 324-395 (397)
92 PRK00578 prfB peptide chain re 55.6 13 0.00033 16.1 11.5 16 198-215 120-135 (367)
93 pfam09133 SANTA SANTA (SANT As 55.6 5.1 0.00013 19.8 1.0 26 270-295 48-73 (93)
94 TIGR01286 nifK nitrogenase mol 54.6 3.4 8.6E-05 21.5 -0.1 226 115-411 128-389 (526)
95 pfam03428 RP-C Replication pro 54.3 11 0.00028 16.7 2.5 33 181-221 93-126 (177)
96 PRK12366 replication factor A; 54.1 14 0.00035 15.9 3.1 14 88-101 41-54 (649)
97 pfam04407 DUF531 Protein of un 54.0 14 0.00035 15.9 5.1 59 318-379 7-76 (174)
98 TIGR02082 metH methionine synt 53.9 8.1 0.00021 18.0 1.8 262 64-378 33-372 (1265)
99 PRK12268 methionyl-tRNA synthe 53.5 14 0.00035 15.8 6.1 27 354-380 340-366 (558)
100 PHA02130 hypothetical protein 53.4 4 0.0001 20.7 0.2 11 38-48 43-53 (81)
101 KOG2767 consensus 53.2 5.9 0.00015 19.2 1.0 39 257-295 92-130 (400)
102 pfam08209 Sgf11 Sgf11 (transcr 53.2 4.8 0.00012 20.1 0.5 72 5-81 13-90 (99)
103 TIGR02684 dnstrm_HI1420 probab 52.9 14 0.00036 15.8 3.4 52 122-179 15-72 (91)
104 PRK12300 leuS leucyl-tRNA synt 52.8 14 0.00036 15.7 5.7 33 355-387 578-611 (888)
105 COG0289 DapB Dihydrodipicolina 52.4 14 0.00036 15.7 4.2 38 278-317 80-118 (266)
106 pfam01780 Ribosomal_L37ae Ribo 52.3 8.2 0.00021 17.9 1.6 26 41-69 36-61 (90)
107 PRK13824 replication initiatio 52.2 12 0.0003 16.4 2.4 33 181-221 105-138 (404)
108 pfam11672 DUF3268 Protein of u 52.0 14 0.00037 15.6 4.7 28 43-70 5-40 (102)
109 cd03770 SR_TndX_transposase Se 50.8 15 0.00038 15.5 3.9 64 296-361 46-113 (140)
110 TIGR01215 minE cell division t 50.6 8.7 0.00022 17.7 1.5 20 5-26 38-57 (89)
111 TIGR00464 gltX_bact glutamyl-t 50.5 13 0.00034 16.0 2.4 33 301-335 232-271 (513)
112 pfam03776 MinE Septum formatio 50.4 11 0.00028 16.7 2.0 23 5-29 23-45 (69)
113 pfam01641 SelR SelR domain. Me 50.4 8.3 0.00021 17.9 1.4 34 24-70 13-46 (124)
114 TIGR03297 Ppyr-DeCO2ase phosph 50.3 8.1 0.00021 18.0 1.3 40 314-356 238-277 (361)
115 pfam06793 UPF0262 Uncharacteri 50.2 11 0.00028 16.8 2.0 50 272-322 92-143 (159)
116 pfam01194 RNA_pol_N RNA polyme 50.1 13 0.00033 16.2 2.3 16 63-78 6-22 (60)
117 PRK01544 bifunctional N5-gluta 50.0 12 0.00031 16.3 2.2 109 249-363 163-274 (503)
118 pfam02631 RecX RecX family. Re 49.7 16 0.0004 15.4 4.4 50 496-547 9-58 (121)
119 KOG0183 consensus 49.7 15 0.00038 15.5 2.6 69 245-334 14-83 (249)
120 COG1644 RPB10 DNA-directed RNA 49.4 14 0.00037 15.7 2.5 30 63-92 6-38 (63)
121 pfam07057 TraI DNA helicase Tr 49.1 14 0.00036 15.8 2.4 22 205-226 93-114 (126)
122 pfam05129 Elf1 Transcription e 49.0 11 0.00027 16.8 1.8 30 41-70 18-50 (74)
123 KOG1422 consensus 48.6 6.7 0.00017 18.7 0.7 53 271-325 18-70 (221)
124 TIGR03364 HpnW_proposed FAD de 48.6 16 0.00041 15.2 4.1 14 87-100 65-78 (365)
125 KOG0435 consensus 48.5 16 0.00041 15.2 3.0 107 278-414 562-677 (876)
126 PRK00750 lysK lysyl-tRNA synth 48.1 16 0.00042 15.2 4.1 32 356-387 293-325 (513)
127 COG0353 RecR Recombinational D 47.5 17 0.00042 15.1 7.6 81 270-356 78-173 (198)
128 PRK05508 methionine sulfoxide 47.1 11 0.00029 16.7 1.6 22 57-80 29-50 (119)
129 PRK12446 N-acetylglucosaminyl 46.9 17 0.00043 15.0 4.4 66 246-324 75-147 (352)
130 KOG0856 consensus 46.8 12 0.0003 16.5 1.7 11 58-68 51-61 (146)
131 COG1422 Predicted membrane pro 46.8 17 0.00043 15.0 8.2 37 587-623 73-109 (201)
132 PRK04016 DNA-directed RNA poly 46.7 16 0.0004 15.3 2.3 15 63-77 6-21 (63)
133 pfam05991 DUF901 Protein of un 46.4 17 0.00044 15.0 3.4 43 315-366 44-86 (166)
134 PTZ00255 60S ribosomal protein 46.1 11 0.00029 16.6 1.5 26 41-69 37-62 (90)
135 PRK06667 motB flagellar motor 46.1 15 0.00039 15.4 2.2 23 271-293 160-183 (254)
136 PRK06163 hypothetical protein; 46.0 11 0.00028 16.8 1.4 60 294-357 55-114 (202)
137 cd01575 PBP1_GntR Ligand-bindi 45.8 17 0.00045 14.9 4.5 50 318-378 95-145 (268)
138 PRK03976 rpl37ae 50S ribosomal 45.2 14 0.00035 15.9 1.8 25 41-69 37-62 (90)
139 cd07048 BMC_PduB_repeat2 1,2-p 45.0 18 0.00046 14.8 2.4 28 297-335 35-62 (70)
140 cd01320 ADA Adenosine deaminas 44.9 18 0.00046 14.8 3.8 28 79-106 10-37 (325)
141 COG1198 PriA Primosomal protei 44.8 18 0.00046 14.8 3.3 97 290-403 268-382 (730)
142 cd00764 Eukaryotic_PFK Phospho 44.7 18 0.00046 14.8 3.2 60 289-351 353-425 (762)
143 pfam00782 DSPc Dual specificit 44.5 18 0.00046 14.7 4.0 40 61-100 75-116 (131)
144 pfam08856 DUF1826 Protein of u 44.4 12 0.00031 16.3 1.5 27 213-239 157-184 (196)
145 TIGR00665 DnaB replicative DNA 44.2 18 0.00047 14.7 13.1 27 395-421 354-380 (465)
146 PRK00296 minE cell division to 44.1 18 0.00047 14.7 2.4 19 516-534 40-58 (85)
147 COG1205 Distinct helicase fami 43.9 17 0.00043 15.1 2.1 17 356-373 421-437 (851)
148 COG0646 MetH Methionine syntha 43.9 17 0.00044 14.9 2.2 53 79-131 45-105 (311)
149 KOG4717 consensus 43.5 19 0.00048 14.6 4.4 26 56-81 87-112 (864)
150 KOG3497 consensus 42.9 11 0.00029 16.7 1.1 25 62-86 5-30 (69)
151 smart00195 DSPc Dual specifici 42.6 19 0.00049 14.5 4.1 37 61-97 82-120 (138)
152 TIGR01058 parE_Gpos DNA topois 42.5 19 0.00049 14.5 3.4 13 343-355 322-335 (655)
153 cd03371 TPP_PpyrDC Thiamine py 42.5 14 0.00036 15.7 1.6 58 294-356 46-104 (188)
154 COG0229 Conserved domain frequ 42.3 16 0.00042 15.1 1.9 12 58-69 39-50 (140)
155 pfam06587 DUF1137 Protein of u 42.1 11 0.00029 16.6 1.0 20 46-65 41-71 (159)
156 cd01971 Nitrogenase_VnfN_like 41.9 20 0.0005 14.4 4.1 10 250-259 134-143 (427)
157 PRK01008 queuine tRNA-ribosylt 41.7 20 0.0005 14.4 6.1 67 302-370 140-219 (372)
158 pfam04405 ScdA_N Domain of Unk 41.6 17 0.00042 15.1 1.8 35 151-185 16-50 (56)
159 PRK05729 valS valyl-tRNA synth 41.3 20 0.00051 14.4 2.2 34 354-387 528-562 (877)
160 cd01987 USP_OKCHK USP domain i 41.0 20 0.00051 14.3 4.8 35 316-353 1-35 (124)
161 pfam04723 GRDA Glycine reducta 40.8 14 0.00037 15.7 1.4 71 278-363 46-126 (150)
162 cd03362 TOPRIM_TopoIA_TopoIII 40.5 20 0.00052 14.3 3.5 36 303-338 85-123 (151)
163 pfam09334 tRNA-synt_1g tRNA sy 40.2 21 0.00053 14.2 5.0 25 355-379 331-356 (388)
164 PRK10026 arsenate reductase; P 40.0 19 0.00047 14.6 1.8 48 136-186 14-61 (141)
165 PRK00726 murG N-acetylglucosam 39.8 21 0.00053 14.2 4.0 65 246-323 75-146 (359)
166 KOG2026 consensus 39.8 17 0.00044 14.9 1.7 26 43-69 24-49 (442)
167 PHA00202 DNA replication initi 39.7 6.9 0.00018 18.6 -0.4 21 67-87 31-51 (379)
168 COG0426 FpaA Uncharacterized f 39.7 21 0.00054 14.2 7.4 63 299-364 223-293 (388)
169 COG2139 RPL21A Ribosomal prote 39.6 19 0.00048 14.6 1.8 36 194-238 49-89 (98)
170 COG2719 SpoVR Uncharacterized 39.4 21 0.00053 14.2 2.0 17 85-101 18-34 (495)
171 cd01525 RHOD_Kc Member of the 39.2 21 0.00054 14.1 4.3 61 291-358 33-101 (105)
172 TIGR00807 s1 malonate transpor 39.2 14 0.00036 15.7 1.2 26 140-170 46-71 (127)
173 COG0535 Predicted Fe-S oxidore 39.2 21 0.00054 14.1 7.3 95 271-368 73-187 (347)
174 PRK13265 glycine/sarcosine/bet 39.1 16 0.00041 15.3 1.4 71 278-363 47-127 (157)
175 cd01724 Sm_D1 The eukaryotic S 39.1 13 0.00033 16.1 0.9 22 344-365 60-81 (90)
176 PRK12655 fructose-6-phosphate 39.0 21 0.00055 14.1 2.7 74 77-150 31-105 (220)
177 PRK05563 DNA polymerase III su 38.8 22 0.00055 14.0 10.9 119 277-417 210-343 (541)
178 PRK05431 seryl-tRNA synthetase 38.5 22 0.00056 14.0 9.4 14 240-253 195-208 (422)
179 KOG1903 consensus 38.5 12 0.00031 16.3 0.7 33 341-373 38-71 (217)
180 TIGR00337 PyrG CTP synthase; I 38.4 20 0.00051 14.3 1.8 90 70-163 151-279 (571)
181 KOG2924 consensus 38.3 1.5 3.8E-05 24.7 -4.0 161 63-239 34-219 (366)
182 pfam01983 CofC Guanylyl transf 38.3 22 0.00056 14.0 2.6 27 302-329 101-129 (217)
183 COG2971 Predicted N-acetylgluc 38.3 22 0.00056 14.0 4.8 28 209-241 20-48 (301)
184 TIGR02279 PaaC-3OHAcCoADH 3-hy 38.1 14 0.00037 15.7 1.0 24 39-62 175-198 (508)
185 TIGR00422 valS valyl-tRNA synt 38.0 20 0.0005 14.4 1.7 121 38-172 285-424 (970)
186 COG1997 RPL43A Ribosomal prote 37.8 22 0.00057 13.9 2.2 26 41-70 36-62 (89)
187 TIGR03652 FeS_repair_RIC iron- 37.8 21 0.00053 14.2 1.8 12 355-366 37-48 (216)
188 PRK10992 cell morphogenesis/ce 37.7 21 0.00054 14.1 1.8 11 355-365 44-54 (220)
189 PRK09358 adenosine deaminase; 37.5 22 0.00057 13.9 5.4 27 79-105 17-43 (333)
190 PRK13782 phosphocarrier protei 37.2 23 0.00058 13.9 5.4 62 306-377 22-83 (85)
191 KOG2802 consensus 37.2 13 0.00033 16.1 0.7 18 47-68 61-78 (503)
192 COG0018 ArgS Arginyl-tRNA synt 37.2 23 0.00058 13.9 15.8 49 482-531 491-539 (577)
193 KOG2164 consensus 37.2 13 0.00033 16.1 0.7 17 298-314 204-220 (513)
194 cd02001 TPP_ComE_PpyrDC Thiami 36.8 16 0.00042 15.2 1.1 40 315-357 59-98 (157)
195 PRK05627 bifunctional riboflav 36.6 23 0.00058 13.8 1.9 39 291-333 230-269 (303)
196 COG0066 LeuD 3-isopropylmalate 36.5 21 0.00053 14.2 1.7 84 207-299 1-98 (191)
197 pfam08271 TF_Zn_Ribbon TFIIB z 36.4 23 0.00059 13.8 2.5 26 42-69 2-27 (40)
198 TIGR00615 recR recombination p 36.3 23 0.00059 13.7 6.6 83 269-356 79-182 (205)
199 COG1794 RacX Aspartate racemas 36.2 23 0.0006 13.7 2.8 50 286-336 112-161 (230)
200 pfam03405 FA_desaturase_2 Fatt 36.1 23 0.0006 13.7 4.0 14 300-313 108-121 (330)
201 PTZ00317 malic enzyme; Provisi 36.0 24 0.0006 13.7 2.6 66 289-356 235-303 (570)
202 PRK13182 racA polar chromosome 35.9 24 0.0006 13.7 6.9 49 590-641 99-147 (178)
203 PRK00222 methionine sulfoxide 35.8 19 0.00049 14.5 1.4 52 23-89 18-73 (141)
204 PRK11020 hypothetical protein; 35.7 24 0.00061 13.7 7.5 39 594-632 13-51 (118)
205 PRK10076 pyruvate formate lyas 35.7 24 0.00061 13.7 7.3 80 285-365 62-149 (213)
206 TIGR01969 minD_arch cell divis 35.4 15 0.00038 15.5 0.8 122 290-433 13-160 (258)
207 pfam08348 PAS_6 YheO-like PAS 35.2 24 0.00061 13.6 4.5 55 158-221 46-100 (118)
208 pfam00500 Late_protein_L1 L1 ( 35.2 24 0.00061 13.6 2.2 24 198-221 90-116 (503)
209 TIGR00963 secA preprotein tran 35.1 24 0.00062 13.6 2.0 91 187-313 348-454 (904)
210 PRK01143 rpl11p 50S ribosomal 35.0 24 0.00062 13.6 3.7 63 301-377 96-159 (163)
211 TIGR00354 polC DNA polymerase 35.0 18 0.00047 14.7 1.2 59 34-98 685-749 (1173)
212 pfam06246 Isy1 Isy1-like splic 34.7 24 0.00062 13.5 4.6 53 394-446 42-95 (253)
213 TIGR00010 TIGR00010 hydrolase, 34.6 17 0.00042 15.1 0.9 21 282-303 22-43 (269)
214 PRK13520 L-tyrosine decarboxyl 34.5 25 0.00063 13.5 2.1 50 278-327 140-196 (375)
215 PRK00283 xerD site-specific ty 34.5 22 0.00055 14.0 1.5 40 139-183 8-48 (296)
216 COG5328 Uncharacterized protei 34.3 23 0.00059 13.8 1.6 106 178-322 33-144 (160)
217 TIGR01426 MGT glycosyltransfer 34.2 25 0.00063 13.5 2.3 103 293-429 262-368 (429)
218 PRK09490 metH B12-dependent me 33.8 24 0.00061 13.6 1.6 63 64-131 48-118 (1229)
219 pfam03393 Pneumo_matrix Pneumo 33.7 16 0.0004 15.3 0.6 16 176-191 10-25 (252)
220 TIGR03287 methan_mark_16 putat 33.6 16 0.00041 15.3 0.7 12 302-313 253-264 (391)
221 PTZ00124 adenosine deaminase; 33.5 25 0.00065 13.4 4.2 125 55-188 10-148 (362)
222 pfam04392 ABC_sub_bind ABC tra 33.4 26 0.00065 13.4 6.1 81 274-357 82-171 (292)
223 KOG3214 consensus 33.4 23 0.00059 13.7 1.5 54 39-94 22-83 (109)
224 cd03372 TPP_ComE Thiamine pyro 32.8 26 0.00066 13.3 4.2 59 294-357 40-98 (179)
225 pfam05566 Pox_vIL-18BP Orthopo 32.8 24 0.00062 13.6 1.5 35 41-75 13-50 (126)
226 TIGR00357 TIGR00357 methionine 32.8 21 0.00054 14.1 1.2 15 55-69 34-48 (135)
227 COG1859 KptA RNA:NAD 2'-phosph 32.6 26 0.00067 13.3 4.4 65 159-234 57-123 (211)
228 COG3454 Metal-dependent hydrol 32.4 26 0.00067 13.3 1.6 11 397-407 189-199 (377)
229 KOG0257 consensus 32.4 26 0.00067 13.3 3.5 104 295-412 182-295 (420)
230 LOAD_USPA consensus 32.4 26 0.00067 13.2 4.7 38 315-355 1-38 (135)
231 PRK08645 bifunctional homocyst 32.0 27 0.00068 13.2 3.9 78 285-364 259-344 (608)
232 pfam00949 Peptidase_S7 Peptida 32.0 27 0.00068 13.2 1.7 18 209-226 118-135 (150)
233 pfam10911 DUF2717 Protein of u 31.8 27 0.00068 13.2 1.7 12 170-181 41-52 (77)
234 cd00817 ValRS_core This is the 31.7 27 0.00069 13.2 2.9 27 355-381 331-357 (363)
235 PRK13804 ileS isoleucyl-tRNA s 31.7 27 0.00069 13.2 4.5 27 354-380 642-668 (966)
236 KOG2361 consensus 31.6 24 0.00061 13.6 1.3 16 330-345 161-176 (264)
237 pfam03976 PPK2 Polyphosphate k 31.6 27 0.00069 13.2 3.5 42 294-336 10-52 (229)
238 COG1206 Gid NAD(FAD)-utilizing 31.6 19 0.00049 14.5 0.8 146 202-366 159-311 (439)
239 cd03785 GT1_MurG MurG is an N- 31.4 27 0.00069 13.1 3.7 66 246-324 73-145 (350)
240 PRK04023 DNA polymerase II lar 31.4 26 0.00066 13.3 1.4 19 83-102 453-471 (1128)
241 TIGR01943 rnfA electron transp 31.2 13 0.00034 16.0 -0.1 13 397-409 37-49 (193)
242 PRK05550 bifunctional methioni 30.9 27 0.00068 13.2 1.4 42 24-80 12-53 (284)
243 TIGR02918 TIGR02918 conserved 30.9 17 0.00043 15.0 0.4 253 158-426 54-402 (511)
244 TIGR03329 Phn_aa_oxid putative 30.8 28 0.00071 13.0 3.9 19 38-56 33-53 (460)
245 TIGR00300 TIGR00300 conserved 30.4 19 0.0005 14.5 0.7 34 278-313 238-288 (418)
246 KOG2518 consensus 30.4 28 0.00072 13.0 2.8 27 284-313 219-245 (556)
247 cd00250 CAS_like Clavaminic ac 30.3 28 0.00072 13.0 2.9 62 207-288 77-140 (262)
248 TIGR01389 recQ ATP-dependent D 30.1 23 0.00059 13.8 1.0 21 169-190 242-262 (607)
249 TIGR02431 pcaR_pcaU beta-ketoa 29.9 22 0.00056 14.0 0.9 19 415-433 78-96 (252)
250 cd00762 NAD_bind_malic_enz NAD 29.9 29 0.00073 12.9 2.7 39 60-98 26-70 (254)
251 cd00763 Bacterial_PFK Phosphof 29.9 29 0.00073 12.9 3.9 16 348-363 185-201 (317)
252 PRK06850 hypothetical protein; 29.8 16 0.0004 15.3 0.1 15 212-226 143-158 (488)
253 TIGR02483 PFK_mixed phosphofru 29.6 25 0.00065 13.4 1.2 13 323-335 9-21 (339)
254 CHL00010 infA translation init 29.6 29 0.00074 12.9 1.5 19 197-215 58-76 (78)
255 COG2957 Peptidylarginine deimi 29.3 29 0.00074 12.8 4.6 27 349-377 199-225 (346)
256 COG1180 PflA Pyruvate-formate 29.3 29 0.00074 12.8 6.6 120 271-394 92-223 (260)
257 KOG2168 consensus 29.3 24 0.0006 13.7 1.0 27 618-644 795-821 (835)
258 cd03361 TOPRIM_TopoIA_RevGyr T 29.3 29 0.00074 12.8 3.9 36 304-339 106-144 (170)
259 TIGR02201 heptsyl_trn_III lipo 29.0 29 0.00075 12.8 1.4 78 270-377 133-211 (347)
260 pfam02969 TAF TATA box binding 28.9 30 0.00075 12.8 5.2 48 85-133 5-53 (66)
261 PRK06645 DNA polymerase III su 28.6 30 0.00076 12.7 5.6 73 276-366 218-297 (507)
262 cd03363 TOPRIM_TopoIA_TopoI TO 28.5 30 0.00076 12.7 3.8 33 305-337 64-96 (123)
263 PRK05362 phosphopentomutase; P 28.3 30 0.00077 12.7 7.4 88 271-360 236-338 (393)
264 pfam12324 HTH_15 Helix-turn-he 28.2 24 0.00062 13.6 0.9 22 518-539 25-46 (77)
265 PRK00048 dihydrodipicolinate r 28.2 30 0.00077 12.7 4.3 42 278-321 80-122 (265)
266 PRK13208 valS valyl-tRNA synth 28.0 30 0.00078 12.7 5.8 31 354-384 544-574 (809)
267 TIGR00539 hemN_rel putative ox 28.0 20 0.00051 14.3 0.4 39 275-315 95-140 (371)
268 cd00293 USP_Like Usp: Universa 27.6 31 0.00079 12.6 4.9 35 316-353 1-35 (130)
269 TIGR00538 hemN oxygen-independ 27.5 31 0.00079 12.6 1.9 12 301-312 117-128 (462)
270 PRK01287 xerC site-specific ty 27.4 28 0.00072 13.0 1.1 34 140-178 30-63 (361)
271 PRK01611 argS arginyl-tRNA syn 27.1 31 0.0008 12.5 15.1 47 481-528 483-529 (570)
272 KOG4657 consensus 26.8 32 0.00081 12.5 3.4 63 199-261 151-220 (246)
273 TIGR02727 MTHFS_bact 5,10-meth 26.8 17 0.00043 15.1 -0.2 18 205-222 118-137 (183)
274 pfam06447 consensus 26.8 32 0.00081 12.5 8.6 13 271-283 253-265 (407)
275 pfam07282 Transposase_35 Putat 26.7 32 0.00081 12.5 2.3 28 42-72 30-57 (69)
276 pfam09445 Methyltransf_15 RNA 26.7 22 0.00056 14.0 0.4 15 65-79 7-21 (165)
277 COG4888 Uncharacterized Zn rib 26.7 32 0.00081 12.5 1.9 28 43-70 25-55 (104)
278 cd05312 NAD_bind_1_malic_enz N 26.6 32 0.00081 12.5 2.8 38 280-317 97-134 (279)
279 pfam06945 DUF1289 Protein of u 26.6 32 0.00082 12.5 1.7 13 63-75 16-28 (56)
280 TIGR02329 propionate_PrpR prop 26.6 32 0.00082 12.5 1.7 12 212-223 214-225 (658)
281 pfam09332 Mcm10 Mcm10 replicat 26.4 32 0.00082 12.4 1.7 12 626-637 229-240 (346)
282 KOG0340 consensus 26.4 32 0.00082 12.4 5.2 24 357-380 333-356 (442)
283 PRK10850 phosphohistidinoprote 26.4 32 0.00082 12.4 6.0 62 306-377 22-83 (85)
284 pfam07014 Hs1pro-1_C Hs1pro-1 26.4 29 0.00075 12.8 1.0 46 334-388 91-136 (261)
285 KOG0177 consensus 26.2 32 0.00083 12.4 1.8 48 46-101 28-76 (200)
286 KOG0456 consensus 26.2 31 0.0008 12.6 1.1 32 141-172 208-239 (559)
287 PRK00380 panC pantoate--beta-a 26.0 33 0.00083 12.4 2.7 59 294-355 25-93 (283)
288 cd01816 Raf_RBD The Raf serine 25.9 21 0.00054 14.1 0.2 33 143-175 29-66 (74)
289 cd00807 Gln_GluRS_non_core Glu 25.9 33 0.00084 12.4 1.8 25 289-313 120-145 (238)
290 COG4230 Delta 1-pyrroline-5-ca 25.8 27 0.0007 13.1 0.8 16 293-308 353-368 (769)
291 pfam00944 Peptidase_S3 Alphavi 25.7 33 0.00084 12.4 1.5 23 186-220 100-122 (157)
292 PRK09040 hypothetical protein; 25.6 28 0.0007 13.1 0.8 23 270-292 121-145 (215)
293 cd01532 4RHOD_Repeat_1 Member 25.6 33 0.00085 12.3 2.1 56 289-351 25-83 (92)
294 COG1915 Uncharacterized conser 25.5 15 0.00038 15.6 -0.6 25 278-304 226-254 (415)
295 cd06325 PBP1_ABC_uncharacteriz 25.5 33 0.00085 12.3 5.7 83 274-362 83-174 (281)
296 KOG0164 consensus 25.4 33 0.00085 12.3 2.6 61 269-331 223-293 (1001)
297 smart00828 PKS_MT Methyltransf 25.4 33 0.00084 12.4 1.1 17 64-80 5-21 (224)
298 cd01196 INT_VanD VanD integras 25.4 33 0.00083 12.4 1.1 18 141-158 2-19 (263)
299 pfam05480 Staph_haemo Staphylo 25.4 30 0.00076 12.8 0.9 25 278-302 2-27 (43)
300 COG3673 Uncharacterized conser 25.4 33 0.00085 12.3 1.3 23 43-66 16-38 (423)
301 KOG2730 consensus 25.2 34 0.00086 12.3 1.3 16 275-290 147-162 (263)
302 KOG4672 consensus 25.1 34 0.00086 12.3 1.6 14 167-180 102-115 (487)
303 pfam03811 Ins_element1 Inserti 25.1 34 0.00086 12.3 2.7 28 42-70 7-38 (88)
304 pfam06819 Arc_PepC Archaeal Pe 25.0 27 0.0007 13.1 0.7 24 292-315 78-101 (111)
305 cd00687 Terpene_cyclase_nonpla 25.0 34 0.00087 12.2 3.9 31 284-314 36-66 (303)
306 PRK00443 nagB glucosamine-6-ph 24.9 34 0.00087 12.2 4.0 16 313-328 231-246 (264)
307 PRK08174 DNA topoisomerase III 24.9 34 0.00087 12.2 3.5 13 481-493 487-499 (670)
308 PRK06674 DNA polymerase III su 24.9 34 0.00087 12.2 12.5 77 277-375 210-293 (563)
309 pfam09393 DUF2001 Protein of u 24.9 30 0.00077 12.7 0.8 35 328-362 66-100 (141)
310 COG0172 SerS Seryl-tRNA synthe 24.8 34 0.00087 12.2 9.8 10 288-297 190-199 (429)
311 PRK05580 primosome assembly pr 24.7 34 0.00087 12.2 2.5 20 293-312 240-259 (699)
312 COG4963 CpaE Flp pilus assembl 24.7 34 0.00088 12.2 8.5 31 354-385 191-221 (366)
313 TIGR01326 OAH_OAS_sulfhy O-ace 24.7 18 0.00046 14.8 -0.3 40 343-385 119-163 (434)
314 PRK09401 reverse gyrase; Revie 24.7 34 0.00088 12.2 6.7 37 305-341 707-746 (1176)
315 cd00127 DSPc Dual specificity 24.6 34 0.00088 12.2 3.5 11 285-295 22-32 (139)
316 COG0125 Tmk Thymidylate kinase 24.5 34 0.00088 12.2 5.0 37 318-356 5-42 (208)
317 COG4847 Uncharacterized protei 24.3 14 0.00035 15.9 -1.0 18 61-78 6-26 (103)
318 pfam10191 COG7 Golgi complex c 24.2 35 0.00089 12.1 12.0 10 354-363 418-427 (768)
319 TIGR00176 mobB molybdopterin-g 24.2 33 0.00083 12.4 0.9 25 250-283 84-108 (165)
320 KOG2185 consensus 24.2 35 0.00089 12.1 8.1 48 590-639 424-471 (486)
321 PRK12267 methionyl-tRNA synthe 24.2 35 0.00089 12.1 5.8 60 355-414 306-368 (644)
322 pfam09740 DUF2043 Uncharacteri 24.2 27 0.00068 13.2 0.5 15 201-217 92-106 (111)
323 TIGR01858 tag_bisphos_ald clas 24.2 30 0.00077 12.7 0.7 89 289-379 165-273 (282)
324 PRK10116 universal stress prot 24.2 35 0.00089 12.1 4.7 43 315-362 4-46 (142)
325 pfam07212 Hyaluronidase_1 Hyal 24.2 35 0.00089 12.1 1.5 14 211-224 105-118 (273)
326 PRK13559 hypothetical protein; 24.1 35 0.00089 12.1 3.4 36 188-227 123-159 (363)
327 KOG0385 consensus 24.0 35 0.0009 12.1 3.8 42 315-361 559-603 (971)
328 COG4026 Uncharacterized protei 24.0 35 0.0009 12.1 13.4 96 270-371 6-116 (290)
329 TIGR02087 LEUD_arch 3-isopropy 24.0 31 0.00079 12.6 0.8 73 215-299 1-84 (159)
330 PRK13209 L-xylulose 5-phosphat 24.0 35 0.0009 12.1 1.9 34 322-356 88-121 (283)
331 KOG2874 consensus 23.8 35 0.0009 12.1 3.4 23 329-351 168-192 (356)
332 TIGR00791 gntP transporter, gl 23.7 26 0.00067 13.3 0.4 15 512-526 273-287 (458)
333 PRK09111 DNA polymerase III su 23.7 36 0.00091 12.1 10.2 48 277-328 222-276 (600)
334 KOG0260 consensus 23.7 27 0.0007 13.1 0.4 21 234-254 789-809 (1605)
335 pfam00396 Granulin Granulin. 23.7 33 0.00084 12.4 0.9 10 39-48 9-18 (43)
336 pfam00282 Pyridoxal_deC Pyrido 23.5 15 0.00038 15.5 -0.9 35 293-327 196-234 (370)
337 pfam11464 Rbsn FYVE-finger-con 23.2 36 0.00092 12.0 4.6 38 593-630 3-40 (42)
338 pfam00365 PFK Phosphofructokin 23.2 36 0.00092 12.0 4.0 14 350-363 188-202 (279)
339 COG2380 Uncharacterized protei 23.0 17 0.00044 14.9 -0.7 23 157-179 1-23 (327)
340 TIGR00036 dapB dihydrodipicoli 22.9 37 0.00093 11.9 2.0 94 277-415 85-186 (281)
341 smart00433 TOP2c Topoisomerase 22.8 37 0.00094 11.9 4.0 11 232-242 194-204 (594)
342 KOG1818 consensus 22.8 34 0.00086 12.3 0.8 39 200-239 167-205 (634)
343 PRK09846 recT recombination an 22.7 37 0.00094 11.9 1.8 79 137-224 85-169 (270)
344 pfam03194 LUC7 LUC7 N_terminus 22.6 37 0.00095 11.9 10.0 42 591-632 128-169 (252)
345 TIGR03183 DNA_S_dndC putative 22.6 26 0.00067 13.3 0.2 15 212-226 135-150 (447)
346 pfam00098 zf-CCHC Zinc knuckle 22.5 31 0.0008 12.6 0.5 11 63-73 2-12 (26)
347 PRK10787 DNA-binding ATP-depen 22.5 37 0.00095 11.9 7.9 13 247-259 323-335 (784)
348 TIGR02410 carnitine_TMLD trime 22.5 37 0.00095 11.9 3.6 25 56-80 216-247 (397)
349 PRK13780 phosphocarrier protei 22.5 37 0.00095 11.9 5.6 62 306-377 22-83 (88)
350 pfam04055 Radical_SAM Radical 22.4 37 0.00095 11.9 5.7 21 343-363 137-159 (165)
351 TIGR02029 AcsF magnesium-proto 22.3 23 0.0006 13.7 -0.1 30 492-524 183-216 (344)
352 PRK12442 translation initiatio 22.3 37 0.00096 11.8 1.6 19 197-215 58-76 (87)
353 pfam05028 PARG_cat Poly (ADP-r 22.3 35 0.00089 12.1 0.7 23 356-378 200-222 (339)
354 COG3313 Predicted Fe-S protein 22.3 38 0.00096 11.8 1.9 25 49-75 7-33 (74)
355 cd06481 ACD_HspB9_like Alpha c 22.2 37 0.00094 11.9 0.9 22 348-369 57-78 (87)
356 KOG4506 consensus 22.2 38 0.00096 11.8 5.2 103 281-392 249-371 (598)
357 PRK10903 peptidyl-prolyl cis-t 22.2 38 0.00096 11.8 3.9 14 275-289 151-164 (190)
358 TIGR00456 argS arginyl-tRNA sy 22.2 38 0.00096 11.8 7.9 54 481-535 513-566 (600)
359 KOG1177 consensus 22.1 13 0.00033 16.1 -1.5 71 51-133 30-100 (596)
360 pfam02330 MAM33 Mitochondrial 22.1 38 0.00096 11.8 1.5 34 351-388 147-183 (203)
361 TIGR00457 asnS asparaginyl-tRN 22.1 35 0.00088 12.2 0.7 32 345-378 101-133 (495)
362 pfam02614 UxaC Glucuronate iso 22.1 38 0.00097 11.8 3.2 15 169-183 57-71 (465)
363 COG5014 Predicted Fe-S oxidore 22.0 16 0.0004 15.4 -1.1 61 301-367 103-165 (228)
364 cd01833 XynB_like SGNH_hydrola 21.9 38 0.00097 11.8 1.9 20 295-330 3-22 (157)
365 cd00223 TOPRIM_TopoIIB_SPO TOP 21.9 38 0.00097 11.8 3.9 88 273-364 2-102 (160)
366 pfam03949 Malic_M Malic enzyme 21.9 38 0.00097 11.8 2.2 38 281-318 99-136 (255)
367 TIGR02009 PGMB-YQAB-SF beta-ph 21.8 38 0.00098 11.8 7.9 82 73-165 44-133 (211)
368 COG0703 AroK Shikimate kinase 21.7 38 0.00098 11.7 3.6 19 356-374 42-60 (172)
369 PRK11460 esterase YpfH; Provis 21.7 38 0.00098 11.7 1.5 42 342-391 175-219 (230)
370 KOG1432 consensus 21.7 38 0.00098 11.7 1.7 37 314-359 318-354 (379)
371 PRK13547 hmuV hemin importer A 21.6 39 0.00098 11.7 3.7 56 302-359 211-268 (273)
372 PRK04025 S-adenosylmethionine 21.4 39 0.00099 11.7 1.9 39 47-97 61-101 (139)
373 KOG2578 consensus 21.4 31 0.00078 12.6 0.3 46 98-157 42-87 (388)
374 KOG1409 consensus 21.3 39 0.00099 11.7 2.1 20 345-364 268-287 (404)
375 KOG2150 consensus 21.3 39 0.001 11.7 11.9 15 318-332 294-308 (575)
376 TIGR02776 NHEJ_ligase_prk DNA 21.3 39 0.001 11.7 1.2 46 284-329 224-275 (645)
377 pfam06189 5-nucleotidase 5'-nu 21.2 39 0.001 11.7 3.5 67 274-374 85-151 (263)
378 TIGR02434 CobF precorrin-6A sy 21.2 39 0.001 11.7 0.9 27 346-374 27-53 (259)
379 PRK13529 malate dehydrogenase; 21.2 39 0.001 11.7 2.7 67 288-357 235-305 (563)
380 KOG0440 consensus 21.1 39 0.001 11.7 2.1 29 345-373 68-96 (243)
381 pfam04710 Pellino Pellino. Pel 21.1 39 0.001 11.6 1.9 11 309-319 131-141 (416)
382 COG0585 Uncharacterized conser 21.1 24 0.00062 13.6 -0.3 45 52-100 31-75 (406)
383 pfam05131 Pep3_Vps18 Pep3/Vps1 21.1 39 0.001 11.6 4.1 17 295-311 34-50 (147)
384 KOG4090 consensus 21.1 24 0.00061 13.6 -0.3 20 271-290 133-152 (157)
385 KOG0402 consensus 21.1 31 0.0008 12.5 0.3 50 41-95 37-89 (92)
386 smart00803 TAF TATA box bindin 21.1 39 0.001 11.6 5.4 50 84-133 3-52 (65)
387 PRK10575 iron-hydroxamate tran 21.0 39 0.001 11.6 2.4 59 303-363 204-264 (265)
388 pfam09059 TyeA TyeA. Members o 21.0 40 0.001 11.6 6.5 44 386-429 26-74 (81)
389 KOG1253 consensus 20.9 40 0.001 11.6 0.9 10 251-260 199-208 (525)
390 pfam04630 Phage_tail Phage maj 20.9 40 0.001 11.6 1.0 20 310-329 163-182 (199)
391 cd06394 PBP1_iGluR_Kainate_KA1 20.9 40 0.001 11.6 3.5 48 315-366 135-182 (333)
392 TIGR02013 rpoB DNA-directed RN 20.9 40 0.001 11.6 1.1 37 293-329 275-311 (1449)
393 TIGR00393 kpsF sugar isomerase 20.9 31 0.0008 12.5 0.3 72 138-219 124-202 (272)
394 pfam04989 CmcI Cephalosporin h 20.8 40 0.001 11.6 3.0 85 303-391 95-186 (202)
395 cd07968 OBF_DNA_ligase_IV The 20.7 36 0.00091 12.0 0.6 18 295-312 46-63 (140)
396 cd01028 TOPRIM_TopoIA TOPRIM_T 20.7 40 0.001 11.6 3.7 55 304-362 78-135 (142)
397 cd04777 HTH_MerR-like_sg1 Heli 20.6 40 0.001 11.6 2.1 10 594-603 89-98 (107)
398 PRK13239 alkylmercury lyase; P 20.5 40 0.001 11.6 1.5 38 210-258 64-101 (206)
399 KOG1207 consensus 20.5 40 0.001 11.5 3.8 60 272-335 7-72 (245)
400 PRK13551 agmatine deiminase; P 20.3 41 0.001 11.5 3.6 54 302-355 207-265 (360)
401 pfam08448 PAS_4 PAS fold. The 20.2 41 0.001 11.5 2.5 23 204-226 82-104 (110)
402 COG3484 Predicted proteasome-t 20.2 34 0.00086 12.3 0.3 16 235-250 139-154 (255)
403 KOG0415 consensus 20.2 14 0.00036 15.7 -1.6 46 39-89 36-81 (479)
404 cd06544 GH18_narbonin Narbonin 20.1 41 0.001 11.5 7.0 84 301-411 55-141 (253)
405 PRK00423 tfb transcription ini 20.1 41 0.001 11.5 2.5 36 42-79 13-50 (310)
406 TIGR02418 acolac_catab acetola 20.1 26 0.00067 13.2 -0.2 43 396-439 212-261 (553)
407 pfam02403 Seryl_tRNA_N Seryl-t 20.1 41 0.001 11.5 10.2 53 584-638 41-93 (108)
408 KOG1597 consensus 20.1 41 0.001 11.5 2.6 68 287-363 17-86 (308)
No 1
>PRK05667 dnaG DNA primase; Validated
Probab=100.00 E-value=0 Score=1218.74 Aligned_cols=592 Identities=36% Similarity=0.583 Sum_probs=500.8
Q ss_pred CCCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf 98788899999874888887541222101588777775575345888858787981789746713688887898998988
Q gi|254780834|r 1 MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSAL 80 (648)
Q Consensus 1 m~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~ 80 (648)
||||+++||+|++++|||||||+||+|+|+|+| ||||||||+||||||+|||+||+|||||||+|||||+|||++
T Consensus 2 grIp~e~Ie~i~~~~dIvdvi~~yv~Lkk~G~~-----~~glCPFH~EktPSF~V~~~k~~~~CFgCg~~Gdv~~Flm~~ 76 (600)
T PRK05667 2 GRIPPEFIDELRARVDIVDVIGEYVKLKKAGRN-----YKGLCPFHDEKTPSFTVSPDKQFYHCFGCGAGGDAIKFLMEY 76 (600)
T ss_pred CCCCHHHHHHHHHHCCHHHHHCCCEEEEECCCC-----CEEECCCCCCCCCCCEEECCCCEEEECCCCCCCCHHHHHHHH
T ss_conf 999989999999849999875162289988998-----378796999999994797899979869999695578978976
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCC
Q ss_conf 59997999999999818858776820-36777889999999999999999973267775789999850688535101244
Q gi|254780834|r 81 LGCSFIESVQRLAAIAGVPLPVVDPK-IEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKL 159 (648)
Q Consensus 81 ~~~~f~ea~~~la~~~gi~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~l 159 (648)
||++|+|||+.||+++||++|..++. .......+..++++|+.|+.|||++|.++.|..|++||++|||++++|++|+|
T Consensus 77 e~lsF~eAv~~LA~~~gi~l~~~~~~~~~~~~~~~~~l~~~~~~a~~~f~~~L~~~~~~~a~~YL~~Rgl~~~~i~~F~l 156 (600)
T PRK05667 77 EGLSFVEAVEELADRAGIELPYEDGGSAQEEKSRRQELYEIMELAAKFYQQQLRTPEGAEARQYLYERGLSEETIERFGI 156 (600)
T ss_pred HCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf 29987999999999959975766775134425689999999999999999984896208999999975999999998383
Q ss_pred CCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCC
Q ss_conf 22567741034554205997345232012100346541000016716888970778588850100146553001038767
Q gi|254780834|r 160 GYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPET 239 (648)
Q Consensus 160 G~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT 239 (648)
||||++|+.|+++|.++||+.++|.++||+..+++| .+||||||||||||+|.+|+|||||||+|+++..|||||||||
T Consensus 157 Gyap~~~~~l~~~l~~~g~~~~~l~~~GL~~~~~~g-~~yDrFr~RimFPI~d~~G~vIgFgGR~l~~~~~pKYlNSpET 235 (600)
T PRK05667 157 GYAPDGWDALLKHLGKKGIEPKLLEEAGLLIKNEDG-RPYDRFRNRIMFPIRDLRGRVIGFGGRVLGKDDEPKYLNSPET 235 (600)
T ss_pred CCCCCCHHHHHHHHHHCCCHHHHHHHHCCEEECCCC-CCCHHHCCCEEEEEECCCCCEEEEECEECCCCCCCCCCCCCCC
T ss_conf 547771789999987369729999982682599999-8751320805676556899876441203488899870179887
Q ss_pred CCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEE
Q ss_conf 65352101108178888643310000235678708997143889998743554211343213662678988512681899
Q gi|254780834|r 240 ILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVL 319 (648)
Q Consensus 240 ~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl 319 (648)
+||+||++|||||.|+++|++. +.+||||||||||+|||+||+|||||||||||++|+++|+|+|++|||
T Consensus 236 ~lF~K~~~Lygl~~A~~~i~~~----------~~~ilvEGymDvIal~q~Gi~naVA~lGTAlT~~h~~~L~r~~~~vil 305 (600)
T PRK05667 236 PLFHKGRELYGLDEARKAIAKK----------DRVIVVEGYMDVIALHQAGITNAVASLGTALTEEHLQLLRRYTDEVIL 305 (600)
T ss_pred CCCHHHHHHHHHHHHHHHHHCC----------CCEEEEECCHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCCEEEE
T ss_conf 3401016886358999986235----------857998063999999984986775334341639999999736893899
Q ss_pred EECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf 61788662257778888887775369730675257888888997203668899886414992799999998530233145
Q gi|254780834|r 320 CFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPD 399 (648)
Q Consensus 320 ~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe 399 (648)
|||||+||++||+||++++++++.+|+.|+|+.||+|+|||||++++|+++|.+++++|.|+++|+|+++..+.++++|+
T Consensus 306 ~fDgD~AG~~Aa~ra~~~~~~~~~~g~~v~v~~lp~g~DPD~~i~~~G~~~f~~~l~~a~~~~~f~~~~~~~~~~l~~~e 385 (600)
T PRK05667 306 CFDGDRAGRKAALRALELALPLLKDGRQLRFLFLPDGKDPDDLVRKEGKEAFRALLEQAIPLSEFLIRRLIPGKDLDTPE 385 (600)
T ss_pred EECCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHH
T ss_conf 96885888999999999878886389779996189998938999875999999999738998999999997148999999
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 79999999998854179989999999999999887657767764332001235555554556643333222233445553
Q gi|254780834|r 400 ERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKK 479 (648)
Q Consensus 400 ~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 479 (648)
+|+.+++.+.++|+.|+|+++|++|++.++++++........................ ...........
T Consensus 386 ~k~~~~~~~~~~i~~i~d~i~r~~y~~~la~~l~i~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~ 454 (600)
T PRK05667 386 GRAALLERAAPLIAKIPDPTLRDSYRQKLAELLGIFDDAQVEQLVPKLRRQRSRLAPP-----------PSPKKLSPRSP 454 (600)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCC-----------CCCCCCCCCCH
T ss_conf 9999999999999968999999999999999859898999999864310246667888-----------77667888987
Q ss_pred HHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH---HHHHHHHHHHHHHH
Q ss_conf 037999999999847788999984430023799889999999999975388999899998851---11289999999998
Q gi|254780834|r 480 PSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLC---ERGFGELLKQLDRQ 556 (648)
Q Consensus 480 ~~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~---~~~l~elL~~L~~~ 556 (648)
....|+.||++|+++|+++..+........|.++.++.|+..+.... +.+..+...+...+. +.....++..+.
T Consensus 455 ~~~aE~~lL~~ll~~p~l~~~~~~~~~~~~~~~~~~~~l~~~i~~~~-~~~~~~~~~l~~~l~~~~~~~~~~~l~~l~-- 531 (600)
T PRK05667 455 KERAERELLALLLQHPELAEEVRELDALEDFKLPGLRLLYELIDAAG-EQPGLTGAQLLELLRDLRDEELAELLERLA-- 531 (600)
T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHCCCHHHHHHHHHHH--
T ss_conf 78999999999982989999875013423138878999999999987-478998799999998436859999999997--
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6543332025689988999999999999985899999999999999872-412798999999999999999999988
Q gi|254780834|r 557 VRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQV-TAKGEAEKTAILISILHEVHIQIHQIE 632 (648)
Q Consensus 557 ~~~~~~~~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~e~-~~~~d~e~~~~l~~el~elk~~L~~l~ 632 (648)
.+. ...+.....+.+++..+.+. .+.+++.++..++... .+..+.+...+++.++++++++++.++
T Consensus 532 -----~~~----~~~e~~~~~i~d~i~~L~~~-~l~~~~~~L~~k~~~~~~~~~e~~el~~ll~el~~l~~~~~~l~ 598 (600)
T PRK05667 532 -----VED----LPAELAEQELEDALAKLRKA-LLELRLEELLKKERRLGLAEEEKEELLALLQELKALEQELRALE 598 (600)
T ss_pred -----CCC----CCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf -----276----78740899999999999983-79999999999984538985539999999999999999999863
No 2
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=939.43 Aligned_cols=413 Identities=43% Similarity=0.689 Sum_probs=391.1
Q ss_pred CCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf 87888999998748888875412221015887777755753458888587879817897467136888878989989885
Q gi|254780834|r 2 NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL 81 (648)
Q Consensus 2 ~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~ 81 (648)
+||+++|++|++++|||||||+||+|+|+|+| ||||||||+||||||+|+|+||+|||||||+|||+|.|||+++
T Consensus 1 ~i~~~~i~~l~~~~dIvdvI~~~v~Lkk~G~~-----y~~lCPFH~EktPSf~V~~~k~~yhCFGCg~~Gd~i~Fl~~~~ 75 (568)
T COG0358 1 RIPREFIDELRERIDIVDVIGEYVKLKKQGAN-----YTGLCPFHAEKTPSFTVSPEKGFYHCFGCGAGGDAIKFLMELL 75 (568)
T ss_pred CCCHHHHHHHHHHCCHHHHHHHCEEEEECCCC-----CEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHH
T ss_conf 99879999998618989876130145775888-----5103888777778748966887698416899851777899970
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCC
Q ss_conf 99979999999998188587768203677788999999999999999997326777578999985068853510124422
Q gi|254780834|r 82 GCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGY 161 (648)
Q Consensus 82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ 161 (648)
|++|.||++.||.++||++|...+ +....+..++++++.++.||+..|. +.+++|++||.+||++.+++..|+|||
T Consensus 76 ~~sf~eav~~La~~~gi~~~~~~~---~~~~~~~~l~~~~~~~~~fy~~~L~-~~~~~a~~yL~~Rgls~~~i~~f~iG~ 151 (568)
T COG0358 76 GLSFDEAVLQLAGRAGIELPYEKG---KRIEKRQKLYDGKEEAAIFYQSSLD-PEGAAALKYLETRGLAAELIAHFRLGY 151 (568)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 997899999998872887775432---2117888888789999999998731-300788999987268888998865088
Q ss_pred CCCCCCHHHHHHHCCC-CCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCC
Q ss_conf 5677410345542059-973452320121003465410000167168889707785888501001465530010387676
Q gi|254780834|r 162 APDSRYSLREHLRQKG-FSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETI 240 (648)
Q Consensus 162 ap~~~~~l~~~l~~~~-~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~ 240 (648)
||++ +.+. ++..++ |+.+.+.++||+..++ | .+|||||+||||||+|.+|+|||||||+++ +++|||+|||||+
T Consensus 152 ap~~-~~~~-~~~~k~~~~~~~l~~~Gl~~~~~-~-~~ydrFr~RImfPI~d~~g~vigFggR~l~-~~~~KYlNspet~ 226 (568)
T COG0358 152 APPN-DSLL-PFLAKKEYREEKLEDLGLLKRKE-G-KIYDRFRNRIMFPIRDLRGDVIGFGGRVLG-DDKPKYLNSPETE 226 (568)
T ss_pred CCCC-CHHH-HHHHCCCCCHHHHHHCCCHHHCC-C-CHHHHHHCHHEEEEECCCCCCCCCCCEECC-CCCCCCCCCCCCC
T ss_conf 9874-3044-54421342477898655134157-7-337888442327510799984240212436-7775334788873
Q ss_pred CCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEE
Q ss_conf 53521011081788886433100002356787089971438899987435542113432136626789885126818996
Q gi|254780834|r 241 LFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLC 320 (648)
Q Consensus 241 if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~ 320 (648)
+|+||++|||++.|++.|++ .+++||||||||||+||++||+||||+||||+|++|+.+|+|++++||+|
T Consensus 227 if~Kg~~Lyg~~~a~~~~~~----------~~~iivVEGymDViaL~~aGi~naVA~lGTalt~ehi~~L~r~~~~vil~ 296 (568)
T COG0358 227 LFKKGEELYGLDPARKKIAK----------ADQIIVVEGYMDVIALHKAGIKNAVASLGTALTEEHIKLLSRGKKKVILC 296 (568)
T ss_pred CCCCCHHCCCCCHHHHHCCC----------CCEEEEEECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHCCCEEEEE
T ss_conf 65677430585455563056----------88399994189999999719752786587679999999998469819999
Q ss_pred ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHHHCCCCCHH
Q ss_conf 178866225777888888777536973067525788888899720366889988641-4992799999998530233145
Q gi|254780834|r 321 FDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETENRSFNTPD 399 (648)
Q Consensus 321 fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~~~dl~spe 399 (648)
||||.||++||+|+++.++++...| |+|+.+|+|+|||||++++|.++|...+.+ +.++++|+++.+... ++++ +
T Consensus 297 fDgD~AG~~Aa~ral~~~~~~~~~~--v~v~~~P~GkDpDel~~k~g~~al~~~l~~~~~~~~~~~~~~~~~~-~~~~-~ 372 (568)
T COG0358 297 FDGDRAGRKAAKRALQLVLPLDFVG--VFVILLPDGKDPDELIRKEGAEALRKKLPNERLPLIEFLIEYLIPS-NLDT-E 372 (568)
T ss_pred ECCCHHHHHHHHHHHHHHHHCCCCC--EEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCH-H
T ss_conf 6896789999999998543315664--4887478999868999873179999875652456899999861453-3212-7
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7999999999885417998999999999999988765776776
Q gi|254780834|r 400 ERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITE 442 (648)
Q Consensus 400 ~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~ 442 (648)
+++.+...+.+.++.++++..|.+|.+.+++.++.........
T Consensus 373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 415 (568)
T COG0358 373 GKARLVEEAVPLIKVIPDEVLRDYYLQKLAELLGISDDALLQL 415 (568)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 7899999976787602765779999999998737546778888
No 3
>TIGR01391 dnaG DNA primase; InterPro: IPR006295 DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. The C-terminal region of these proteins is poorly conserved between species. In Escherichia coli, primase (DnaG) interacts with the replicative DnaB helicase, single-stranded DNA binding protein (SSB), and DNA polymerase III holoenzyme , , , . Although DnaG is capable of synthesizing 60-nucleotide-long primers in vitro this primer length is restrained to 11 (±1) nucleotides in the context of the replisome . Members of this entry are homologs of DnaG and have been identified in all prokaryotes, as well as in several bacteriophage. On the basis of sequence analysis, these proteins appear structurally distinct from primases known to act in archaeal, eukaryotic replication or to either of the two subunits, p50 and p60, of the heterodimeric eukaryotic DNA primase (IPR002755 from INTERPRO). DnaG has been shown by proteolysis to comprise three structural domains: a 12-kD NH2-terminal Zn2+-binding domain (ZBD), a 36-kD core domain containing the polymerase region, and a 15-kD COOH-terminal DnaB-interaction domain (DnaB-ID) , .; GO: 0003896 DNA primase activity, 0006269 DNA replication synthesis of RNA primer.
Probab=100.00 E-value=0 Score=702.79 Aligned_cols=413 Identities=44% Similarity=0.749 Sum_probs=391.3
Q ss_pred CCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf 87888999998748888875412221015887777755753458888587879817897467136888878989989885
Q gi|254780834|r 2 NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL 81 (648)
Q Consensus 2 ~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~ 81 (648)
++|+++++++++++||++||++||.|+|+|+| |+||||||+||||||+|+|+|++|||||||++||+|.|+|+++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~-----~~~~cPfh~~~~ps~~~~~~~~~~~cfgc~~~G~~~~f~~~~~ 75 (424)
T TIGR01391 1 RIPEEVIDELKERVDIVDLVSEYVKLKKKGKN-----YVGLCPFHHEKTPSFSVSPEKGFYHCFGCGAGGDAIKFLMEIE 75 (424)
T ss_pred CCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCC-----CEEECCCCCCCCCCEEEECCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf 97467899998620057776544311004774-----0453365455676224301335355530466660577777761
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHCCCCHHHH
Q ss_conf 9997999999999818858776820367------778899999999999999999732677-757899998506885351
Q gi|254780834|r 82 GCSFIESVQRLAAIAGVPLPVVDPKIEK------KEKIQTDLIRLIEVATDFFHHSLKNAR-DKRLHYYLDERGIDSHAI 154 (648)
Q Consensus 82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~a~~yl~~Rg~~~~~~ 154 (648)
+++|.||++.||.++|++++... .... ....+..++.+++.+..||+..|.... +..+++||.+||++++++
T Consensus 76 ~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~yl~~rg~~~~~~ 154 (424)
T TIGR01391 76 GLSFVEAVKELAKRAGLDLPLEK-ESEKSPDKAEEKSERKELLELLELAAEFFKNELKNTPEGNRALDYLLSRGLSDETI 154 (424)
T ss_pred CCCHHHHHHHHHHHHCCCCCHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHH
T ss_conf 57678999999987377321000-22210233343335678999999999999987520101468899998628888789
Q ss_pred CCCCCCCCCCCCCHHHHHHHCC-CCCHHHHHHHCCCEECCCC-CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCE
Q ss_conf 0124422567741034554205-9973452320121003465-4100001671688897077858885010014655300
Q gi|254780834|r 155 EMFKLGYAPDSRYSLREHLRQK-GFSEEKIIEAGLLIDGDNS-ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVK 232 (648)
Q Consensus 155 ~~f~lG~ap~~~~~l~~~l~~~-~~~~~~~~~~gl~~~~~~~-~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~K 232 (648)
.+|++||+|..|..+..++..+ +++.+.+.++|++...++| ..+||+|++||||||+|..|++||||||.++ +..||
T Consensus 155 ~~f~~G~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~f~~r~~~p~~~~~g~~~~fggr~~~-~~~~k 233 (424)
T TIGR01391 155 SRFGLGYAPDNWDFLLDFLENKKGFDLELLLEAGLLVKKENGDQKYYDRFRNRIIFPIHDPKGKVVGFGGRALG-DEKPK 233 (424)
T ss_pred HHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCCCEECCCCCCHHHHHHHCEEEEEEECCCCCEEEECCCCCC-CCCCC
T ss_conf 87403677552467888763201555567865033000145541023222220254433367865540430015-66663
Q ss_pred ECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf 10387676535210110817888864331000023567870899714388999874355421134321366267898851
Q gi|254780834|r 233 YLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 233 YlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r 312 (648)
|+|||||++|+|+++|||++.|++.+.+ .+.+++||||||||++|++|+.++||++||++|++|+.++++
T Consensus 234 y~n~p~~~~~~k~~~l~~~~~~~~~~~~----------~~~~~~~eG~~d~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~ 303 (424)
T TIGR01391 234 YLNSPETPLFKKGELLYGLDKARKEIRK----------EKELLLVEGYMDVIALHQAGIKNAVASLGTALTEEHLKLLKR 303 (424)
T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHHHC----------CCEEEEECCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 1156533000010356546677776512----------660688602567788765055402444312201789999863
Q ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf 26818996178866225777888888777536973067525788888899720366889988641-49927999999985
Q gi|254780834|r 313 LSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETE 391 (648)
Q Consensus 313 ~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~ 391 (648)
+++++++|||||.||.+|++|+++.+++....+..++++.+|+|+|||++++++|.+.|..++.+ +.++.+|++.....
T Consensus 304 ~~~~~~~~~dgd~aG~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~dpd~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 383 (424)
T TIGR01391 304 YADEIILCFDGDSAGLKAALRALELLLPLGKDGISVKVVLLPGGKDPDELLRKEGAEALKKLLENGSLPLIEFLLEYLLS 383 (424)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 25727898557412378899999987641256622789865777887999862047889999741664079999998730
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 3023314579999999998854179989999999999999
Q gi|254780834|r 392 NRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDR 431 (648)
Q Consensus 392 ~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~ 431 (648)
..++++++++..+...+.+.+..++++..+..|.+.+++.
T Consensus 384 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 423 (424)
T TIGR01391 384 GYNLDSPEEKAKLLEELLPLLKKLPDPLLRDSYLQKLAEL 423 (424)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf 1355435689999999988875202157899999998750
No 4
>pfam08275 Toprim_N DNA primase catalytic core, N-terminal domain.
Probab=99.97 E-value=1.5e-31 Score=309.83 Aligned_cols=128 Identities=49% Similarity=0.854 Sum_probs=123.1
Q ss_pred HHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEE
Q ss_conf 99997326777578999985068853510124422567741034554205997345232012100346541000016716
Q gi|254780834|r 127 FFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRL 206 (648)
Q Consensus 127 ~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri 206 (648)
|||.+|.++.+..|++||.+||+++++|++|+|||||++|+.|.++|.++||+.+++.++||+..+++|. +||+|+|||
T Consensus 1 fy~~~L~~~~~~~a~~YL~~Rgi~~~~i~~F~iGyap~~~~~L~~~l~~~~~~~~~l~~~Gl~~~~~~~~-~~D~F~~Ri 79 (128)
T pfam08275 1 FYHELLKTKEGAAARDYLKSRGLSPETIKRFGLGYAPDGWDNLLNHLEKKGFDLELLLEAGLLVKREDGG-YYDRFRNRI 79 (128)
T ss_pred CHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCCEEECCCCC-EEEEECCEE
T ss_conf 9378857975589999999859999999984878787606899998753289899998689869879998-855441248
Q ss_pred EEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHH
Q ss_conf 8889707785888501001465530010387676535210110817888
Q gi|254780834|r 207 IFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGAL 255 (648)
Q Consensus 207 ~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~ 255 (648)
||||+|.+|+|||||||+|+++.+|||||||||+||+||++||||++|+
T Consensus 80 ~fPI~d~~g~vigFgGR~l~~~~~~KYlNS~et~iF~K~~~Lygl~~Ak 128 (128)
T pfam08275 80 MFPIRDESGRVVGFGGRALDDEEPPKYLNSPETPLFKKGKVLYGLDEAK 128 (128)
T ss_pred EEEEECCCCCEEEEEEEECCCCCCCCEECCCCCCCEECCCCEECCCCCC
T ss_conf 9988779998999871577999998704799984685640103831049
No 5
>PRK08624 hypothetical protein; Provisional
Probab=99.97 E-value=3.7e-29 Score=287.80 Aligned_cols=273 Identities=18% Similarity=0.250 Sum_probs=198.7
Q ss_pred HHHHHHCCHHHH------HHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEEC-CCCCCCCHHHHH----
Q ss_conf 999874888887------541222101588777775575345888858787981789746713-688887898998----
Q gi|254780834|r 9 KDLLIHIPISNL------IGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF-SCHVKGDHLSFL---- 77 (648)
Q Consensus 9 ~~i~~~~~i~~v------v~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf-~c~~~gd~~~f~---- 77 (648)
+++++....-|+ +|.--.+.+.|.- =+.-.|-=|+--+--+.-+++.+.|||| |||++||||+|+
T Consensus 5 ~e~k~sLT~edI~kil~~lg~~~~~~k~g~~----i~~t~ch~~~g~s~kL~yY~e~~~FHCytgCG~~~DV~~li~k~~ 80 (373)
T PRK08624 5 DELKESLTPEDIIKILEEVGCENVRGKDGNT----IAETACHNDGGGSTKLYYYIENDNFHCYTRCGDIFDVFELLCKRL 80 (373)
T ss_pred HHHHHHCCHHHHHHHHHHHCCCCCCCCCCCE----EEEEEEECCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHH
T ss_conf 7887636898999999995777876889978----766543058999458999616853665426787511999999887
Q ss_pred -HHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHHCCCCHHHH
Q ss_conf -9885999799999999981885877682036777889999999999999999973267--7757899998506885351
Q gi|254780834|r 78 -SALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNA--RDKRLHYYLDERGIDSHAI 154 (648)
Q Consensus 78 -~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~a~~yl~~Rg~~~~~~ 154 (648)
|+.+++||.|||+.||.++||.+-..+. ....+.. ..++++..|.. +.++...+.- |.++..++
T Consensus 81 kmeg~~lSF~eAi~~la~i~Gis~~~~~k----~~~ik~~--------~~ki~d~~w~~k~e~~k~i~~~L-k~~~e~Il 147 (373)
T PRK08624 81 KMEGKALSFSKAIRKITKILGLSYFYEPK----QQGIKPS--------FLKILDWVWTGKKEKKEKIQPQL-KSFNENIL 147 (373)
T ss_pred HHCCCCCCHHHHHHHHHHHHCCCCCCCCH----HHHHHHH--------HHHHHHHHHHCCHHHHHHHHHHH-HCCCHHHH
T ss_conf 61043565999999999985853456810----3102477--------99988787650111467788776-05668889
Q ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC--CCE
Q ss_conf 012442256774103455420599734523201210034654100001671688897077858885010014655--300
Q gi|254780834|r 155 EMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE--SVK 232 (648)
Q Consensus 155 ~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~--~~K 232 (648)
..| ++|+|+.| .+.|++.+.+.+.++ +.|||.|+|||||||+|..|++|||+||.|+++. .+|
T Consensus 148 ~~F-~~yp~~~W-------i~EGIS~et~kk~~i-------~yY~d~f~NrIiIPh~D~~G~lVGirgR~L~ke~~~~~K 212 (373)
T PRK08624 148 NQF-VKIPNRKW-------LDEGISEKTQKYWEI-------KFYLDVISQRIIIPHRDESGELIGIRGRLLDKELVDKNK 212 (373)
T ss_pred HHH-HCCCHHHH-------HHCCCCHHHHHHHCC-------CCCCCHHCCEEEEEEECCCCCEEEEEECCCCHHHHHCCC
T ss_conf 875-35671778-------875889999987464-------542120036468666457887888960115586752476
Q ss_pred ECCCC-CCCC--CCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHH---HHHHCCCCCCHHHHHCCCCHHH
Q ss_conf 10387-6765--3521011081788886433100002356787089971438899---9874355421134321366267
Q gi|254780834|r 233 YLNSP-ETIL--FHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVL---SLCQAGVQNVVSSLGTALTEYQ 306 (648)
Q Consensus 233 YlNSp-eT~i--f~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi---~l~~~G~~n~va~~Gtalt~~~ 306 (648)
|+-.- .... +.+|..||||++-+++|.. .+.+|||||.--|+ .++.-+ ..+||.||..+|+.|
T Consensus 213 Y~Pl~~~~~~ynhp~g~nLYGL~~N~~~I~~----------~~kviifEsEKSVl~~~t~y~~~-n~~VAicGs~~s~~Q 281 (373)
T PRK08624 213 YFPIYVNDTGYNHPKGKILYGLWQNKKYIKE----------KKKVIIVESEKSVLFSDKFYGEG-NFVVAICGSNISEVQ 281 (373)
T ss_pred EEEEEECCCCCCCCCHHHHHHHHHCHHHHHH----------CCCEEEEECCCCEEEHHHHCCCC-CEEEEECCCCCCHHH
T ss_conf 2579976713578330245412326899985----------48289997140301315442578-736996367679999
Q ss_pred HHHHHHCCC-EEEEEECCC
Q ss_conf 898851268-189961788
Q gi|254780834|r 307 LRLLWKLSP-RIVLCFDGD 324 (648)
Q Consensus 307 ~~~l~r~~~-~vvl~fDgD 324 (648)
.++|.++.- +|+|+||-+
T Consensus 282 ~~~ll~LgVeeviiA~Dke 300 (373)
T PRK08624 282 AEKLLRLGVEEVTIALDKE 300 (373)
T ss_pred HHHHHHCCCEEEEEEECCH
T ss_conf 9999847964898774205
No 6
>pfam01807 zf-CHC2 CHC2 zinc finger. This domain is principally involved in DNA binding in DNA primases.
Probab=99.96 E-value=2.5e-28 Score=280.14 Aligned_cols=96 Identities=46% Similarity=0.823 Sum_probs=94.0
Q ss_pred CCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCC
Q ss_conf 78889999987488888754122210158877777557534588885878798178974671368888789899898859
Q gi|254780834|r 3 YPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLG 82 (648)
Q Consensus 3 i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~ 82 (648)
||+++|++||+++||++|||+||+|+|+|+| |||+||||+||||||+|+|+||+|||||||+|||+|+|||++||
T Consensus 1 I~~~~I~~ik~~~~i~~vv~~~v~L~~~G~~-----~~~~CPFH~ek~PS~~V~~~k~~f~CF~Cg~~Gd~i~fv~~~e~ 75 (98)
T pfam01807 1 IPEESIDDLKNRIDIVDIIGQYVKLKKKGRD-----YKGLCPFHDEKTPSFSVSPDKQFYHCFGCGAGGDAISFLMKIDK 75 (98)
T ss_pred CCHHHHHHHHHHCCHHHHHHHCCEEEECCCC-----EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHHC
T ss_conf 9889999999859999998622516888986-----58879988999982799769996997789999767878998859
Q ss_pred CCHHHHHHHHHHHHCCCCCCC
Q ss_conf 997999999999818858776
Q gi|254780834|r 83 CSFIESVQRLAAIAGVPLPVV 103 (648)
Q Consensus 83 ~~f~ea~~~la~~~gi~~~~~ 103 (648)
++|+|||++||+++||++|..
T Consensus 76 ~~f~eAv~~LA~~~gi~l~~~ 96 (98)
T pfam01807 76 LSFVEAVKKLADRAGIDLPYE 96 (98)
T ss_pred CCHHHHHHHHHHHHCCCCCCC
T ss_conf 799999999999969988876
No 7
>smart00400 ZnF_CHCC zinc finger.
Probab=99.75 E-value=1.3e-18 Score=190.84 Aligned_cols=55 Identities=47% Similarity=0.894 Sum_probs=54.3
Q ss_pred EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 5753458888587879817897467136888878989989885999799999999
Q gi|254780834|r 39 YWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLA 93 (648)
Q Consensus 39 ~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la 93 (648)
|||+||||+||||||+|||+||+|||||||+|||+|+|||+++|++|+|||++||
T Consensus 1 ~~~~CPFH~d~~pS~~V~~~k~~~~CF~Cg~~Gd~i~fv~~~~~~~f~eAv~~LA 55 (55)
T smart00400 1 YKGLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55 (55)
T ss_pred CEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHHCCCHHHHHHHHC
T ss_conf 9466949899999879977999799678999986554689884989999999869
No 8
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=99.70 E-value=5e-17 Score=176.18 Aligned_cols=78 Identities=54% Similarity=0.823 Sum_probs=73.9
Q ss_pred EEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf 08997143889998743554211343213662678988512681899617886622577788888877753697306752
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVL 352 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~ 352 (648)
.+||||||||||++||+|++|+||++||++|++|+++|++++.+|++|||+|+||++|+.|+++.++ +.|++++|+.
T Consensus 2 ~viivEG~~D~i~~~~~G~~n~VA~~Gt~~t~~q~~~L~~~~~~vil~~D~D~AG~~Aa~r~~~~l~---~~g~~v~i~~ 78 (79)
T cd03364 2 KVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLL---KLGLNVRVLT 78 (79)
T ss_pred EEEEEECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHH---HCCCEEEEEE
T ss_conf 8999967799999998599625625665471999997723158679997898899999999999999---7799699997
Q ss_pred C
Q ss_conf 5
Q gi|254780834|r 353 L 353 (648)
Q Consensus 353 L 353 (648)
|
T Consensus 79 l 79 (79)
T cd03364 79 L 79 (79)
T ss_pred C
T ss_conf 9
No 9
>PHA02415 DNA primase domain-containing protein
Probab=99.68 E-value=8.7e-14 Score=146.42 Aligned_cols=314 Identities=20% Similarity=0.305 Sum_probs=206.4
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEEC---CCC-EEEECCCCCCCCHHHHHHHHC
Q ss_conf 8999998748888875412221015887777755753458888587879817---897-467136888878989989885
Q gi|254780834|r 6 DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCND---SKG-FYYCFSCHVKGDHLSFLSALL 81 (648)
Q Consensus 6 ~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~---~~~-~~~cf~c~~~gd~~~f~~~~~ 81 (648)
..||++|.++|+-|+..+ +.|+| |.+.-++.| .+|-|.||+||+++.. .++ -|+.++.++||..||.||.-.
T Consensus 2 as~dqLK~~IDLhdLA~R-Lgl~R-~~~G~~~~Y--hsP~h~Dk~pSlSIf~nh~~~g~~WkDhs~~~gGSciDLV~~~r 77 (930)
T PHA02415 2 ATIDELKQRIDLHDLADR-LGLKR-GRGGDKALY--HSPQHEDKSPSLSIYVNHPKHGTGWRDHSADAGGSCIDLVIHAR 77 (930)
T ss_pred CCHHHHHHCCCHHHHHHH-HCCCC-CCCCCCCCC--CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf 657888610669889998-47603-689985555--69988888985578734743576423356788974678888606
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHC----CC
Q ss_conf 99979999999998188587768203677788999999999999999997326777578999985068853510----12
Q gi|254780834|r 82 GCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIE----MF 157 (648)
Q Consensus 82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~----~f 157 (648)
+-+-.||+++|.+.|||+.+...+.. ..++.++- ..+ ..++..+ ..|+.||.+|||++..|+ .=
T Consensus 78 ~~~~~dA~k~L~d~ygiP~~~pA~~~---~~~kSt~e----yIA---erc~a~~--~~a~aYLagRGI~~av~~~ai~~~ 145 (930)
T PHA02415 78 GGTVADAVRYLHDAYGIPLDRPAPAE---RREKSTVE----YIA---DRCLAER--ERVREYLGGRGISAAAIDAAFAAR 145 (930)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCC---CCCCCHHH----HHH---HHHHCCC--HHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 99889999998897579988876200---24313799----999---8873261--256777621796389999999846
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEEC-CCCEEEEECCCCCCCCC--CEEC
Q ss_conf 44225677410345542059973452320121003465410000167168889707-78588850100146553--0010
Q gi|254780834|r 158 KLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSS-RGQVIAFGGRTLSKGES--VKYL 234 (648)
Q Consensus 158 ~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~-~g~~i~f~gR~l~~~~~--~KYl 234 (648)
-+||. .|++-... +|=+. -.| + -..|+++.. .|+|||.-=|-.|+.-+ .|--
T Consensus 146 ~lG~n--~WtS~kv~-------------aGe~G--hgG--P------AaaFivr~~~~~~VvaVDlRy~DPAlNG~vKTq 200 (930)
T PHA02415 146 SLGFN--TWTSSKVA-------------AGEVG--HAG--P------AAAFIVREPADGRVVAVDMRYVDPALNGGVKTQ 200 (930)
T ss_pred CCCCC--CCCCCCCC-------------CCCCC--CCC--C------CEEEEEECCCCCCEEEEEEEECCCCCCCCCCCC
T ss_conf 57635--45676778-------------98878--787--5------135577227887379987112270016885210
Q ss_pred CCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCC--HHHHHCCCCHHHHHHHHH
Q ss_conf 387676535210110817888864331000023567870899714388999874355421--134321366267898851
Q gi|254780834|r 235 NSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNV--VSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 235 NSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~--va~~Gtalt~~~~~~l~r 312 (648)
--- .|.-.-|--+.++- + ....|+|||....++|..-+-.+++ +|.-|+|-.++ |-.-+-
T Consensus 201 ~qG-----eK~G~gwt~D~~rL--~----------rA~~VyiVESpINAlSi~~c~~pg~aa~alRG~aNvd~-IDwsfl 262 (930)
T PHA02415 201 TQG-----DKAGYGWTADARRL--D----------KAKRVFIVESAINALSIDTCAMPGAAALALRGLANVDA-IDFSSL 262 (930)
T ss_pred CCC-----CCCCCCCCCCHHHH--H----------HCCEEEEEECCCHHHHHHHHCCCCCEEEEEECCCCCCC-CCHHHH
T ss_conf 145-----44577876798888--3----------27489998245014436663389830133104455553-110111
Q ss_pred CCCEEEEEECCCC------------CCHHHHHHHHHHHHHHHHCCCCEEEEEC-------CCC-------CCHHHHHHCC
Q ss_conf 2681899617886------------6225777888888777536973067525-------788-------8888997203
Q gi|254780834|r 313 LSPRIVLCFDGDD------------PGLRAAYKAIDLVLCHLIPGNRVNFVLL-------SRG-------EDPDSFIRCY 366 (648)
Q Consensus 313 ~~~~vvl~fDgD~------------AG~kAa~Ra~e~~l~~l~~g~~v~vv~L-------P~G-------~DPDe~ir~~ 366 (648)
-.++|++|+|.|+ +|..||++.-|.+..+ ++....|-. .+| .|-.||++.+
T Consensus 263 rGKrvvi~lD~~dp~~e~~pr~g~RPG~eAAW~l~E~lta~---~I~~~LVD~~~W~~gl~~~e~~~~~i~DiND~Lq~~ 339 (930)
T PHA02415 263 RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLASL---NISAVLVDQAGWLADLADGETKQQPINDVNDYLQLR 339 (930)
T ss_pred CCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC---CCCCEEEEHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 58769999368875445785447898778899999988763---853124516544324554422235510278999971
Q ss_pred CHHHHHHHHHHCCCH
Q ss_conf 668899886414992
Q gi|254780834|r 367 GKTAFEKLIVESLPL 381 (648)
Q Consensus 367 G~eaf~~ll~~A~~l 381 (648)
|++.+...+++=.|+
T Consensus 340 Ga~el~~~l~~lepW 354 (930)
T PHA02415 340 GPEELARALEQLEPW 354 (930)
T ss_pred CHHHHHHHHHHCCCC
T ss_conf 789999999724411
No 10
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=99.31 E-value=6.8e-12 Score=129.01 Aligned_cols=77 Identities=52% Similarity=0.796 Sum_probs=70.3
Q ss_pred EEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf 08997143889998743554211343213662678988512681899617886622577788888877753697306752
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVL 352 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~ 352 (648)
.++|||||+||++++|+|+.++||++||+.+..|+..+++..++|+||||+|.||++|+.|+.+.++.. +..++++.
T Consensus 2 ~v~i~EG~~Dals~~~~g~~~~va~~G~~~~~~~~~~l~~~~~~vii~~D~D~aG~~~~~~~~~~~~~~---~~~~~i~~ 78 (79)
T cd01029 2 EVIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLAL---GGRVRVPP 78 (79)
T ss_pred EEEEEECHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEE
T ss_conf 399996479999999718654425887677499999985557765999688899999999999999977---99699851
No 11
>PHA02031 putative DnaG-like primase
Probab=99.13 E-value=4.5e-10 Score=112.23 Aligned_cols=165 Identities=21% Similarity=0.287 Sum_probs=116.2
Q ss_pred CCHHHHHHHCCCCCHHHHHH-HCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEEC---CCCCCCC
Q ss_conf 41034554205997345232-0121003465410000167168889707785888501001465530010---3876765
Q gi|254780834|r 166 RYSLREHLRQKGFSEEKIIE-AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYL---NSPETIL 241 (648)
Q Consensus 166 ~~~l~~~l~~~~~~~~~~~~-~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYl---NSpeT~i 241 (648)
+.+++.++..||++.-.+.. .|| ||-.=.+||+||+.+. .-||..+ +.+|||+ |-+-
T Consensus 93 ~~~iy~~ll~Kgi~~~~~~~~l~l---------y~S~r~~Rlilp~~~g------W~gRs~~-~~~PKW~gYg~p~~--- 153 (274)
T PHA02031 93 YQSLYGLLLSKGIDYNVMTPGLPL---------LYSERQHRLIFPTDAG------WIGRATA-DQNPKWVGYGYPAP--- 153 (274)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCC---------HHHHHCCEEEEECCCC------HHHHCCC-CCCCCCCCCCCCCC---
T ss_conf 777655421046555546775332---------0021068389753430------3121115-67873003799973---
Q ss_pred CCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCC----CCHHHHHCCCCHHHHHHHHH-CCCE
Q ss_conf 352101108178888643310000235678708997143889998743554----21134321366267898851-2681
Q gi|254780834|r 242 FHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQ----NVVSSLGTALTEYQLRLLWK-LSPR 316 (648)
Q Consensus 242 f~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~----n~va~~Gtalt~~~~~~l~r-~~~~ 316 (648)
-+.++..+. ...+.+||+| |+||.+.-|.- .++|.|||.|+.-|...|-. .+++
T Consensus 154 -----~~~~~~~~~-------------~~g~~~VLTE---D~lSA~KV~~a~~~~~A~alLGT~L~~~~AA~Llq~~~k~ 212 (274)
T PHA02031 154 -----DYHGWPQEL-------------SMGRPWVLTE---DYLSALKVRWACPEVFAVGLNGTRLRDRLAAIMLQQTCKR 212 (274)
T ss_pred -----CCCCCCCCC-------------CCCCCEEEEH---HHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCC
T ss_conf -----313434223-------------7887279754---5554554431036412321105653368999999844995
Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 8996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r 317 IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 317 vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
|+++||||.||..++-.+...+-++ |++++++.-|+|.||-++= ....+++|..
T Consensus 213 V~~wLD~D~AG~~Ga~~i~k~LR~~---gl~~~~~~~~~~~DPKd~~----~~qI~~ii~g 266 (274)
T PHA02031 213 AFIFLDGDPAGVRGSAGVMRRLRSL---LIEGQVIHTPDGFDPKDLT----REQIRSLVIG 266 (274)
T ss_pred EEEEECCCCCCCHHHHHHHHHHHHH---HCCCEEEECCCCCCCCCCC----HHHHHHHHCC
T ss_conf 7999569831213589999998874---0512256247789922089----9999999746
No 12
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI; InterPro: IPR014129 This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein ..
Probab=98.88 E-value=2.3e-07 Score=87.43 Aligned_cols=303 Identities=19% Similarity=0.293 Sum_probs=197.8
Q ss_pred CCCCCCCCEEEE---CCCCEEEECCCCCCCCHHHHHHHHCCCC-HHHHHHHHHHHHCCCCC---CCCCCHHH-HHHHHHH
Q ss_conf 888858787981---7897467136888878989989885999-79999999998188587---76820367-7788999
Q gi|254780834|r 45 FHDEKTPSFHCN---DSKGFYYCFSCHVKGDHLSFLSALLGCS-FIESVQRLAAIAGVPLP---VVDPKIEK-KEKIQTD 116 (648)
Q Consensus 45 fh~ektpsf~v~---~~~~~~~cf~c~~~gd~~~f~~~~~~~~-f~ea~~~la~~~gi~~~---~~~~~~~~-~~~~~~~ 116 (648)
|-.-|. ++.|+ ..||+||-|+.|.+|..|+.+|..++|| |.||+..=+...|++=- .-...+++ .......
T Consensus 1759 fg~~KG-~Lkv~L~g~yrG~w~~f~tG~~G~li~li~~~~~LSG~KEal~~A~~l~~~p~~~~~~i~~~a~~~~~~~~~k 1837 (2193)
T TIGR02760 1759 FGTAKG-SLKVSLTGKYRGLWKDFETGEKGTLIDLIEAKKGLSGFKEALNKAASLLGEPEHYQLSINKKAPQLLNTEPEK 1837 (2193)
T ss_pred ECCCCC-CEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 006752-2588750453422242467888768888751058877799999999862787412544142341234344566
Q ss_pred HHHHHH-----HHHHHHHHHHCCCCCHHHHHHH-HHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCE
Q ss_conf 999999-----9999999973267775789999-8506885351012442256774103455420599734523201210
Q gi|254780834|r 117 LIRLIE-----VATDFFHHSLKNARDKRLHYYL-DERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLI 190 (648)
Q Consensus 117 ~~~~~~-----~~~~~~~~~l~~~~~~~a~~yl-~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~ 190 (648)
+-++-. .|..+|..-. .-+|..|-.|| ..||+. .++.-.|-|+|....+ +-|.+. |++.
T Consensus 1838 ~~~~e~r~kvi~A~~~f~~s~-~~~gTlAe~YL~~~~G~~--~~D~~~~Rf~P~vy~W--knCneq----------G~~~ 1902 (2193)
T TIGR02760 1838 LAQLEKRNKVILAKKLFQESQ-ELKGTLAEKYLKQHRGLA--SIDNDDIRFHPSVYSW--KNCNEQ----------GKLS 1902 (2193)
T ss_pred HHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCC--CCCCCC----------CCCC
T ss_conf 765544456788899863480-167889999998617863--3456451132576751--010112----------5555
Q ss_pred ECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCC
Q ss_conf 034654100001671688897077858885010014655--300103876765352101108178888643310000235
Q gi|254780834|r 191 DGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRR 268 (648)
Q Consensus 191 ~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~ 268 (648)
. +....|+ ++.+++|..|++-|..=--|+++. .-|-+.++--.+=.|+...-.|+...+.
T Consensus 1903 ~-~~~~~PA------li~~~~~~~g~~~gi~~~yL~~~~a~k~~~~~~~krv~G~~s~~~~~ln~g~~g----------- 1964 (2193)
T TIGR02760 1903 D-KKKKHPA------LIAAAKDEKGEIKGIQITYLDKDDANKDKDMDSNKRVLGSKSGQFVVLNKGRQG----------- 1964 (2193)
T ss_pred C-CCCCCCE------EEEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEECCCEEECCCCCCH-----------
T ss_conf 6-4345530------010111889854116851368655567663656874112013624430477640-----------
Q ss_pred CCCCEEEEECCHHHHHHHHHCCCCC--CHHHHHC-------CCCHHH---------HHHHH--HCCCEEEEEECCCCCCH
Q ss_conf 6787089971438899987435542--1134321-------366267---------89885--12681899617886622
Q gi|254780834|r 269 NSSSFIILVEGYMDVLSLCQAGVQN--VVSSLGT-------ALTEYQ---------LRLLW--KLSPRIVLCFDGDDPGL 328 (648)
Q Consensus 269 ~~~~~~i~vEGy~Dvi~l~~~G~~n--~va~~Gt-------alt~~~---------~~~l~--r~~~~vvl~fDgD~AG~ 328 (648)
+..||.||.=+.++-.++--.+ +|+..|- |+|-.. ++-+. ..-.+||||.|.|.-=.
T Consensus 1965 ---~~~~~a~G~E~g~~I~~~n~~~~~~~~v~~~~~PWnPvaitGGrvWGdiPd~n~~~i~~~~~~~~v~I~l~n~~~~~ 2041 (2193)
T TIGR02760 1965 ---DISYLAEGIETGLSIAEANPKATVVIAVVGKNRPWNPVAITGGRVWGDIPDNNVSPIAPKDIPKNVVIVLDNDGEEA 2041 (2193)
T ss_pred ---HHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEECCEEECCCCCCCCCCCCCCCCCEEEEEEECCCCHHH
T ss_conf ---07888886899999975489960699980488764664640660233577334788888887306999724773689
Q ss_pred -----HHHHHHH-HHHHHHHHCCCCEEEEECCC------CCCHHHHHHCCCHHHHHHHHHH----CCCHHHHH
Q ss_conf -----5777888-88877753697306752578------8888899720366889988641----49927999
Q gi|254780834|r 329 -----RAAYKAI-DLVLCHLIPGNRVNFVLLSR------GEDPDSFIRCYGKTAFEKLIVE----SLPLVDML 385 (648)
Q Consensus 329 -----kAa~Ra~-e~~l~~l~~g~~v~vv~LP~------G~DPDe~ir~~G~eaf~~ll~~----A~~l~dFl 385 (648)
+-.-|.+ ++...+-.+|..+.+|+ |+ .-|=.+..-+.|.+.+.+-|.. +...+++.
T Consensus 2042 yky~~~e~~~~i~ki~~kl~~d~~~~~i~~-P~GlqGK~~TD~Nd~~l~~~~~~~~k~~~~kDiG~i~~~~~k 2113 (2193)
T TIGR02760 2042 YKYVKRESQRAIEKIIKKLKEDNISASIVI-PDGLQGKEKTDLNDVLLKKGEEELKKQLKRKDIGAISSIEDK 2113 (2193)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEEE-CCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999853534329999999616898089981-378676111660001003863799999745422012010036
No 13
>pfam01751 Toprim Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Probab=98.83 E-value=1e-08 Score=99.90 Aligned_cols=79 Identities=39% Similarity=0.578 Sum_probs=72.1
Q ss_pred EEEEECCHHHHHHHHHCCC--CCCHHHHHCC-----CCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 0899714388999874355--4211343213-----662678988512681--899617886622577788888877753
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTA-----LTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLI 343 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gta-----lt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~ 343 (648)
.++||||++||+++.+.|+ .++++++|+. ++++|++.|++..++ ||+|+|+|.+|+.++++..+.+.+.
T Consensus 2 ~l~IVE~~~d~~~i~~~~~~~~~~~~~~G~~~~l~~~~~~~~~~l~~~~~~~eViiatD~D~eGe~~a~~l~~~l~~~-- 79 (89)
T pfam01751 2 VLIIVEGPSDAIALAKAGGYKGNVVALLGHLSDVIPLTKEQLKLLKKLAKKDEVILATDPDREGEAIAWKLLELLKPL-- 79 (89)
T ss_pred EEEEECCHHHHHHHHHHCCCCEEEEEEECEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHC--
T ss_conf 899989889999999624888799984157057655424679999986237749998798948999999999983122--
Q ss_pred CCCCEEEEECC
Q ss_conf 69730675257
Q gi|254780834|r 344 PGNRVNFVLLS 354 (648)
Q Consensus 344 ~g~~v~vv~LP 354 (648)
+..++.+.+|
T Consensus 80 -~~~v~ri~~~ 89 (89)
T pfam01751 80 -GKKVRRIFLP 89 (89)
T ss_pred -CCCEEEEECC
T ss_conf -9816999669
No 14
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.75 E-value=2.1e-08 Score=96.93 Aligned_cols=68 Identities=34% Similarity=0.468 Sum_probs=63.0
Q ss_pred EEEEECCHHHHHHHHHCCC--CCCHHHHHCCCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf 0899714388999874355--4211343213662678988512681--899617886622577788888877
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLC 340 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gtalt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~ 340 (648)
.++||||++||+++++.|. .++++++|+..+.+|+..|++..++ ||||+|+|.+|+++++++.+.+.+
T Consensus 2 ~liIVEg~~d~~~i~~~~~~~~~~~~~~G~~~~~~~i~~l~~~~~~~eViiatD~D~eGe~~a~~i~~~l~~ 73 (76)
T smart00493 2 VLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKLAELLKP 73 (76)
T ss_pred EEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 799987888999999856999799982152350448999998633897999769894469999999998776
No 15
>PRK04031 DNA primase; Provisional
Probab=98.43 E-value=1.8e-06 Score=79.13 Aligned_cols=102 Identities=27% Similarity=0.420 Sum_probs=78.4
Q ss_pred CCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHC-CCCE
Q ss_conf 787089971438899987435542113432136626789885126818996178866225777888888777536-9730
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIP-GNRV 348 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~-g~~v 348 (648)
..+.+|||||--||+-|-.+||+|+||..||.+-+.-+.+-++ +.|+.+.|||. +.++.|..|.+ +.--
T Consensus 167 ~sd~iIvVEGRaDV~nLLk~GikN~ia~~G~~ip~~i~~L~~~--k~vtaF~DGDr--------GG~liLKELlqVadID 236 (420)
T PRK04031 167 DSDAIIVVEGRADVLNLLRYGIKNVIAVEGTSVPETIIELSKK--KTVTAFLDGDR--------GGELILKELLQVADID 236 (420)
T ss_pred CCCEEEEEECHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHCC--CEEEEEECCCC--------CHHHHHHHHHHHCCEE
T ss_conf 8880899956588999987363327862688888899998638--65899953885--------4378999998546735
Q ss_pred EEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH
Q ss_conf 6752578888889972036688998864149927999
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDML 385 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl 385 (648)
+|++-|+|+---++-++ .....|.+..|...|+
T Consensus 237 YVArAP~GKEVEeLT~K----EI~KALR~KVP~eq~~ 269 (420)
T PRK04031 237 YVARAPPGKEVEELTKK----EIAKALRNKVPVEQYL 269 (420)
T ss_pred EEEECCCCCCHHHCCHH----HHHHHHHCCCCHHHHH
T ss_conf 99979899635326887----9999987248889998
No 16
>TIGR00646 MG010 DNA primase homolog; InterPro: IPR004611 The DNA primase DnaG of Escherichia coli and its apparent orthologs in other bacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein found in this family, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown..
Probab=98.43 E-value=1e-06 Score=81.42 Aligned_cols=197 Identities=22% Similarity=0.299 Sum_probs=141.4
Q ss_pred HHHHHHHHHCCC---CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCC
Q ss_conf 999999973267---77578999985068853510124422567741034554205997345232012100346541000
Q gi|254780834|r 124 ATDFFHHSLKNA---RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYD 200 (648)
Q Consensus 124 ~~~~~~~~l~~~---~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d 200 (648)
..-.||..|++. +-..+..|+.+||++-+..-..+=|.+ |+
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~d~~~~ggg~~---------~~--------------------------- 54 (218)
T TIGR00646 11 LFFVYHKNLKNQSKSKYRCPVNYLKKRGFNLQDLLKVGGGLG---------YL--------------------------- 54 (218)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHCCCCHH---------HC---------------------------
T ss_conf 666554210100012455567777632775356654044200---------00---------------------------
Q ss_pred CCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCH
Q ss_conf 01671688897077858885010014655300103876765352101108178888643310000235678708997143
Q gi|254780834|r 201 RFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGY 280 (648)
Q Consensus 201 ~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy 280 (648)
.-+.-+-.|+.+..|.++||-.|.+.- ..+++-+|-..-=.|+....|+....- ....+++|||-
T Consensus 55 ~~~~w~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~p~~~pp~~~~~~~g~~~~~~-------------~~~~~~~~~gd 119 (218)
T TIGR00646 55 GEKEWLNLPLYNFDGNLVGFLNRKVGF--EKEFLYLPFNKPPSKSEAFLGLKELPT-------------EDNTIYLVEGD 119 (218)
T ss_pred CCCCCCCCEEECCCCCCHHHHHHHCCC--CCCEEECCCCCCCCCCHHHHHHHHHCC-------------CCCEEEEEECC
T ss_conf 342100000001366101122211011--100022146788541012310122000-------------25505886166
Q ss_pred HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC-CC
Q ss_conf 889998743554211343213662678988512-6818996178866225777888888777536973067525788-88
Q gi|254780834|r 281 MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG-ED 358 (648)
Q Consensus 281 ~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G-~D 358 (648)
+|-++....|+-|.+..||..++..+++.+.+- ..++++|+|.|-||..++...-+. +...|..++++.+... +|
T Consensus 120 ~dw~~~~~~g~~~~~p~cg~~~~~~~~~~~~~~~~~~~~~c~d~d~~g~~~~~~~~~~---~~~~g~~~~~~~~~~~~~d 196 (218)
T TIGR00646 120 FDWLAFRKGGILNCLPLCGLTLSDKQVKWLKQKKIEKVFLCLDNDLAGKNGAKNLEEY---LKNAGFITKVVELKGKAKD 196 (218)
T ss_pred CHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH---HHHCCCEEEHHHHHHHHCC
T ss_conf 2011221033100000103100203566655411004566523530000235568888---7404731210002100012
Q ss_pred HHHHHHCCCHHHHHHHH
Q ss_conf 88997203668899886
Q gi|254780834|r 359 PDSFIRCYGKTAFEKLI 375 (648)
Q Consensus 359 PDe~ir~~G~eaf~~ll 375 (648)
=.+++.-+ +..+...+
T Consensus 197 w~~~~~~~-~~~w~~~~ 212 (218)
T TIGR00646 197 WNDLLLLY-PKNWAKAL 212 (218)
T ss_pred CCCEEEEC-CCCHHHHH
T ss_conf 00012421-64045666
No 17
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.32 E-value=4e-05 Score=66.75 Aligned_cols=266 Identities=23% Similarity=0.285 Sum_probs=147.1
Q ss_pred ECCCCCCCCCCEEEECCC--CEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCH-HHHHHHHHHHH
Q ss_conf 345888858787981789--746713688887898998988599979999999998188587768203-67778899999
Q gi|254780834|r 42 CCPFHDEKTPSFHCNDSK--GFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKI-EKKEKIQTDLI 118 (648)
Q Consensus 42 ~cPfh~ektpsf~v~~~~--~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~-~~~~~~~~~~~ 118 (648)
.||-..-|. -|-+.++| |.|.||-|+ +||=.+.|....+.++.|+........|...|...... .....+.+..-
T Consensus 34 ~cpvcg~k~-RFr~dD~kGrGtw~c~y~~-~GDGl~lvs~v~~~~~~eaa~~i~~~i~~~~~~~~a~~~s~a~~~~~~~~ 111 (366)
T COG4643 34 PCPVCGGKD-RFRFDDRKGRGTWFCNYCG-HGDGLPLVSLVRQRTGIEAAWEIKGDIGNDAPESKAMRASIAPAKADRAA 111 (366)
T ss_pred CCCCCCCCC-CCCCCCCCCCCCEEEEEEC-CCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 898557766-3015675677646886404-67885315530577258999987311047613212334221335577788
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCC
Q ss_conf 99999999999973267775789999850688535101244225677410345542059973452320121003465410
Q gi|254780834|r 119 RLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATS 198 (648)
Q Consensus 119 ~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~ 198 (648)
+--..+...+... .+.-.-.|+.++|. -||..++++.. ++.+
T Consensus 112 ~~~~la~~~a~~~----~gts~~a~~~~~g~---------------------p~Lp~~~it~~-------------~~i~ 153 (366)
T COG4643 112 ERAKLAALLAAKS----RGTSGYAYLVSLGH---------------------PYLPAKGITPA-------------AGIG 153 (366)
T ss_pred HHHHHHHHHHHHH----HHHHHHHHHCCCCC---------------------CCCCCCCCCCC-------------CCCC
T ss_conf 9999999999863----30235688735896---------------------15424546512-------------3356
Q ss_pred CCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf 00016716888970778588850100146553001038767653521011081788886433100002356787089971
Q gi|254780834|r 199 YDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVE 278 (648)
Q Consensus 199 ~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vE 278 (648)
-+-|+.--++|..|..|...+.- .+.++ -|.=|.||.--=|.+........ ....+|++|
T Consensus 154 ~~~~~~~slip~~d~~Gel~~lq--~I~~d---------G~Krf~~Ggr~kg~f~p~~g~~~---------~aa~lvi~E 213 (366)
T COG4643 154 GVQLRDGSLIPLRDADGELTGLQ--LIQPD---------GTKRFLKGGRVKGCFIPLGGLAG---------PAARLVIAE 213 (366)
T ss_pred CCCCCCCCEEEEECCCCCEEEEE--EECCC---------CCCEECCCCCCCCCEEECCCCCC---------CCCCEEEEE
T ss_conf 54446663687772788775368--87678---------65000358742340432588754---------343057740
Q ss_pred CHHHHHHHHHCC-CCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCC-----CCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 438899987435-54211343213662678988512-681899617886-----62257778888887775369730675
Q gi|254780834|r 279 GYMDVLSLCQAG-VQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDD-----PGLRAAYKAIDLVLCHLIPGNRVNFV 351 (648)
Q Consensus 279 Gy~Dvi~l~~~G-~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~-----AG~kAa~Ra~e~~l~~l~~g~~v~vv 351 (648)
||--+.+++|+= ..-++|-.-+.|+.--..+-++| +..||||=|.|. +|+.++..+..-+ +..+ .
T Consensus 214 GyATal~i~~~~ga~v~aAi~agNll~VA~al~~~~Pda~iIIaAD~D~~~~nnpG~t~A~eaA~Av------ng~~--~ 285 (366)
T COG4643 214 GYATALSISQATGAPVAAAIDAGNLLAVASALRKKFPDAQIIIAADDDINTANNPGLTKAEEAAQAV------NGTV--A 285 (366)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHH------CCEE--E
T ss_conf 2367879998741066544402358999999997689763699745654467880167899998752------7666--3
Q ss_pred ECCCC-CCHHHHHHCCCHHHHHHHH
Q ss_conf 25788-8888997203668899886
Q gi|254780834|r 352 LLSRG-EDPDSFIRCYGKTAFEKLI 375 (648)
Q Consensus 352 ~LP~G-~DPDe~ir~~G~eaf~~ll 375 (648)
.+|-+ -|=+|+...+|..+-+.-+
T Consensus 286 lP~~~~adwpD~~tq~n~la~r~~~ 310 (366)
T COG4643 286 LPPFGPADWPDGFTQFNDLATRCAF 310 (366)
T ss_pred CCCCCCCCCCHHHHHCCHHHHHHHH
T ss_conf 6887887784054332205555332
No 18
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.94 E-value=3.4e-05 Score=67.36 Aligned_cols=67 Identities=34% Similarity=0.430 Sum_probs=59.2
Q ss_pred EEEEECCHHHHHHHHHCCC--CCCHHHHHCCC--CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf 0899714388999874355--42113432136--6267898851268189961788662257778888887
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGV--QNVVSSLGTAL--TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVL 339 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~--~n~va~~Gtal--t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l 339 (648)
.++||||..|++++.+.+. ..++++.|+.. +..++..+.+...+|++++|+|.+|..++.+......
T Consensus 2 ~viivEG~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~vii~~D~D~~g~~~~~~~~~~~~ 72 (83)
T cd00188 2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK 72 (83)
T ss_pred EEEEECCHHHHHHHHHHCCCCEEEEEEEEEECCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf 79998888999999985699979999755738438999999876899999974989379999999999732
No 19
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.84 E-value=4.3e-05 Score=66.47 Aligned_cols=66 Identities=23% Similarity=0.357 Sum_probs=59.8
Q ss_pred CEEEEECCHHHHHHHHHCCCC-CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 708997143889998743554-211343213662678988512681899617886622577788888
Q gi|254780834|r 272 SFIILVEGYMDVLSLCQAGVQ-NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDL 337 (648)
Q Consensus 272 ~~~i~vEGy~Dvi~l~~~G~~-n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~ 337 (648)
+.+|||||-.|..++.++|++ ..+.+.|++++..-+.++++....|+++.|.|.+|.+-+.+-.+.
T Consensus 2 ~evIvVEGk~D~~~l~~~~~~~~ii~t~g~~~~~~~~~~i~~~~~~VIIlTD~D~~Gekirk~i~~~ 68 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEY 68 (81)
T ss_pred CEEEEEECCCHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf 7699995561899999863781399989903459999999985598599968996707999999998
No 20
>pfam10410 DnaB_bind DnaB-helicase binding domain of primase. This domain is the C-terminal region three-helical domain of primase. Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase. It is associated with the Toprim domain (pfam01751) which is the central catalytic core.
Probab=97.83 E-value=3.9e-05 Score=66.88 Aligned_cols=56 Identities=30% Similarity=0.361 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 27999999985302331457999999999885417998999999999999988765
Q gi|254780834|r 381 LVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLF 436 (648)
Q Consensus 381 l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~ 436 (648)
+++|+|+++.++.|+++|++|+++.+.+.|+|++|+|++.|+.|+++++++++...
T Consensus 1 l~~f~~~~l~~~~dl~~~egk~~~~~~~~pli~~i~~~~~r~~y~~~la~~~gi~~ 56 (59)
T pfam10410 1 LSEFLFRRLLEGYDLDTPEGRAALLREALPLIAKIPDPVLRELYLQELAELLGISE 56 (59)
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 92889999873589999889999999970787559838899999999999878284
No 21
>PRK06904 replicative DNA helicase; Validated
Probab=97.47 E-value=0.022 Score=41.60 Aligned_cols=48 Identities=15% Similarity=0.117 Sum_probs=32.3
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|=.+||- + =|+..+.++.|..+..+. ..+|.+.--.|..-.+..
T Consensus 220 ~g~LiViAaRP---s---------------mGKTa~alnia~n~A~~~---------~~~V~~fSLEM~~~~l~~ 267 (472)
T PRK06904 220 PSDLIIVAARP---S---------------MGKTTFAMNLCENAAMAS---------EKPVLVFSLEMPAEQIMM 267 (472)
T ss_pred CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHH
T ss_conf 57579997379---8---------------756899999999999955---------995799778799999999
No 22
>LOAD_Toprim consensus
Probab=97.43 E-value=0.00077 Score=54.96 Aligned_cols=66 Identities=30% Similarity=0.374 Sum_probs=54.3
Q ss_pred EEEEECCHHHHHHHHHCC-CCCCHHHHHCCC--CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf 089971438899987435-542113432136--626789885126818996178866225777888888
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAG-VQNVVSSLGTAL--TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLV 338 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G-~~n~va~~Gtal--t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~ 338 (648)
.+|||||..|+-.+.+.+ -.+++|++|... +...++...+-+++|+|+.|.|..|..-++...+++
T Consensus 2 ~liIVEsp~k~k~I~~~l~~~~vias~GHi~~~~~~~~~~~~~~~~~VilATDpDrEGEaIa~hl~~~l 70 (98)
T LOAD_Toprim 2 KIIVVEGPADAKAIERFGGDKNVIASKGHARKKSVLELIKLALKAKEVIIATDPDREGEKIAKKLLELL 70 (98)
T ss_pred EEEEEECHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf 499992848899999985998799795883251699999998469929994696965289999999983
No 23
>PRK08760 replicative DNA helicase; Provisional
Probab=97.31 E-value=0.036 Score=39.62 Aligned_cols=48 Identities=19% Similarity=0.108 Sum_probs=31.2
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||-= -|+.-+.++.|.....+. ...|.+.--.|..-.+.+
T Consensus 228 ~G~LiViaaRPs------------------mGKTalalnia~~~A~~~---------~~~V~~fSLEMs~~ql~~ 275 (476)
T PRK08760 228 PTDLIILAARPA------------------MGKTTFALNIAEYAAIKS---------KKGVAVFSMEMSASQLAM 275 (476)
T ss_pred CCCEEEEEECCC------------------CCHHHHHHHHHHHHHHHC---------CCCEEEEECCCCHHHHHH
T ss_conf 777799987788------------------747899999999999837---------997899703699999999
No 24
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=97.28 E-value=0.032 Score=40.10 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=28.7
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 78588850100146553001038767653521011081788886433100002356787089971438899987
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~ 287 (648)
.|..|-.+||. + =|+..+.++.|.....+ ...+|.+.=-.|..-.+.
T Consensus 193 ~g~LiIiaARP---s---------------mGKTafalnia~n~A~~---------~g~~Vl~fSLEMs~eql~ 239 (421)
T TIGR03600 193 KGDLIVIGARP---S---------------MGKTTLALNIAENVALR---------EGKPVLFFSLEMSAEQLG 239 (421)
T ss_pred CCCEEEEEEEC---C---------------CCHHHHHHHHHHHHHHH---------CCCEEEEEECCCCHHHHH
T ss_conf 88689998546---7---------------87459999999999986---------698389992579999999
No 25
>PRK08006 replicative DNA helicase; Provisional
Probab=97.15 E-value=0.05 Score=38.31 Aligned_cols=48 Identities=13% Similarity=0.059 Sum_probs=31.1
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||-= -|+.-+.++.|.....+ ...+|.+.--.|..-.+..
T Consensus 223 ~G~LiviaaRPs------------------mGKTalalnia~~~a~~---------~~~~V~~fSlEMs~~ql~~ 270 (471)
T PRK08006 223 PSDLIIVAARPS------------------MGKTTFAMNLCENAAML---------QDKPVLIFSLEMPGEQIMM 270 (471)
T ss_pred CCCEEEEEECCC------------------CCHHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHH
T ss_conf 173899994699------------------87699999999999986---------6995799816799999999
No 26
>PRK07004 replicative DNA helicase; Provisional
Probab=97.11 E-value=0.051 Score=38.20 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=31.0
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||- + -|++-+.++.|+....+ ....|.++=-.|..-.+.+
T Consensus 212 ~gdLiIIAARP---s---------------mGKTafAlniA~n~A~~---------~g~~V~~FSLEMs~eql~~ 259 (460)
T PRK07004 212 GGELIIVAGRP---S---------------MGKTAFSMNIGEYVAVE---------YGLPVAVFSMEMPGTQLAM 259 (460)
T ss_pred CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHH---------CCCCEEEECCCCCHHHHHH
T ss_conf 77579997368---7---------------64269999999999872---------5886699847799999999
No 27
>PRK05748 replicative DNA helicase; Provisional
Probab=96.98 E-value=0.067 Score=37.09 Aligned_cols=48 Identities=21% Similarity=0.184 Sum_probs=30.4
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||-=- |+.-+.++.|.....+. ...|.+.--.|..-.+.+
T Consensus 202 ~g~LiviaaRP~m------------------GKTa~alnia~~~a~~~---------~~~v~~fSlEM~~~~l~~ 249 (448)
T PRK05748 202 PNDLIIVAARPSV------------------GKTAFALNIAQNVATKT---------DKNVAIFSLEMGAESLVM 249 (448)
T ss_pred CCCEEEEEECCCC------------------CHHHHHHHHHHHHHHHC---------CCEEEEEECCCCHHHHHH
T ss_conf 6737999847998------------------76899999999999856---------980899817788889999
No 28
>PRK08082 consensus
Probab=96.93 E-value=0.052 Score=38.13 Aligned_cols=48 Identities=21% Similarity=0.214 Sum_probs=31.5
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||- + -|+.-+.++.|....-+ ....|.+.-..|..-.+..
T Consensus 202 ~g~LiviaaRP---s---------------mGKTa~alnia~~~a~~---------~~~~V~~fSlEM~~~~l~~ 249 (453)
T PRK08082 202 RNDLIIVAARP---S---------------VGKTAFALNIAQNVATK---------TDENVAIFSLEMGADQLVM 249 (453)
T ss_pred CCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHH
T ss_conf 58579998678---8---------------75789999999999985---------5994899731389899999
No 29
>PRK08694 consensus
Probab=96.92 E-value=0.074 Score=36.72 Aligned_cols=49 Identities=18% Similarity=0.175 Sum_probs=31.9
Q ss_pred CCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 7785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 213 SRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 213 ~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
..|..|-.+||- + -|+.-+.++.|.....+. ...+.++--.|..-.+.+
T Consensus 216 ~~G~LiVIaaRP---s---------------mGKTalalnia~~~a~~~---------~~~V~~fSLEMs~~~l~~ 264 (468)
T PRK08694 216 QPGDLIIVAGRP---S---------------MGKTAFSINIAEHVAVEG---------KLPVAVFSMEMGGAQLVM 264 (468)
T ss_pred CCCCEEEEEECC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHH
T ss_conf 878479996178---6---------------537899999999999847---------984799778899999999
No 30
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.
Probab=96.90 E-value=0.033 Score=39.91 Aligned_cols=109 Identities=17% Similarity=0.207 Sum_probs=77.8
Q ss_pred HHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999847788999984430023799889999999999975388999899998851112899999999986543332
Q gi|254780834|r 484 EAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLW 563 (648)
Q Consensus 484 E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~elL~~L~~~~~~~~~~ 563 (648)
+|.+|+++++||++...+.+......|.+|.+. +...+++.+..++......+.++..+.....++..+...-.
T Consensus 1 ~R~~I~llLq~P~la~~v~~~~~~~~~~~~~~~-ll~~L~~~~~~~p~~~t~~Lle~~rd~~~~~~L~~La~~~~----- 74 (125)
T smart00766 1 MRELIRLLLQNPELASLVPDLLTLEDFTHPGLA-LLAELLATCRGNPGLTTGQLLEHWRDTPYEELLSELAVWDH----- 74 (125)
T ss_pred CHHHHHHHHHCHHHHHHCCCCHHHHHCCCCHHH-HHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCC-----
T ss_conf 989999998692988658881345545681079-99999999854999879999989549808999999985574-----
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0256899889999999999999858999999999999998
Q gi|254780834|r 564 SATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIA 603 (648)
Q Consensus 564 ~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~ 603 (648)
....++....+.+++....+. .+.+++..+..+.+
T Consensus 75 ----~~~~~~~~~ef~d~l~~L~~~-~~~~ri~~L~~k~~ 109 (125)
T smart00766 75 ----LIDEENLEEEFLDTLARLRKQ-LLERRIEELIAKLR 109 (125)
T ss_pred ----CCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
T ss_conf ----578067999999999999999-99999999999873
No 31
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=96.87 E-value=0.0019 Score=51.40 Aligned_cols=63 Identities=29% Similarity=0.312 Sum_probs=57.1
Q ss_pred CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCC-HHHHHHHHH--CCCEEEEEECCCCCCHHHHHH
Q ss_conf 870899714388999874355421134321366-267898851--268189961788662257778
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALT-EYQLRLLWK--LSPRIVLCFDGDDPGLRAAYK 333 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt-~~~~~~l~r--~~~~vvl~fDgD~AG~kAa~R 333 (648)
.+.+|||||--|..++-+.|+..++-++|-|+. .+-+.+|++ ....||+..|.|.+|.+=..+
T Consensus 9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~ 74 (127)
T COG1658 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKK 74 (127)
T ss_pred CCCEEEEECCCHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
T ss_conf 496699967767999998546863897586542788999999864258779986898562899999
No 32
>PRK08840 replicative DNA helicase; Provisional
Probab=96.84 E-value=0.085 Score=36.17 Aligned_cols=47 Identities=15% Similarity=0.131 Sum_probs=31.0
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 78588850100146553001038767653521011081788886433100002356787089971438899987
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~ 287 (648)
.|..|-.+||- +. |+.-+.++.|..++.+. ...|.+.-..|..-.+.
T Consensus 216 ~G~LiviaaRP---sm---------------GKTalalnia~n~a~~~---------~~~v~~fSlEMs~~ql~ 262 (464)
T PRK08840 216 GSDLIIVAARP---SM---------------GKTTFAMNLCENAAMDQ---------DKPVLIFSLEMPAEQLM 262 (464)
T ss_pred CCCEEEEEECC---CC---------------CHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHH
T ss_conf 57679998379---87---------------36899999999999965---------99679976779989999
No 33
>PRK04017 hypothetical protein; Provisional
Probab=96.82 E-value=0.0099 Score=44.74 Aligned_cols=82 Identities=27% Similarity=0.221 Sum_probs=60.6
Q ss_pred CCCEEEEECCHHHHHHHHHCCCCCC-HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE
Q ss_conf 7870899714388999874355421-134321366267898851268189961788662257778888887775369730
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQAGVQNV-VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV 348 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~G~~n~-va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v 348 (648)
..+.+|||||-=|+.||-..||+.- +-.....+.+ -...+.++..+||+++|-|..|.+=+.+..+.+..
T Consensus 21 ~~g~~IlVEGkRD~~ALr~LG~~G~Ii~l~r~~l~~-ia~~~~~~~~~vIlL~DwDr~G~~L~~kl~~~L~~-------- 91 (132)
T PRK04017 21 ENGAVIIVEGKRDELSLRKLGVRGEIIKLSRLPLFE-IALRASRLKKEVIILTDFDRKGEELAKKLSEYLQG-------- 91 (132)
T ss_pred CCCCEEEEECCCHHHHHHHCCCCCEEEEECCCCHHH-HHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHH--------
T ss_conf 599879996363699999849983189874840999-99999855983999971363217999999999986--------
Q ss_pred EEEECCCCCCHHHHHHCC
Q ss_conf 675257888888997203
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCY 366 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~ 366 (648)
-|..||..+|+.
T Consensus 92 ------~g~kvD~~~R~~ 103 (132)
T PRK04017 92 ------YGIKVDLEIRRK 103 (132)
T ss_pred ------CCCCCCHHHHHH
T ss_conf ------899757899999
No 34
>PRK07263 consensus
Probab=96.73 E-value=0.099 Score=35.54 Aligned_cols=70 Identities=21% Similarity=0.161 Sum_probs=37.8
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH------
Q ss_conf 78588850100146553001038767653521011081788886433100002356787089971438899987------
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC------ 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~------ 287 (648)
.|..|-.+||- +. |+.-+.++.|....-+ ....|.+.---|..-.+.
T Consensus 202 ~GdLiviaaRP---sm---------------GKTa~alnia~~iA~~---------~~~~V~~fSlEMs~~ql~~R~la~ 254 (453)
T PRK07263 202 PDQLIILAARP---AV---------------GKTAFVLNIAQNVGTK---------QKKTVAIFSLEMGAESLVDRMLAA 254 (453)
T ss_pred CCCEEEEEECC---CC---------------CHHHHHHHHHHHHHHH---------CCCEEEEEECCCCHHHHHHHHHHH
T ss_conf 78689997278---88---------------4789999999999985---------598289992469989999999998
Q ss_pred HCCCCCCHHHHHCCCCHHHHHHHH
Q ss_conf 435542113432136626789885
Q gi|254780834|r 288 QAGVQNVVSSLGTALTEYQLRLLW 311 (648)
Q Consensus 288 ~~G~~n~va~~Gtalt~~~~~~l~ 311 (648)
..||...---.| .+|+++...+.
T Consensus 255 ~~~i~~~~i~~g-~l~~~e~~~~~ 277 (453)
T PRK07263 255 EGMVDSHSLRTG-QLTDQDWNNVT 277 (453)
T ss_pred HCCCCHHCCCCC-CCCHHHHHHHH
T ss_conf 617331033136-52479999999
No 35
>PRK07773 replicative DNA helicase; Validated
Probab=96.73 E-value=0.1 Score=35.52 Aligned_cols=23 Identities=13% Similarity=0.374 Sum_probs=9.8
Q ss_pred CEECCCCCCCCCCC-CHHCCCHHH
Q ss_conf 00103876765352-101108178
Q gi|254780834|r 231 VKYLNSPETILFHK-GKNLYNFFG 253 (648)
Q Consensus 231 ~KYlNSpeT~if~K-~~~Ly~l~~ 253 (648)
-|+...+-|.+|.- .+.+|.+..
T Consensus 421 ~~~~~~~~~~v~~~G~k~v~~l~t 444 (868)
T PRK07773 421 LRMVARPMSNVFPTGRKEVFRLRT 444 (868)
T ss_pred CEEEECCCCCEECCCCCEEEEEEE
T ss_conf 518750333200056534899985
No 36
>PRK06321 replicative DNA helicase; Provisional
Probab=96.70 E-value=0.1 Score=35.39 Aligned_cols=71 Identities=17% Similarity=0.168 Sum_probs=37.6
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH------H
Q ss_conf 7858885010014655300103876765352101108178888643310000235678708997143889998------7
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL------C 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l------~ 287 (648)
.|..|=.+||- + -|++-+.++.|.....+. ...|.+.--.|..-.+ .
T Consensus 225 ~GdliviaaRP---s---------------mGKTalalnia~~~a~~~---------~~~v~~fSLEMs~~ql~~R~ls~ 277 (472)
T PRK06321 225 PSNLMILAARP---A---------------MGKTALALNIAENFCFQN---------RLPVGIFSLEMTVDQLIHRIICS 277 (472)
T ss_pred CCCEEEEECCC---C---------------CCHHHHHHHHHHHHHHHC---------CCCEEEECCCCCHHHHHHHHHHH
T ss_conf 67579985389---9---------------977999999999999856---------99469975779999999999874
Q ss_pred HCCCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf 4355421134321366267898851
Q gi|254780834|r 288 QAGVQNVVSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 288 ~~G~~n~va~~Gtalt~~~~~~l~r 312 (648)
.+||...--..| .+|.++...+..
T Consensus 278 ~s~i~~~~i~~g-~l~~~e~~~~~~ 301 (472)
T PRK06321 278 RSEVESKKISVG-DLSGRDFQRIVS 301 (472)
T ss_pred HCCCCCCCCCCC-CCCHHHHHHHHH
T ss_conf 037675521047-999999999999
No 37
>PRK05636 replicative DNA helicase; Provisional
Probab=96.64 E-value=0.11 Score=35.06 Aligned_cols=10 Identities=40% Similarity=0.640 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q ss_conf 1244225677
Q gi|254780834|r 156 MFKLGYAPDS 165 (648)
Q Consensus 156 ~f~lG~ap~~ 165 (648)
.|.=||.|++
T Consensus 8 ~~~~~~~~~~ 17 (507)
T PRK05636 8 SFDDDYVPPS 17 (507)
T ss_pred CCCCCCCCCC
T ss_conf 6777778999
No 38
>PRK08506 replicative DNA helicase; Provisional
Probab=96.58 E-value=0.12 Score=34.73 Aligned_cols=69 Identities=17% Similarity=0.168 Sum_probs=37.9
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH------H
Q ss_conf 7858885010014655300103876765352101108178888643310000235678708997143889998------7
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL------C 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l------~ 287 (648)
.|..|=.+||- +. |++-+.++.|..+++. ...|.+.=-.|..-.+ .
T Consensus 192 ~gdLiIIAARP---sm---------------GKTAfAlniA~~~a~~----------~~~V~~FSLEMs~~ql~~Rlls~ 243 (473)
T PRK08506 192 KGDLIIIAARP---SM---------------GKTTLVLNMVLKALNQ----------GKGVAFFSLEMPAEQLMLRMLSA 243 (473)
T ss_pred CCCEEEEECCC---CC---------------CHHHHHHHHHHHHHHC----------CCCEEEEECCCCHHHHHHHHHHH
T ss_conf 56279995079---98---------------6789999999999965----------99658982247999999999997
Q ss_pred HCCCCCCHHHHHCCCCHHHHHHHH
Q ss_conf 435542113432136626789885
Q gi|254780834|r 288 QAGVQNVVSSLGTALTEYQLRLLW 311 (648)
Q Consensus 288 ~~G~~n~va~~Gtalt~~~~~~l~ 311 (648)
.+||+..---.| .+|++....+.
T Consensus 244 ~s~V~~~~lr~g-~l~~~e~~~~~ 266 (473)
T PRK08506 244 KTSIPLQNLRTG-DLDDDEWENLS 266 (473)
T ss_pred HCCCCCCCCCCC-CCCHHHHHHHH
T ss_conf 288783100068-99999999999
No 39
>PRK05595 replicative DNA helicase; Provisional
Probab=96.52 E-value=0.13 Score=34.43 Aligned_cols=69 Identities=17% Similarity=0.213 Sum_probs=35.5
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH------
Q ss_conf 78588850100146553001038767653521011081788886433100002356787089971438899987------
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC------ 287 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~------ 287 (648)
.|..|=.+||- + -|+.-+.++.|.....+ ....|.+.---|..-.+.
T Consensus 200 ~GdLiiiaaRP---~---------------mGKTa~alnia~~~a~~---------~g~~V~~fSlEMs~~ql~~R~ls~ 252 (444)
T PRK05595 200 KGDMILIAARP---S---------------MGKTTFALNIAEYAALR---------EGKSVVIFSLEMSKEQLAYKLLCS 252 (444)
T ss_pred CCCEEEEEECC---C---------------CCCHHHHHHHHHHHHHH---------CCCCEEEEECCCCHHHHHHHHHHH
T ss_conf 57779998579---8---------------98079999999999986---------699379995889999999999996
Q ss_pred HCCCCCCHHHHHCCCCHHHHHHH
Q ss_conf 43554211343213662678988
Q gi|254780834|r 288 QAGVQNVVSSLGTALTEYQLRLL 310 (648)
Q Consensus 288 ~~G~~n~va~~Gtalt~~~~~~l 310 (648)
..|++..---.| .+++++...+
T Consensus 253 ~s~i~~~~i~~g-~l~~~~~~~~ 274 (444)
T PRK05595 253 EANVDMLRLRTG-NLEDKDWENI 274 (444)
T ss_pred HCCCCCCCCCCC-CCCHHHHHHH
T ss_conf 469884423268-9799999999
No 40
>pfam08278 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. Eubacterial DnaG primases interact with several factors to from the replisome. One of these factors in DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB.
Probab=96.36 E-value=0.16 Score=33.69 Aligned_cols=109 Identities=19% Similarity=0.165 Sum_probs=75.5
Q ss_pred HHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999847788999984430023799889999999999975388999899998851112899999999986543332
Q gi|254780834|r 484 EAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLW 563 (648)
Q Consensus 484 E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~elL~~L~~~~~~~~~~ 563 (648)
.+.+|.++++||.+...+.+......+.+|... ++..+++.+..++..+...+.++..+......+..+....
T Consensus 2 ~r~ai~LLLq~P~LA~~v~~~~~l~~~~~~~~~-lL~~L~~~~~~~P~~~t~~Lle~~r~t~~~~~L~~La~~~------ 74 (126)
T pfam08278 2 MRRAIALLLQNPALAALVPDLLALEDLKDPGLA-LLLELVELCRGNPNINTGQLLEHWRGTPYGELLAKLATWE------ 74 (126)
T ss_pred HHHHHHHHHHCHHHHHHCCCHHHHHHCCCHHHH-HHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHCC------
T ss_conf 899999998694987568774544115670289-9999999998589985999999970991799999998642------
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0256899889999999999999858999999999999998
Q gi|254780834|r 564 SATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIA 603 (648)
Q Consensus 564 ~~~~e~~~~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~ 603 (648)
...+.++....+.+++...... .+.+++.++..+..
T Consensus 75 ---~~~~~~~~~~ef~d~l~~L~~~-~~~~r~~~L~~k~~ 110 (126)
T pfam08278 75 ---HLIDEDNIEQEFDDTLARLQEQ-LLERRIEELIAKSR 110 (126)
T ss_pred ---CCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
T ss_conf ---2466067999999999999999-99999999998774
No 41
>PRK09165 replicative DNA helicase; Provisional
Probab=96.23 E-value=0.18 Score=33.14 Aligned_cols=48 Identities=17% Similarity=0.095 Sum_probs=25.7
Q ss_pred CEEEECCCCEEEECC----CCCCCCHHHHHHHHCC---CCHHHHHHHHHHHHCCC
Q ss_conf 879817897467136----8888789899898859---99799999999981885
Q gi|254780834|r 52 SFHCNDSKGFYYCFS----CHVKGDHLSFLSALLG---CSFIESVQRLAAIAGVP 99 (648)
Q Consensus 52 sf~v~~~~~~~~cf~----c~~~gd~~~f~~~~~~---~~f~ea~~~la~~~gi~ 99 (648)
.|+....+.+|.|.. -|..-|+++....+.. +.-..-+.+|++.+.-.
T Consensus 41 dFy~~~H~~If~ai~~L~~~g~~iD~itv~~~L~~~~~l~~vGG~~yL~~L~~~~ 95 (484)
T PRK09165 41 HFFEPLHQRIYEAIAKIIRKGKLATPVTLKTFLENDEALGELGGVQYLAKLATEA 95 (484)
T ss_pred HCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHCCCHHHHHHHHHCC
T ss_conf 7798999999999999997699987989999986458723227799999999708
No 42
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=96.12 E-value=0.086 Score=36.10 Aligned_cols=85 Identities=21% Similarity=0.213 Sum_probs=57.9
Q ss_pred CCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHH----HCCCCC---CHHHHH--CCCCHHHHHHHHHC
Q ss_conf 521011081788886433100002356787089971438899987----435542---113432--13662678988512
Q gi|254780834|r 243 HKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLC----QAGVQN---VVSSLG--TALTEYQLRLLWKL 313 (648)
Q Consensus 243 ~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~----~~G~~n---~va~~G--talt~~~~~~l~r~ 313 (648)
.|+++.|+++-+|...- =.+.+|+|||..++|-+. ++|+.- .|+..+ -+=...=++.-.++
T Consensus 378 ~~r~i~r~l~~trs~~l----------FAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs~~k~f~kf~~~~ 447 (581)
T COG3593 378 DKRRIKRHLDATRSSLL----------FARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGLKPFIKFAEAM 447 (581)
T ss_pred CHHHHHHHCCCCCCHHH----------HHCEEEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHCC
T ss_conf 30456641464520123----------33336997133021017999998445644374799960555737888776504
Q ss_pred CCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 681899617886622577788888
Q gi|254780834|r 314 SPRIVLCFDGDDPGLRAAYKAIDL 337 (648)
Q Consensus 314 ~~~vvl~fDgD~AG~kAa~Ra~e~ 337 (648)
..++.+..|||+||.++..+.-.+
T Consensus 448 gI~~~vitD~D~~g~~~~~~~~~l 471 (581)
T COG3593 448 GIRVHVITDGDEAGKKYEATVRDL 471 (581)
T ss_pred CCEEEEEECCCCCCCHHHHHHHHC
T ss_conf 945999935885413456655301
No 43
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=95.99 E-value=0.23 Score=32.24 Aligned_cols=49 Identities=12% Similarity=0.084 Sum_probs=25.7
Q ss_pred CEEEECCCCEE----EECCCCCCCCHHHHHHHHCCCCHHHH---HHHHHHHHCCCC
Q ss_conf 87981789746----71368888789899898859997999---999999818858
Q gi|254780834|r 52 SFHCNDSKGFY----YCFSCHVKGDHLSFLSALLGCSFIES---VQRLAAIAGVPL 100 (648)
Q Consensus 52 sf~v~~~~~~~----~cf~c~~~gd~~~f~~~~~~~~f~ea---~~~la~~~gi~~ 100 (648)
.|...+.+-+| .+|.-|..=|++++-.+....+-.+. ..+|++.+.-..
T Consensus 35 dFy~~~H~~IF~a~~~l~~~~~~id~vtv~~~l~~~~~~~~igg~~yl~~L~~~~p 90 (435)
T COG0305 35 DFYRPAHRLIYQAILDLYGQGEPIDLVTVSEELSDRGLLTRIGGANYLATLIDRTP 90 (435)
T ss_pred HCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHCCCHHHHHHHHHCCC
T ss_conf 20767899999999999866898767289999864144766075899999986288
No 44
>pfam00772 DnaB DnaB-like helicase N terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity.
Probab=95.95 E-value=0.069 Score=36.97 Aligned_cols=65 Identities=17% Similarity=0.209 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 79999999998477889999844300237998899999999999753889998999988511128
Q gi|254780834|r 482 LREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGF 546 (648)
Q Consensus 482 ~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l 546 (648)
-.|+.+|..++.+|+.+.++.+.+...+|.++.++.+|..+.+.+.++...+...+...+...+.
T Consensus 7 eaE~~lLg~lL~~~~~~~~i~~~l~~edF~~~~h~~If~~i~~l~~~~~~iD~~tl~~~l~~~~~ 71 (103)
T pfam00772 7 EAEQAVLGALLLDPEAIDEVADILKPEDFYDPAHRLIFEAILELYDKGKPIDPVTVAEELERKGK 71 (103)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCC
T ss_conf 99999999999697489999972799984959999999999999845699689999999976798
No 45
>PRK06749 replicative DNA helicase; Provisional
Probab=95.37 E-value=0.36 Score=30.39 Aligned_cols=47 Identities=19% Similarity=0.274 Sum_probs=31.3
Q ss_pred CCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 785888501001465530010387676535210110817888864331000023567870899714388999874
Q gi|254780834|r 214 RGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQ 288 (648)
Q Consensus 214 ~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~ 288 (648)
.|..|-.+||- + -|+.-+.++.|....+. ...+.+.---|..-.+..
T Consensus 185 ~g~LiviaaRP---s---------------mGKTa~alnia~~~a~~----------g~~v~~fSlEMs~~~l~~ 231 (428)
T PRK06749 185 EGDFVVLGARP---S---------------MGKTAFALNVGLHAAKS----------GAAVGLFSLEMSSKQLLK 231 (428)
T ss_pred CCCEEEEECCC---C---------------CCHHHHHHHHHHHHHHC----------CCCEEEEECCCCHHHHHH
T ss_conf 88689996279---8---------------97689999999999964----------992799837899999999
No 46
>TIGR00334 primaseG_like primase homolog; InterPro: IPR004466 This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases..
Probab=90.81 E-value=0.52 Score=28.92 Aligned_cols=65 Identities=28% Similarity=0.338 Sum_probs=56.5
Q ss_pred CEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHH
Q ss_conf 70899714388999874355421134321366267898851268--189961788662257778888
Q gi|254780834|r 272 SFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAID 336 (648)
Q Consensus 272 ~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e 336 (648)
+.+++|||-.|.-.+.+.---.++.+.|.|+..+-+.+++.... .+++..|.|.+|.+-..+..+
T Consensus 3 ~~~~~~~g~~d~~~~~~~~d~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~dpd~~g~~~~~~~~~ 69 (176)
T TIGR00334 3 KGVIVCEGKDDLARLKELFDVDVIETNGSALKDETINLLKKALKKKGVILLLDPDKPGEKIRKKLEE 69 (176)
T ss_pred CCEEEEECCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHH
T ss_conf 7426640761467777764001100354023578899999877536736875687322689999998
No 47
>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional
Probab=90.56 E-value=1.6 Score=24.34 Aligned_cols=85 Identities=20% Similarity=0.234 Sum_probs=58.2
Q ss_pred CCCEEEEECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECCCCC-------C----HHHHHHHHH
Q ss_conf 7870899714388999-8743554211343213662678988512-6818996178866-------2----257778888
Q gi|254780834|r 270 SSSFIILVEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDGDDP-------G----LRAAYKAID 336 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDgD~A-------G----~kAa~Ra~e 336 (648)
.+++-.+-...++.+. +...|+...+.|.||-+|++-++.|+.. ...|.+.+||-.+ | ...++++++
T Consensus 70 tGGEPllr~D~~ei~~~a~~~G~~~~l~TNG~lit~~~a~~L~~~gl~~v~vSlDg~~~e~hD~~rG~~G~f~~~~~~i~ 149 (375)
T PRK05301 70 SGGEPLLRKDLEELVAHARRLGLYTNLITSGVGLTEARLAALKAAGLDHIQLSFQDSDPELADRIAGTRGAFAQKLEVAR 149 (375)
T ss_pred CCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 18652456689999999997697589960674557999999985099889995677987787776378862999999999
Q ss_pred HHHHHHHCCCCEEEEE--CCCCC
Q ss_conf 8877753697306752--57888
Q gi|254780834|r 337 LVLCHLIPGNRVNFVL--LSRGE 357 (648)
Q Consensus 337 ~~l~~l~~g~~v~vv~--LP~G~ 357 (648)
. +.+.|+.+.+-+ -..+.
T Consensus 150 ~---l~~~Gi~v~i~~ti~r~N~ 169 (375)
T PRK05301 150 L---VKAHGYPLTLNAVIHRHNI 169 (375)
T ss_pred H---HHHCCCCEEEEEEECCCCH
T ss_conf 9---9974981699987230568
No 48
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=89.81 E-value=0.27 Score=31.52 Aligned_cols=33 Identities=36% Similarity=0.759 Sum_probs=26.8
Q ss_pred EEECCCCCCCCCCEEEECCC---CEEEECCCCCCCCH
Q ss_conf 75345888858787981789---74671368888789
Q gi|254780834|r 40 WACCPFHDEKTPSFHCNDSK---GFYYCFSCHVKGDH 73 (648)
Q Consensus 40 ~~~cPfh~ektpsf~v~~~~---~~~~cf~c~~~gd~ 73 (648)
-+.||-+.-+. -|.+.+++ +.|+|+.||..||-
T Consensus 3 h~pCP~CGg~D-rfr~fdd~~g~G~~~C~~Cg~~GDG 38 (39)
T pfam08273 3 HGPCPNCGGSD-RFRIFDDKDGRGTWFCFSCGYAGDG 38 (39)
T ss_pred CCCCCCCCCCC-CCEECCCCCCCCCEECCCCCCCCCC
T ss_conf 66777777857-5256557899757783888777888
No 49
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=89.07 E-value=0.79 Score=27.25 Aligned_cols=55 Identities=25% Similarity=0.370 Sum_probs=40.7
Q ss_pred CEEEEECCHHHHHHHH-----------HCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCH
Q ss_conf 7089971438899987-----------43554211343213662678988512681899617886622
Q gi|254780834|r 272 SFIILVEGYMDVLSLC-----------QAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGL 328 (648)
Q Consensus 272 ~~~i~vEGy~Dvi~l~-----------~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~ 328 (648)
+.+|+|||..|.+.+. ++|| .+|..-|.++-.. ++++..+.-.+++..|.|....
T Consensus 4 ~~viLVEG~tE~~~l~~~~~~~~~~l~~~~i-~ii~v~G~~~~~~-~~l~~~l~i~~~vi~D~D~~~~ 69 (97)
T cd01026 4 DKVILVEGDSEEILLPALAKKLGLDLDEAGI-SIIPVGGKNFKPF-IKLLNALGIPVAVLTDLDAKRN 69 (97)
T ss_pred CEEEEEECHHHHHHHHHHHHHHCCCHHHCCC-EEEEECCCCHHHH-HHHHHHCCCCEEEEECCCCCCC
T ss_conf 7799994413999999999996979778797-8998589274999-9999976993899971898746
No 50
>PRK13758 anaerobic sulfatase-maturase; Provisional
Probab=88.99 E-value=1.2 Score=25.47 Aligned_cols=72 Identities=18% Similarity=0.192 Sum_probs=48.9
Q ss_pred CCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCC----------C---HHHHHHHHHHHHHHHHCCCC--EEEEECC
Q ss_conf 5542113432136626789885126818996178866----------2---25777888888777536973--0675257
Q gi|254780834|r 290 GVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDP----------G---LRAAYKAIDLVLCHLIPGNR--VNFVLLS 354 (648)
Q Consensus 290 G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~A----------G---~kAa~Ra~e~~l~~l~~g~~--v~vv~LP 354 (648)
.+.+++.|.||-||++.+..|+++.-.|-+.+||.++ | -..+.++++++ .+.+.. +..+.-.
T Consensus 92 ~i~~~i~TNGtLL~~e~~~~l~~~~~~I~ISlDG~~~~HD~~R~~~~G~Gsf~~v~~~i~~l---~~~~~~~~i~~~i~~ 168 (370)
T PRK13758 92 KIYNSLQTNGTLIDESWAKFLSENKFLVGLSMDGPKEIHNLNRKDCCGLDTFSKVERAAELF---KKYKVEFNILCVVTS 168 (370)
T ss_pred EEEEEEEECCEECCHHHHHHHHHCCEEEEEECCCCHHHHHHHCCCCCCCCHHHHHHHHHHHH---HHCCCCEEEEEEEEC
T ss_conf 69999851887668999999997694899964688888740068889970599999999999---973997008999918
Q ss_pred CC-CCHHHHHH
Q ss_conf 88-88889972
Q gi|254780834|r 355 RG-EDPDSFIR 364 (648)
Q Consensus 355 ~G-~DPDe~ir 364 (648)
++ .+++++++
T Consensus 169 ~~~~~~~~i~~ 179 (370)
T PRK13758 169 NTARHVNKIYK 179 (370)
T ss_pred CCCCCHHHHHH
T ss_conf 73118999999
No 51
>KOG2373 consensus
Probab=86.18 E-value=2.9 Score=22.09 Aligned_cols=133 Identities=15% Similarity=0.164 Sum_probs=90.5
Q ss_pred CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCC-CCCCHHHHHCCCCH-HHH
Q ss_conf 3001038767653521011081788886433100002356787089971438899987435-54211343213662-678
Q gi|254780834|r 230 SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG-VQNVVSSLGTALTE-YQL 307 (648)
Q Consensus 230 ~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G-~~n~va~~Gtalt~-~~~ 307 (648)
+.-|=-.-||++=++-+.+|||+.|-.. ...++++--..|.|+++++- +..+.-|-|+-+-+ .-+
T Consensus 94 g~~ye~~~~~~~r~a~~~~fGL~l~~rr-------------d~~vVltsne~D~lal~~~t~~~t~~LP~g~~~lP~~~L 160 (514)
T KOG2373 94 GENYELPDETSVRQAFNGVFGLHLATRR-------------DRSVVLTSNERDALALYEATKALTFALPHGEILLPQLVL 160 (514)
T ss_pred CCCCCCCCCCCHHHHHCCEECEEECCCC-------------CCEEEEEECCHHHHHHHHHCCCEEEECCCCCCCCCHHHH
T ss_conf 6667997665334454212030312434-------------544897505145777764148637872665434827777
Q ss_pred HHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHCCCHHHHHHHHHHCCCHHH
Q ss_conf 9885126818996178866225777888888777536973067525-788888899720366889988641499279
Q gi|254780834|r 308 RLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL-SRGEDPDSFIRCYGKTAFEKLIVESLPLVD 383 (648)
Q Consensus 308 ~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L-P~G~DPDe~ir~~G~eaf~~ll~~A~~l~d 383 (648)
--|-+| ++||++|--|.....||. ..-.. + . ..|++.. |+..-|.-...-.+.=.+..+++.|.|.-+
T Consensus 161 PyLE~F-~~i~fWl~~d~~sw~aAk-~fa~k--L-n---~~rClLvrp~e~~p~p~~al~~rlnl~~il~~a~p~~h 229 (514)
T KOG2373 161 PYLEEF-DKIYFWLPVDHVSWSAAK-DFASK--L-N---TLRCLLVRPEERPPEPVRALDHRLNLNSILNSAVPMRH 229 (514)
T ss_pred HHHHHH-HEEEEEECCCCCCHHHHH-HHHHH--C-C---CCEEEEECCCCCCCCHHHHHCCCCCHHHHHHHHCHHHH
T ss_conf 889865-259998025442368999-99862--2-8---41379977888896556653455028888755122465
No 52
>COG0641 AslB Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]
Probab=85.68 E-value=3 Score=21.90 Aligned_cols=131 Identities=15% Similarity=0.176 Sum_probs=68.0
Q ss_pred CCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCC-------------CCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf 355421134321366267898851268189961788-------------6622577788888877753697306752578
Q gi|254780834|r 289 AGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGD-------------DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR 355 (648)
Q Consensus 289 ~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD-------------~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~ 355 (648)
.-|.|++-|.||.||++-+..+++.--.|-+..||- ..--.+++|+++.+.. -+..+.+..-
T Consensus 89 ~~i~~siqTNg~LL~~e~~e~l~~~~~~IgISiDGp~eihD~~R~~~~GkgTfd~i~~~i~~L~~---~~v~~~~~~v-- 163 (378)
T COG0641 89 KTISNALQTNGTLLNDEWAEFLAEHDFLIGISIDGPEEIHDKYRVTKSGKGTFDRVMKGLELLQA---HGVDFNTLTV-- 163 (378)
T ss_pred CCEEEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHH---CCCCEEEEEE--
T ss_conf 82578998760325799999998529669996668177611103578998569999999999997---5884699999--
Q ss_pred CCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHHHHHHHCC--------CCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 88888997203668899886-4149927999999985302--------33145799999999988541799899999999
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWKRETENRS--------FNTPDERAELEIHLKNCINHIKDQKLRYYYSQ 426 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~~l~~~~d--------l~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~ 426 (648)
.+++.+ .+ ..++-+++ +.....+.|+ . +.+..+ ..++++-..+...+.....+.. ....+++
T Consensus 164 -v~~~n~--~~-~~ei~~~l~~~g~~~i~fi-p-~~~~~~~~~~~~~~~~~~~~~~~fl~~~~~~~~~~~---~~~i~i~ 234 (378)
T COG0641 164 -VNRQNV--LH-PEEIYHFLKSEGSKFIQFI-P-LVESDNRGDSLLEFSVTAEEYGQFLIAIFDEWVRHD---VGRIFIQ 234 (378)
T ss_pred -ECHHHH--HC-HHHHHHHHHHCCCCEEEEE-E-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC---CCCCCHH
T ss_conf -764453--07-9999999997376638988-5-116888775322123466679999999999999714---7741014
Q ss_pred HHHHHHH
Q ss_conf 9999988
Q gi|254780834|r 427 AIRDRLQ 433 (648)
Q Consensus 427 ~la~~L~ 433 (648)
.+...+.
T Consensus 235 ~f~~~~~ 241 (378)
T COG0641 235 NFDQLLK 241 (378)
T ss_pred HHHHHHH
T ss_conf 7999999
No 53
>PRK09897 hypothetical protein; Provisional
Probab=85.33 E-value=2.1 Score=23.27 Aligned_cols=191 Identities=17% Similarity=0.198 Sum_probs=107.0
Q ss_pred HHHHHCCCCHHHHCCCC------CC-CCCCCCCHHHHHHHCCCCCHHHHHHHCCCEE--CCCCCCCCCCCCCEEEEEEEE
Q ss_conf 99985068853510124------42-2567741034554205997345232012100--346541000016716888970
Q gi|254780834|r 142 YYLDERGIDSHAIEMFK------LG-YAPDSRYSLREHLRQKGFSEEKIIEAGLLID--GDNSATSYDRFRNRLIFPIRS 212 (648)
Q Consensus 142 ~yl~~Rg~~~~~~~~f~------lG-~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~--~~~~~~~~d~Fr~Ri~fPi~~ 212 (648)
+||...|++.+.+...+ +| |--+....|++...++|++......+-+.-. +.+|.. +.....
T Consensus 79 ~~L~~~~id~~~l~~rqflPRiLlGeYl~~QF~~Lve~a~~~G~~i~Vh~~~~VtDi~~~~~gv~---------l~~~~~ 149 (535)
T PRK09897 79 SHLQRYGVKKETLHDRQFLPRILLGEYFRDQFLRLVDQARQQKFAVAVYESCQVTDLQITNAGVM---------LATNQD 149 (535)
T ss_pred HHHHHCCCCHHHCCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECCCCEE---------EEECCC
T ss_conf 78987199832264101004888889999999999999986596699975766676443699559---------983378
Q ss_pred CC----CCEEEEECCCCCC--CCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 77----8588850100146--55300103876765352101108178888643310000235678708997143889998
Q gi|254780834|r 213 SR----GQVIAFGGRTLSK--GESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSL 286 (648)
Q Consensus 213 ~~----g~~i~f~gR~l~~--~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l 286 (648)
.. -.+|==+|-...+ +.+++|.-||=+ |+-.|
T Consensus 150 ~~~~~FD~vVIaTGH~WP~~~e~~~~YF~SPw~----------~l~~a-------------------------------- 187 (535)
T PRK09897 150 LPSETFDLAVIATGHVWPDEEEATRTYFPSPWS----------GLMEA-------------------------------- 187 (535)
T ss_pred CCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC----------CHHHC--------------------------------
T ss_conf 876432079980798799877677666789997----------36542--------------------------------
Q ss_pred HHCCCC-CCHHHHHCCCCH-HHHHHHHHC----C---C-EEEEEECCCCCCHHHHHHHHHHHHHHHHCCC--CEEEEECC
Q ss_conf 743554-211343213662-678988512----6---8-1899617886622577788888877753697--30675257
Q gi|254780834|r 287 CQAGVQ-NVVSSLGTALTE-YQLRLLWKL----S---P-RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN--RVNFVLLS 354 (648)
Q Consensus 287 ~~~G~~-n~va~~Gtalt~-~~~~~l~r~----~---~-~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~--~v~vv~LP 354 (648)
-++ ..||.+||+||- +-+..|.+- + + .+.+..|.|.-+.+=++-+ ..|+ +++|- .|
T Consensus 188 ---~ip~~~VgI~GSSLSAIDAa~ala~~hG~F~~~~d~~l~F~~~~~se~~~I~mmS--------r~GiLPeadFy-~p 255 (535)
T PRK09897 188 ---KVDACNVGIMGTSLSGLDAAMAVAIQHGSFIEDDKQHVVFHRDNASEKLNITLMS--------RTGILPEADFY-CP 255 (535)
T ss_pred ---CCCCCEEEEECCCHHHHHHHHHHHHHCCEEEECCCCEEEEEECCCCCCEEEEEEE--------CCCCCCCCCCC-CC
T ss_conf ---5787527762376578999999998768058768850788878998652699972--------37877653203-78
Q ss_pred CCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHHHCCCCCH
Q ss_conf 88888899720366889988641-499279999999853023314
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETENRSFNTP 398 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~~~dl~sp 398 (648)
.-..|=+++ ..++....+++ +..++||+|+...+.....+|
T Consensus 256 ~pye~L~il---T~~ai~~~ia~g~~gLLDrVF~l~~~el~~~DP 297 (535)
T PRK09897 256 IPYEPLHIV---TDQALNAEIQKGEEGLLDRVFRLIVEEIKFADP 297 (535)
T ss_pred CCCCCHHHC---CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCH
T ss_conf 998713217---899999999748883189999999999986684
No 54
>PRK13745 anaerobic sulfatase-maturase; Provisional
Probab=81.10 E-value=3.7 Score=21.05 Aligned_cols=70 Identities=21% Similarity=0.254 Sum_probs=48.2
Q ss_pred CCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCC----------CH---HHHHHHHHHHHHHHHCCCCEEEE--EC-C
Q ss_conf 542113432136626789885126818996178866----------22---57778888887775369730675--25-7
Q gi|254780834|r 291 VQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDP----------GL---RAAYKAIDLVLCHLIPGNRVNFV--LL-S 354 (648)
Q Consensus 291 ~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~A----------G~---kAa~Ra~e~~l~~l~~g~~v~vv--~L-P 354 (648)
|.|++-|.||.||++.+..++++-=.|-+..||..+ |+ .+.+|+++++. +.|.+..++ .- .
T Consensus 102 i~~siQTNGtLL~dew~~ff~~~~f~VgiSiDGp~~~HD~~R~~~~G~gs~~~v~~~i~lL~---~~~v~fn~L~vv~~~ 178 (412)
T PRK13745 102 IDNCIQTNGTLLTDEWCEFFRENNWLVGVSIDGPQEFHDEYRKNKMGKPSFVKVMKGINLLK---KHGVEWNAMAVVNDF 178 (412)
T ss_pred EEEEEEECCEECCHHHHHHHHHCCCEEEEECCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHH---HCCCCEEEEEEEECH
T ss_conf 68999877875499999999985967999625887887402798899877999999999999---849964699998111
Q ss_pred CCCCHHHHH
Q ss_conf 888888997
Q gi|254780834|r 355 RGEDPDSFI 363 (648)
Q Consensus 355 ~G~DPDe~i 363 (648)
....|.++.
T Consensus 179 n~~~p~~iY 187 (412)
T PRK13745 179 NADYPLDFY 187 (412)
T ss_pred HHHCHHHHH
T ss_conf 545889999
No 55
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=80.34 E-value=4.6 Score=20.26 Aligned_cols=89 Identities=18% Similarity=0.101 Sum_probs=57.6
Q ss_pred CCEEEEECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCC-EEEEEECCCCC----------CHHHHHHHHHHH
Q ss_conf 870899714388999-874355421134321366267898851268-18996178866----------225777888888
Q gi|254780834|r 271 SSFIILVEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSP-RIVLCFDGDDP----------GLRAAYKAIDLV 338 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~-~vvl~fDgD~A----------G~kAa~Ra~e~~ 338 (648)
+++-++-....+.+. +.+.|+.-++.|.|| |.++.+..++.... .+-+.+||.+. .-..|++++..+
T Consensus 80 GGEPLLr~dl~eIv~~a~~~g~~v~l~TNG~-Ll~k~i~~~~~~~~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~aIr~a 158 (318)
T TIGR03470 80 GGEPLLHPEIDEIVRGLVARKKFVYLCTNAL-LLEKKLDKFEPSPYLTFSVHLDGLREHHDASVCREGVFDRAVEAIREA 158 (318)
T ss_pred CCCCCCCCCHHHHHHHHHHCCCEEEEECCHH-HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 8874556479999999997599799977552-009999998518883699980178788668871797799999999999
Q ss_pred HHHHHCCCCEEEEE-CCCCCCHHHHH
Q ss_conf 77753697306752-57888888997
Q gi|254780834|r 339 LCHLIPGNRVNFVL-LSRGEDPDSFI 363 (648)
Q Consensus 339 l~~l~~g~~v~vv~-LP~G~DPDe~i 363 (648)
. +.|+.|.+-+ +=++.||++..
T Consensus 159 k---~~G~~V~iN~Tvf~~~n~~~i~ 181 (318)
T TIGR03470 159 K---ARGFRVTTNTTLFNDTDPEEVA 181 (318)
T ss_pred H---HCCCCEEEEEEEECCCCHHHHH
T ss_conf 9---8699467998970689999999
No 56
>pfam03291 Pox_MCEL mRNA capping enzyme. This family of enzymes are related to pfam03919.
Probab=80.29 E-value=0.71 Score=27.71 Aligned_cols=75 Identities=16% Similarity=0.215 Sum_probs=45.2
Q ss_pred HHHCCHHHHH-HHHCCCEECCCC---CCCCCEEEECCCCC-----------CCCCCEEEECCCCEEEECCCCCCCCHHHH
Q ss_conf 8748888875-412221015887---77775575345888-----------85878798178974671368888789899
Q gi|254780834|r 12 LIHIPISNLI-GQYVDWDRRKTN---AVKGDYWACCPFHD-----------EKTPSFHCNDSKGFYYCFSCHVKGDHLSF 76 (648)
Q Consensus 12 ~~~~~i~~vv-~~~v~l~~~g~n---~~~~~~~~~cPfh~-----------ektpsf~v~~~~~~~~cf~c~~~gd~~~f 76 (648)
...-||++|| .+|=+++.+|.. +....-.+|.=||| .+++ ....+..-=..+||+|||..+|
T Consensus 5 ~~~~~~~~~V~~HYN~~~~~~~~~~~R~~S~I~~LR~FNNwVKs~LI~~~~~~~~---~~~~~~~VLDl~CGkGGDL~Kw 81 (327)
T pfam03291 5 ETESNIVDIVAAHYNELPESGIDLKKRQDSTIDQLRNFNNWIKSLLISLYASKTF---QDKPKRKVLDLDCGKGGDLEKY 81 (327)
T ss_pred CCCCCHHHHHHHHHCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCEEEEECCCCCCCHHHH
T ss_conf 2048853699987331101261223341385177887318999999999988751---4688987998368664457889
Q ss_pred HHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf 898859997999999999818858
Q gi|254780834|r 77 LSALLGCSFIESVQRLAAIAGVPL 100 (648)
Q Consensus 77 ~~~~~~~~f~ea~~~la~~~gi~~ 100 (648)
... +++| ..||++
T Consensus 82 ~~~--~i~~---------~vgiDi 94 (327)
T pfam03291 82 FKG--GISG---------LIGTDI 94 (327)
T ss_pred HHC--CCCE---------EEEECC
T ss_conf 747--9868---------999668
No 57
>PRK12383 putative mutase; Provisional
Probab=79.32 E-value=4.9 Score=20.00 Aligned_cols=140 Identities=18% Similarity=0.217 Sum_probs=60.1
Q ss_pred CCCCEEEEECCCCCCCC--------CCEE--CCCCCCCCCCCCHHC----CCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf 77858885010014655--------3001--038767653521011----081788886433100002356787089971
Q gi|254780834|r 213 SRGQVIAFGGRTLSKGE--------SVKY--LNSPETILFHKGKNL----YNFFGALNYLQKSIRKDVRRNSSSFIILVE 278 (648)
Q Consensus 213 ~~g~~i~f~gR~l~~~~--------~~KY--lNSpeT~if~K~~~L----y~l~~a~~~~~~~~~~~~~~~~~~~~i~vE 278 (648)
.-||||+|+++-...+. .+.+ +|+|.+-.|.+.... |++........... .....|+.|=
T Consensus 178 ~v~RvIa~~~~g~~~~~~~~~~~~~~~~~~g~~~P~~~~~~~~~~~rh~~y~~~P~~~v~~~L~------~aG~~V~~VG 251 (406)
T PRK12383 178 QVGRVIAFGGLLTDSQRILDAAESKEGGFIGINAPKSGVYDNGFQVVHLGYGVDPKVQVPQLLY------EAGVPVVLVG 251 (406)
T ss_pred CCCEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH------HCCCEEEEEE
T ss_conf 7213897556677513321000124766543458877755665321235557898510569999------7799389995
Q ss_pred CHHHHHHHHHCCCCCCHHHHHCCCCHHHHHH-HHHCCCEEEEE----EC-----CCCCCHHHHHHHHHHHHHHHHCCC--
Q ss_conf 4388999874355421134321366267898-85126818996----17-----886622577788888877753697--
Q gi|254780834|r 279 GYMDVLSLCQAGVQNVVSSLGTALTEYQLRL-LWKLSPRIVLC----FD-----GDDPGLRAAYKAIDLVLCHLIPGN-- 346 (648)
Q Consensus 279 Gy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~-l~r~~~~vvl~----fD-----gD~AG~kAa~Ra~e~~l~~l~~g~-- 346 (648)
=--|..+ .-||...+-+.+++-.-+++.. +++-.+-.+++ || -|.+|...++..++.-|+.+.+.+
T Consensus 252 KI~DIfa--~~Gi~~~~~~~~n~~~~~~t~~~~~~~~~gliF~NlVdfDl~GHRrD~~GYa~aLe~fD~~L~ell~~l~~ 329 (406)
T PRK12383 252 KVADIVN--NPYGASWQPLVDTQRVLDITLDEFNTHPTAFICANIQETDLAGHAEDVARYAERLEVVDRNLARLLEAMQP 329 (406)
T ss_pred CHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 3598317--88864345579889999999999960699569972223125445558889999999999989999983898
Q ss_pred -CEEEEECCCCCCHH
Q ss_conf -30675257888888
Q gi|254780834|r 347 -RVNFVLLSRGEDPD 360 (648)
Q Consensus 347 -~v~vv~LP~G~DPD 360 (648)
++-|++-..|-||-
T Consensus 330 dDLLiITADHGnDPT 344 (406)
T PRK12383 330 DDCLVVMADHGNDPT 344 (406)
T ss_pred CCEEEEECCCCCCCC
T ss_conf 878999387788988
No 58
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=76.08 E-value=5.2 Score=19.74 Aligned_cols=67 Identities=21% Similarity=0.312 Sum_probs=54.7
Q ss_pred CHHHHHCC-----------------------CCHHHHHHHHHC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf 11343213-----------------------662678988512--------68189961788662257778888887775
Q gi|254780834|r 294 VVSSLGTA-----------------------LTEYQLRLLWKL--------SPRIVLCFDGDDPGLRAAYKAIDLVLCHL 342 (648)
Q Consensus 294 ~va~~Gta-----------------------lt~~~~~~l~r~--------~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l 342 (648)
.|.|-|.+ +..+|||.|.++ ..+|||..|.|.=..+||---+.. +-
T Consensus 68 ~~~P~~~~~~~~~de~~~~~~g~a~~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~AANALLKt---LE 144 (216)
T TIGR00678 68 RLEPEGQSKSLTADEAAEGEEGSAKRRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEAAANALLKT---LE 144 (216)
T ss_pred EEEEECCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHHHH---EE
T ss_conf 874234777777645897625642113678787278999999986064214751799767323258989865101---01
Q ss_pred HCCCCEEEEECCCCCCHHHHH
Q ss_conf 369730675257888888997
Q gi|254780834|r 343 IPGNRVNFVLLSRGEDPDSFI 363 (648)
Q Consensus 343 ~~g~~v~vv~LP~G~DPDe~i 363 (648)
++.-++.|+++-..-||+.++
T Consensus 145 EPp~~t~fiL~~~~~DP~~lL 165 (216)
T TIGR00678 145 EPPPNTLFILITHSPDPERLL 165 (216)
T ss_pred CCCCCEEEEEECCCCCHHHHC
T ss_conf 279870798850888843322
No 59
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=74.39 E-value=2.4 Score=22.87 Aligned_cols=30 Identities=23% Similarity=0.641 Sum_probs=22.2
Q ss_pred EEECCCCCCCCCCEEEE--CCCCEEEECCCCCC
Q ss_conf 75345888858787981--78974671368888
Q gi|254780834|r 40 WACCPFHDEKTPSFHCN--DSKGFYYCFSCHVK 70 (648)
Q Consensus 40 ~~~cPfh~ektpsf~v~--~~~~~~~cf~c~~~ 70 (648)
-+.||.+.-|. -|... ...+.|+|+.||+|
T Consensus 3 h~pCP~CGG~D-rfrf~dk~g~G~~~C~~Cg~G 34 (37)
T smart00778 3 HGPCPNCGGSD-RFRFDDKDGRGTWFCSVCGAG 34 (37)
T ss_pred CCCCCCCCCCC-CEEEECCCCCEEEECCCCCCC
T ss_conf 66788677865-536746999740782788789
No 60
>KOG2593 consensus
Probab=73.81 E-value=2.7 Score=22.42 Aligned_cols=48 Identities=21% Similarity=0.349 Sum_probs=24.6
Q ss_pred CCCCCCCCCCEEE----ECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 4588885878798----1789746713688887898998988599979999999998
Q gi|254780834|r 43 CPFHDEKTPSFHC----NDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAI 95 (648)
Q Consensus 43 cPfh~ektpsf~v----~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~ 95 (648)
||+++-|=-|+-+ +.+.+.|||.-||-- .|+.-..+.-.+++..|+.+
T Consensus 131 Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge-----lveDe~~~~~~e~~~~l~~~ 182 (436)
T KOG2593 131 CPNCQKKYTSLEALQLLDNETGEFHCENCGGE-----LVEDENKLPSKESRTALNRL 182 (436)
T ss_pred CCCCCCCHHHHHHHHHHCCCCCEEEEECCCCC-----HHCCCCCCCHHHHHHHHHHH
T ss_conf 87412411266787752146766987247970-----21022447448888888998
No 61
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=73.17 E-value=3.4 Score=21.46 Aligned_cols=60 Identities=10% Similarity=0.140 Sum_probs=43.1
Q ss_pred CCCCHHHHHHCCCHHHHHHHHHHCCC----HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 88888899720366889988641499----2799999998530233145799999999988541
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLIVESLP----LVDMLWKRETENRSFNTPDERAELEIHLKNCINH 414 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll~~A~~----l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~ 414 (648)
...||++++.++|+|+++-++-...| -.+|=|+.+....+-+-...--.+++++..++.+
T Consensus 334 nvv~p~~~l~~yg~D~lRY~l~~~~p~~~~D~dfs~~~~~~r~NsdLan~lGNl~~R~~~~~~k 397 (666)
T PRK00133 334 TFIWARTYLDHLDPDYLRYYLAAKLPSRIDDIDFNWEDFQQRVNSDLVGKLVNFASRAAGFINK 397 (666)
T ss_pred EEEEHHHHHHHCCCCCEEHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 1761799998669645302033107898767786999999998688887666899999999998
No 62
>TIGR00396 leuS_bact leucyl-tRNA synthetase; InterPro: IPR002302 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes the eubacterial and mitochondrial synthetases. The crystal structure of leucyl-tRNA synthetase from the hyperthermophile Thermus thermophilus has an overall architecture that is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain . ; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=72.11 E-value=5.3 Score=19.66 Aligned_cols=56 Identities=21% Similarity=0.370 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH-HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 78888889972036688998864149927999-9999853023314579999999998854179
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDML-WKRETENRSFNTPDERAELEIHLKNCINHIK 416 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl-~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~ 416 (648)
-+|-||+++|.+||+|+.+-++==+-|+.+-+ |+ -+..+|..++++++-.+...+.
T Consensus 669 ~N~i~P~e~~~~yGADa~Rlf~mF~~P~~~~L~W~-------~~g~~G~~RFL~RVw~l~~~~~ 725 (916)
T TIGR00396 669 GNGIDPQEIVKKYGADALRLFIMFMGPIAASLEWN-------ESGLEGARRFLDRVWNLVKEIL 725 (916)
T ss_pred CCCCCCHHHHHHCCHHHHHHHHHHCCCHHHCCCCC-------CCCHHHHHHHHHHHHHHHHHHC
T ss_conf 79887038974048027999997048831414777-------1110135688899999998732
No 63
>PRK00076 recR recombination protein RecR; Reviewed
Probab=71.05 E-value=7.4 Score=18.33 Aligned_cols=81 Identities=27% Similarity=0.299 Sum_probs=54.9
Q ss_pred CCEEEEECCHHHHHHHHHCCCCCCH-HHHHCCCC------HHHH---HHHHHC----CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf 8708997143889998743554211-34321366------2678---988512----68189961788662257778888
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAGVQNVV-SSLGTALT------EYQL---RLLWKL----SPRIVLCFDGDDPGLRAAYKAID 336 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtalt------~~~~---~~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e 336 (648)
...+.|||-..|++++-+.|.-+.. -.||-.++ ++++ .++.|. .++|||++..+--|+.-|.=..+
T Consensus 78 ~~~icVVE~~~Dl~~iE~s~~y~G~YhVLgG~lSpl~gi~pe~l~i~~L~~Ri~~~~v~EVIlA~~~t~EGe~Ta~yi~~ 157 (197)
T PRK00076 78 RSLLCVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGIGPEDLNIDELLERLADGEVKEVILATNPTVEGEATAHYIAR 157 (197)
T ss_pred CCEEEEECCHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf 76799986899999997579454783585662482128983226889999986579951799864898650899999999
Q ss_pred HHHHHHHCCCCEEEEECCCC
Q ss_conf 88777536973067525788
Q gi|254780834|r 337 LVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 337 ~~l~~l~~g~~v~vv~LP~G 356 (648)
. ++ +..++|-.|-.|
T Consensus 158 ~----lk-~~~ikitrlA~G 172 (197)
T PRK00076 158 L----LK-PLGVKVTRLAHG 172 (197)
T ss_pred H----HH-HCCCEEEEEEEC
T ss_conf 8----65-549707776544
No 64
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=71.01 E-value=4 Score=20.82 Aligned_cols=42 Identities=21% Similarity=0.434 Sum_probs=26.6
Q ss_pred ECCCCCCCCC----CEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 3458888587----8798178974671368888789899898859997999999
Q gi|254780834|r 42 CCPFHDEKTP----SFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQR 91 (648)
Q Consensus 42 ~cPfh~ektp----sf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~ 91 (648)
.|||.....= ++.......++.|=+||+.|.+ .-+-.+|++.
T Consensus 3 pCPFCG~~~~~~~~~~~~~~~~~~~~C~~CgA~~~~--------~~~~~~ai~~ 48 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV--------EEDEAEAIEA 48 (53)
T ss_pred CCCCCCCCHHHEECCCCCCCCEEEEECCCCCCCCCC--------CCCHHHHHHH
T ss_conf 888789753100025787665268877777787663--------1279999999
No 65
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=70.71 E-value=7.5 Score=18.27 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=9.3
Q ss_pred EEEEEEECCCCEEEEECC
Q ss_conf 688897077858885010
Q gi|254780834|r 206 LIFPIRSSRGQVIAFGGR 223 (648)
Q Consensus 206 i~fPi~~~~g~~i~f~gR 223 (648)
|-||+.+..+.+..|+-|
T Consensus 231 v~F~~~~~~~~l~v~TTr 248 (822)
T PRK00390 231 VTFKVKGSDEKLEVFTTR 248 (822)
T ss_pred EEEECCCCCCEEEEEECC
T ss_conf 863316998559999688
No 66
>TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319 This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis.
Probab=69.97 E-value=7.7 Score=18.15 Aligned_cols=281 Identities=14% Similarity=0.224 Sum_probs=121.8
Q ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCC
Q ss_conf 99999999818858776820367778899999999999999999732677757899998506885351012442256774
Q gi|254780834|r 87 ESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSR 166 (648)
Q Consensus 87 ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~ 166 (648)
-||..+.++|||....+.-+.. +=..|-.+-...-++|...- -.| |=++-|=++.|.||.. +
T Consensus 294 PavaevvekyGirPd~fsL~De----Ei~~LA~~a~~IE~HY~k~~--------g~y---rPMDIEWAkD~~LG~~--g- 355 (877)
T TIGR01418 294 PAVAEVVEKYGIRPDKFSLSDE----EILELAKLAVKIEKHYSKKA--------GRY---RPMDIEWAKDFDLGED--G- 355 (877)
T ss_pred CHHHHHHHHHCCCCCCCCCCHH----HHHHHHHHHHHHHHHHCCCC--------CCC---CCCCEEEEEECCCCCC--C-
T ss_conf 4265777761788886517878----99999888633532107898--------830---6862252001037989--7-
Q ss_pred CHHHHHHHCCCCCHHHHHHHCCCEECCCCCC-CCCCCCCEEEEEEEE----CCCCEEEEECCCCCCC--C-CCEECCCCC
Q ss_conf 1034554205997345232012100346541-000016716888970----7785888501001465--5-300103876
Q gi|254780834|r 167 YSLREHLRQKGFSEEKIIEAGLLIDGDNSAT-SYDRFRNRLIFPIRS----SRGQVIAFGGRTLSKG--E-SVKYLNSPE 238 (648)
Q Consensus 167 ~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~-~~d~Fr~Ri~fPi~~----~~g~~i~f~gR~l~~~--~-~~KYlNSpe 238 (648)
+.+ -++.. +++..... ..++.+. ...+ |++.+ .+|+||.= ||...+. . ++|=+
T Consensus 356 ~if--ivQAR---PETv~S~k---~~E~~n~P~~e~------~~~~~P~Eerkg~vlv~-G~a~g~~Ia~GkvkVi---- 416 (877)
T TIGR01418 356 EIF--IVQAR---PETVQSRK---KKEAENKPVEER------YELKGPEEERKGKVLVK-GRAAGPGIASGKVKVI---- 416 (877)
T ss_pred CEE--EEECC---CCCEEECC---CCCCCCCCCEEE------ECCCCCCCCCCCEEEEE-EECCCCCCCCCCCEEE----
T ss_conf 578--99758---73110124---530023870565------02887860136718999-6322664035652687----
Q ss_pred CCCCCCCHHCCCHHHH-HHHHHHHHCCCCCCCCCCEEEEE--------------------CCHHH---HHHHHHCCCCCC
Q ss_conf 7653521011081788-88643310000235678708997--------------------14388---999874355421
Q gi|254780834|r 239 TILFHKGKNLYNFFGA-LNYLQKSIRKDVRRNSSSFIILV--------------------EGYMD---VLSLCQAGVQNV 294 (648)
Q Consensus 239 T~if~K~~~Ly~l~~a-~~~~~~~~~~~~~~~~~~~~i~v--------------------EGy~D---vi~l~~~G~~n~ 294 (648)
..+.++ -..+ ..|.++|+ ||=|= +|-.=..|||-|
T Consensus 417 ----------~~~~e~k~~~~-----------~~GdiLVT~mTDPDWeP~MK~AsAIVTn~GG~TcHAAIVaRELGiPAV 475 (877)
T TIGR01418 417 ----------LDLKEMKVDKF-----------EEGDILVTDMTDPDWEPVMKRASAIVTNEGGRTCHAAIVARELGIPAV 475 (877)
T ss_pred ----------CCHHHHCCCCC-----------CCCCEEEECCCCCCCHHHCCCCCEEEECCCCCHHHHHHHHHHCCCCCE
T ss_conf ----------57434320443-----------886468757874281212213030470788750089999875588826
Q ss_pred HHHHHCCCCHHHHHHHHHCCCEEEEE-ECCCC----CCHHH-HHHHHHH-HHHHHH--CCCCEEEEECCCCCCHHH--HH
Q ss_conf 13432136626789885126818996-17886----62257-7788888-877753--697306752578888889--97
Q gi|254780834|r 295 VSSLGTALTEYQLRLLWKLSPRIVLC-FDGDD----PGLRA-AYKAIDL-VLCHLI--PGNRVNFVLLSRGEDPDS--FI 363 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~r~~~~vvl~-fDgD~----AG~kA-a~Ra~e~-~l~~l~--~g~~v~vv~LP~G~DPDe--~i 363 (648)
|.+-. |-+. |+- ...|++| ==||+ ||+-- |--+.+. +-+.+. ... =+.|+.--.+.. ++
T Consensus 476 VG~~~-AT~~-----lkd-G~~VTVdc~eGdtG~VY~Gr~~~T~E~~~~~~~~ev~iq~~~---~v~l~~~P~t~Tki~m 545 (877)
T TIGR01418 476 VGTGD-ATKK-----LKD-GEEVTVDCAEGDTGYVYAGRVEKTEEAVEEKLEYEVEIQEDA---EVELSNMPETATKIYM 545 (877)
T ss_pred ECCCH-HHHH-----HCC-CCEEEEECCCCCCCCEECCCEEECHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCEEEE
T ss_conf 64703-4565-----108-786898544488131345702300232544315674112665---3316767876647898
Q ss_pred HCCCH---HHHH-HHHHHCCC--HHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHH--------------------HH
Q ss_conf 20366---8899-88641499--279999999853023---31457999999999885--------------------41
Q gi|254780834|r 364 RCYGK---TAFE-KLIVESLP--LVDMLWKRETENRSF---NTPDERAELEIHLKNCI--------------------NH 414 (648)
Q Consensus 364 r~~G~---eaf~-~ll~~A~~--l~dFl~~~l~~~~dl---~spe~ka~~~~~l~~~I--------------------~~ 414 (648)
+=-.| +.|. .+=.+... =+||++-..+..+++ +.++.+...-.++.+++ ++
T Consensus 546 Nvg~Pe~Af~~ar~lP~dGVGLaR~EfII~~~i~~HP~aLi~~~d~~~~~K~EI~el~dekGfvqfkliyhyanGrlanK 625 (877)
T TIGR01418 546 NVGNPERAFRFARALPNDGVGLARIEFIILNWIKIHPLALIDDDDLKEVEKAEIEELMDEKGFVQFKLIYHYANGRLANK 625 (877)
T ss_pred ECCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEECCCHHHHH
T ss_conf 53885457899752578862278899999857765468745776877588899986320576056677654204326677
Q ss_pred CCCH--HHHHHHHHHHHHHHHHH
Q ss_conf 7998--99999999999998876
Q gi|254780834|r 415 IKDQ--KLRYYYSQAIRDRLQQL 435 (648)
Q Consensus 415 I~d~--~~R~~yl~~la~~L~~~ 435 (648)
+.-- .-+++|+++|++-+...
T Consensus 626 L~aGY~~~~~~fv~kLaeGia~v 648 (877)
T TIGR01418 626 LAAGYANPRDFFVDKLAEGIAKV 648 (877)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 65045881257889999999999
No 67
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659 This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=69.95 E-value=3.8 Score=21.01 Aligned_cols=48 Identities=21% Similarity=0.492 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCH-HHHHHH
Q ss_conf 775789999850688535101244225677410345542059973-452320
Q gi|254780834|r 136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSE-EKIIEA 186 (648)
Q Consensus 136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~-~~~~~~ 186 (648)
++..+++||+.+|+.+++++...= |.+...|.+.+.+.|++. .+++..
T Consensus 11 kSR~tLalL~dkgi~P~vV~YL~~---pp~~seL~~~~~~LG~~~ar~~~R~ 59 (114)
T TIGR00014 11 KSRQTLALLEDKGIEPEVVKYLKN---PPTKSELKALLAKLGISSAREMIRT 59 (114)
T ss_pred HHHHHHHHHHHCCCCCEEEECCCC---CCCHHHHHHHHHHCCCCHHHHHCCC
T ss_conf 468999999856999547414589---7486889999987089703630117
No 68
>TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161 Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal). Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis. For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm.
Probab=68.26 E-value=6 Score=19.16 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=7.4
Q ss_pred ECCCCCCHHHHHHHH
Q ss_conf 178866225777888
Q gi|254780834|r 321 FDGDDPGLRAAYKAI 335 (648)
Q Consensus 321 fDgD~AG~kAa~Ra~ 335 (648)
==|=..|.=|++=++
T Consensus 582 tmGG~sGYLAt~~GL 596 (777)
T TIGR02478 582 TMGGYSGYLATMAGL 596 (777)
T ss_pred EECCCHHHHHHHHHH
T ss_conf 708971689999988
No 69
>pfam01921 tRNA-synt_1f tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes.
Probab=67.95 E-value=8.2 Score=17.92 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=12.9
Q ss_pred CCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf 8888899720366889988641499
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEKLIVESLP 380 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~ll~~A~~ 380 (648)
|.=|+++++-.-++.++-++-+..|
T Consensus 286 ~is~~e~L~~~~pE~Lr~l~~~~~P 310 (355)
T pfam01921 286 GITIEEWLEYAPPESLRFLMFRVKP 310 (355)
T ss_pred CCCHHHHHHHCCHHHHHHHHCCCCC
T ss_conf 7699999986699999999804288
No 70
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=67.51 E-value=8.5 Score=17.75 Aligned_cols=99 Identities=17% Similarity=0.241 Sum_probs=65.0
Q ss_pred HHHCCCCCCHHHHHCCCCHHHHHHHH-HCCCEEEEEECCCCCCHHHHHHHHHHHH------HHHHCCCCEEEEECCCCCC
Q ss_conf 87435542113432136626789885-1268189961788662257778888887------7753697306752578888
Q gi|254780834|r 286 LCQAGVQNVVSSLGTALTEYQLRLLW-KLSPRIVLCFDGDDPGLRAAYKAIDLVL------CHLIPGNRVNFVLLSRGED 358 (648)
Q Consensus 286 l~~~G~~n~va~~Gtalt~~~~~~l~-r~~~~vvl~fDgD~AG~kAa~Ra~e~~l------~~l~~g~~v~vv~LP~G~D 358 (648)
|.-.-|.+-|+.|||.+-++-.-+=+ || .+||||=|+|==|.. .|++-|.. ++++.|. |+++..|
T Consensus 477 l~N~Ei~~~ItALG~GI~~d~Fdl~KLRY-HKIIIMTDADVDGSH--IRTLLLTFFYR~M~~LIE~Gy-vYIAqPP---- 548 (818)
T TIGR01059 477 LSNDEIQAIITALGCGIGKDEFDLEKLRY-HKIIIMTDADVDGSH--IRTLLLTFFYRYMRPLIENGY-VYIAQPP---- 548 (818)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCEEEEECCCCCHHH--HHHHHHHHHHHHHHHHHHCCC-EEEECCC----
T ss_conf 21253388899736886766787232464-436884067878368--999999988740158874587-2650786----
Q ss_pred HHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCC
Q ss_conf 88997203668899886414992799999998530233
Q gi|254780834|r 359 PDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFN 396 (648)
Q Consensus 359 PDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~ 396 (648)
=|=-+.|++. .+|.+..-+-.|++...++...+-
T Consensus 549 --LYKvk~gk~~--~Yikdd~e~d~yll~~~~~~~~l~ 582 (818)
T TIGR01059 549 --LYKVKKGKKE--RYIKDDKELDHYLLNLGINEAELV 582 (818)
T ss_pred --CHHHHCCCCC--CCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf --0212046551--122277899889887532420265
No 71
>COG2604 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.38 E-value=8.2 Score=17.91 Aligned_cols=55 Identities=29% Similarity=0.469 Sum_probs=31.2
Q ss_pred HHHHHCCCCHHHHHHHHHCCCEE-EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf 13432136626789885126818-9961788662257778888887775369730675257888888997203
Q gi|254780834|r 295 VSSLGTALTEYQLRLLWKLSPRI-VLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY 366 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~r~~~~v-vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~ 366 (648)
|-+-|-+|+ -|+.+|+.|.++. |+|=| ||+.+ +++.|+.+.+|. -.||||++-+.
T Consensus 229 IVSaGPSL~-Kql~lLK~y~~k~~IFcad----------sal~~---L~k~GIkPDyVc---~ld~~di~~e~ 284 (594)
T COG2604 229 IVSAGPSLE-KQLPLLKKYQDKATIFCAD----------SALPI---LAKHGIKPDYVC---SLDPDDIAYEF 284 (594)
T ss_pred EECCCCCHH-HCCHHHHHHCCCEEEEECC----------CCCHH---HHHCCCCCCEEE---EECCHHHHHHH
T ss_conf 980786744-4368888605553999889----------75457---986799977699---85641889999
No 72
>TIGR01430 aden_deam adenosine deaminase; InterPro: IPR006330 This family includes the experimentally verified adenosine deaminases of mammals and Escherichia coli. Other members of this family are predicted also to be adenosine deaminase, an enzyme of nucleotide degradation. This family is distantly related to AMP deaminase. ; GO: 0004000 adenosine deaminase activity, 0009168 purine ribonucleoside monophosphate biosynthetic process.
Probab=66.33 E-value=8.1 Score=17.94 Aligned_cols=68 Identities=21% Similarity=0.267 Sum_probs=39.8
Q ss_pred HHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HHHC-CCCC--HHHHHHHHH
Q ss_conf 9885999799999999981885877682036777889999999999999999--9732-6777--578999985
Q gi|254780834|r 78 SALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFH--HSLK-NARD--KRLHYYLDE 146 (648)
Q Consensus 78 ~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~-~~~~--~~a~~yl~~ 146 (648)
+++||-==||-+-.||.|+||.+| ..++..+-...-..-.++...-..||. .+|. +... .-|.+|+.+
T Consensus 8 ~HleG~~~P~l~l~la~k~gi~LP-~~~~~~e~~~~~~~~~~L~~FL~~yd~~~~~L~G~~~d~~rlAy~~~~~ 80 (346)
T TIGR01430 8 LHLEGSLRPELLLELAQKNGIPLP-DLQSLEELKEAYEKFRDLQDFLAKYDFGVEVLRGTEDDFKRLAYEYVEK 80 (346)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCCC-CCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 574325567889988864389888-6312100232111267878999999999887428998999999999999
No 73
>TIGR01696 deoB phosphopentomutase; InterPro: IPR010045 This entry describes bacterial phosphopentomutase. This protein is involved in the purine and pyrimidine salvage pathway of nucleotide synthesis. It catalyses a phosphotransfer on ribose and deoxyribose, converting D-ribose 1-phosphate to D-ribose 5-phosphate, and 2-deoxy-D-ribose 1-phosphate to 2-deoxy-D-ribose 5-phosphate . ; GO: 0000287 magnesium ion binding, 0008973 phosphopentomutase activity, 0009117 nucleotide metabolic process, 0043094 metabolic compound salvage, 0005737 cytoplasm.
Probab=66.11 E-value=5.6 Score=19.46 Aligned_cols=85 Identities=26% Similarity=0.344 Sum_probs=54.7
Q ss_pred ECCHHHHHHH-------HHCCCCCCHHHHHC-CCCHHHHHHHHHCCCE-EEEE----ECC------CCCCHHHHHHHHHH
Q ss_conf 7143889998-------74355421134321-3662678988512681-8996----178------86622577788888
Q gi|254780834|r 277 VEGYMDVLSL-------CQAGVQNVVSSLGT-ALTEYQLRLLWKLSPR-IVLC----FDG------DDPGLRAAYKAIDL 337 (648)
Q Consensus 277 vEGy~Dvi~l-------~~~G~~n~va~~Gt-alt~~~~~~l~r~~~~-vvl~----fDg------D~AG~kAa~Ra~e~ 337 (648)
=+||-||||. ...||+..|-+.|. ++-..-++.++.-..+ |+|. ||+ |.+|..++++-.+.
T Consensus 246 D~~~G~VisiGKI~DIY~~~GiT~~~~~~s~~~~~D~~i~~~k~~f~~ti~F~NlVDFDa~~GHRRD~~GYa~al~~FD~ 325 (404)
T TIGR01696 246 DEGYGDVISIGKIADIYDGEGITKKVRTTSNMDGMDKVIKELKEDFTGTISFTNLVDFDALYGHRRDKAGYAAALEEFDR 325 (404)
T ss_pred CCCCCCEEEECCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 17776568853200110578844223310036788999999853137717885200100246756582578999998742
Q ss_pred HHHHHHCCC---CEEEEECCCCCCHHH
Q ss_conf 877753697---306752578888889
Q gi|254780834|r 338 VLCHLIPGN---RVNFVLLSRGEDPDS 361 (648)
Q Consensus 338 ~l~~l~~g~---~v~vv~LP~G~DPDe 361 (648)
=||.+-..+ ++-|++--.|-||=-
T Consensus 326 RLPEl~s~lr~DDllI~TADHG~DP~~ 352 (404)
T TIGR01696 326 RLPELFSKLREDDLLIITADHGNDPTA 352 (404)
T ss_pred HHHHHHHHCCCCCEEEEECCCCCCCCC
T ss_conf 226887403768579983067887788
No 74
>TIGR02482 PFKA_ATP 6-phosphofructokinase; InterPro: IPR012828 6-phosphofructokinase (2.7.1.11 from EC) catalyses the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This entry contains bacterial ATP-dependent 6-phosphofructokinases, which lack a beta-hairpin loop present in IPR012829 from INTERPRO family members. IPR012829 from INTERPRO contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. IPR011183 from INTERPRO represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (2.7.1.90 from EC).; GO: 0003872 6-phosphofructokinase activity, 0005524 ATP binding, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=65.36 E-value=7 Score=18.55 Aligned_cols=29 Identities=24% Similarity=0.517 Sum_probs=15.1
Q ss_pred CCEEEEECC---HHHHHHHHHCC-CCCCHHHHHC
Q ss_conf 870899714---38899987435-5421134321
Q gi|254780834|r 271 SSFIILVEG---YMDVLSLCQAG-VQNVVSSLGT 300 (648)
Q Consensus 271 ~~~~i~vEG---y~Dvi~l~~~G-~~n~va~~Gt 300 (648)
-+.+||+=| ||=+-.||+-| |+ +|+.=||
T Consensus 92 I~~LVViGGDGSy~GA~~L~~~gg~~-~iGlPGT 124 (302)
T TIGR02482 92 IEALVVIGGDGSYTGAQKLYEEGGIP-VIGLPGT 124 (302)
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCC-EEEECCC
T ss_conf 86689986844068899999717984-7874585
No 75
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=64.92 E-value=9.4 Score=17.36 Aligned_cols=45 Identities=18% Similarity=0.273 Sum_probs=16.6
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 999984430023799889999999999975388999899998851112
Q gi|254780834|r 498 LQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERG 545 (648)
Q Consensus 498 ~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~ 545 (648)
+..+++.+....+.|. .......+..-...+ ..+..+.+.|...+
T Consensus 54 Ie~Vi~~l~~~~~ldD--~~fAe~~i~~r~~~g-~G~~rl~qeL~qkG 98 (174)
T COG2137 54 IEEVIDRLAEEGYLDD--TRFAEAYIRSRSRKG-KGPARLKQELKQKG 98 (174)
T ss_pred HHHHHHHHHHCCCCCH--HHHHHHHHHHHHHCC-CCHHHHHHHHHHCC
T ss_conf 9999999999286567--999999999987646-67299999999849
No 76
>TIGR00600 rad2 DNA excision repair protein (rad2); InterPro: IPR001044 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XPGC, an acidic protein that confers normal UV resistance in expressing cells, can correct XP-G. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms. XPGC cleaves one strand of the duplex at the border with the single-stranded region , .; GO: 0003697 single-stranded DNA binding, 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=64.63 E-value=3.8 Score=21.03 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=11.4
Q ss_pred CCHHHHHHHHHHCCHHHHHHHH
Q ss_conf 7888999998748888875412
Q gi|254780834|r 3 YPRDFIKDLLIHIPISNLIGQY 24 (648)
Q Consensus 3 i~~~~i~~i~~~~~i~~vv~~~ 24 (648)
|++==|+.|+.+.++-.-|..+
T Consensus 265 FS~yQl~~l~~kN~L~q~l~~~ 286 (1127)
T TIGR00600 265 FSRYQLKGLLKKNDLNQKLENV 286 (1127)
T ss_pred HHHHHHHHHHHHCHHHHHHHHH
T ss_conf 1089999876522034568865
No 77
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=64.16 E-value=9.7 Score=17.25 Aligned_cols=79 Identities=24% Similarity=0.292 Sum_probs=51.7
Q ss_pred EEEEECCHHHHHHHHHCCCCCCH-HHHHCCCCH------HHH---HHHHHC----CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf 08997143889998743554211-343213662------678---988512----6818996178866225777888888
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGVQNVV-SSLGTALTE------YQL---RLLWKL----SPRIVLCFDGDDPGLRAAYKAIDLV 338 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtalt~------~~~---~~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e~~ 338 (648)
.+.|||-..|++++-+.|.-+.. -.||-.+++ +++ .++.|. .++|||++...--|..-|.=-.+.
T Consensus 2 ~lcVVe~~~Dl~~iE~s~~y~G~YhVL~G~lspl~g~~p~~l~i~~L~~ri~~~~i~EvIlA~~~t~EGe~Ta~yi~~~- 80 (112)
T cd01025 2 KLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL- 80 (112)
T ss_pred EEEEECCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH-
T ss_conf 7999898999999972175656999852634755699833031999999983589418999748996608999999998-
Q ss_pred HHHHHCCCCEEEEECCCC
Q ss_conf 777536973067525788
Q gi|254780834|r 339 LCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 339 l~~l~~g~~v~vv~LP~G 356 (648)
++ ...++|-.|-.|
T Consensus 81 ---l~-~~~ikitrLA~G 94 (112)
T cd01025 81 ---LK-DFGVKVTRLAQG 94 (112)
T ss_pred ---HH-HCCCCEEEEEEC
T ss_conf ---54-359727988744
No 78
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=64.09 E-value=7 Score=18.53 Aligned_cols=57 Identities=32% Similarity=0.387 Sum_probs=37.3
Q ss_pred CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHH-HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC
Q ss_conf 1134321366267898851268189961788662257778-88888777536973067525788888899720
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYK-AIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~R-a~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~ 365 (648)
++-.+|++++.+|.+-|+.+..+ .+ .+ +..+-..++.-| |.|..+|.-.||-++.-.
T Consensus 56 viVA~gi~ls~eH~~al~aL~~e-----------~R--~efi~~l~~dLlr~~--v~F~~~Pn~~~pqsiqvs 113 (161)
T COG5440 56 VIVAIGIALSQEHRRALMALNPE-----------KR--EEFIWKLRRDLLRLG--VDFQALPNPRDPQSIQVS 113 (161)
T ss_pred EEEEEEECCCHHHHHHHHHCCHH-----------HH--HHHHHHHHHHHHHCC--CCEEECCCCCCCCEEEEE
T ss_conf 99997633299999998840967-----------78--999999999999638--735954996677436744
No 79
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=63.82 E-value=9.8 Score=17.20 Aligned_cols=82 Identities=24% Similarity=0.299 Sum_probs=47.1
Q ss_pred CCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCC
Q ss_conf 12100346541000016716888970778588850100146553001038767653521011081788886433100002
Q gi|254780834|r 187 GLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDV 266 (648)
Q Consensus 187 gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~ 266 (648)
||....+....+||-. =.+-..|.|..|+|++=.|-.+++ -.|+.-+++.+|=-++--=-+..|+.....
T Consensus 75 gl~~a~~~rt~~~DPS-~tl~~DI~d~~G~via~aGt~vNP---Ld~v~~~~~LvF~DgdD~~Qv~Wa~~~~~~------ 144 (210)
T PRK13738 75 GIGRAEKYGSRLFDPS-VRLAADIRDNEGRVFARQGEVMNP---LQYVPFNQTLYFINGDDPAQVAWMKRQTPP------ 144 (210)
T ss_pred CCCCCCCCCEEEECCC-EEECCCCCCCCCCEEECCCCEECC---CCCCCCCCEEEEEECCCHHHHHHHHHHCCC------
T ss_conf 8755434625995786-884575238999899758877786---412468872899959899999999974005------
Q ss_pred CCCCCCEEEEECCH
Q ss_conf 35678708997143
Q gi|254780834|r 267 RRNSSSFIILVEGY 280 (648)
Q Consensus 267 ~~~~~~~~i~vEGy 280 (648)
.....+|+|.|-
T Consensus 145 --~~~~K~ILv~Gs 156 (210)
T PRK13738 145 --TLESKIILVQGS 156 (210)
T ss_pred --CCCCEEEEECCC
T ss_conf --777139996898
No 80
>PRK13844 recombination protein RecR; Provisional
Probab=63.47 E-value=9.9 Score=17.15 Aligned_cols=80 Identities=15% Similarity=0.247 Sum_probs=51.0
Q ss_pred CCEEEEECCHHHHHHHHHCCCCCCH-HHHHCCC------CHHHHH--HH-HHC----CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf 8708997143889998743554211-3432136------626789--88-512----68189961788662257778888
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAGVQNVV-SSLGTAL------TEYQLR--LL-WKL----SPRIVLCFDGDDPGLRAAYKAID 336 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G~~n~v-a~~Gtal------t~~~~~--~l-~r~----~~~vvl~fDgD~AG~kAa~Ra~e 336 (648)
...+-|||-..|++++-+.|.-+.+ -.||-.+ ++++++ .| .|. .++|||+++.+--|..-|.= +.
T Consensus 82 ~~~iCVVE~~~Dl~aiE~s~~y~G~YhVL~G~iSpl~gigp~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~y-i~ 160 (200)
T PRK13844 82 DTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGIGPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHF-IS 160 (200)
T ss_pred CCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHCHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH-HH
T ss_conf 98899983689999999744106688874874473238882230679999886379974799967999650999999-99
Q ss_pred HHHHHHHCCCCEEEEECCCC
Q ss_conf 88777536973067525788
Q gi|254780834|r 337 LVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 337 ~~l~~l~~g~~v~vv~LP~G 356 (648)
. +++. .|+|-.|-.|
T Consensus 161 ~---~l~~--~ikitrLA~G 175 (200)
T PRK13844 161 Q---MIAK--DIKISRIGFG 175 (200)
T ss_pred H---HHCC--CCCEEEEEEC
T ss_conf 9---8449--9727766544
No 81
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a superfamily IPR000352 from INTERPRO of RF-1, RF-2, mitochondrial, RF-H, etc proteins.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=62.23 E-value=10 Score=16.97 Aligned_cols=95 Identities=15% Similarity=0.326 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH-
Q ss_conf 9999885111289999999998654333202568998-89999999999999858999999999999998724127989-
Q gi|254780834|r 535 EEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANI-VDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAE- 612 (648)
Q Consensus 535 ~~l~~~L~~~~l~elL~~L~~~~~~~~~~~~~~e~~~-~d~~e~~~~~l~l~~r~~~L~r~l~ele~~l~e~~~~~d~e- 612 (648)
..+...|..+.+..-|+++.........|.-...+.. ......++..+. +...|.+.+.++..- .++....+.+
T Consensus 19 ~~~~~~Ld~e~~~~rle~le~e~~dP~fW~D~~rAq~v~~e~~~l~~~l~---~~~~l~~~~~dl~~L-~Ela~ee~d~a 94 (373)
T TIGR00020 19 DDVRGILDPEKLKARLEELEKEMEDPNFWNDQERAQKVIKERSSLEEELD---TLEELKNSLDDLSEL-LELAKEEDDEA 94 (373)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH-HHHHCCCCHHH
T ss_conf 98775138668999999998775078666125899999999999998632---799987553257889-98743760357
Q ss_pred ------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf ------999999999999999999884
Q gi|254780834|r 613 ------KTAILISILHEVHIQIHQIES 633 (648)
Q Consensus 613 ------~~~~l~~el~elk~~L~~l~~ 633 (648)
...++-.|+..|.+++++++-
T Consensus 95 aasGm~~~~el~~El~~Le~~~~~lE~ 121 (373)
T TIGR00020 95 AASGMETFAELEEELKALEKELEELEL 121 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 778999999999999999999999999
No 82
>pfam04273 DUF442 Putative phosphatase (DUF442). Although this domain is uncharacterized it seems likely that it performs a phosphatase function.
Probab=60.90 E-value=11 Score=16.79 Aligned_cols=84 Identities=14% Similarity=0.184 Sum_probs=49.4
Q ss_pred CCCHHHHHCCCCHHHHHHHHHCCCEEEEEEC--CCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHH
Q ss_conf 4211343213662678988512681899617--88662257778888887775369730675257888888997203668
Q gi|254780834|r 292 QNVVSSLGTALTEYQLRLLWKLSPRIVLCFD--GDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKT 369 (648)
Q Consensus 292 ~n~va~~Gtalt~~~~~~l~r~~~~vvl~fD--gD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~e 369 (648)
..-++..| .++++++..|....=+.|||.= +.+.|+-....--+.+. ..|++..-+.+..|.-.++- .+
T Consensus 6 ~~~~~vs~-Qi~~~di~~la~~GfktIInnRPd~E~~~qp~~~~~~~~a~---~~Gl~y~~iPv~~~~~t~~~-----v~ 76 (110)
T pfam04273 6 NEDLSVSP-QIQPDDIAAAARAGFRSVINNRPDGEEPGQPSNAAEQAAAR---AAGLAYRFIPVISGQITEAD-----VE 76 (110)
T ss_pred CCCEEECC-CCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHHH---HCCCEEEEEECCCCCCCHHH-----HH
T ss_conf 78875759-98999999999859838853388877789988899999999---83997999644778989999-----99
Q ss_pred HHHHHHHHC-CCHHHH
Q ss_conf 899886414-992799
Q gi|254780834|r 370 AFEKLIVES-LPLVDM 384 (648)
Q Consensus 370 af~~ll~~A-~~l~dF 384 (648)
.|.++++++ .|.+-|
T Consensus 77 ~f~~~l~~~~~Pvl~~ 92 (110)
T pfam04273 77 AFQRALAAAEGPVLAH 92 (110)
T ss_pred HHHHHHHHCCCCEEEE
T ss_conf 9999998589989998
No 83
>PRK02853 hypothetical protein; Provisional
Probab=60.85 E-value=9.1 Score=17.50 Aligned_cols=81 Identities=22% Similarity=0.428 Sum_probs=43.0
Q ss_pred CCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHH
Q ss_conf 67168889707785888501001465530010387676535210110817888864331000023567870899714388
Q gi|254780834|r 203 RNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMD 282 (648)
Q Consensus 203 r~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~D 282 (648)
-+|++|-|++..|..+.= ....|..-|..++ ++..+||.|+|
T Consensus 63 d~rLvfdI~~~~~~~~~~--------------------------~~lsl~pfRriik------------DYf~iCeSYy~ 104 (161)
T PRK02853 63 ENRLVFDIRREDGEPVAT--------------------------HILSLTPFRRIVK------------DYFMICESYYQ 104 (161)
T ss_pred CCEEEEEEECCCCCEEEE--------------------------EEECCHHHHHHHH------------HHHHHHHHHHH
T ss_conf 798999973688982058--------------------------9962444899999------------99999999999
Q ss_pred HHHHHHCCCCCCHHHHH-CCCCHHHHHHHH-HCCCEEEEEEC
Q ss_conf 99987435542113432-136626789885-12681899617
Q gi|254780834|r 283 VLSLCQAGVQNVVSSLG-TALTEYQLRLLW-KLSPRIVLCFD 322 (648)
Q Consensus 283 vi~l~~~G~~n~va~~G-talt~~~~~~l~-r~~~~vvl~fD 322 (648)
+|.-....-=.+| -|| -++-.+-..+|. |+..+|.+=||
T Consensus 105 AIk~~~p~qIEaI-DMgRRglHnEga~lL~eRL~gki~~D~~ 145 (161)
T PRK02853 105 AIRTATPSQIEAI-DMGRRGLHNEGSELLQERLEGKIDVDFD 145 (161)
T ss_pred HHHHCCHHHHHHH-HHHHHCCCHHHHHHHHHHHHCCEEECHH
T ss_conf 9960998786787-6542022247899999998287354202
No 84
>TIGR01980 sufB FeS assembly protein SufB; InterPro: IPR010231 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, which is part of the SUF system and forms a complex with SufBCD.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=60.13 E-value=5.3 Score=19.69 Aligned_cols=34 Identities=24% Similarity=0.192 Sum_probs=18.9
Q ss_pred HCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf 21366267898851268189961788662257778888887
Q gi|254780834|r 299 GTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVL 339 (648)
Q Consensus 299 Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l 339 (648)
+--||++=|+.|.+.-.++=-|+|= =|||+|...
T Consensus 18 ~kGLt~~VV~~IS~~K~EP~WMLd~-------RLrale~f~ 51 (469)
T TIGR01980 18 EKGLTEEVVREISEKKGEPDWMLDF-------RLRALELFL 51 (469)
T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHH-------HHHHHHHHH
T ss_conf 7898889999997305888689999-------999999884
No 85
>pfam06840 DUF1241 Protein of unknown function (DUF1241). This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.
Probab=58.29 E-value=10 Score=16.93 Aligned_cols=28 Identities=21% Similarity=0.078 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 8999999999997538899989999885
Q gi|254780834|r 514 ELQKLWSFLFSDFVEQKYFLPEEIHQRL 541 (648)
Q Consensus 514 ~~~~L~~~i~~~~~~~~~~~~~~l~~~L 541 (648)
..+.|+.++...-.+.+.+..+-+..-+
T Consensus 31 a~q~Lr~Af~kaE~~~PGf~~d~v~~il 58 (154)
T pfam06840 31 AAQKLRAAFTKAEKENPGFTYDLVKGIL 58 (154)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9999999999987218966999999999
No 86
>KOG3578 consensus
Probab=57.15 E-value=3.3 Score=21.49 Aligned_cols=35 Identities=11% Similarity=0.057 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHCC------------CCHHHHHHHHHHHHCCCCCC
Q ss_conf 888789899898859------------99799999999981885877
Q gi|254780834|r 68 HVKGDHLSFLSALLG------------CSFIESVQRLAAIAGVPLPV 102 (648)
Q Consensus 68 ~~~gd~~~f~~~~~~------------~~f~ea~~~la~~~gi~~~~ 102 (648)
+--|.++.|++++.- +-|.-|.+.+++.+|..+..
T Consensus 79 ~~mg~~~~~~qe~~~fv~~~y~~irn~v~~l~a~~~~~~~~~~~i~~ 125 (1058)
T KOG3578 79 AYMGTVGKVYQESRKFVFAHYKNIRNMVLFLTAEESLMDTDGHRINN 125 (1058)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECC
T ss_conf 77568999998877999999999999999999999974005812001
No 87
>pfam00133 tRNA-synt_1 tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included.
Probab=56.90 E-value=7.9 Score=18.04 Aligned_cols=19 Identities=16% Similarity=0.599 Sum_probs=10.3
Q ss_pred EEEEEEEECCC-CEEEEECC
Q ss_conf 16888970778-58885010
Q gi|254780834|r 205 RLIFPIRSSRG-QVIAFGGR 223 (648)
Q Consensus 205 Ri~fPi~~~~g-~~i~f~gR 223 (648)
.+-||+.+..+ .++.|+-|
T Consensus 189 ~v~f~l~~~~~~~l~i~TTr 208 (606)
T pfam00133 189 HVAFPLADGKGASLVIWTTT 208 (606)
T ss_pred EEECCCCCCCCCEEEEEECC
T ss_conf 65044578987669999435
No 88
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis . The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=56.76 E-value=12 Score=16.49 Aligned_cols=70 Identities=19% Similarity=0.182 Sum_probs=45.4
Q ss_pred HHHH--HHHHC----CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf 6789--88512----68189961788662257778888887775369730675257888888997203668899886414
Q gi|254780834|r 305 YQLR--LLWKL----SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES 378 (648)
Q Consensus 305 ~~~~--~l~r~----~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A 378 (648)
||.- .|+.. .+++-+.|=||. +|=.--+ |++.-.+-|++++|+. |+|.+||+.|.+. ..++.+--..+
T Consensus 147 E~~g~~~l~g~nkGinsklk~vy~GDg--RNNVcnS--L~la~a~~Gm~~~v~t-P~gyeP~~~~v~~-A~~~a~e~Gg~ 220 (341)
T TIGR00658 147 EHFGEKKLKGVNKGINSKLKVVYVGDG--RNNVCNS--LLLAAAKLGMDVVVAT-PEGYEPDAEIVKK-AKKIAKENGGS 220 (341)
T ss_pred HHCCCCCCCHHCCCCCCCCEEEEECCC--CHHHHHH--HHHHHHHHCCEEEEEC-CCCCCCCHHHHHH-HHHHHHHCCCE
T ss_conf 746795600000352442168997378--5126889--9999997285478878-8888878789999-99999717985
Q ss_pred CC
Q ss_conf 99
Q gi|254780834|r 379 LP 380 (648)
Q Consensus 379 ~~ 380 (648)
..
T Consensus 221 ~~ 222 (341)
T TIGR00658 221 VE 222 (341)
T ss_pred EE
T ss_conf 99
No 89
>pfam01113 DapB_N Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.
Probab=56.73 E-value=7.4 Score=18.31 Aligned_cols=42 Identities=26% Similarity=0.313 Sum_probs=30.9
Q ss_pred CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEE
Q ss_conf 14388999-874355421134321366267898851268189961
Q gi|254780834|r 278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCF 321 (648)
Q Consensus 278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~f 321 (648)
++-++.+. +..+|++-||+| |-||++|...|+++++++-+++
T Consensus 76 ~~~~~~~~~~~~~~~~~ViGT--TG~s~~~~~~i~~~a~~ipi~~ 118 (122)
T pfam01113 76 EATLENLELALKHGKPLVIGT--TGFTEEQLAELKEAAKKIPIVI 118 (122)
T ss_pred HHHHHHHHHHHHCCCCEEEEC--CCCCHHHHHHHHHHHCCCCEEE
T ss_conf 899999999996799889989--9999999999999844598898
No 90
>pfam01458 UPF0051 Uncharacterized protein family (UPF0051).
Probab=56.57 E-value=6.9 Score=18.62 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=5.1
Q ss_pred CCHHH--HHHCCCH
Q ss_conf 88889--9720366
Q gi|254780834|r 357 EDPDS--FIRCYGK 368 (648)
Q Consensus 357 ~DPDe--~ir~~G~ 368 (648)
.|||. |++..|.
T Consensus 204 id~e~lfYL~sRGi 217 (230)
T pfam01458 204 LDEEQLFYLMSRGL 217 (230)
T ss_pred CCHHHHHHHHHCCC
T ss_conf 79899999987698
No 91
>TIGR01981 sufD FeS assembly protein SufD; InterPro: IPR011542 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 SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=55.95 E-value=6.3 Score=19.00 Aligned_cols=69 Identities=19% Similarity=0.205 Sum_probs=34.4
Q ss_pred CCCEEEEECCCC-CCHHHHHHC-CCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHH-HHHHHHHHHHCCCHHHH
Q ss_conf 973067525788-888899720-366889988641499279999999853023314579999-99999885417998999
Q gi|254780834|r 345 GNRVNFVLLSRG-EDPDSFIRC-YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAEL-EIHLKNCINHIKDQKLR 421 (648)
Q Consensus 345 g~~v~vv~LP~G-~DPDe~ir~-~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka~~-~~~l~~~I~~I~d~~~R 421 (648)
+...++..-|.= -|=||..-. ||+. .-.+=+ +-+|- +....++..+-|.-+ ..++.++|..|+++.+|
T Consensus 324 s~~A~~d~~P~LeI~~ddV~~~gHgAt-Vg~iD~------e~LFY--LrSRGi~~~~A~~L~i~gF~~e~i~~i~~~~l~ 394 (397)
T TIGR01981 324 SDKARADTKPQLEIDADDVKCSGHGAT-VGQIDD------EQLFY--LRSRGIDEEEARRLLIRGFLGEIIEEIPDESLK 394 (397)
T ss_pred CCCCEEEECEEEEEECCCEEECCEECC-CCCCCH------HHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 787628712167997582432110110-033574------46576--763788989999999998864333213881565
Q ss_pred H
Q ss_conf 9
Q gi|254780834|r 422 Y 422 (648)
Q Consensus 422 ~ 422 (648)
+
T Consensus 395 ~ 395 (397)
T TIGR01981 395 E 395 (397)
T ss_pred H
T ss_conf 2
No 92
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=55.62 E-value=13 Score=16.10 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=7.0
Q ss_pred CCCCCCCEEEEEEEECCC
Q ss_conf 000016716888970778
Q gi|254780834|r 198 SYDRFRNRLIFPIRSSRG 215 (648)
Q Consensus 198 ~~d~Fr~Ri~fPi~~~~g 215 (648)
+||. +|-|| -|+-..|
T Consensus 120 ~~D~-~nail-eI~aGaG 135 (367)
T PRK00578 120 EYDA-NNAIL-TIHAGAG 135 (367)
T ss_pred CCCC-CCEEE-EEECCCC
T ss_conf 8867-88479-9984899
No 93
>pfam09133 SANTA SANTA (SANT Associated). The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota. It is sometimes found in association with the SANT domain (pfam00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes. Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions.
Probab=55.57 E-value=5.1 Score=19.80 Aligned_cols=26 Identities=15% Similarity=0.351 Sum_probs=17.0
Q ss_pred CCCEEEEECCHHHHHHHHHCCCCCCH
Q ss_conf 78708997143889998743554211
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQAGVQNVV 295 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~G~~n~v 295 (648)
..+..|+..|.||...++++|++.-|
T Consensus 48 ~dG~~~~L~G~in~~~~~~nGfs~~v 73 (93)
T pfam09133 48 VDGITYVLVGFIDRSRMLKNGFPSEV 73 (93)
T ss_pred CCCEEEEEECCCCHHHHHHCCCCHHH
T ss_conf 58709999465688889885999899
No 94
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain; InterPro: IPR005976 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=54.64 E-value=3.4 Score=21.46 Aligned_cols=226 Identities=16% Similarity=0.182 Sum_probs=100.0
Q ss_pred HHHHHHHHHHHHHHH-------HHHCCC-CCHHHHHHHHHCCCCHHHHCCCCCCCCC---------CCCCHH----HHHH
Q ss_conf 999999999999999-------973267-7757899998506885351012442256---------774103----4554
Q gi|254780834|r 115 TDLIRLIEVATDFFH-------HSLKNA-RDKRLHYYLDERGIDSHAIEMFKLGYAP---------DSRYSL----REHL 173 (648)
Q Consensus 115 ~~~~~~~~~~~~~~~-------~~l~~~-~~~~a~~yl~~Rg~~~~~~~~f~lG~ap---------~~~~~l----~~~l 173 (648)
+.|.+.++=....|. ..++.. .|..-.+|+.+=.=.+-+-+.|-+-||. .+||.. .++|
T Consensus 128 ~NmvdGL~N~~alYkPkmIAVSTTCMAEVIGdDL~AFi~nAk~~g~ip~dfPVpFAHTPsFVGSHitGYD~M~kGil~~l 207 (526)
T TIGR01286 128 KNMVDGLQNIYALYKPKMIAVSTTCMAEVIGDDLRAFIGNAKEEGVIPDDFPVPFAHTPSFVGSHITGYDSMLKGILETL 207 (526)
T ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEECCCCHHHHHHHHHH
T ss_conf 77999997404325896466304544011013589999875306888888767865477732650025322689999985
Q ss_pred HCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECC--CCE---------EEEECCCCCCCCCCEECCCCCCCCC
Q ss_conf 20599734523201210034654100001671688897077--858---------8850100146553001038767653
Q gi|254780834|r 174 RQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSR--GQV---------IAFGGRTLSKGESVKYLNSPETILF 242 (648)
Q Consensus 174 ~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~--g~~---------i~f~gR~l~~~~~~KYlNSpeT~if 242 (648)
.++. .++ |.=.....+++. =++|=+|.. |.+ .|.++-+|. | ...||-||.-==|
T Consensus 208 ~~~~--~~d---as~~~~~~~~~i--------N~ipGFdTYCiGN~R~~Kr~L~~mGv~~~~L~-D-~~~~LDsP~dGey 272 (526)
T TIGR01286 208 TKGS--EDD---ASDKKKSANGKI--------NIIPGFDTYCIGNVREIKRILSLMGVEYTLLS-D-AEESLDSPADGEY 272 (526)
T ss_pred HCCC--HHH---HHHHHHCCCCEE--------EEEECCCCCEECCHHHHHHHHHHHCCCCEEEC-C-CHHHCCCCCCCCC
T ss_conf 0585--113---345442038627--------78407675111656889789987289830304-6-5543679888871
Q ss_pred CCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE----EE
Q ss_conf 52101108178888643310000235678708997143889998743554211343213662678988512681----89
Q gi|254780834|r 243 HKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR----IV 318 (648)
Q Consensus 243 ~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~----vv 318 (648)
-|| -+|-. ---.++=.|+-||+ .|=+.+++.=+.|+.+ =+
T Consensus 273 ----~mY---------------------------~gGT~---lee~~~A~nA~atl--~LQ~y~l~kT~eYie~~W~~et 316 (526)
T TIGR01286 273 ----RMY---------------------------DGGTK---LEELKDALNAEATL--VLQEYTLRKTKEYIEKKWKQET 316 (526)
T ss_pred ----CCC---------------------------CCCCC---HHHHHCCCCHHHEE--ECCCCCCHHHHHHHCCCCCCEE
T ss_conf ----226---------------------------77886---57642360101122--2124342356886527775124
Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCH
Q ss_conf 96178866225777888888777536973067525788888899720366889988641499279999999853023314
Q gi|254780834|r 319 LCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTP 398 (648)
Q Consensus 319 l~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~sp 398 (648)
..|. =.=|.++|.--+ |.++. +-+..=|.++-.+.|. +-+.+.++..+ =+-.+-.--.+|
T Consensus 317 ~~l~-~PlGv~~TDeFL-m~vs~-----------isg~eiP~~l~~eRGR--lVDamtDs~aw-----lHGKr~Ai~GDP 376 (526)
T TIGR01286 317 VKLE-IPLGVKGTDEFL-MKVSE-----------ISGQEIPAELTIERGR--LVDAMTDSQAW-----LHGKRVAIYGDP 376 (526)
T ss_pred EEEC-CCCCCCHHHHHH-HHHHH-----------HCCCCCHHHHHHHCCC--HHHHHHHHHHH-----HHHCCEEEECCC
T ss_conf 4524-788740778999-99998-----------5078762788851033--02555543343-----400304540581
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 5799999999988
Q gi|254780834|r 399 DERAELEIHLKNC 411 (648)
Q Consensus 399 e~ka~~~~~l~~~ 411 (648)
+=-..+.++++++
T Consensus 377 DlV~al~~F~LEl 389 (526)
T TIGR01286 377 DLVMALVRFVLEL 389 (526)
T ss_pred HHHHHHHHHHHHH
T ss_conf 5899999999981
No 95
>pfam03428 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
Probab=54.32 E-value=11 Score=16.70 Aligned_cols=33 Identities=33% Similarity=0.701 Sum_probs=21.1
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEE-EEE
Q ss_conf 45232012100346541000016716888970778588-850
Q gi|254780834|r 181 EKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVI-AFG 221 (648)
Q Consensus 181 ~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i-~f~ 221 (648)
..|+++||+..+|..++ -|| +.+|..|.|+ +||
T Consensus 93 a~LveaGLi~rrDS~Ng--KRy------~rR~~~G~i~~A~G 126 (177)
T pfam03428 93 AALVDAGLIIRRDSPNG--KRY------ARRGGDGEIEEAFG 126 (177)
T ss_pred HHHHHCCCEEECCCCCC--CCC------CEECCCCCEEEEEC
T ss_conf 99998897452369998--501------62379987763446
No 96
>PRK12366 replication factor A; Reviewed
Probab=54.08 E-value=14 Score=15.90 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=6.2
Q ss_pred HHHHHHHHHCCCCC
Q ss_conf 99999998188587
Q gi|254780834|r 88 SVQRLAAIAGVPLP 101 (648)
Q Consensus 88 a~~~la~~~gi~~~ 101 (648)
|+..+|...|++++
T Consensus 41 AamlVA~elG~~~~ 54 (649)
T PRK12366 41 AVMLVAQEIGIEIT 54 (649)
T ss_pred HHHHHHHHHCCCCC
T ss_conf 99999998544555
No 97
>pfam04407 DUF531 Protein of unknown function (DUF531). Family of hypothetical archaeal proteins.
Probab=54.02 E-value=14 Score=15.90 Aligned_cols=59 Identities=12% Similarity=0.128 Sum_probs=42.1
Q ss_pred EEEECCC---CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC--------CCHHHHHHHHHHCC
Q ss_conf 9961788---66225777888888777536973067525788888899720--------36688998864149
Q gi|254780834|r 318 VLCFDGD---DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC--------YGKTAFEKLIVESL 379 (648)
Q Consensus 318 vl~fDgD---~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~--------~G~eaf~~ll~~A~ 379 (648)
|=.||++ +|-.+|..||+.+|..+ |+.+-.+-.|-...|.+++.. .|.+.+.+++++.+
T Consensus 7 yNtYd~~k~~e~H~RaIARAapic~Af---~~~LAL~~FP~~~~~~el~~~v~~~TtIG~~G~yl~~L~~~nr 76 (174)
T pfam04407 7 YNTYDKKKVHEAHYRAIARAAPICYAF---GFHLALFGFPFDMTPKELAEYVADKTTIGESGKYLLELAESNK 76 (174)
T ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHC---CCCEEEECCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHCCC
T ss_conf 844687756608999998460476641---7877987798877879999997642732776799999987496
No 98
>TIGR02082 metH methionine synthase; InterPro: IPR011822 Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin. This enzyme is a large protein composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate , the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.Recent studies suggest that this enzyme exists as an ensemble of conformations with equilibria dependent on the oxidation and methylation state of the cobalamin and on the concentrations of substrates or products .; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0050897 cobalt ion binding, 0009086 methionine biosynthetic process.
Probab=53.87 E-value=8.1 Score=17.96 Aligned_cols=262 Identities=18% Similarity=0.181 Sum_probs=132.7
Q ss_pred ECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 136888878989989885999799999999981---8858776820-----36777889999999999999999973267
Q gi|254780834|r 64 CFSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPLPVVDPK-----IEKKEKIQTDLIRLIEVATDFFHHSLKNA 135 (648)
Q Consensus 64 cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 135 (648)
.+-|.-.||- ++-++|-||+|+..=..| |=++=+.++. ...........|+++..+++.=+.+
T Consensus 33 d~~~~l~GnN-----d~L~~TkPdvi~~iHr~YfEAGADiiETNTF~sT~i~~aDY~~~~~~y~~N~~gA~lAr~v---- 103 (1265)
T TIGR02082 33 DHARELKGNN-----DILNLTKPDVIATIHRAYFEAGADIIETNTFNSTTIALADYDLEDLIYDLNFKGAKLARRV---- 103 (1265)
T ss_pred CCCCCCCCCC-----HHHHCCCHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH----
T ss_conf 8887766760-----0320684379999988773318867873577765032532127999999879999999999----
Q ss_pred CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHH-------CCCCCHHHHHHH------CCCEECCCC-------
Q ss_conf 775789999850688535101244225677410345542-------059973452320------121003465-------
Q gi|254780834|r 136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLR-------QKGFSEEKIIEA------GLLIDGDNS------- 195 (648)
Q Consensus 136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~-------~~~~~~~~~~~~------gl~~~~~~~------- 195 (648)
-+|+..| +++ .+||=.|--=+++.. --|. =++++.+.|.+| ||+ |.|
T Consensus 104 -----A~E~~~~--~p~-kpRfVAGs~GPtnkt--~tlsPdVe~P~FRnvtyD~L~~AY~e~~~gL~---dGGvDllLiE 170 (1265)
T TIGR02082 104 -----ADEFTAL--TPE-KPRFVAGSLGPTNKT--ATLSPDVERPEFRNVTYDELVDAYKEQIKGLL---DGGVDLLLIE 170 (1265)
T ss_pred -----HHHHHHC--CCC-CCEEEEECCCCCCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH---HCCCHHHHHH
T ss_conf -----8776410--889-865887315775557--74588888778875787989999999999877---3260354774
Q ss_pred ------------CCCCCCCC-CEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHH------HH
Q ss_conf ------------41000016-716888970778588850100146553001038767653521011081788------88
Q gi|254780834|r 196 ------------ATSYDRFR-NRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGA------LN 256 (648)
Q Consensus 196 ------------~~~~d~Fr-~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a------~~ 256 (648)
...-+-|. --.-.||. .+|=++-=+||+|-..+..=.++| +=+-+=...|||.| ++
T Consensus 171 T~fDtLnaKAAlfA~~~~F~~~g~~lPi~-iSGti~d~sGr~LsGqt~~Af~~s----l~~~~~~~iGLNCAlGpdel~~ 245 (1265)
T TIGR02082 171 TVFDTLNAKAALFAAETVFEEKGRELPIM-ISGTIVDTSGRTLSGQTLEAFLAS----LEHAEILIIGLNCALGPDELRP 245 (1265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCEE-EEEEEECCCCCCCCCCCHHHHHHH----HCCCCCCEECCCCCCCHHHHHH
T ss_conf 79999999999999999999728978768-860262276872026208999998----5468730241231147778999
Q ss_pred HHHHHHCCCCCCCCCCEEEEE---------CC---H---------HHHHHHHHCCCCCCH-HHHHCCCCHHHHHHHHHCC
Q ss_conf 643310000235678708997---------14---3---------889998743554211-3432136626789885126
Q gi|254780834|r 257 YLQKSIRKDVRRNSSSFIILV---------EG---Y---------MDVLSLCQAGVQNVV-SSLGTALTEYQLRLLWKLS 314 (648)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~i~v---------EG---y---------~Dvi~l~~~G~~n~v-a~~Gtalt~~~~~~l~r~~ 314 (648)
.++...+.. ...|.| =| . +-+--+.+.|.-|+| ..||| |++||+-|.+-+
T Consensus 246 h~~~Ls~~~------~~~Vs~~PNAGLPn~~G~~AeY~l~P~~~A~~l~~fa~eg~lniVGGCCGT--TP~HIraiA~aV 317 (1265)
T TIGR02082 246 HVKELSEHA------EAYVSVHPNAGLPNAFGKQAEYDLTPDELAKALKDFAEEGGLNIVGGCCGT--TPDHIRAIAEAV 317 (1265)
T ss_pred HHHHHHHHC------CEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCC--CHHHHHHHHHHH
T ss_conf 999987008------813888337888100477768755578999999999986390377426899--678999999998
Q ss_pred CE----EEEE--ECCCCCCHHHHHHHHHHHHHHHHC---CCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf 81----8996--178866225777888888777536---9730675257888888997203668899886414
Q gi|254780834|r 315 PR----IVLC--FDGDDPGLRAAYKAIDLVLCHLIP---GNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES 378 (648)
Q Consensus 315 ~~----vvl~--fDgD~AG~kAa~Ra~e~~l~~l~~---g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A 378 (648)
++ ..-- +-.- +.++.+++ +.+-.||.+- |=.+-.|...|+++|..-
T Consensus 318 k~i~Pr~~~~ta~~~~------------~~~Sgle~~~~~~~~~FvniG------ERtNv~GS~KF~~li~ae 372 (1265)
T TIGR02082 318 KDIKPRKRPETALYEP------------SRLSGLEAITIAQESNFVNIG------ERTNVAGSKKFRKLIIAE 372 (1265)
T ss_pred HCCCCCCCCCCCCCHH------------HHHHCCCCCCCCCCCCEEEEE------EEECCCCCHHHHHHHHCC
T ss_conf 1687688876556324------------676303134636635668874------300787686799985123
No 99
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=53.45 E-value=14 Score=15.82 Aligned_cols=27 Identities=11% Similarity=0.073 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf 788888899720366889988641499
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVESLP 380 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A~~ 380 (648)
-...||++++.++|.|+++-++-...|
T Consensus 340 Gnvi~p~~~i~~yg~D~lRy~L~~~~~ 366 (558)
T PRK12268 340 GWGIWVDDALERLPPDYLRYYLAANAP 366 (558)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 887798999987490777899885488
No 100
>PHA02130 hypothetical protein
Probab=53.40 E-value=4 Score=20.73 Aligned_cols=11 Identities=36% Similarity=1.340 Sum_probs=7.4
Q ss_pred CEEEECCCCCC
Q ss_conf 55753458888
Q gi|254780834|r 38 DYWACCPFHDE 48 (648)
Q Consensus 38 ~~~~~cPfh~e 48 (648)
-|||||||.++
T Consensus 43 v~w~lcp~~qd 53 (81)
T PHA02130 43 VYWDLCPYAQD 53 (81)
T ss_pred EEECCCCCHHH
T ss_conf 54135732465
No 101
>KOG2767 consensus
Probab=53.21 E-value=5.9 Score=19.20 Aligned_cols=39 Identities=13% Similarity=0.146 Sum_probs=20.3
Q ss_pred HHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCH
Q ss_conf 643310000235678708997143889998743554211
Q gi|254780834|r 257 YLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVV 295 (648)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~v 295 (648)
.|+|..-+-.+.++...++|.--.|=...+-.+|+...+
T Consensus 92 FIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~ 130 (400)
T KOG2767 92 FIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDM 130 (400)
T ss_pred HHHHHEECCCCCCCCEEEEECCCCHHHHHHHHCCCCCCC
T ss_conf 998824676889975047753662265678872885543
No 102
>pfam08209 Sgf11 Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation.
Probab=53.17 E-value=4.8 Score=20.06 Aligned_cols=72 Identities=15% Similarity=0.282 Sum_probs=43.2
Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECC------CCEEEECCCCCCCCHHHHHH
Q ss_conf 889999987488888754122210158877777557534588885878798178------97467136888878989989
Q gi|254780834|r 5 RDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDS------KGFYYCFSCHVKGDHLSFLS 78 (648)
Q Consensus 5 ~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~------~~~~~cf~c~~~gd~~~f~~ 78 (648)
+++.+.|... =|-|+|++++...+- ...+|=++=|+|-+..|+..|+-. -+.|+|--||..=-+=.|-.
T Consensus 13 ~sIy~NLL~~-~i~divsr~~~~~s~----~~~~~p~~k~y~~d~~~~lDi~g~~~~~~~s~yf~C~nC~R~v~~~rfa~ 87 (99)
T pfam08209 13 DSIYNNLLTS-MIQDIVSRETSRQKL----LKSRYPDLKSYHIDPNGSLDIYGNPKQQESSQYFHCENCGRDVSGNRFAA 87 (99)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHH----HHCCCCCCCCEEECCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHH
T ss_conf 9999999999-999999999888888----86149987666766898736679956776253667777675445552399
Q ss_pred HHC
Q ss_conf 885
Q gi|254780834|r 79 ALL 81 (648)
Q Consensus 79 ~~~ 81 (648)
++|
T Consensus 88 Hl~ 90 (99)
T pfam08209 88 HLQ 90 (99)
T ss_pred HHH
T ss_conf 999
No 103
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=52.86 E-value=14 Score=15.75 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHCCC--CC---HHHHHHH-HHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf 99999999973267--77---5789999-85068853510124422567741034554205997
Q gi|254780834|r 122 EVATDFFHHSLKNA--RD---KRLHYYL-DERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFS 179 (648)
Q Consensus 122 ~~~~~~~~~~l~~~--~~---~~a~~yl-~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~ 179 (648)
+..+.|-.++|-+. .. ..|+-|+ +.||+| ++.++=||| +.+||+.|..+|=+
T Consensus 15 E~~a~YL~~a~e~gGdDp~~~~~ALG~iArArGMt-qlA~~tGls-----REsLYkALs~~GnP 72 (91)
T TIGR02684 15 EEVAEYLAQALEDGGDDPALIAAALGVIARARGMT-QLAKKTGLS-----RESLYKALSGGGNP 72 (91)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHH-HHHHHHCCC-----HHHHHHHHCCCCCC
T ss_conf 89999999997436999889999988998651657-899982876-----78878873568895
No 104
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=52.77 E-value=14 Score=15.74 Aligned_cols=33 Identities=12% Similarity=0.045 Sum_probs=25.0
Q ss_pred CCCCHHHHHHCCCHHHHHHHHH-HCCCHHHHHHH
Q ss_conf 8888889972036688998864-14992799999
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLIV-ESLPLVDMLWK 387 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll~-~A~~l~dFl~~ 387 (648)
+..||++.+.++|+|+++-++- .|.+.-|.-|.
T Consensus 578 NvV~P~eiI~~YGADalRl~l~~~a~~~~d~~~~ 611 (888)
T PRK12300 578 NVLPLREAIEEYGADVVRLYLASTAELSQDADFR 611 (888)
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHCCCCCCCCCCC
T ss_conf 9899899997619629999999718855686457
No 105
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=52.44 E-value=14 Score=15.70 Aligned_cols=38 Identities=26% Similarity=0.354 Sum_probs=25.2
Q ss_pred CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE
Q ss_conf 14388999-87435542113432136626789885126818
Q gi|254780834|r 278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI 317 (648)
Q Consensus 278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v 317 (648)
|+-+..+. +.++|+.-||.| |-||++|+..|..++.++
T Consensus 80 ~~~~~~l~~~~~~~~~lVIGT--TGf~~e~~~~l~~~a~~v 118 (266)
T COG0289 80 EATLENLEFALEHGKPLVIGT--TGFTEEQLEKLREAAEKV 118 (266)
T ss_pred HHHHHHHHHHHHCCCCEEEEC--CCCCHHHHHHHHHHHHHC
T ss_conf 546999999997699869979--999989999999998538
No 106
>pfam01780 Ribosomal_L37ae Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
Probab=52.28 E-value=8.2 Score=17.89 Aligned_cols=26 Identities=23% Similarity=0.594 Sum_probs=18.8
Q ss_pred EECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf 53458888587879817897467136888
Q gi|254780834|r 41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV 69 (648)
Q Consensus 41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~ 69 (648)
-.|||.+-.. .--..-|+|+|=.||.
T Consensus 36 y~Cp~Cgk~~---vkR~a~GIW~C~~C~~ 61 (90)
T pfam01780 36 YTCPFCGKDA---VKRKAVGIWKCRKCGK 61 (90)
T ss_pred CCCCCCCCCE---EEEEEEEEEECCCCCC
T ss_conf 3089999887---7888888887279899
No 107
>PRK13824 replication initiation protein RepC; Provisional
Probab=52.23 E-value=12 Score=16.42 Aligned_cols=33 Identities=33% Similarity=0.648 Sum_probs=24.1
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEE-EEE
Q ss_conf 45232012100346541000016716888970778588-850
Q gi|254780834|r 181 EKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVI-AFG 221 (648)
Q Consensus 181 ~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i-~f~ 221 (648)
..|+++||+..+|..+ +-|| ..+|..|+|+ |||
T Consensus 105 a~LveaGLI~rrDSpN--GKRY------arR~~~G~I~~AyG 138 (404)
T PRK13824 105 AALVEAGLIIRRDSPN--GKRY------ARKGRGGEIEEAFG 138 (404)
T ss_pred HHHHHCCCEEECCCCC--CCCC------CEECCCCCEEEEEC
T ss_conf 9999769556123889--8871------13479997875646
No 108
>pfam11672 DUF3268 Protein of unknown function (DUF3268). This family of proteins has no known function.
Probab=52.02 E-value=14 Score=15.65 Aligned_cols=28 Identities=25% Similarity=0.577 Sum_probs=15.9
Q ss_pred CCCCCCCC---CCEEEEC-----CCCEEEECCCCCC
Q ss_conf 45888858---7879817-----8974671368888
Q gi|254780834|r 43 CPFHDEKT---PSFHCND-----SKGFYYCFSCHVK 70 (648)
Q Consensus 43 cPfh~ekt---psf~v~~-----~~~~~~cf~c~~~ 70 (648)
||+...++ ++=.|++ .+-+|.|=+|++-
T Consensus 5 CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~Ay 40 (102)
T pfam11672 5 CPYCGGKVELRPAEVVYGRGYGDWPYLYLCTGCDAY 40 (102)
T ss_pred CCCCCCEEEEEECCEECCCCCCCCCEEEECCCCCCE
T ss_conf 799999558821664057667888347888999854
No 109
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=50.82 E-value=15 Score=15.50 Aligned_cols=64 Identities=19% Similarity=0.148 Sum_probs=32.9
Q ss_pred HHHHCCCCHHHHHHHHHCCC----EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHH
Q ss_conf 34321366267898851268----1899617886622577788888877753697306752578888889
Q gi|254780834|r 296 SSLGTALTEYQLRLLWKLSP----RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDS 361 (648)
Q Consensus 296 a~~Gtalt~~~~~~l~r~~~----~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe 361 (648)
+..||.+...++..|...+. .+|+|++=|.=|++...= +. .+..+.+...|+|+.+-++.|..+
T Consensus 46 g~SG~~~~Rp~~~~ml~~~~~g~~d~vlv~~ldRl~R~~~~~-~~-~~~~l~~~~gv~~is~~e~iDt~~ 113 (140)
T cd03770 46 GFSGTTFDRPGFNRMIEDIEAGKIDIVIVKDMSRLGRNYLKV-GL-YMEILFPKKGVRFIAINDGVDSAD 113 (140)
T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCHHCCCHHHH-HH-HHHHHHHHCCCEEEEECCCCCCCC
T ss_conf 867763358889999999986997589998583433677999-99-999998767938999357877998
No 110
>TIGR01215 minE cell division topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerization, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD . MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for 'topological specificity' - that is, the ability of MinE to antagonize MinCD inhibition of Z rings at the midcell position but not at the poles..
Probab=50.60 E-value=8.7 Score=17.69 Aligned_cols=20 Identities=30% Similarity=0.571 Sum_probs=7.7
Q ss_pred HHHHHHHHHHCCHHHHHHHHCC
Q ss_conf 8899999874888887541222
Q gi|254780834|r 5 RDFIKDLLIHIPISNLIGQYVD 26 (648)
Q Consensus 5 ~~~i~~i~~~~~i~~vv~~~v~ 26 (648)
|+.++++|. ||++||..||+
T Consensus 38 P~yle~lR~--dileVi~KYv~ 57 (89)
T TIGR01215 38 PDYLEELRK--DILEVIQKYVP 57 (89)
T ss_pred CHHHHHHHH--HHHHHHHHHCC
T ss_conf 712388899--99988773113
No 111
>TIGR00464 gltX_bact glutamyl-tRNA synthetase; InterPro: IPR004527 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure . ; GO: 0000166 nucleotide binding, 0004818 glutamate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006424 glutamyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=50.48 E-value=13 Score=16.02 Aligned_cols=33 Identities=15% Similarity=0.157 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHHCCCE-------EEEEECCCCCCHHHHHHHH
Q ss_conf 3662678988512681-------8996178866225777888
Q gi|254780834|r 301 ALTEYQLRLLWKLSPR-------IVLCFDGDDPGLRAAYKAI 335 (648)
Q Consensus 301 alt~~~~~~l~r~~~~-------vvl~fDgD~AG~kAa~Ra~ 335 (648)
+=|+-||.+.+-+.-. +-|.. |+-|+|=+.|=.
T Consensus 232 sNTPkQI~iy~Alg~~~iP~f~H~p~I~--~~~gKKLSKRdg 271 (513)
T TIGR00464 232 SNTPKQILIYKALGWKRIPTFAHLPLIL--NEDGKKLSKRDG 271 (513)
T ss_pred CCCHHHHHHHHHCCCCCCCCEEEEEEEE--CCCCCEEECCCC
T ss_conf 6718999999970889888155353585--698840012064
No 112
>pfam03776 MinE Septum formation topological specificity factor MinE. The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites.
Probab=50.38 E-value=11 Score=16.73 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=12.2
Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCEE
Q ss_conf 8899999874888887541222101
Q gi|254780834|r 5 RDFIKDLLIHIPISNLIGQYVDWDR 29 (648)
Q Consensus 5 ~~~i~~i~~~~~i~~vv~~~v~l~~ 29 (648)
+++++.++. ||.+||+.||....
T Consensus 23 ~d~l~~lk~--dil~VI~KYv~id~ 45 (69)
T pfam03776 23 QDYLPQLKE--EILEVISKYVEIDP 45 (69)
T ss_pred HHHHHHHHH--HHHHHHHHHEECCH
T ss_conf 999999999--99999998763063
No 113
>pfam01641 SelR SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfo
Probab=50.37 E-value=8.3 Score=17.86 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=19.9
Q ss_pred HCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCC
Q ss_conf 22210158877777557534588885878798178974671368888
Q gi|254780834|r 24 YVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVK 70 (648)
Q Consensus 24 ~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~ 70 (648)
|--|+..|.- --...|+.+++ ++|+|+|-+||.-
T Consensus 13 y~Vlr~~gTE-----~pfsg~y~~~~--------~~G~Y~C~~C~~~ 46 (124)
T pfam01641 13 YRVLRNKGTE-----KPFTGEYDDHF--------EEGIYVCIGCGEP 46 (124)
T ss_pred HHHHHHCCCC-----CCCCCCCCCCC--------CCEEEEECCCCCC
T ss_conf 9999856888-----99877776888--------9889981689983
No 114
>TIGR03297 Ppyr-DeCO2ase phosphonopyruvate decarboxylase. This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a precursor of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the glycosylinositolphospholipids of Trypanosoma cruzi. This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (A
Probab=50.25 E-value=8.1 Score=17.97 Aligned_cols=40 Identities=25% Similarity=0.353 Sum_probs=22.0
Q ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 6818996178866225777888888777536973067525788
Q gi|254780834|r 314 SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 314 ~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G 356 (648)
.++-|+|+|||.|=.- .-..++.--.....++..+.|.+|
T Consensus 238 ~~~~Vi~lDGDGs~LM---h~Gslati~~~~~~Nl~hivlnN~ 277 (361)
T TIGR03297 238 PDQRVVCLDGDGAALM---HMGGLATIGTQGPANLIHVLFNNG 277 (361)
T ss_pred CCCEEEEEECCHHHHH---CCCHHHHHHHCCCCCEEEEEEECC
T ss_conf 8970899908689985---440687887438874799998288
No 115
>pfam06793 UPF0262 Uncharacterized protein family (UPF0262).
Probab=50.24 E-value=11 Score=16.77 Aligned_cols=50 Identities=20% Similarity=0.439 Sum_probs=26.6
Q ss_pred CEEEEECCHHHHHHHHHCCCCCCHHHHH-CCCCHHHHHHHH-HCCCEEEEEEC
Q ss_conf 7089971438899987435542113432-136626789885-12681899617
Q gi|254780834|r 272 SFIILVEGYMDVLSLCQAGVQNVVSSLG-TALTEYQLRLLW-KLSPRIVLCFD 322 (648)
Q Consensus 272 ~~~i~vEGy~Dvi~l~~~G~~n~va~~G-talt~~~~~~l~-r~~~~vvl~fD 322 (648)
++..+||.|+|+|.-...+-=.+| -|| -++-.+-..+|. |+..+|.+=+|
T Consensus 92 DYf~iCeSYy~AIk~~~p~qIEaI-DMgRRglHNEGa~lL~eRL~gki~~D~d 143 (159)
T pfam06793 92 DYFMICESYYEAIRTATPSQIEAI-DMGRRGLHNEGSELLRERLEGKIEVDFD 143 (159)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHH-HHHHHCCCHHHHHHHHHHHHCCEEECCH
T ss_conf 999999999999960999887787-7642032248899999998397341230
No 116
>pfam01194 RNA_pol_N RNA polymerases N / 8 kDa subunit.
Probab=50.08 E-value=13 Score=16.15 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=9.4
Q ss_pred EECCCCC-CCCHHHHHH
Q ss_conf 7136888-878989989
Q gi|254780834|r 63 YCFSCHV-KGDHLSFLS 78 (648)
Q Consensus 63 ~cf~c~~-~gd~~~f~~ 78 (648)
.||+||+ =||.+..+.
T Consensus 6 RCftCGkvi~~k~~~y~ 22 (60)
T pfam01194 6 RCFTCGKVIGDKWEEYL 22 (60)
T ss_pred CCCCCCCCHHHHHHHHH
T ss_conf 65789888699899999
No 117
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=50.03 E-value=12 Score=16.31 Aligned_cols=109 Identities=10% Similarity=0.099 Sum_probs=55.9
Q ss_pred CCHHHHHHHHHHHHCCCCCCCCCCEEEEECCH-HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC--CCEEEEEECCCC
Q ss_conf 08178888643310000235678708997143-889998743554211343213662678988512--681899617886
Q gi|254780834|r 249 YNFFGALNYLQKSIRKDVRRNSSSFIILVEGY-MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL--SPRIVLCFDGDD 325 (648)
Q Consensus 249 y~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy-~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~--~~~vvl~fDgD~ 325 (648)
.+.|...++..-..++....+-.+.+-+++|- |+.+.- .-+.-.|+.= -=+....+..|..- .-++-+++||.+
T Consensus 163 ~avDIS~~AL~vAk~Na~~~~v~~ri~fi~sdwfe~l~~--~kFDlIVSNP-PYI~~~e~~~L~~eV~~yEP~lAL~gge 239 (503)
T PRK01544 163 IATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFENIGK--QKFDFIVSNP-PYISHSEKSEMAIETINYEPSIALFAEE 239 (503)
T ss_pred EEEECCHHHHHHHHHHHHHCCCCCCEEEEECCCHHCCCC--CCCCEEEECC-CCCCHHHHHHCCHHHHCCCCHHHHCCCC
T ss_conf 999898999999999999808820179996553101588--8724798389-9887566665276653169378864887
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf 62257778888887775369730675257888888997
Q gi|254780834|r 326 PGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI 363 (648)
Q Consensus 326 AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i 363 (648)
-|..+-.+.++.+..+|+++= .+.+--|.|=.+-|
T Consensus 240 DGL~~Yr~Ia~~a~~~Lkp~G---~l~lEIGy~Q~e~V 274 (503)
T PRK01544 240 DGLQAYFIIAENAKQFLKPNG---KIILEIGFKQAEAV 274 (503)
T ss_pred CCHHHHHHHHHHHHHHCCCCC---EEEEEECCCHHHHH
T ss_conf 628999999998898528898---89999787868999
No 118
>pfam02631 RecX RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.
Probab=49.68 E-value=16 Score=15.36 Aligned_cols=50 Identities=18% Similarity=0.325 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 8899998443002379988999999999997538899989999885111289
Q gi|254780834|r 496 AILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFG 547 (648)
Q Consensus 496 ~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~~l~~~L~~~~l~ 547 (648)
+.+..+++.+....+.+.. ......+..........+..+...|...++.
T Consensus 9 ~~I~~vi~~L~~~gyldD~--rya~~~i~~~~~~~~~G~~~I~~~L~~kGI~ 58 (121)
T pfam02631 9 EVIEAVLERLKELGYLDDE--RFAESFVRSRLRTKGKGPRRIRQELRQKGVD 58 (121)
T ss_pred HHHHHHHHHHHHCCCCCHH--HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 9999999999996997999--9999999999882681199999999995999
No 119
>KOG0183 consensus
Probab=49.68 E-value=15 Score=15.51 Aligned_cols=69 Identities=26% Similarity=0.357 Sum_probs=32.3
Q ss_pred CHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCC-CHHHHHCCCCHHHHHHHHHCCCEEEEEECC
Q ss_conf 1011081788886433100002356787089971438899987435542-113432136626789885126818996178
Q gi|254780834|r 245 GKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQN-VVSSLGTALTEYQLRLLWKLSPRIVLCFDG 323 (648)
Q Consensus 245 ~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n-~va~~Gtalt~~~~~~l~r~~~~vvl~fDg 323 (648)
--+|+..-.|..+.+|. ..++-|-|- |+|. .|++- .|+-|- -+.-++.|.-+-++|++.|
T Consensus 14 DGhL~QVEYAqEAvrkG----------staVgvrg~-~~vv---lgvEkkSv~~Lq---~~r~~rkI~~ld~hV~maf-- 74 (249)
T KOG0183 14 DGHLFQVEYAQEAVRKG----------STAVGVRGN-NCVV---LGVEKKSVPKLQ---DERTVRKISMLDDHVVMAF-- 74 (249)
T ss_pred CCCEEEEHHHHHHHHCC----------CEEEEECCC-CEEE---EEEEECCHHHHH---HHHHHHHHEEECCEEEEEE--
T ss_conf 98777327589998627----------637986068-5599---998405526652---1110322101045146773--
Q ss_pred CCCCHHHHHHH
Q ss_conf 86622577788
Q gi|254780834|r 324 DDPGLRAAYKA 334 (648)
Q Consensus 324 D~AG~kAa~Ra 334 (648)
||.+|-.|.
T Consensus 75 --aGl~aDAri 83 (249)
T KOG0183 75 --AGLTADARI 83 (249)
T ss_pred --CCCCCCCEE
T ss_conf --378864001
No 120
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=49.36 E-value=14 Score=15.66 Aligned_cols=30 Identities=27% Similarity=0.309 Sum_probs=14.5
Q ss_pred EECCCCC-CCCHHHHHHHH--CCCCHHHHHHHH
Q ss_conf 7136888-87898998988--599979999999
Q gi|254780834|r 63 YCFSCHV-KGDHLSFLSAL--LGCSFIESVQRL 92 (648)
Q Consensus 63 ~cf~c~~-~gd~~~f~~~~--~~~~f~ea~~~l 92 (648)
.||+||+ =|+.+.=+.+. ++-+-.+|+-.|
T Consensus 6 RCFsCGkvi~~~w~~y~~rv~~ge~p~~vLDdL 38 (63)
T COG1644 6 RCFSCGKVIGHKWEEYKRRVEEGEDPGEVLDDL 38 (63)
T ss_pred EEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 752388787888999999998489888888870
No 121
>pfam07057 TraI DNA helicase TraI. This family represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer.
Probab=49.08 E-value=14 Score=15.76 Aligned_cols=22 Identities=14% Similarity=0.190 Sum_probs=16.9
Q ss_pred EEEEEEEECCCCEEEEECCCCC
Q ss_conf 1688897077858885010014
Q gi|254780834|r 205 RLIFPIRSSRGQVIAFGGRTLS 226 (648)
Q Consensus 205 Ri~fPi~~~~g~~i~f~gR~l~ 226 (648)
.++||++|..|+.-|.-=.-|.
T Consensus 93 ~vAlPv~D~NGK~AG~~L~~l~ 114 (126)
T pfam07057 93 HVALPVWDRNGKSAGALLVELT 114 (126)
T ss_pred CEECEEECCCCCEEEEEEEEEE
T ss_conf 3402105478843005776545
No 122
>pfam05129 Elf1 Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Elf1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae.
Probab=49.05 E-value=11 Score=16.83 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=21.3
Q ss_pred EECCCCC-CCCCCEEEECC--CCEEEECCCCCC
Q ss_conf 5345888-85878798178--974671368888
Q gi|254780834|r 41 ACCPFHD-EKTPSFHCNDS--KGFYYCFSCHVK 70 (648)
Q Consensus 41 ~~cPfh~-ektpsf~v~~~--~~~~~cf~c~~~ 70 (648)
=-|||.+ |++=+..+.-. .+.-+|-.||..
T Consensus 18 F~CpfC~h~~sv~vkidk~~~~g~l~C~vCg~~ 50 (74)
T pfam05129 18 FDCPFCNHKKSVSVKIDKKTGIAKLHCRVCGLS 50 (74)
T ss_pred EECCCCCCCCEEEEEEECCCCEEEEEEECCCCE
T ss_conf 747867998759999981479899996217885
No 123
>KOG1422 consensus
Probab=48.64 E-value=6.7 Score=18.73 Aligned_cols=53 Identities=15% Similarity=0.004 Sum_probs=37.7
Q ss_pred CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 8708997143889998743554211343213662678988512681899617886
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDD 325 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~ 325 (648)
-|.+..+.-+| +.|+..|.+.-|-+.-+.-+++-++.+.--+.=+++.||++.
T Consensus 18 ~Gdcpf~qr~~--m~L~~k~~~f~vttVd~~~kp~~f~~~sp~~~~P~l~~d~~~ 70 (221)
T KOG1422 18 LGDCPFCQRLF--MTLELKGVPFKVTTVDLSRKPEWFLDISPGGKPPVLKFDEKW 70 (221)
T ss_pred CCCCHHHHHHH--HHHHHCCCCCEEEEEECCCCCHHHHHHCCCCCCCEEEECCCE
T ss_conf 78974478999--999981887348986168896999952888899869758724
No 124
>TIGR03364 HpnW_proposed FAD dependent oxidoreductase TIGR03364. This clade of FAD dependent oxidoreductases (members of the pfam01266 family) is syntenically associated with a family of proposed phosphonatase-like enzymes (TIGR03351) and is also found (less frequently) in association with phosphonate transporter components. A likely role for this enzyme involves the oxidative deamination of an aminophosphonate differring slightly from 2-aminoethylphosphonate, possibly 1-hydroxy-2-aminoethylphosphonate (see the comments for TIGR03351). Many members of the larger FAD dependent oxidoreductase family act as amino acid oxidative deaminases.
Probab=48.63 E-value=16 Score=15.23 Aligned_cols=14 Identities=43% Similarity=0.325 Sum_probs=7.0
Q ss_pred HHHHHHHHHHCCCC
Q ss_conf 99999999818858
Q gi|254780834|r 87 ESVQRLAAIAGVPL 100 (648)
Q Consensus 87 ea~~~la~~~gi~~ 100 (648)
+..+.|++..|+.+
T Consensus 65 ~~~~~l~~~~~~~~ 78 (365)
T TIGR03364 65 EIWLELAAKAGIWV 78 (365)
T ss_pred HHHHHHHHHCCCCE
T ss_conf 99999887349897
No 125
>KOG0435 consensus
Probab=48.49 E-value=16 Score=15.22 Aligned_cols=107 Identities=16% Similarity=0.187 Sum_probs=56.5
Q ss_pred CCHHHHHHH-HHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC---
Q ss_conf 143889998-7435542113432136626789885126818996178866225777888888777536973067525---
Q gi|254780834|r 278 EGYMDVLSL-CQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL--- 353 (648)
Q Consensus 278 EGy~Dvi~l-~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L--- 353 (648)
|-+.++|.- .-.|-...++..|-=|.++-+..+.---+.+|+-=| .++.++.-
T Consensus 562 EPF~~Li~QGmV~G~tf~~~~sG~yl~~~ev~~~nd~~~~~vlk~~-----------------------~e~~v~t~eKM 618 (876)
T KOG0435 562 EPFTKLITQGMVRGKTFRTKESGKYLGPEEVQQVNDHQNKFVLKND-----------------------KEVVVVTYEKM 618 (876)
T ss_pred CCHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHCCCCCEEEECCC-----------------------CCCEEEEHHHH
T ss_conf 7488887510003417862777762787776663477663575379-----------------------95035448873
Q ss_pred ----CCCCCHHHHHHCCCHHHHHHHHH-HCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf ----78888889972036688998864-14992799999998530233145799999999988541
Q gi|254780834|r 354 ----SRGEDPDSFIRCYGKTAFEKLIV-ESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINH 414 (648)
Q Consensus 354 ----P~G~DPDe~ir~~G~eaf~~ll~-~A~~l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~ 414 (648)
-+|.||++.+.++|.|..+.++= .|.+--.-.|+ -+...|.-+...++-.++..
T Consensus 619 SKSK~NGVdP~~~v~~yG~D~tRl~ilf~ap~~~~~nW~-------es~i~Gi~rwl~riw~l~~~ 677 (876)
T KOG0435 619 SKSKHNGVDPADVVLEYGVDTTRLYILFAAPPRDPINWN-------ESAIPGIKRWLQRIWALVSQ 677 (876)
T ss_pred HHCCCCCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC-------CCCCHHHHHHHHHHHHHHHH
T ss_conf 202357989899998848317789998617865666666-------33245499999999999887
No 126
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=48.13 E-value=16 Score=15.17 Aligned_cols=32 Identities=6% Similarity=0.285 Sum_probs=15.6
Q ss_pred CCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHH
Q ss_conf 88888997203668899886-414992799999
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWK 387 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~ 387 (648)
|.=|+|+++=.-+|++..++ .+.+|.=.+-|+
T Consensus 293 git~~ewL~~~~PEsl~rfm~~~pkpaK~l~fd 325 (513)
T PRK00750 293 GISIEDWLEYAPPESLARFMYARPKPAKRLYFD 325 (513)
T ss_pred CCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCHH
T ss_conf 238999997559999999997188988401565
No 127
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.49 E-value=17 Score=15.10 Aligned_cols=81 Identities=26% Similarity=0.267 Sum_probs=53.2
Q ss_pred CCCEEEEECCHHHHHHHHHCCCCCC--------HHHHHCCCCHHHH--H-HHHHC---CC-EEEEEECCCCCCHHHHHHH
Q ss_conf 7870899714388999874355421--------1343213662678--9-88512---68-1899617886622577788
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQAGVQNV--------VSSLGTALTEYQL--R-LLWKL---SP-RIVLCFDGDDPGLRAAYKA 334 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~G~~n~--------va~~Gtalt~~~~--~-~l~r~---~~-~vvl~fDgD~AG~kAa~Ra 334 (648)
....+.|||-.-||+++-+.|.-+. ++|+ .-..++++ . ++.|. .. +|||+.+.--.|+.-|.=.
T Consensus 78 d~~~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl-~gigpe~l~i~~L~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI 156 (198)
T COG0353 78 DKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPL-DGIGPEDLNIDELLQRLAEGSIKEVILATNPTVEGEATALYI 156 (198)
T ss_pred CCCEEEEECCHHHHHHHHHHCCCCEEEEEECCCCCCC-CCCCCCCCCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHH
T ss_conf 8866899866499999997452572788845733734-589910126799999984699755999658986436899999
Q ss_pred HHHHHHHHHCCCCEEEEECCCC
Q ss_conf 8888777536973067525788
Q gi|254780834|r 335 IDLVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 335 ~e~~l~~l~~g~~v~vv~LP~G 356 (648)
.+++. +..++|-.|-.|
T Consensus 157 ~~~l~-----~~~ikvtRlA~G 173 (198)
T COG0353 157 ARLLK-----PLGLKVTRLAQG 173 (198)
T ss_pred HHHHH-----HCCCEEEEEEEC
T ss_conf 99975-----359717877605
No 128
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=47.05 E-value=11 Score=16.67 Aligned_cols=22 Identities=23% Similarity=0.378 Sum_probs=13.7
Q ss_pred CCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf 789746713688887898998988
Q gi|254780834|r 57 DSKGFYYCFSCHVKGDHLSFLSAL 80 (648)
Q Consensus 57 ~~~~~~~cf~c~~~gd~~~f~~~~ 80 (648)
.+.|+|+|-+||.- .|+--.++
T Consensus 29 ~~~G~Y~C~~C~~~--LF~S~~Kf 50 (119)
T PRK05508 29 YEKGTYICRQCGAP--LYKSEDKF 50 (119)
T ss_pred CCCEEEEECCCCCC--CCCCCCCC
T ss_conf 88859993799960--02743223
No 129
>PRK12446 N-acetylglucosaminyl transferase; Reviewed
Probab=46.90 E-value=17 Score=15.02 Aligned_cols=66 Identities=15% Similarity=0.235 Sum_probs=50.7
Q ss_pred HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf 01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV 318 (648)
Q Consensus 246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv 318 (648)
++++++.++...+++.++ +-||-+=||.-+ ++.+-.+++-++ |..|.| -+++.++++.|.
T Consensus 75 ~l~~~~~~s~~il~~~kP--------d~Vig~GGY~S~P~~lAA~ll~iP~~ihEqNav~G~a-----Nr~l~~~a~~i~ 141 (352)
T PRK12446 75 LVMKGVMDAYVRIRKLKP--------DVIFSKGGFVSVPVVIGGWLNRVPVLLHESDMTPGLA-----NKIALRFASKIF 141 (352)
T ss_pred HHHHHHHHHHHHHHHCCC--------CEEEECCCHHHHHHHHHHHHCCCCEEEECCCHHHHHH-----HHHHHHHHCCEE
T ss_conf 999999999999996399--------9999749877799999999859996998874677789-----999998707128
Q ss_pred EEECCC
Q ss_conf 961788
Q gi|254780834|r 319 LCFDGD 324 (648)
Q Consensus 319 l~fDgD 324 (648)
++|+..
T Consensus 142 ~~f~~~ 147 (352)
T PRK12446 142 VTFEEA 147 (352)
T ss_pred ECCHHH
T ss_conf 996245
No 130
>KOG0856 consensus
Probab=46.82 E-value=12 Score=16.46 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=4.5
Q ss_pred CCCEEEECCCC
Q ss_conf 89746713688
Q gi|254780834|r 58 SKGFYYCFSCH 68 (648)
Q Consensus 58 ~~~~~~cf~c~ 68 (648)
+.|+|+|-+||
T Consensus 51 e~GvY~C~~C~ 61 (146)
T KOG0856 51 EEGVYVCAGCG 61 (146)
T ss_pred CCCEEEEEECC
T ss_conf 88448875059
No 131
>COG1422 Predicted membrane protein [Function unknown]
Probab=46.78 E-value=17 Score=15.01 Aligned_cols=37 Identities=19% Similarity=0.303 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 5899999999999999872412798999999999999
Q gi|254780834|r 587 RFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHE 623 (648)
Q Consensus 587 r~~~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~e 623 (648)
+...++++.++.+++..++..++|..+.+.+.++.+|
T Consensus 73 km~~~qk~m~efq~e~~eA~~~~d~~~lkkLq~~qme 109 (201)
T COG1422 73 KMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQME 109 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 9999999999999999999980889999999999999
No 132
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=46.70 E-value=16 Score=15.34 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=9.5
Q ss_pred EECCCCC-CCCHHHHH
Q ss_conf 7136888-87898998
Q gi|254780834|r 63 YCFSCHV-KGDHLSFL 77 (648)
Q Consensus 63 ~cf~c~~-~gd~~~f~ 77 (648)
.||+||+ =||.+..+
T Consensus 6 RCFTCGkvi~~k~~~y 21 (63)
T PRK04016 6 RCFTCGKVIGELWEEF 21 (63)
T ss_pred CCCCCCCCHHHHHHHH
T ss_conf 5478978789889999
No 133
>pfam05991 DUF901 Protein of unknown function (DUF901). This family consists of several hypothetical bacterial proteins as well as some uncharacterized sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=46.36 E-value=17 Score=14.96 Aligned_cols=43 Identities=21% Similarity=0.246 Sum_probs=29.4
Q ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf 8189961788662257778888887775369730675257888888997203
Q gi|254780834|r 315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY 366 (648)
Q Consensus 315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~ 366 (648)
-+|++.|||....-..... ..--.+.|++=++|+.-|+||...
T Consensus 44 ~~v~vVFDa~~~~~~~~~~---------~~~~~i~vvfT~~~etAD~~IEr~ 86 (166)
T pfam05991 44 YRVIVVFDAHYVPGSEEEY---------EKYGGIEVVFTKEGETADSYIEKL 86 (166)
T ss_pred CEEEEEEECCCCCCCCCCE---------EECCCEEEEECCCCCCHHHHHHHH
T ss_conf 6799998566489998743---------450988999888999878999999
No 134
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=46.14 E-value=11 Score=16.64 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=18.1
Q ss_pred EECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf 53458888587879817897467136888
Q gi|254780834|r 41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV 69 (648)
Q Consensus 41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~ 69 (648)
-.|||.+-. ++ --..-|+|+|=.||.
T Consensus 37 y~Cp~Cgk~--~v-kR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 37 YFCSFCGKH--AT-KRKAVGIWRCKGCSK 62 (90)
T ss_pred CCCCCCCCC--EE-EEEEEEEEECCCCCC
T ss_conf 628999997--66-888888887689999
No 135
>PRK06667 motB flagellar motor protein MotB; Validated
Probab=46.06 E-value=15 Score=15.42 Aligned_cols=23 Identities=17% Similarity=0.351 Sum_probs=15.0
Q ss_pred CCEEEEECCHHHHHHHHHCC-CCC
Q ss_conf 87089971438899987435-542
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAG-VQN 293 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G-~~n 293 (648)
...-|.||||+|-....-.+ +++
T Consensus 160 ~~~~I~VeGHTD~~pi~~~~~~~s 183 (254)
T PRK06667 160 AGYNFRIEGHTDNVDVNPEGAWKS 183 (254)
T ss_pred CCCEEEEEECCCCCCCCCCCCCCC
T ss_conf 574289994378776687888886
No 136
>PRK06163 hypothetical protein; Provisional
Probab=45.95 E-value=11 Score=16.79 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=29.9
Q ss_pred CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 1134321366267898851268189961788662257778888887775369730675257888
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE 357 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~ 357 (648)
.|.+||-|..-.---.|.+ .++-|+|+|||.+=.- .-.+++.--.....++.++.|.+|.
T Consensus 55 ~vGsMG~as~iaLG~Ala~-p~k~Vi~iDGDGs~LM---~mGsLaTi~~~~p~Nl~hIvlnN~~ 114 (202)
T PRK06163 55 MLGSMGLAFPIALGVALAQ-PKRRVIALEGDGSLLM---QLGALGTIAALAPKNLTIIVMDNGV 114 (202)
T ss_pred EECCCCCHHHHHHHHHHHC-CCCEEEEEECCHHHHH---CHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf 7522101889999999878-9982899947668873---5688999997178856999986964
No 137
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=45.76 E-value=17 Score=14.89 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=26.6
Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf 99617886622577788888877753697-30675257888888997203668899886414
Q gi|254780834|r 318 VLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRGEDPDSFIRCYGKTAFEKLIVES 378 (648)
Q Consensus 318 vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A 378 (648)
.+++|..+||..|+...+ +.|. .+-++.- ++++..-..-.++|.+.++++
T Consensus 95 ~V~~Dn~~~~~~a~~~L~-------~~G~~~i~~i~~----~~~~~~~~~R~~G~~~al~~~ 145 (268)
T cd01575 95 AVGFSHAEAGRAMARHLL-------ARGYRRIGFLGA----RMDDTRAQQRLEGFRAALRAA 145 (268)
T ss_pred EEECCHHHHHHHHHHHHH-------HCCCCEEEEECC----CCCCHHHHHHHHHHHHHHHHC
T ss_conf 897388999999999999-------749976999848----988736999999999999976
No 138
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=45.22 E-value=14 Score=15.91 Aligned_cols=25 Identities=20% Similarity=0.592 Sum_probs=18.0
Q ss_pred EECCCCCCCCCCEEEE-CCCCEEEECCCCC
Q ss_conf 5345888858787981-7897467136888
Q gi|254780834|r 41 ACCPFHDEKTPSFHCN-DSKGFYYCFSCHV 69 (648)
Q Consensus 41 ~~cPfh~ektpsf~v~-~~~~~~~cf~c~~ 69 (648)
-.|||.+-. .|. ..-|+|+|=.||.
T Consensus 37 y~Cp~Cg~~----~vkR~a~GIW~C~kC~~ 62 (90)
T PRK03976 37 HVCPVCGRP----KVKRIATGIWQCRKCGA 62 (90)
T ss_pred CCCCCCCCC----EEEEEEEEEEECCCCCC
T ss_conf 649989997----45888888888899998
No 139
>cd07048 BMC_PduB_repeat2 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 2. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduB).
Probab=44.97 E-value=18 Score=14.79 Aligned_cols=28 Identities=32% Similarity=0.490 Sum_probs=20.8
Q ss_pred HHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf 432136626789885126818996178866225777888
Q gi|254780834|r 297 SLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI 335 (648)
Q Consensus 297 ~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~ 335 (648)
.-||++| ++|++++-||..-.+.++.+.
T Consensus 35 ~~gts~s-----------NEvi~~isGDsgAVrqAv~aa 62 (70)
T cd07048 35 SGGTSFS-----------NEVILTISGDSGAVRQALIAA 62 (70)
T ss_pred CCCCCCC-----------CEEEEEEECCHHHHHHHHHHH
T ss_conf 9986204-----------359999935779999999999
No 140
>cd01320 ADA Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in the purine pathway. Low, as well as high levels of ADA activity have been linked to several diseases.
Probab=44.86 E-value=18 Score=14.78 Aligned_cols=28 Identities=32% Similarity=0.396 Sum_probs=22.4
Q ss_pred HHCCCCHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 8859997999999999818858776820
Q gi|254780834|r 79 ALLGCSFIESVQRLAAIAGVPLPVVDPK 106 (648)
Q Consensus 79 ~~~~~~f~ea~~~la~~~gi~~~~~~~~ 106 (648)
+.+|-=-++.+..||.+.|+++|..+..
T Consensus 10 HL~Gsi~~~tl~~la~~~~~~lp~~~~~ 37 (325)
T cd01320 10 HLDGSLRPETILELAKKNGITLPASDVE 37 (325)
T ss_pred CCCCCCCHHHHHHHHHHCCCCCCCCCHH
T ss_conf 7778889999999999719999988877
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.83 E-value=18 Score=14.78 Aligned_cols=97 Identities=16% Similarity=0.252 Sum_probs=44.6
Q ss_pred CCCCCHHHHHCCCCHHHHHHHHHCCC----EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHC
Q ss_conf 55421134321366267898851268----18996178866225777888888777536973067525788888899720
Q gi|254780834|r 290 GVQNVVSSLGTALTEYQLRLLWKLSP----RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365 (648)
Q Consensus 290 G~~n~va~~Gtalt~~~~~~l~r~~~----~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~ 365 (648)
=|..-||.+--.|++.+-...|+-+. +||+ |- |++ +.+|+-. +..+.+-+-.|+ +|-+.
T Consensus 268 rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVI-------Gt----RSA-lF~Pf~~----LGLIIvDEEHD~-sYKq~ 330 (730)
T COG1198 268 RFGAKVAVLHSGLSPGERYRVWRRARRGEARVVI-------GT----RSA-LFLPFKN----LGLIIVDEEHDS-SYKQE 330 (730)
T ss_pred HHCCCHHHHCCCCCHHHHHHHHHHHHCCCCEEEE-------EE----CHH-HCCCHHH----CCEEEEECCCCC-CCCCC
T ss_conf 8678745314657927899999998559715999-------71----223-3072312----576997024564-32477
Q ss_pred CCH--------------HHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 366--------------88998864149927999999985302331457999
Q gi|254780834|r 366 YGK--------------TAFEKLIVESLPLVDMLWKRETENRSFNTPDERAE 403 (648)
Q Consensus 366 ~G~--------------eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka~ 403 (648)
.++ +...-.|.+|+|.+|-+.......+.+.....|+.
T Consensus 331 ~~prYhARdvA~~Ra~~~~~pvvLgSATPSLES~~~~~~g~y~~~~L~~R~~ 382 (730)
T COG1198 331 DGPRYHARDVAVLRAKKENAPVVLGSATPSLESYANAESGKYKLLRLTNRAG 382 (730)
T ss_pred CCCCCCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCCEEEEECCCCCC
T ss_conf 7777678999999988609988982688778999866538558997035455
No 142
>cd00764 Eukaryotic_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include eukaryotic ATP-dependent phosphofructokinases. These have evolved from the bacterial PFKs by gene duplication and fusion events and exhibit complex allosteric behavior.
Probab=44.74 E-value=18 Score=14.77 Aligned_cols=60 Identities=17% Similarity=0.191 Sum_probs=35.6
Q ss_pred CCCCCCHHHHHCCCCHHHHHHHHHC------------CCEE-EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 3554211343213662678988512------------6818-9961788662257778888887775369730675
Q gi|254780834|r 289 AGVQNVVSSLGTALTEYQLRLLWKL------------SPRI-VLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFV 351 (648)
Q Consensus 289 ~G~~n~va~~Gtalt~~~~~~l~r~------------~~~v-vl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv 351 (648)
.-|..++..=|.+|.+.. ...+.. .-+| ||.--||++|.|||.||+=.. -+..|.+|.-+
T Consensus 353 k~f~~a~~lr~~~F~~~~-~~~~~~~~~~~~~~~~~~~~rIaIlt~GgdapGMNAAiRA~Vr~--~~~~G~~v~gI 425 (762)
T cd00764 353 KRFDEAAALRGKSFDKNW-NLYKLLAIELPQPLPEKTNLNIAIVNVGAPAAGMNAAVRSAVRY--GLAHGHRPYAI 425 (762)
T ss_pred CCHHHHHHHCCHHHHHHH-HHHHHHCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHH--HHHCCCEEEEE
T ss_conf 278999974377789999-99998603477778866770699985688961477999999999--99889999999
No 143
>pfam00782 DSPc Dual specificity phosphatase, catalytic domain. Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
Probab=44.55 E-value=18 Score=14.74 Aligned_cols=40 Identities=10% Similarity=0.068 Sum_probs=26.6
Q ss_pred EEEECC-CCCCCCH-HHHHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf 467136-8888789-899898859997999999999818858
Q gi|254780834|r 61 FYYCFS-CHVKGDH-LSFLSALLGCSFIESVQRLAAIAGVPL 100 (648)
Q Consensus 61 ~~~cf~-c~~~gd~-~~f~~~~~~~~f~ea~~~la~~~gi~~ 100 (648)
+-||.. -+.++-+ +-++|.++++++.+|+..+-.+-.+-.
T Consensus 75 LVHC~~G~sRS~~i~~aYLm~~~~~~~~~A~~~v~~~R~~~~ 116 (131)
T pfam00782 75 LVHCQAGISRSATLIIAYLMKTRNLSLNEAYSFVKERRPIIS 116 (131)
T ss_pred EEECCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCC
T ss_conf 999999874019999999999829999999999999899889
No 144
>pfam08856 DUF1826 Protein of unknown function (DUF1826). These proteins are functionally uncharacterized.
Probab=44.38 E-value=12 Score=16.32 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=14.4
Q ss_pred CCCCEEEEECCCCCCCCCCEECC-CCCC
Q ss_conf 77858885010014655300103-8767
Q gi|254780834|r 213 SRGQVIAFGGRTLSKGESVKYLN-SPET 239 (648)
Q Consensus 213 ~~g~~i~f~gR~l~~~~~~KYlN-SpeT 239 (648)
..|.|+=|-|-....++..--+- ||..
T Consensus 157 ~~G~vallKG~~W~~~~~~glvHRSP~~ 184 (196)
T pfam08856 157 PTGDVALLKGELWPGNEGAGLVHRSPPI 184 (196)
T ss_pred CCCCEEEEECCCCCCCCCCCEEECCCCC
T ss_conf 8998899867857888999817579898
No 145
>TIGR00665 DnaB replicative DNA helicase; InterPro: IPR007692 This family includes the replicative DNA helicases, helicase DnaB, which exhibit DNA-dependent ATPase activity. Helicase DnaB is a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of more than 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. Replication protein, GP12 from Bacteriophage P22 also belongs to this family .; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication.
Probab=44.18 E-value=18 Score=14.70 Aligned_cols=27 Identities=22% Similarity=0.165 Sum_probs=15.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 331457999999999885417998999
Q gi|254780834|r 395 FNTPDERAELEIHLKNCINHIKDQKLR 421 (648)
Q Consensus 395 l~spe~ka~~~~~l~~~I~~I~d~~~R 421 (648)
.+-.++.+...+.+..+...+.-|++.
T Consensus 354 ~~r~~~~~~i~~~lk~~a~e~~~P~~a 380 (465)
T TIGR00665 354 DNRHQEVAEISRSLKALARELNVPVIA 380 (465)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf 404688999989999888774141665
No 146
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=44.10 E-value=18 Score=14.69 Aligned_cols=19 Identities=11% Similarity=0.067 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHCCCCCCH
Q ss_conf 9999999999753889998
Q gi|254780834|r 516 QKLWSFLFSDFVEQKYFLP 534 (648)
Q Consensus 516 ~~L~~~i~~~~~~~~~~~~ 534 (648)
..+...|++.+......+.
T Consensus 40 ~~lk~eil~VI~KYv~Id~ 58 (85)
T PRK00296 40 PQLRKEILEVICKYVQIDP 58 (85)
T ss_pred HHHHHHHHHHHHHHEEECH
T ss_conf 9999999999987603662
No 147
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=43.90 E-value=17 Score=15.05 Aligned_cols=17 Identities=12% Similarity=0.090 Sum_probs=7.9
Q ss_pred CCCHHHHHHCCCHHHHHH
Q ss_conf 888889972036688998
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEK 373 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~ 373 (648)
...=|+|...+ ++.|.+
T Consensus 421 ~~~~d~yy~~~-p~~~~~ 437 (851)
T COG1205 421 SDPLDSYYLRH-PEELLE 437 (851)
T ss_pred CCCCCHHHHHC-CHHHHH
T ss_conf 88400445508-375654
No 148
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=43.89 E-value=17 Score=14.90 Aligned_cols=53 Identities=8% Similarity=0.061 Sum_probs=28.1
Q ss_pred HHCCCCHHHHHHHHHHHH---CCCCCCCCCCH-----HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 885999799999999981---88587768203-----677788999999999999999997
Q gi|254780834|r 79 ALLGCSFIESVQRLAAIA---GVPLPVVDPKI-----EKKEKIQTDLIRLIEVATDFFHHS 131 (648)
Q Consensus 79 ~~~~~~f~ea~~~la~~~---gi~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~ 131 (648)
+.-+++-||.|+.+-..| |-++-+.++.. ..........++++..+++.-+..
T Consensus 45 E~LnlT~Pd~I~~IH~aY~eAGADiIeTNTFgat~i~lady~led~v~~in~~aa~iAR~a 105 (311)
T COG0646 45 ELLNLTKPDVIEAIHRAYIEAGADIIETNTFGATTIKLADYGLEDKVYEINQKAARIARRA 105 (311)
T ss_pred HHHHCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_conf 7875479499999999999646767873477865365755073889999999999999999
No 149
>KOG4717 consensus
Probab=43.54 E-value=19 Score=14.62 Aligned_cols=26 Identities=12% Similarity=0.241 Sum_probs=22.0
Q ss_pred ECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf 17897467136888878989989885
Q gi|254780834|r 56 NDSKGFYYCFSCHVKGDHLSFLSALL 81 (648)
Q Consensus 56 ~~~~~~~~cf~c~~~gd~~~f~~~~~ 81 (648)
..+..+|--.--|.+||.|+|+|++|
T Consensus 87 DTQTKlyLiLELGD~GDl~DyImKHe 112 (864)
T KOG4717 87 DTQTKLYLILELGDGGDLFDYIMKHE 112 (864)
T ss_pred CCCCEEEEEEEECCCCCHHHHHHHHC
T ss_conf 25533899998167730899998610
No 150
>KOG3497 consensus
Probab=42.89 E-value=11 Score=16.66 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=15.1
Q ss_pred EEECCCCC-CCCHHHHHHHHCCCCHH
Q ss_conf 67136888-87898998988599979
Q gi|254780834|r 62 YYCFSCHV-KGDHLSFLSALLGCSFI 86 (648)
Q Consensus 62 ~~cf~c~~-~gd~~~f~~~~~~~~f~ 86 (648)
-.||.||+ -||-+.-+.+.-+.++.
T Consensus 5 iRCFtCGKvig~KWe~Yl~lLq~d~~ 30 (69)
T KOG3497 5 IRCFTCGKVIGDKWETYLELLQADYT 30 (69)
T ss_pred EEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf 57521356230108999999987520
No 151
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=42.62 E-value=19 Score=14.51 Aligned_cols=37 Identities=8% Similarity=0.060 Sum_probs=20.5
Q ss_pred EEEEC-CCCCCC-CHHHHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf 46713-688887-89899898859997999999999818
Q gi|254780834|r 61 FYYCF-SCHVKG-DHLSFLSALLGCSFIESVQRLAAIAG 97 (648)
Q Consensus 61 ~~~cf-~c~~~g-d~~~f~~~~~~~~f~ea~~~la~~~g 97 (648)
+-||. |.+.++ =|+.|+|.+.++++.+|++.+..+-.
T Consensus 82 LVHC~~G~sRS~~vv~aYLm~~~~~~~~~A~~~v~~~Rp 120 (138)
T smart00195 82 LVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKDRRP 120 (138)
T ss_pred EEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCC
T ss_conf 999998775549999999999839999999999999799
No 152
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit; InterPro: IPR005740 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=42.54 E-value=19 Score=14.50 Aligned_cols=13 Identities=23% Similarity=0.082 Sum_probs=5.4
Q ss_pred HCCCC-EEEEECCC
Q ss_conf 36973-06752578
Q gi|254780834|r 343 IPGNR-VNFVLLSR 355 (648)
Q Consensus 343 ~~g~~-v~vv~LP~ 355 (648)
.+|++ |=-|.+|+
T Consensus 322 ReGL~avi~v~~PE 335 (655)
T TIGR01058 322 REGLSAVISVRIPE 335 (655)
T ss_pred HHHHHHEEEEECCH
T ss_conf 53202115532575
No 153
>cd03371 TPP_PpyrDC Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors.
Probab=42.47 E-value=14 Score=15.70 Aligned_cols=58 Identities=26% Similarity=0.224 Sum_probs=30.5
Q ss_pred CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCC
Q ss_conf 11343213662678988512681899617886622577788888877753697-3067525788
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRG 356 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G 356 (648)
.+.+||-++.-.--..+. .-++-|+|+|||.+=.- ...+++. ..+.+. .+.++.+.++
T Consensus 46 ~~GsMG~a~p~AiG~ala-~p~r~Vv~l~GDGs~lM---~~geL~T-~~~~~~~n~~~vv~nN~ 104 (188)
T cd03371 46 TVGSMGHASQIALGIALA-RPDRKVVCIDGDGAALM---HMGGLAT-IGGLAPANLIHIVLNNG 104 (188)
T ss_pred EECHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHH---HHHHHHH-HHHHCCCCEEEEEECCC
T ss_conf 543123178999999983-99981899957338888---8579999-99727887799998796
No 154
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=42.31 E-value=16 Score=15.13 Aligned_cols=12 Identities=42% Similarity=1.038 Sum_probs=5.9
Q ss_pred CCCEEEECCCCC
Q ss_conf 897467136888
Q gi|254780834|r 58 SKGFYYCFSCHV 69 (648)
Q Consensus 58 ~~~~~~cf~c~~ 69 (648)
++|+|+|-+||.
T Consensus 39 ~~GiY~c~~cg~ 50 (140)
T COG0229 39 EKGIYVCIVCGE 50 (140)
T ss_pred CCCEEEEECCCC
T ss_conf 885698614797
No 155
>pfam06587 DUF1137 Protein of unknown function (DUF1137). This family consists of several hypothetical proteins specific to Chlamydia species. The function of this family is unknown.
Probab=42.09 E-value=11 Score=16.57 Aligned_cols=20 Identities=35% Similarity=0.748 Sum_probs=13.8
Q ss_pred CCCCCCCE-----------EEECCCCEEEEC
Q ss_conf 88858787-----------981789746713
Q gi|254780834|r 46 HDEKTPSF-----------HCNDSKGFYYCF 65 (648)
Q Consensus 46 h~ektpsf-----------~v~~~~~~~~cf 65 (648)
|-++.|-| .++|+||||||-
T Consensus 41 ~~~~aPPFLKIKKlgV~KqI~SPekqfF~C~ 71 (159)
T pfam06587 41 HFTPAPPFLKIKKLGVRKQIISPEKQFFYCT 71 (159)
T ss_pred CCCCCCCCEEEEECCCEEEECCCHHHEEEEE
T ss_conf 6778998147666152003258268648867
No 156
>cd01971 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protien for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=41.91 E-value=20 Score=14.43 Aligned_cols=10 Identities=10% Similarity=-0.147 Sum_probs=4.3
Q ss_pred CHHHHHHHHH
Q ss_conf 8178888643
Q gi|254780834|r 250 NFFGALNYLQ 259 (648)
Q Consensus 250 ~l~~a~~~~~ 259 (648)
|++.|..++-
T Consensus 134 G~~~a~~aiv 143 (427)
T cd01971 134 GHEIVLKAII 143 (427)
T ss_pred HHHHHHHHHH
T ss_conf 9999999999
No 157
>PRK01008 queuine tRNA-ribosyltransferase; Provisional
Probab=41.73 E-value=20 Score=14.40 Aligned_cols=67 Identities=16% Similarity=0.158 Sum_probs=41.9
Q ss_pred CCHHH-HHHHHHCCCEEEEEEC---CCCCCHHHHHHHHHHHHHHHH---------CCCCEEEEECCCCCCHHHHHHCCCH
Q ss_conf 66267-8988512681899617---886622577788888877753---------6973067525788888899720366
Q gi|254780834|r 302 LTEYQ-LRLLWKLSPRIVLCFD---GDDPGLRAAYKAIDLVLCHLI---------PGNRVNFVLLSRGEDPDSFIRCYGK 368 (648)
Q Consensus 302 lt~~~-~~~l~r~~~~vvl~fD---gD~AG~kAa~Ra~e~~l~~l~---------~g~~v~vv~LP~G~DPDe~ir~~G~ 368 (648)
||++. +..-..+..-|+++|| +-.+..+-+.+++++...+++ ++.+.-|...-.|.||| +|+...
T Consensus 140 ltPE~~i~~Q~~iGsDI~m~lD~~~~~~~~~~~~~~s~~rT~rW~~r~~~~~~~~~~~q~lfgIVQGG~~~d--LR~~sa 217 (372)
T PRK01008 140 LSPEVSVQAQKDLGADIIIPLDELLPFHTDPTYFLQSCSRTYVWEKRSLDYHLKNPRHQSMYGVIHGGIDPD--QRKIGC 217 (372)
T ss_pred ECHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHH--HHHHHH
T ss_conf 289999999997489889987878899977999999999999999999999852975526874246788799--999999
Q ss_pred HH
Q ss_conf 88
Q gi|254780834|r 369 TA 370 (648)
Q Consensus 369 ea 370 (648)
+.
T Consensus 218 ~~ 219 (372)
T PRK01008 218 AF 219 (372)
T ss_pred HH
T ss_conf 99
No 158
>pfam04405 ScdA_N Domain of Unknown function (DUF542). This domain is always found in conjunction with the HHE domain (pfam03794) at the N-terminus.
Probab=41.63 E-value=17 Score=15.09 Aligned_cols=35 Identities=17% Similarity=0.450 Sum_probs=27.2
Q ss_pred HHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHH
Q ss_conf 53510124422567741034554205997345232
Q gi|254780834|r 151 SHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE 185 (648)
Q Consensus 151 ~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~ 185 (648)
..+-++|+|-|+=.+...|.+.+.++|.+.+.+++
T Consensus 16 a~vF~~~gIDFCCgG~~~L~eA~~~~~ld~~~vl~ 50 (56)
T pfam04405 16 ARVFRKYGIDFCCGGKVSLAEACKEKGLDPEEVLA 50 (56)
T ss_pred HHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 99999949665689980699999882989999999
No 159
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=41.29 E-value=20 Score=14.35 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHH
Q ss_conf 7888888997203668899886-414992799999
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLI-VESLPLVDMLWK 387 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~ 387 (648)
-+..||.+.+.++|+|+++-.+ ..+.+..|..|+
T Consensus 528 GNvidP~~vi~~yGaDalR~~l~~~~~~g~di~~~ 562 (877)
T PRK05729 528 GNVIDPLDLIDKYGADALRFTLAALASPGRDIRFD 562 (877)
T ss_pred CCCCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf 89899899998719199999999707767660006
No 160
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=41.03 E-value=20 Score=14.32 Aligned_cols=35 Identities=23% Similarity=0.268 Sum_probs=27.5
Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 18996178866225777888888777536973067525
Q gi|254780834|r 316 RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL 353 (648)
Q Consensus 316 ~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L 353 (648)
+|..|.|+...+.++..||..++..+ +-++.++..
T Consensus 1 rILV~vd~s~~s~~lir~a~rlA~~~---~a~l~vl~V 35 (124)
T cd01987 1 RILVCISGGPNAERLIRRAARLADRL---KAPWYVVYV 35 (124)
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHHC---CCCEEEEEE
T ss_conf 99999589850799999999999964---998999999
No 161
>pfam04723 GRDA Glycine reductase complex selenoprotein A. Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. A member of this family may also exist in Treponema denticola.
Probab=40.76 E-value=14 Score=15.67 Aligned_cols=71 Identities=28% Similarity=0.276 Sum_probs=36.9
Q ss_pred CCHHHHH-------HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf 1438899-------987435542113432136626789885126818996178866225777888888777536973067
Q gi|254780834|r 278 EGYMDVL-------SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNF 350 (648)
Q Consensus 278 EGy~Dvi-------~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~v 350 (648)
-|-||.= ..-+.|-+|+|-.+|.|=.+. ..++-+-|-.=|.--||--|- +++ |+.|+-
T Consensus 46 agaMDLEnQ~rVK~~aEk~G~ENvvVvlGaaeaE~-----aglaaETVt~GDPTfAGPLAG---V~L-------gL~vYH 110 (150)
T pfam04723 46 AGAMDLENQQKVKDATESIGAENLVVLLGAAEAES-----AGLAAETVTAGDPTFAGPLAG---VEL-------GLRVYH 110 (150)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHH-----CCCEEEEEECCCCCCCCCCCC---CCC-------CCEEEE
T ss_conf 44122687899999998709752899964667001-----144334540689865555556---652-------856566
Q ss_pred EECCC---CCCHHHHH
Q ss_conf 52578---88888997
Q gi|254780834|r 351 VLLSR---GEDPDSFI 363 (648)
Q Consensus 351 v~LP~---G~DPDe~i 363 (648)
+.=|+ --||+-|=
T Consensus 111 i~EpEiK~~~d~~vye 126 (150)
T pfam04723 111 AVEPEFKAEVDEAIYD 126 (150)
T ss_pred ECCHHHHHHCCHHHHH
T ss_conf 4689898456888999
No 162
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=40.54 E-value=20 Score=14.26 Aligned_cols=36 Identities=25% Similarity=0.372 Sum_probs=27.0
Q ss_pred CHHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf 62678988512---6818996178866225777888888
Q gi|254780834|r 303 TEYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLV 338 (648)
Q Consensus 303 t~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~ 338 (648)
+..|++.|+++ ++.||++-|.|.=|..=++..++.+
T Consensus 85 ~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~ei~~~~ 123 (151)
T cd03362 85 KKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYA 123 (151)
T ss_pred HHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 899999999998539989987788720459999999984
No 163
>pfam09334 tRNA-synt_1g tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.
Probab=40.21 E-value=21 Score=14.22 Aligned_cols=25 Identities=28% Similarity=0.444 Sum_probs=18.3
Q ss_pred CCCCHHHHHHCCCHHHHHHHH-HHCC
Q ss_conf 888888997203668899886-4149
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLI-VESL 379 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll-~~A~ 379 (648)
+..||++++.++|+|+++-+| .++.
T Consensus 331 N~i~~~d~i~~ygaDalR~~L~~~~~ 356 (388)
T pfam09334 331 NVVDPDELLDRYGVDALRYYLAREAP 356 (388)
T ss_pred CCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 87888999988782899999995399
No 164
>PRK10026 arsenate reductase; Provisional
Probab=39.96 E-value=19 Score=14.65 Aligned_cols=48 Identities=13% Similarity=0.182 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHH
Q ss_conf 775789999850688535101244225677410345542059973452320
Q gi|254780834|r 136 RDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEA 186 (648)
Q Consensus 136 ~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~ 186 (648)
++..|+++|++.|+..+++..+.-... .+.|...+...|.+..+++..
T Consensus 14 KSR~aL~lL~e~g~e~~vv~YLk~p~s---~~eL~~l~~~Lg~~~~~liRk 61 (141)
T PRK10026 14 TSRNTLEMIRNSGTEPTIIYYLETPPT---RDELVKLIADMGISVRALLRK 61 (141)
T ss_pred HHHHHHHHHHHCCCCCEEEHHHCCCCC---HHHHHHHHHHCCCCHHHHHHC
T ss_conf 899999999986999587156217999---999999999859999999873
No 165
>PRK00726 murG N-acetylglucosaminyl transferase; Provisional
Probab=39.80 E-value=21 Score=14.17 Aligned_cols=65 Identities=22% Similarity=0.319 Sum_probs=45.3
Q ss_pred HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf 01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV 318 (648)
Q Consensus 246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv 318 (648)
+.+.++.+++..+++.++ +-+|-+=||.-+ ++.+..|++-++ +.+|.|- +++.++++.|.
T Consensus 75 ~l~~~~~~~~~il~~~kP--------d~Vig~GGY~s~P~~laA~l~~iP~iiHEqN~v~G~aN-----r~l~~~a~~i~ 141 (359)
T PRK00726 75 KLLKGVLQARKILKRFKP--------DVVVGFGGYVSGPAGLAARLLGIPLVIHEQNAVPGLAN-----KLLARFAKKVA 141 (359)
T ss_pred HHHHHHHHHHHHHHHCCC--------CEEEECCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCH-----HHHHHHCCEEE
T ss_conf 999999999999997499--------99997897412899999998299869974542356233-----78888509789
Q ss_pred EEECC
Q ss_conf 96178
Q gi|254780834|r 319 LCFDG 323 (648)
Q Consensus 319 l~fDg 323 (648)
++|+.
T Consensus 142 ~~f~~ 146 (359)
T PRK00726 142 TAFEE 146 (359)
T ss_pred ECCHH
T ss_conf 97755
No 166
>KOG2026 consensus
Probab=39.79 E-value=17 Score=14.91 Aligned_cols=26 Identities=27% Similarity=0.425 Sum_probs=22.9
Q ss_pred CCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf 458888587879817897467136888
Q gi|254780834|r 43 CPFHDEKTPSFHCNDSKGFYYCFSCHV 69 (648)
Q Consensus 43 cPfh~ektpsf~v~~~~~~~~cf~c~~ 69 (648)
--||.||-||.+.|+ -..|-|--||.
T Consensus 24 ldfd~ek~c~vslsn-LnvyAclvcg~ 49 (442)
T KOG2026 24 LDFDFEKPCSVSLSN-LNVYACLVCGK 49 (442)
T ss_pred CCCCCCCCCCCCCCC-CCEEEEEEECC
T ss_conf 246578999623466-65145542070
No 167
>PHA00202 DNA replication initiation protein
Probab=39.71 E-value=6.9 Score=18.62 Aligned_cols=21 Identities=19% Similarity=0.143 Sum_probs=12.0
Q ss_pred CCCCCCHHHHHHHHCCCCHHH
Q ss_conf 888878989989885999799
Q gi|254780834|r 67 CHVKGDHLSFLSALLGCSFIE 87 (648)
Q Consensus 67 c~~~gd~~~f~~~~~~~~f~e 87 (648)
|...+....+-..+-++.|+.
T Consensus 31 ~~~a~~~~~~~~~~~~~~~~~ 51 (379)
T PHA00202 31 CHDAVRRLHKHEEYKGFAKSG 51 (379)
T ss_pred HHHHCCCCCCCCCCCCCCCCC
T ss_conf 554023345621024567755
No 168
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=39.71 E-value=21 Score=14.16 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=34.4
Q ss_pred HCCCCHHHHHHHHHC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHH
Q ss_conf 213662678988512--------681899617886622577788888877753697306752578888889972
Q gi|254780834|r 299 GTALTEYQLRLLWKL--------SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIR 364 (648)
Q Consensus 299 Gtalt~~~~~~l~r~--------~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir 364 (648)
|--++..-.+++.+| +.+|.+.||.+--=-.-..++ ++..+.+.|..|.++.+-.. ||-+.++
T Consensus 223 G~i~~~~~~~i~~~Y~~W~~~~~~~~V~l~Y~smyg~T~~ma~a--iaegl~~~gv~v~~~~~~~~-~~~eI~~ 293 (388)
T COG0426 223 GPIWRGNPKEIVEAYRDWAEGQPKGKVDLIYDSMYGNTEKMAQA--IAEGLMKEGVDVEVINLEDA-DPSEIVE 293 (388)
T ss_pred CCEEECCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHH--HHHHHHHCCCCEEEEECCCC-CHHHHHH
T ss_conf 85255798999999999970687661799984223787999999--98776115996299991558-8999999
No 169
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=39.57 E-value=19 Score=14.63 Aligned_cols=36 Identities=31% Similarity=0.542 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCEEEEEEEECCCCEEEEECCCCC----CCCCCEECC-CCC
Q ss_conf 654100001671688897077858885010014----655300103-876
Q gi|254780834|r 194 NSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLS----KGESVKYLN-SPE 238 (648)
Q Consensus 194 ~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~----~~~~~KYlN-Spe 238 (648)
+|. ++-||-|+ .|.|+|-.||... .+..-|+|+ +||
T Consensus 49 kGm-Ph~rf~G~--------TG~Vvg~~g~ay~V~v~~G~k~K~liv~pe 89 (98)
T COG2139 49 KGM-PHPRFQGK--------TGTVVGVRGRAYKVEVYDGNKEKTLIVRPE 89 (98)
T ss_pred CCC-CCCCCCCC--------CEEEEECCCCEEEEEEECCCCEEEEEECHH
T ss_conf 698-77530476--------307984148779999961894589986778
No 170
>COG2719 SpoVR Uncharacterized conserved protein [Function unknown]
Probab=39.43 E-value=21 Score=14.19 Aligned_cols=17 Identities=24% Similarity=0.479 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHCCCCC
Q ss_conf 79999999998188587
Q gi|254780834|r 85 FIESVQRLAAIAGVPLP 101 (648)
Q Consensus 85 f~ea~~~la~~~gi~~~ 101 (648)
..+.+..+|..+|.+..
T Consensus 18 ~~~eI~~ia~~~gLD~Y 34 (495)
T COG2719 18 YLEEIERIAKEYGLDTY 34 (495)
T ss_pred HHHHHHHHHHHHCCCCC
T ss_conf 99999999997087877
No 171
>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.
Probab=39.23 E-value=21 Score=14.10 Aligned_cols=61 Identities=13% Similarity=0.139 Sum_probs=41.9
Q ss_pred CCCCHH-HHHCCCCH-------HHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf 542113-43213662-------678988512681899617886622577788888877753697306752578888
Q gi|254780834|r 291 VQNVVS-SLGTALTE-------YQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGED 358 (648)
Q Consensus 291 ~~n~va-~~Gtalt~-------~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~D 358 (648)
|+++|- |..|++++ .++..|.++-.++|++.+. +|+.|+.=|-. +.+.|. .+|+.|-.|.+
T Consensus 33 i~~siniPf~~~~~~~~~L~~~~~~~~Lek~Kgk~VViV~~--~g~~a~~fa~~----Lvk~Gf-~rVcvL~GGi~ 101 (105)
T cd01525 33 IEGSINIPFSSVFLKEGELEQLPTVPRLENYKGKIIVIVSH--SHKHAALFAAF----LVKCGV-PRVCILDGGIN 101 (105)
T ss_pred ECCCCCCCCHHHCCCCCCCCCCCCHHHHHHCCCCEEEEECC--CCCCHHHHHHH----HHHCCC-CEEEEECCHHH
T ss_conf 12755057302015544221364258999758982999889--98679999999----998499-86999338275
No 172
>TIGR00807 s1 malonate transporter, MadL subunit; InterPro: IPR004690 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM. The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity..
Probab=39.20 E-value=14 Score=15.69 Aligned_cols=26 Identities=15% Similarity=0.328 Sum_probs=19.3
Q ss_pred HHHHHHHCCCCHHHHCCCCCCCCCCCCCHHH
Q ss_conf 8999985068853510124422567741034
Q gi|254780834|r 140 LHYYLDERGIDSHAIEMFKLGYAPDSRYSLR 170 (648)
Q Consensus 140 a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~ 170 (648)
+++||.+||-= ....+|++|| |+..|
T Consensus 46 ~~~~l~k~G~l-~q~~qfGvgf----W~aMY 71 (127)
T TIGR00807 46 AKELLAKKGKL-KQVSQFGVGF----WSAMY 71 (127)
T ss_pred HHHHHHHCCCC-CCCCCCCCEE----ECCEE
T ss_conf 99998743999-7220156010----04501
No 173
>COG0535 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=39.17 E-value=21 Score=14.09 Aligned_cols=95 Identities=20% Similarity=0.247 Sum_probs=57.6
Q ss_pred CCEEEEECCHHHHHHHHH--CCCCCCHHHHHCCCCHHHHHHHHHC-CCEEEEEECC-CCCC------H----HHHHHHHH
Q ss_conf 870899714388999874--3554211343213662678988512-6818996178-8662------2----57778888
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQ--AGVQNVVSSLGTALTEYQLRLLWKL-SPRIVLCFDG-DDPG------L----RAAYKAID 336 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~--~G~~n~va~~Gtalt~~~~~~l~r~-~~~vvl~fDg-D~AG------~----kAa~Ra~e 336 (648)
.++..+-.-.++.+.... .|+.-++.|.||.++++=++.+... .+.|.+.+|| |... . +++.+++.
T Consensus 73 gGEPll~~~~~ei~~~~~~~~~~~~~~~TnG~~~~~~~~~~l~~~g~~~v~iSld~~~~e~hd~~rg~~g~~~~~~~~i~ 152 (347)
T COG0535 73 GGEPLLRPDLLEIVEYARKKGGIRVSLSTNGTLLTEEVLEKLKEAGLDYVSISLDGLDPETHDPIRGVKGVFKRAVEAIK 152 (347)
T ss_pred CCCCEECCCHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 98733345799999998513872898826875453889998876688769999745885321400277626999999999
Q ss_pred HHHHHHHCCC--CEEEEECCCC----CCHHHHHHCCCH
Q ss_conf 8877753697--3067525788----888899720366
Q gi|254780834|r 337 LVLCHLIPGN--RVNFVLLSRG----EDPDSFIRCYGK 368 (648)
Q Consensus 337 ~~l~~l~~g~--~v~vv~LP~G----~DPDe~ir~~G~ 368 (648)
.+ .+.|+ .+.+...... .+..+++...|.
T Consensus 153 ~~---~~~g~~~~~~~~v~~~n~~~l~~~~~~~~~~g~ 187 (347)
T COG0535 153 NL---KEAGILVVINTTVTKINYDELPEIADLAAELGV 187 (347)
T ss_pred HH---HHHCCEEEEEEEEECCCHHHHHHHHHHHHHCCC
T ss_conf 99---873970489999956634658999999986597
No 174
>PRK13265 glycine/sarcosine/betaine reductase complex protein A; Reviewed
Probab=39.11 E-value=16 Score=15.25 Aligned_cols=71 Identities=28% Similarity=0.277 Sum_probs=36.9
Q ss_pred CCHHHHH-------HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf 1438899-------987435542113432136626789885126818996178866225777888888777536973067
Q gi|254780834|r 278 EGYMDVL-------SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNF 350 (648)
Q Consensus 278 EGy~Dvi-------~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~v 350 (648)
-|-||.= ..-+.|-+|+|-.+|.|=.+. ..++-+-|-.=|.--||--|- +++ |+.|+-
T Consensus 47 agaMDLEnQ~rVK~~aek~G~ENvvVvlGaaeaE~-----aglaaETVT~GDPTfAGPLAG---V~L-------gL~vYH 111 (157)
T PRK13265 47 AGAMDLENQKRVKDLTEKHGAENIVVILGAAEAEA-----AGLAAETVTNGDPTFAGPLAG---VQL-------GLRVYH 111 (157)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHH-----CCCEEEEECCCCCCCCCCCCC---CCC-------CCEEEE
T ss_conf 44122687899999998709752899964667001-----144323440689865555556---642-------866566
Q ss_pred EECCC---CCCHHHHH
Q ss_conf 52578---88888997
Q gi|254780834|r 351 VLLSR---GEDPDSFI 363 (648)
Q Consensus 351 v~LP~---G~DPDe~i 363 (648)
+.=|+ --||+-|=
T Consensus 112 i~EpEiK~~~d~~vye 127 (157)
T PRK13265 112 AVEPEIKEEVDEEVYE 127 (157)
T ss_pred ECCHHHHHHCCHHHHH
T ss_conf 4689898456888999
No 175
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.07 E-value=13 Score=16.09 Aligned_cols=22 Identities=18% Similarity=0.434 Sum_probs=19.2
Q ss_pred CCCCEEEEECCCCCCHHHHHHC
Q ss_conf 6973067525788888899720
Q gi|254780834|r 344 PGNRVNFVLLSRGEDPDSFIRC 365 (648)
Q Consensus 344 ~g~~v~vv~LP~G~DPDe~ir~ 365 (648)
-|-+||++.||+..|.|+++..
T Consensus 60 RGs~IRyi~lPD~l~~d~lL~d 81 (90)
T cd01724 60 RGNNIRYFILPDSLNLDTLLVD 81 (90)
T ss_pred CCCCEEEEECCCCCCCCCCEEE
T ss_conf 5773899988787766451210
No 176
>PRK12655 fructose-6-phosphate aldolase; Reviewed
Probab=39.01 E-value=21 Score=14.08 Aligned_cols=74 Identities=16% Similarity=0.069 Sum_probs=33.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCC
Q ss_conf 898859997999999999818858776-82036777889999999999999999973267775789999850688
Q gi|254780834|r 77 LSALLGCSFIESVQRLAAIAGVPLPVV-DPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGID 150 (648)
Q Consensus 77 ~~~~~~~~f~ea~~~la~~~gi~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~ 150 (648)
+|..+|.+|.+.++.+++..+-+.|-. +......++.-..-..+.++....+-+.-.+..|-.|...|.+.|+.
T Consensus 31 ll~k~g~~~~~~~~~i~~~~~~~~~l~~ev~~~d~~~m~~~a~~l~~~~~~ivVKIP~t~~Gl~ai~~L~~~gi~ 105 (220)
T PRK12655 31 IIAASKESIWEVLPRLQKAIGGEGILFAQTMSRDAQGMVEEAKRLRNAIPGIVVKIPVTAEGLAAIKKLKKEGIP 105 (220)
T ss_pred HHHHCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHCCCC
T ss_conf 998659987999999999828999789999559999999999999974787399868877899999999986997
No 177
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=38.75 E-value=22 Score=14.04 Aligned_cols=119 Identities=18% Similarity=0.105 Sum_probs=62.8
Q ss_pred ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 71438-89998743554211343213662678988512681------899617886622577788888877753697306
Q gi|254780834|r 277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVN 349 (648)
Q Consensus 277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~ 349 (648)
-+|=| |++++-. .+++..+..+|.+.+..+-.+++. +-.++++|.+ +++..++- +.
T Consensus 210 s~GsmRDAlslLd----Q~is~~~~~it~~~v~~~lG~~~~~~l~~l~~~i~~~d~~---~~l~~~~~---i~------- 272 (541)
T PRK05563 210 SDGAMRDALSILD----QAISMGDGKVDYDDVVSMLGLVTNENLFDITDSIIEKDIE---KSMEIIDD---IV------- 272 (541)
T ss_pred CCCCHHHHHHHHH----HHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHH---HHHHHHHH---HH-------
T ss_conf 5997788999999----9998359986699999996899989999999999858999---99999999---99-------
Q ss_pred EEECCCCCCHHHHHHCCCHHHHHHHHH-H-CCCHH------HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 752578888889972036688998864-1-49927------99999998530233145799999999988541799
Q gi|254780834|r 350 FVLLSRGEDPDSFIRCYGKTAFEKLIV-E-SLPLV------DMLWKRETENRSFNTPDERAELEIHLKNCINHIKD 417 (648)
Q Consensus 350 vv~LP~G~DPDe~ir~~G~eaf~~ll~-~-A~~l~------dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d 417 (648)
-.|.||-.|++.- ..-|++++- + +.... +-.++.+......-+.+.-..+++.+......++-
T Consensus 273 ----~~G~d~~~fl~dL-i~~~R~lll~k~~~~~~~~l~~~~e~~~~l~~~a~~~~~~~l~~~~~~L~~~~~~lk~ 343 (541)
T PRK05563 273 ----LSGKDIYNFIKDL-ITHFRNLLMVKVSSNPEEILDMSEENIELLKEQSKKIRIEEIMRCIRILQEAEEQSKW 343 (541)
T ss_pred ----HCCCCHHHHHHHH-HHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf ----8699999999999-9999999997606973765217999999999999708999999999999999999614
No 178
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=38.49 E-value=22 Score=14.01 Aligned_cols=14 Identities=7% Similarity=0.052 Sum_probs=7.4
Q ss_pred CCCCCCHHCCCHHH
Q ss_conf 65352101108178
Q gi|254780834|r 240 ILFHKGKNLYNFFG 253 (648)
Q Consensus 240 ~if~K~~~Ly~l~~ 253 (648)
|.+-++..++|--+
T Consensus 195 P~lv~~~~~~gtGq 208 (422)
T PRK05431 195 PYLVNEESMYGTGQ 208 (422)
T ss_pred HHHHHHHHHHHHCC
T ss_conf 37636788744537
No 179
>KOG1903 consensus
Probab=38.48 E-value=12 Score=16.33 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=24.6
Q ss_pred HHHCCCCEE-EEECCCCCCHHHHHHCCCHHHHHH
Q ss_conf 753697306-752578888889972036688998
Q gi|254780834|r 341 HLIPGNRVN-FVLLSRGEDPDSFIRCYGKTAFEK 373 (648)
Q Consensus 341 ~l~~g~~v~-vv~LP~G~DPDe~ir~~G~eaf~~ 373 (648)
-+..|+++| +|.||.|+|-|||+--|-.|-|..
T Consensus 38 sL~sG~dLr~aV~LPpgEn~nDW~AVHvVDFFNR 71 (217)
T KOG1903 38 SLNSGLDLRSAVRLPPGENLNDWLAVHVVDFFNR 71 (217)
T ss_pred HHHCCCCHHHHCCCCCCCCCCCEEEEEHHHHHHH
T ss_conf 7743725687510899887443023211335556
No 180
>TIGR00337 PyrG CTP synthase; InterPro: IPR004468 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5 upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium .; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=38.42 E-value=20 Score=14.33 Aligned_cols=90 Identities=19% Similarity=0.325 Sum_probs=45.7
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHHHHCCC---------CCCCC-------CCHHHH-HHHHH--------------HH-
Q ss_conf 878989989885999799999999981885---------87768-------203677-78899--------------99-
Q gi|254780834|r 70 KGDHLSFLSALLGCSFIESVQRLAAIAGVP---------LPVVD-------PKIEKK-EKIQT--------------DL- 117 (648)
Q Consensus 70 ~gd~~~f~~~~~~~~f~ea~~~la~~~gi~---------~~~~~-------~~~~~~-~~~~~--------------~~- 117 (648)
||.|= .+|++.|.||++.+....|=+ +|.-. ..++.+ .+.|. .|
T Consensus 151 GGTVG----DIEs~PFLEAiRQ~~~e~G~Env~~iHvTLVP~i~aagE~KTKPTQhSVKeLRs~Gi~PD~i~cRs~~~l~ 226 (571)
T TIGR00337 151 GGTVG----DIESLPFLEAIRQLKKEVGRENVLFIHVTLVPYIAAAGELKTKPTQHSVKELRSLGIQPDIIICRSSEPLD 226 (571)
T ss_pred CCCCC----CCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf 77000----00362589999999987389867999840026314487478775127899998609888689981887689
Q ss_pred HHHHHHHHHHHH---HHHCCCCCHH----HHHHHHHCCCCHHHHCCCCCCCCC
Q ss_conf 999999999999---9732677757----899998506885351012442256
Q gi|254780834|r 118 IRLIEVATDFFH---HSLKNARDKR----LHYYLDERGIDSHAIEMFKLGYAP 163 (648)
Q Consensus 118 ~~~~~~~~~~~~---~~l~~~~~~~----a~~yl~~Rg~~~~~~~~f~lG~ap 163 (648)
-.+-++.|-|++ .+.-+..++. .---|.+-|+.+-+.++|+|.-.|
T Consensus 227 ~~~k~KiAlFCdV~~~aVI~~~Da~sIY~vPl~L~~egl~~~~~~rl~L~~~~ 279 (571)
T TIGR00337 227 KSLKKKIALFCDVEEEAVINAEDASSIYEVPLLLKKEGLDDYLCRRLNLNEKP 279 (571)
T ss_pred HHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCEECCCCHHHHHHHHHCCCCCC
T ss_conf 77764521005889732578655524011352100043357999984378777
No 181
>KOG2924 consensus
Probab=38.35 E-value=1.5 Score=24.72 Aligned_cols=161 Identities=22% Similarity=0.267 Sum_probs=81.9
Q ss_pred EECCCCCCCCHHHHHHHHCCCCH-----HHHHHHHHHHHCCCCCCC---CCCHHHHHHHHHHHHHHHHHHHHH--HHHHH
Q ss_conf 71368888789899898859997-----999999999818858776---820367778899999999999999--99973
Q gi|254780834|r 63 YCFSCHVKGDHLSFLSALLGCSF-----IESVQRLAAIAGVPLPVV---DPKIEKKEKIQTDLIRLIEVATDF--FHHSL 132 (648)
Q Consensus 63 ~cf~c~~~gd~~~f~~~~~~~~f-----~ea~~~la~~~gi~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l 132 (648)
+.|.-+. |.-..+.-+....| -+||+.+-.......... +.+.....-.+... ....-| |-.+|
T Consensus 34 ~Dfnk~~--~~~~l~~s~~t~GFQatnl~~Av~~in~M~~~rd~~~~~d~d~~~~~~~~~r~~----~~ctIFlGyTSNl 107 (366)
T KOG2924 34 YDFNKGV--DYSALLESFGTTGFQATNLGRAVQQINRMLNWRDEPLSADDDSHEDLTFSRRPL----TSCTIFLGYTSNL 107 (366)
T ss_pred CCCCCCC--CHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC----CCEEEEEECCHHH
T ss_conf 6656520--599999998602641000889999999998434576644455444467121455----3148997423033
Q ss_pred CCCCCHHHHHHHHHC-----------CCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCC
Q ss_conf 267775789999850-----------688535101244225677410345542059973452320121003465410000
Q gi|254780834|r 133 KNARDKRLHYYLDER-----------GIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDR 201 (648)
Q Consensus 133 ~~~~~~~a~~yl~~R-----------g~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~ 201 (648)
-+.--.+...||-+| |+.++.|+-+.--|.-+ +..--..|+.+|.+.- -+|+++|++ |-.
T Consensus 108 iSSGlRetirylvqh~mVdviVttaGGvEEDlIKclaPTy~g~-F~L~G~~LR~~GlNRi----GNllvPndN----Yck 178 (366)
T KOG2924 108 ISSGLRETIRYLVQHNMVDVIVTTAGGVEEDLIKCLAPTYLGD-FSLDGKELRENGLNRI----GNLLVPNDN----YCK 178 (366)
T ss_pred HHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHCCCCEEE-EECCHHHHHHHHHHHH----CCEECCCCC----HHH
T ss_conf 3350899999999746135999548862788998707530202-5347287776013332----467247865----155
Q ss_pred CCCEEEEEEEECCCCEEEEECCCCCCCCC----CEECCCCCC
Q ss_conf 16716888970778588850100146553----001038767
Q gi|254780834|r 202 FRNRLIFPIRSSRGQVIAFGGRTLSKGES----VKYLNSPET 239 (648)
Q Consensus 202 Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~----~KYlNSpeT 239 (648)
|.+-|| ||.|..=.--.=-|+++.++.. .|-+|-+.|
T Consensus 179 fEdWl~-pIld~mleeq~~~~~iwTPSk~I~rlGk~IndesS 219 (366)
T KOG2924 179 FEDWLM-PILDEMLEEQKTEGVIWTPSKMIARLGKEINDESS 219 (366)
T ss_pred HHHHHH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf 899988-99999998765248624879999998655089221
No 182
>pfam01983 CofC Guanylyl transferase CofC like. Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis. This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis. CofC has been shown to catalyse the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP.
Probab=38.31 E-value=22 Score=13.99 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=11.7
Q ss_pred CCHHHHHHHHHCCC--EEEEEECCCCCCHH
Q ss_conf 66267898851268--18996178866225
Q gi|254780834|r 302 LTEYQLRLLWKLSP--RIVLCFDGDDPGLR 329 (648)
Q Consensus 302 lt~~~~~~l~r~~~--~vvl~fDgD~AG~k 329 (648)
+|.+.+..+-.... .|+||=|-|. |-|
T Consensus 101 i~~~~l~~ll~~~~~~~vvI~P~r~g-GTN 129 (217)
T pfam01983 101 ISKEVLKRFLETEGRADVVIAPGRGG-GTN 129 (217)
T ss_pred CCHHHHHHHHHHCCCCCEEECCCCCC-CEE
T ss_conf 99899999998377888897456789-633
No 183
>COG2971 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=38.26 E-value=22 Score=13.98 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=18.7
Q ss_pred EEEECCCCEEEEECCCCCCCCCCEECCCC-CCCC
Q ss_conf 89707785888501001465530010387-6765
Q gi|254780834|r 209 PIRSSRGQVIAFGGRTLSKGESVKYLNSP-ETIL 241 (648)
Q Consensus 209 Pi~~~~g~~i~f~gR~l~~~~~~KYlNSp-eT~i 241 (648)
-+.|.+|+|+|.| ..-++-|.|+| |+.+
T Consensus 20 ~l~~~~g~vlg~g-----~sGpAN~~~~~~e~A~ 48 (301)
T COG2971 20 VLADEDGNVLGRG-----KSGPANIQLVGKEEAV 48 (301)
T ss_pred EEECCCCCEEEEE-----CCCCCEECCCCHHHHH
T ss_conf 9975897589775-----1688521356367899
No 184
>TIGR02279 PaaC-3OHAcCoADH 3-hydroxyacyl-CoA dehydrogenase PaaC; InterPro: IPR011967 This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring . The sequences included in this entry are all found in possible operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN . Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. .
Probab=38.06 E-value=14 Score=15.66 Aligned_cols=24 Identities=33% Similarity=0.578 Sum_probs=19.5
Q ss_pred EEEECCCCCCCCCCEEEECCCCEE
Q ss_conf 575345888858787981789746
Q gi|254780834|r 39 YWACCPFHDEKTPSFHCNDSKGFY 62 (648)
Q Consensus 39 ~~~~cPfh~ektpsf~v~~~~~~~ 62 (648)
=||.-|-|-..||-|.||-==.=|
T Consensus 175 aWGK~PVh~~STPGFIVNRVARPy 198 (508)
T TIGR02279 175 AWGKQPVHARSTPGFIVNRVARPY 198 (508)
T ss_pred HCCCCCCCCCCCCCCEECCCCCCH
T ss_conf 328856323469882342656731
No 185
>TIGR00422 valS valyl-tRNA synthetase; InterPro: IPR002303 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=38.04 E-value=20 Score=14.43 Aligned_cols=121 Identities=12% Similarity=0.190 Sum_probs=69.6
Q ss_pred CEEEECCCCC---------CCC-CCEEEECCCCE--EEE--CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCC
Q ss_conf 5575345888---------858-78798178974--671--36888878989989885999799999999981---8858
Q gi|254780834|r 38 DYWACCPFHD---------EKT-PSFHCNDSKGF--YYC--FSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPL 100 (648)
Q Consensus 38 ~~~~~cPfh~---------ekt-psf~v~~~~~~--~~c--f~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~ 100 (648)
-=+=+||||| .+= |--+|-.++|. =+| |+.|.. +++..=-++.||+-.||=+.+-+.. |.-+
T Consensus 285 G~VKvTPAHD~ND~~~g~RH~LLe~i~~l~~dG~Lne~a~~~~tG~~-~~Y~iP~~y~GL~~~eAR~kiv~~L~~~glL~ 363 (970)
T TIGR00422 285 GAVKVTPAHDFNDYEVGKRHNLLEFINILDEDGLLNENAEVIDTGKE-DVYAIPGEYQGLERFEARKKIVEDLKEEGLLV 363 (970)
T ss_pred CEEEEECCCCCCCHHHCCEECCCCHHHHCCCCCCCCCEECEEECCCC-CCCCCCHHCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 12776087497760013412114143331799750110011007772-33106522058888999999999998668800
Q ss_pred CCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHH
Q ss_conf 776820367--778899999999999999999732677757899998506885351012442256774103455
Q gi|254780834|r 101 PVVDPKIEK--KEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREH 172 (648)
Q Consensus 101 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~ 172 (648)
.. .+.... ...+-....+.+ ....||...=. -...|++-+++-| .+-|.|..|...+.+
T Consensus 364 k~-~p~~~~VG~c~Rsg~vvEP~-ls~QWFV~~~~--La~~a~~~~~~~g---------~~~fvP~~~~~~y~~ 424 (970)
T TIGR00422 364 KI-EPHTHNVGHCERSGTVVEPL-LSKQWFVKVEK--LADKALEAAEEDG---------EIKFVPKRFEKRYLN 424 (970)
T ss_pred CC-CEECCCCCEECCCCCEEECC-CCCCCEECHHH--HHHHHHHHHHHCC---------CCEEECHHHHHHHHH
T ss_conf 11-10003456214789343042-69986217177--7899999985458---------833602167889999
No 186
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.79 E-value=22 Score=13.93 Aligned_cols=26 Identities=31% Similarity=0.727 Sum_probs=19.8
Q ss_pred EECCCCCCCCCCEEEE-CCCCEEEECCCCCC
Q ss_conf 5345888858787981-78974671368888
Q gi|254780834|r 41 ACCPFHDEKTPSFHCN-DSKGFYYCFSCHVK 70 (648)
Q Consensus 41 ~~cPfh~ektpsf~v~-~~~~~~~cf~c~~~ 70 (648)
-.|||..-++ |. -..++|.|=.||..
T Consensus 36 ~~Cp~C~~~~----VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 36 HVCPFCGRTT----VKRIATGIWKCRKCGAK 62 (89)
T ss_pred CCCCCCCCCC----EEEECCCEEECCCCCCE
T ss_conf 7699789740----45523675871788873
No 187
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=37.78 E-value=21 Score=14.21 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=7.1
Q ss_pred CCCCHHHHHHCC
Q ss_conf 888888997203
Q gi|254780834|r 355 RGEDPDSFIRCY 366 (648)
Q Consensus 355 ~G~DPDe~ir~~ 366 (648)
.|.||+.++..-
T Consensus 37 ~~ld~~~ll~~L 48 (216)
T TIGR03652 37 KGLDPDEILAEL 48 (216)
T ss_pred CCCCHHHHHHHH
T ss_conf 498999999999
No 188
>PRK10992 cell morphogenesis/cell wall metabolism regulator; Provisional
Probab=37.71 E-value=21 Score=14.12 Aligned_cols=11 Identities=18% Similarity=0.015 Sum_probs=6.2
Q ss_pred CCCCHHHHHHC
Q ss_conf 88888899720
Q gi|254780834|r 355 RGEDPDSFIRC 365 (648)
Q Consensus 355 ~G~DPDe~ir~ 365 (648)
.|.||+.++.+
T Consensus 44 ~~ld~~~l~~e 54 (220)
T PRK10992 44 KELDIDVIEAR 54 (220)
T ss_pred CCCCHHHHHHH
T ss_conf 49899999999
No 189
>PRK09358 adenosine deaminase; Provisional
Probab=37.46 E-value=22 Score=13.89 Aligned_cols=27 Identities=33% Similarity=0.383 Sum_probs=22.2
Q ss_pred HHCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 885999799999999981885877682
Q gi|254780834|r 79 ALLGCSFIESVQRLAAIAGVPLPVVDP 105 (648)
Q Consensus 79 ~~~~~~f~ea~~~la~~~gi~~~~~~~ 105 (648)
+.+|.--+|.+..||.+.|+++|..+.
T Consensus 17 HL~Gsi~~etl~~la~~~~~~lp~~~~ 43 (333)
T PRK09358 17 HLDGSLRPETILELARRNGIDLPATDI 43 (333)
T ss_pred CCCCCCCHHHHHHHHHHCCCCCCCCCH
T ss_conf 776888999999999982999997899
No 190
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=37.24 E-value=23 Score=13.86 Aligned_cols=62 Identities=15% Similarity=0.281 Sum_probs=40.5
Q ss_pred HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
=++...+|...|.+.+||..+--|..+..+-+ -...|-.|.|. -+|.|-++-+ +++.+++++
T Consensus 22 lv~~a~~f~s~I~l~~~~~~~naKSil~lm~L---g~~~G~~i~i~--a~G~De~~Al-----~~l~~lie~ 83 (85)
T PRK13782 22 FVQEANRFHADIFIEKDGKKVNAKSIMGLMSL---AIGTGSMITII--TEGSDEEEAL-----EALAAYVQE 83 (85)
T ss_pred HHHHHHCCCCEEEEEECCEEECHHHHHHHHHC---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHC
T ss_conf 99999728986999989999835829999851---77898999999--9788999999-----999999845
No 191
>KOG2802 consensus
Probab=37.22 E-value=13 Score=16.09 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=8.0
Q ss_pred CCCCCCEEEECCCCEEEECCCC
Q ss_conf 8858787981789746713688
Q gi|254780834|r 47 DEKTPSFHCNDSKGFYYCFSCH 68 (648)
Q Consensus 47 ~ektpsf~v~~~~~~~~cf~c~ 68 (648)
.+|.|-|-|+.-. ||+..
T Consensus 61 ~~k~~~l~vs~vp----s~sta 78 (503)
T KOG2802 61 KEKSQTLRVSKVP----SFSTA 78 (503)
T ss_pred HCCCCEEEEECCC----CCCCC
T ss_conf 0578357851255----54336
No 192
>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.17 E-value=23 Score=13.85 Aligned_cols=49 Identities=27% Similarity=0.233 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 79999999998477889999844300237998899999999999753889
Q gi|254780834|r 482 LREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKY 531 (648)
Q Consensus 482 ~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~ 531 (648)
..|+.|+..|..+|+++....+.+..- .....+..|....-.+|...+.
T Consensus 491 ~~E~~L~~~L~~fp~vl~~aa~~~~Ph-~la~YL~~LA~~Fn~fY~~~~V 539 (577)
T COG0018 491 LEERELVKKLLEFPEVLEEAAEELEPH-RLANYLYDLAGSFNSFYNACPV 539 (577)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHCCC
T ss_conf 279999999998499999999856955-9999999999999999850877
No 193
>KOG2164 consensus
Probab=37.15 E-value=13 Score=16.06 Aligned_cols=17 Identities=18% Similarity=0.303 Sum_probs=7.8
Q ss_pred HHCCCCHHHHHHHHHCC
Q ss_conf 32136626789885126
Q gi|254780834|r 298 LGTALTEYQLRLLWKLS 314 (648)
Q Consensus 298 ~Gtalt~~~~~~l~r~~ 314 (648)
||-.|--.=+-..|++.
T Consensus 204 CGHiFC~~CiLqy~~~s 220 (513)
T KOG2164 204 CGHIFCGPCILQYWNYS 220 (513)
T ss_pred CCCEEEHHHHHHHHHHH
T ss_conf 67331068999998553
No 194
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=36.81 E-value=16 Score=15.17 Aligned_cols=40 Identities=23% Similarity=0.210 Sum_probs=21.1
Q ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 8189961788662257778888887775369730675257888
Q gi|254780834|r 315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE 357 (648)
Q Consensus 315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~ 357 (648)
++-|+|+|||.+=.- ...+++..--.....+.++.|.++-
T Consensus 59 p~kVi~idGDGs~lM---~lg~LaTi~~~~~~nl~~ivlnN~~ 98 (157)
T cd02001 59 SRKVIVVDGDGSLLM---NPGVLLTAGEFTPLNLILVVLDNRA 98 (157)
T ss_pred CCCEEEEECCHHHHH---CCCHHHHHHHCCCCCEEEEEEECCC
T ss_conf 996899957558875---2461999986389887999997975
No 195
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=36.65 E-value=23 Score=13.85 Aligned_cols=39 Identities=26% Similarity=0.170 Sum_probs=19.8
Q ss_pred CCCCHHHHHCCCCHHHHHHHHHCCCEE-EEEECCCCCCHHHHHH
Q ss_conf 542113432136626789885126818-9961788662257778
Q gi|254780834|r 291 VQNVVSSLGTALTEYQLRLLWKLSPRI-VLCFDGDDPGLRAAYK 333 (648)
Q Consensus 291 ~~n~va~~Gtalt~~~~~~l~r~~~~v-vl~fDgD~AG~kAa~R 333 (648)
.-.+|+..|+.-|-+.- +.+-++ +|=||+|-=|+.-...
T Consensus 230 ~y~gv~niG~rPTf~~~----~~~iE~hildf~~dlYg~~i~v~ 269 (303)
T PRK05627 230 PYPGVANIGTRPTVDGG----RQLLEVHLLDFSGDLYGEHIAVE 269 (303)
T ss_pred EEEEEEEECCCCCCCCC----CEEEEEEECCCCCCCCCCEEEEE
T ss_conf 78744440468844898----55899996478977089879999
No 196
>COG0066 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]
Probab=36.51 E-value=21 Score=14.17 Aligned_cols=84 Identities=12% Similarity=0.154 Sum_probs=46.1
Q ss_pred EEEEEECCCCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHH---H-HHHHHHCCCCCCCCCCEEEEECCH
Q ss_conf 88897077858885010014655--30010387676535210110817888---8-643310000235678708997143
Q gi|254780834|r 207 IFPIRSSRGQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGAL---N-YLQKSIRKDVRRNSSSFIILVEGY 280 (648)
Q Consensus 207 ~fPi~~~~g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~---~-~~~~~~~~~~~~~~~~~~i~vEGy 280 (648)
|-++.-..|+++-|+.--+|.|. +.+||.+-+-.-|-| .+| +..| + ...+..+ -..+.++|+---
T Consensus 1 m~~f~~~~G~~~pl~~dnIDTD~IIP~~fLk~i~~~gl~k--~~f--~~~r~~~PdF~~n~~~-----yq~g~IlVag~N 71 (191)
T COG0066 1 MEKFTKITGRVWPLGRDNVDTDQIIPKRFLKTITRTGLGK--HLF--EDWRYLDPDFVLNVPP-----YQGGDILVAGEN 71 (191)
T ss_pred CCCEEEEEEEEEECCCCCCCCCCCCCHHHHCCCCHHHHHH--CCC--CCCCCCCCCHHHCCCC-----CCCCCEEEECCC
T ss_conf 9853888525970688877604386288745368746642--153--1010249643215886-----678648996688
Q ss_pred --------HHHHHHHHCCCCCCHHHHH
Q ss_conf --------8899987435542113432
Q gi|254780834|r 281 --------MDVLSLCQAGVQNVVSSLG 299 (648)
Q Consensus 281 --------~Dvi~l~~~G~~n~va~~G 299 (648)
--+++|..+||..|||++-
T Consensus 72 FGcGSSREHApwALk~~Gi~~VIA~SF 98 (191)
T COG0066 72 FGCGSSREHAPWALKDYGIRAVIAPSF 98 (191)
T ss_pred CCCCCCHHHHHHHHHHCCEEEEEECCH
T ss_conf 778852778999999759249993629
No 197
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=36.43 E-value=23 Score=13.76 Aligned_cols=26 Identities=23% Similarity=0.562 Sum_probs=21.1
Q ss_pred ECCCCCCCCCCEEEECCCCEEEECCCCC
Q ss_conf 3458888587879817897467136888
Q gi|254780834|r 42 CCPFHDEKTPSFHCNDSKGFYYCFSCHV 69 (648)
Q Consensus 42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~ 69 (648)
.||.... +++..++++|-+-|-.||.
T Consensus 2 ~Cp~Cg~--~~~~~D~~~Ge~vC~~CG~ 27 (40)
T pfam08271 2 KCPNCGS--TEIVFDYERGEYVCTECGL 27 (40)
T ss_pred CCCCCCC--CCEEEECCCCCEECCCCCE
T ss_conf 3887999--7067727789787057971
No 198
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=36.26 E-value=23 Score=13.74 Aligned_cols=83 Identities=25% Similarity=0.318 Sum_probs=58.4
Q ss_pred CC-CCEEEEECCHHHHHHHHHCC--------CCCCHHHHHCCCCHHHHH---HHH----HC----CCEEEEEECCCCCCH
Q ss_conf 67-87089971438899987435--------542113432136626789---885----12----681899617886622
Q gi|254780834|r 269 NS-SSFIILVEGYMDVLSLCQAG--------VQNVVSSLGTALTEYQLR---LLW----KL----SPRIVLCFDGDDPGL 328 (648)
Q Consensus 269 ~~-~~~~i~vEGy~Dvi~l~~~G--------~~n~va~~Gtalt~~~~~---~l~----r~----~~~vvl~fDgD~AG~ 328 (648)
++ ++.+-|||-.=||.++-+.+ ..+++||| +...++|++ +++ |+ .++|||++|.=-.|-
T Consensus 79 Rde~s~iCvV~~p~Dv~a~E~~~~f~G~YhVL~G~isPl-~Gigp~~~~i~~L~~riGeRl~~~~~~EVIlA~nPt~EGe 157 (205)
T TIGR00615 79 RDENSVICVVEDPKDVFALEKTKEFRGRYHVLGGLISPL-DGIGPEDLKIAALLKRIGERLQEESVKEVILATNPTVEGE 157 (205)
T ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCEEEECCEECCC-CCCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCCHHH
T ss_conf 344753687447267999876542166014315641764-5768322146889988600000057977886078984134
Q ss_pred HHHHHHHHHHHHHHHCCC-CEEEEECCCC
Q ss_conf 577788888877753697-3067525788
Q gi|254780834|r 329 RAAYKAIDLVLCHLIPGN-RVNFVLLSRG 356 (648)
Q Consensus 329 kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G 356 (648)
.-|+=..++ +++-. .|+|-.+-.|
T Consensus 158 aTa~Yi~~~----l~~~fP~~~~tRiA~G 182 (205)
T TIGR00615 158 ATALYIARL----LRPLFPGVKVTRIASG 182 (205)
T ss_pred HHHHHHHHH----HHHCCCCCEEEEEEEC
T ss_conf 799999999----8623898378655422
No 199
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=36.19 E-value=23 Score=13.73 Aligned_cols=50 Identities=24% Similarity=0.136 Sum_probs=29.4
Q ss_pred HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf 874355421134321366267898851268189961788662257778888
Q gi|254780834|r 286 LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAID 336 (648)
Q Consensus 286 l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e 336 (648)
.-.+|++ .|+.|||.+|-+|----+|+..+=+=..=.|+++|.+..|.+-
T Consensus 112 ik~~g~k-kvgLLgT~~Tm~~~fY~~~l~~~gievvvPdd~~q~~v~~iIy 161 (230)
T COG1794 112 IKAAGAK-KVGLLGTRFTMEQGFYRKRLEEKGIEVVVPDDDEQAEVNRIIY 161 (230)
T ss_pred HHHCCCC-EEEEEECCCHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHH
T ss_conf 8765886-1588613005776899999997796475677788999999999
No 200
>pfam03405 FA_desaturase_2 Fatty acid desaturase.
Probab=36.13 E-value=23 Score=13.72 Aligned_cols=14 Identities=36% Similarity=0.126 Sum_probs=8.0
Q ss_pred CCCCHHHHHHHHHC
Q ss_conf 13662678988512
Q gi|254780834|r 300 TALTEYQLRLLWKL 313 (648)
Q Consensus 300 talt~~~~~~l~r~ 313 (648)
||=-.-|--+|.+|
T Consensus 108 TAEEnRHg~~Lr~Y 121 (330)
T pfam03405 108 TAEENRHGDLLNKY 121 (330)
T ss_pred CCCCCHHHHHHHHH
T ss_conf 64434147899765
No 201
>PTZ00317 malic enzyme; Provisional
Probab=35.98 E-value=24 Score=13.70 Aligned_cols=66 Identities=17% Similarity=0.079 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHCCC-CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHH-HHHHHHHCC-CCEEEEECCCC
Q ss_conf 35542113432136-6267898851268189961788662257778888-887775369-73067525788
Q gi|254780834|r 289 AGVQNVVSSLGTAL-TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAID-LVLCHLIPG-NRVNFVLLSRG 356 (648)
Q Consensus 289 ~G~~n~va~~Gtal-t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e-~~l~~l~~g-~~v~vv~LP~G 356 (648)
.-+++++ ..---| +.+-.++|.||-++ +.||.-|-=|-.|..=|.- .++...... .+.+||+.-.|
T Consensus 235 ~~~P~~l-iqfEDF~~~nA~~lL~~Yr~~-~~~FNDDiQGTaaV~LAgll~Alritg~~l~d~riv~~GAG 303 (570)
T PTZ00317 235 ATWPSAV-VQFEDFSNNHCFDMLERYQKK-YRCFNDDIQGTGAVIAAGFLNAVKLSGVPPLEQRIVFFGAG 303 (570)
T ss_pred HHCCCEE-EEECCCCCHHHHHHHHHHHHC-CCEECCCCHHHHHHHHHHHHHHHHHHCCCHHHCEEEEECCC
T ss_conf 8789828-972448954489999999853-76421442138899999999999984998646179997788
No 202
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=35.93 E-value=24 Score=13.70 Aligned_cols=49 Identities=22% Similarity=0.356 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999872412798999999999999999999988413267621
Q gi|254780834|r 590 LLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGF 641 (648)
Q Consensus 590 ~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~e~~ 641 (648)
.+..++.++++++.+ +.|+--+-+|+++.+|+..-+.+++.-|+.+.-.
T Consensus 99 ~~~~Rl~~LE~qL~q---KADDVVSyQLLqHRrEiEEm~~~lq~Le~ri~kl 147 (178)
T PRK13182 99 TITRRLDELEEQLQQ---KADDVVSYQLLQHRREMEEMLERIQKLEARLKKL 147 (178)
T ss_pred HHHHHHHHHHHHHHH---HCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999986---4232001899987999999999999999999986
No 203
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=35.83 E-value=19 Score=14.48 Aligned_cols=52 Identities=27% Similarity=0.369 Sum_probs=25.1
Q ss_pred HHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC---CC-CHHHHH
Q ss_conf 12221015887777755753458888587879817897467136888878989989885---99-979999
Q gi|254780834|r 23 QYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL---GC-SFIESV 89 (648)
Q Consensus 23 ~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~---~~-~f~ea~ 89 (648)
+|--|+..|..+ -...++-+++ +.|+|+|-+||.- .|+--.+++ |. +|.+++
T Consensus 18 ~y~V~r~~gTE~-----pfsg~y~~~~--------~~G~Y~C~~Cg~~--LF~S~~KfdSg~GWPSF~~~i 73 (141)
T PRK00222 18 QYRVTQEHGTER-----PFTGEYLDNK--------RKGIYVCIVCGEP--LFSSDTKFDSGCGWPSFTKPI 73 (141)
T ss_pred HHHHHHHCCCCC-----CCCCCCCCCC--------CCEEEEECCCCCE--EEECCCCCCCCCCCCHHHHHC
T ss_conf 999998659889-----9887775888--------9989984699898--441155147999872031224
No 204
>PRK11020 hypothetical protein; Provisional
Probab=35.68 E-value=24 Score=13.67 Aligned_cols=39 Identities=18% Similarity=0.330 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999872412798999999999999999999988
Q gi|254780834|r 594 QKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIE 632 (648)
Q Consensus 594 ~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~ 632 (648)
++.....++..+...+|.+.+.+...++..+.+++.+++
T Consensus 13 rLD~~r~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk 51 (118)
T PRK11020 13 RLDAIRHKLAAASLRGDADKIAQFEKEKATLEKEIARLK 51 (118)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999988999974788999999999999999999998
No 205
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=35.65 E-value=24 Score=13.66 Aligned_cols=80 Identities=15% Similarity=0.077 Sum_probs=52.0
Q ss_pred HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHH------HHHHHHHHHHHHCCC--CEEEEECCCC
Q ss_conf 98743554211343213662678988512681899617886622577------788888877753697--3067525788
Q gi|254780834|r 285 SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAA------YKAIDLVLCHLIPGN--RVNFVLLSRG 356 (648)
Q Consensus 285 ~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa------~Ra~e~~l~~l~~g~--~v~vv~LP~G 356 (648)
.+++.||..+|=|+|.+ ..+.+..+..+++-+.+.+-.=+.-..-. .+.++.+.-+.+.|. -+|++.+|.=
T Consensus 62 ~~k~~gihtaieTsG~~-~~~~~~~~~~~~Dl~L~DiK~~d~~~h~~~TG~~n~~il~Nl~~l~~~~~~v~iR~pvIPg~ 140 (213)
T PRK10076 62 RLRLWGVSCAIETAGDA-PASKLLPLAKLCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGF 140 (213)
T ss_pred HHHHCCCCEEEECCCCC-CHHHHHHHHHHCCEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf 99866998899768888-89999999984598998617798489999979993999999999996799689988677997
Q ss_pred CCHHHHHHC
Q ss_conf 888899720
Q gi|254780834|r 357 EDPDSFIRC 365 (648)
Q Consensus 357 ~DPDe~ir~ 365 (648)
-|=++-++.
T Consensus 141 nd~~e~i~~ 149 (213)
T PRK10076 141 TLSRENMQQ 149 (213)
T ss_pred CCCHHHHHH
T ss_conf 899999999
No 206
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224 Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=35.40 E-value=15 Score=15.50 Aligned_cols=122 Identities=18% Similarity=0.234 Sum_probs=68.0
Q ss_pred CCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHH---------------------HCCCC-
Q ss_conf 55421134321366267898851268189961788662257778888887775---------------------36973-
Q gi|254780834|r 290 GVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHL---------------------IPGNR- 347 (648)
Q Consensus 290 G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l---------------------~~g~~- 347 (648)
|=+.+.|+||+||.+- -+=|+..|||=| +-=+++.|-+- +--..
T Consensus 13 GKTT~tANLgVALA~~---------Gk~V~~~DADI~-----MANL~LiLgmE~~~VTLhDVLAGeA~i~DAIY~gp~Gn 78 (258)
T TIGR01969 13 GKTTITANLGVALAKL---------GKKVLVLDADIT-----MANLELILGMEDKPVTLHDVLAGEADIKDAIYEGPEGN 78 (258)
T ss_pred CHHHEEEHHHHHHHHC---------CCEEEEEECCHH-----HHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC
T ss_conf 6140000077889860---------976899946766-----77689884468889675221344561001100288984
Q ss_pred EEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHH-HHHHHHCCCCCHHHHHHHHHH---HHHHHHHCCCHHHHHH
Q ss_conf 067525788888899720366889988641499279999-999853023314579999999---9988541799899999
Q gi|254780834|r 348 VNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLW-KRETENRSFNTPDERAELEIH---LKNCINHIKDQKLRYY 423 (648)
Q Consensus 348 v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~-~~l~~~~dl~spe~ka~~~~~---l~~~I~~I~d~~~R~~ 423 (648)
|+| +|.|.+=--|-|.+ +|-+++.+++=....||++ |. =-+-..+...-.+...+- +.|-|+.|.|...-.
T Consensus 79 V~V--~PagvSLEg~rKA~-~~~L~dV~~~i~~~~D~lLIDA-PAGL~~~a~~Al~~a~elLLVvNPEi~SItDaLK~k- 153 (258)
T TIGR01969 79 VKV--IPAGVSLEGLRKAD-PDKLEDVLKEIIDDTDFLLIDA-PAGLERDAVTALAAADELLLVVNPEISSITDALKVK- 153 (258)
T ss_pred EEE--ECCCCCHHHCCCCC-HHHHHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHHHHCCCCEEEECCCHHHHHHHHHHH-
T ss_conf 478--50612210001268-3332899998720437788747-898337899999861866486676544677788999-
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999988
Q gi|254780834|r 424 YSQAIRDRLQ 433 (648)
Q Consensus 424 yl~~la~~L~ 433 (648)
.++++++
T Consensus 154 ---~va~~lG 160 (258)
T TIGR01969 154 ---IVAEKLG 160 (258)
T ss_pred ---HHHHHCC
T ss_conf ---9987608
No 207
>pfam08348 PAS_6 YheO-like PAS domain. This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO. Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.
Probab=35.24 E-value=24 Score=13.61 Aligned_cols=55 Identities=20% Similarity=0.205 Sum_probs=29.1
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEE
Q ss_conf 4422567741034554205997345232012100346541000016716888970778588850
Q gi|254780834|r 158 KLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFG 221 (648)
Q Consensus 158 ~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~ 221 (648)
++| +|.. +...+.+.+..+..+.+ .+....+.+|+.. .-..|+|+|..|++||.=
T Consensus 46 ~vG-~p~t-~~~l~~l~~~~~~~~~~--~~Y~~~~~dGr~l-----kSsT~~ird~~g~~iG~L 100 (118)
T pfam08348 46 KVG-DPIT-DLALELLKEDESEEDVL--GNYETRTADGRLL-----KSSTIVIRDSDGKPIGML 100 (118)
T ss_pred CCC-CCCC-HHHHHHHHCCCCCCCCC--CCCEEECCCCCEE-----EEEEEEEECCCCCEEEEE
T ss_conf 679-8616-89999986445467725--2640277999899-----999999999999999999
No 208
>pfam00500 Late_protein_L1 L1 (late) protein.
Probab=35.19 E-value=24 Score=13.61 Aligned_cols=24 Identities=33% Similarity=0.673 Sum_probs=10.1
Q ss_pred CCCCCCCEEEEEEEE---CCCCEEEEE
Q ss_conf 000016716888970---778588850
Q gi|254780834|r 198 SYDRFRNRLIFPIRS---SRGQVIAFG 221 (648)
Q Consensus 198 ~~d~Fr~Ri~fPi~~---~~g~~i~f~ 221 (648)
.||.=+.|+++-++- .+|+..|.|
T Consensus 90 ~ynPe~eRLVW~l~Giei~RG~PLGvg 116 (503)
T pfam00500 90 LYNPDKERLVWACRGVEVGRGQPLGVG 116 (503)
T ss_pred CCCCCCCEEEEEEEEEEECCCCCCCCC
T ss_conf 779875467778888982378888127
No 209
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=35.13 E-value=24 Score=13.60 Aligned_cols=91 Identities=20% Similarity=0.270 Sum_probs=44.3
Q ss_pred CCCEECCCC----CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCC-CCEECCCCCCCCCCCCHHCCCHH-----HHHH
Q ss_conf 121003465----4100001671688897077858885010014655-30010387676535210110817-----8888
Q gi|254780834|r 187 GLLIDGDNS----ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE-SVKYLNSPETILFHKGKNLYNFF-----GALN 256 (648)
Q Consensus 187 gl~~~~~~~----~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~-~~KYlNSpeT~if~K~~~Ly~l~-----~a~~ 256 (648)
|+-+.+++- =.|.-+| .||| +.-|.+|-+.++.. --| .|+|. ..|+
T Consensus 348 ~V~I~~En~T~AtITyQNfF---rlY~------KLsGMTGTA~TE~~EF~~---------------IYnL~Vv~vPTNrp 403 (904)
T TIGR00963 348 GVEIQNENQTLATITYQNFF---RLYE------KLSGMTGTAKTEEEEFEK---------------IYNLEVVVVPTNRP 403 (904)
T ss_pred CCEEECCCCEEEEHHHHHHH---HHHH------HHCCCCCCHHHHHHHHHC---------------CCCCEEEECCCCCC
T ss_conf 86010355224404457676---5426------544687756899998404---------------57751355166772
Q ss_pred HHHHHHCCCCCCCCCCEEEEECCH------HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHC
Q ss_conf 643310000235678708997143------889998743554211343213662678988512
Q gi|254780834|r 257 YLQKSIRKDVRRNSSSFIILVEGY------MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKL 313 (648)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~i~vEGy------~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~ 313 (648)
.+|+. ..|.|+..|=- -||..+|+.|=|-=|.|- +-+.-.+|.++
T Consensus 404 ~~R~D--------~~DlvY~te~~Kw~Av~~e~~~~h~~GqPvLvGT~----svE~SE~LS~l 454 (904)
T TIGR00963 404 VIRKD--------LPDLVYKTEEEKWKAVVDEIKEIHAKGQPVLVGTT----SVEKSELLSKL 454 (904)
T ss_pred CCCCC--------CCCCEECCHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHH
T ss_conf 34467--------77734647688999999999998746898777522----17778999999
No 210
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=35.04 E-value=24 Score=13.59 Aligned_cols=63 Identities=21% Similarity=0.262 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH-HHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 36626789885126818996178866225777888-888777536973067525788888899720366889988641
Q gi|254780834|r 301 ALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI-DLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 301 alt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~-e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
.+|-+|+..|.+.-.. |--..-.+++.|.+ -.|.++ |+.| +|+||-|.++.-...+|.+++..
T Consensus 96 ~is~~qv~eIAk~K~~-----dl~~~~l~~a~k~V~GTarSm---Gi~V------eG~~Pkev~~~i~~G~~d~~~~~ 159 (163)
T PRK01143 96 NLSIEQVIKIAIMKKP-----DLLAYDLKAAVKEVLGTCVSM---GVTV------EGKDPKEVQKEVDEGKYDDLLAK 159 (163)
T ss_pred CCCHHHHHHHHHHHCC-----CCCCCCHHHHHHHHHHHHHCC---EEEE------ECCCHHHHHHHCCCCCHHHHHHH
T ss_conf 2379999999998573-----547899999999999876135---4898------57798999987176327799986
No 211
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=34.96 E-value=18 Score=14.66 Aligned_cols=59 Identities=24% Similarity=0.312 Sum_probs=30.4
Q ss_pred CCCCCEEEECCCCCCCC------CCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf 77775575345888858------787981789746713688887898998988599979999999998188
Q gi|254780834|r 34 AVKGDYWACCPFHDEKT------PSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGV 98 (648)
Q Consensus 34 ~~~~~~~~~cPfh~ekt------psf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi 98 (648)
+...++|-.|||+.++| ||+.... ..--|=+||..-.- +|+. +++..+=.+.=+++.||
T Consensus 685 Cgk~s~~~~Cp~CG~~te~~~~gPsCrmkn--tssvCesCGreCeG---ymkr-k~~L~~l~~~A~~nlg~ 749 (1173)
T TIGR00354 685 CGKESLYRVCPVCGEKTELDEYGPSCRMKN--TSSVCESCGRECEG---YMKR-KVDLKELYKEALKNLGV 749 (1173)
T ss_pred CCCCCEEEECCCCCCEEEECCCCCCCCCCC--CCCHHHCCCCCCCC---CEEE-CCCHHHHHHHHHHHCCC
T ss_conf 664000014577885454457788530035--42022105754453---1121-14389999999985752
No 212
>pfam06246 Isy1 Isy1-like splicing family. Isy1 protein is important in the optimisation of splicing.
Probab=34.72 E-value=24 Score=13.55 Aligned_cols=53 Identities=17% Similarity=0.313 Sum_probs=41.3
Q ss_pred CCCCHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2331457-9999999998854179989999999999999887657767764332
Q gi|254780834|r 394 SFNTPDE-RAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGY 446 (648)
Q Consensus 394 dl~spe~-ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~~~~~~~~ 446 (648)
++...+. |..++++|-..|+.|.|+.+=++-++++.+.++.+++.-..-....
T Consensus 42 ~L~~AekWR~~vikEIs~kvt~Iqn~~L~e~~iRdLNDeiNkL~rEK~~WE~~I 95 (253)
T pfam06246 42 SLPEAEKWRSQVIKEISRKVTEIQDPSLGEYQIRDLNDEINKLFREKRHWEDRI 95 (253)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999999999999888831899777899999999999999999999999
No 213
>TIGR00010 TIGR00010 hydrolase, TatD family; InterPro: IPR015991 Escherichia coli TatD (synonym MttC) has been shown experimentally to be a DNase . On the basis of operon structure, it was originally thought to be involved in the Sec-independent export of protein precursors bearing twin arginine signal peptides by the Tat system . This alternative membrane targeting and translocation system (Mtt), also called twin arginine translocase (Tat) (MttA1A2BC or TatABCD), has been shown to transport fully folded proteins to, or across, the membrane , . However, it was later determined that TatD is not required for this translocation process , . Furthermore, it was noted that no exact correlation exists between the ability of an organism to synthesise a TatD-like protein and whether that organism has a Tat protein transport pathway . Also, with the exception of Escherichia coli , the genetic linkage between TatD and other Tat genes (operon structure) is not maintained. Members of this group may be distantly related to a large 3D fold-based domain superfamily of metalloenzymes . The description of this fold superfamily was based on an analysis of conservation patterns in three dimensions, and the discovery that the same active-site architecture occurs in a large set of enzymes involved primarily in nucleotide metabolism. The group is thought to include urease, dihydroorotase, allantoinase, hydantoinase, AMP-, adenine- and cytosine- deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolase, formylmethanofuran dehydrogenase, and other enzymes ..
Probab=34.56 E-value=17 Score=15.11 Aligned_cols=21 Identities=38% Similarity=0.534 Sum_probs=10.2
Q ss_pred HHHH-HHHCCCCCCHHHHHCCCC
Q ss_conf 8999-874355421134321366
Q gi|254780834|r 282 DVLS-LCQAGVQNVVSSLGTALT 303 (648)
Q Consensus 282 Dvi~-l~~~G~~n~va~~Gtalt 303 (648)
+||. +.+.|++.+|++ ||.+.
T Consensus 22 ~v~~ra~~~~v~~~v~v-g~~l~ 43 (269)
T TIGR00010 22 EVIERAKAEGVTAVVDV-GTDLE 43 (269)
T ss_pred HHHHHHHHCCCEEEEEE-CCCCC
T ss_conf 99999997499299973-46700
No 214
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=34.53 E-value=25 Score=13.52 Aligned_cols=50 Identities=26% Similarity=0.172 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHCCCCC---CHHHHHCCCCH--HHHHHHHHCCCE--EEEEECCCCCC
Q ss_conf 1438899987435542---11343213662--678988512681--89961788662
Q gi|254780834|r 278 EGYMDVLSLCQAGVQN---VVSSLGTALTE--YQLRLLWKLSPR--IVLCFDGDDPG 327 (648)
Q Consensus 278 EGy~Dvi~l~~~G~~n---~va~~Gtalt~--~~~~~l~r~~~~--vvl~fDgD~AG 327 (648)
+|-||+-.+..+==+| +||+.||-.|- +-+..|..++.+ +.|=-||=-.|
T Consensus 140 ~~~~d~~~l~~~i~~~ti~vvatagtt~~G~iDpi~~i~~i~~~~~i~lHVDaa~GG 196 (375)
T PRK13520 140 DYRVDVKSVEDLIDDNTIGIVGIAGTTELGQVDPIPELSKIALENDIFLHVDAAFGG 196 (375)
T ss_pred CCCCCHHHHHHHHHHCCEEEEEECCCCCCEEECCHHHHHHHHHHCCCEEEEECCCCE
T ss_conf 886989999998864957999925887882235999999999975974998625520
No 215
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=34.51 E-value=22 Score=14.02 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=24.7
Q ss_pred HHHHHHH-HCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHH
Q ss_conf 7899998-50688535101244225677410345542059973452
Q gi|254780834|r 139 RLHYYLD-ERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKI 183 (648)
Q Consensus 139 ~a~~yl~-~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~ 183 (648)
+-++||. .||+++.|++.|.-.. ..+..|+..++.+.+.+
T Consensus 8 ~fl~~L~~erg~S~~Ti~~Y~~~l-----~~f~~~l~~~~~~~~~i 48 (296)
T PRK00283 8 QFLDALWVERGLAENTLSSYRRDL-----ELFAEWLAARGLSLAEA 48 (296)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHCCCCHHHC
T ss_conf 999999998790799999999999-----99999998759994779
No 216
>COG5328 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.35 E-value=23 Score=13.78 Aligned_cols=106 Identities=18% Similarity=0.312 Sum_probs=54.1
Q ss_pred CCHHHHHHHCCCEECCCCCCCCCC----CCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHH
Q ss_conf 973452320121003465410000----1671688897077858885010014655300103876765352101108178
Q gi|254780834|r 178 FSEEKIIEAGLLIDGDNSATSYDR----FRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFG 253 (648)
Q Consensus 178 ~~~~~~~~~gl~~~~~~~~~~~d~----Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~ 253 (648)
+..-++++-+.|-+-..+.++|+- --.|++|.|..+.|.-++- ++.-|..
T Consensus 33 VAIFDLiEeN~FeP~~~~~GPYrl~lSL~e~rLvF~i~~e~g~~v~t--------------------------HiLSLtP 86 (160)
T COG5328 33 VAIFDLIEENSFEPVGHGGGPYRLKLSLVEARLVFAIAREGGTAVAT--------------------------HILSLTP 86 (160)
T ss_pred HHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCHHHHH--------------------------HHHCCCC
T ss_conf 68988762036554778999767774402004356751168606777--------------------------6331470
Q ss_pred HHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHC-CCCHHHHH-HHHHCCCEEEEEEC
Q ss_conf 88864331000023567870899714388999874355421134321-36626789-88512681899617
Q gi|254780834|r 254 ALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGT-ALTEYQLR-LLWKLSPRIVLCFD 322 (648)
Q Consensus 254 a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gt-alt~~~~~-~l~r~~~~vvl~fD 322 (648)
-+..+ ++++++||.|.++|.-..-.--.++ -||- .+-.+--+ +..|+..+|-+-||
T Consensus 87 fRriv------------kDYfmICeSYY~AIRsstPsqIEAi-DMGRRGlHNeGSqtL~dRL~GKi~~DfD 144 (160)
T COG5328 87 FRRIV------------KDYFMICESYYQAIRSSTPSQIEAI-DMGRRGLHNEGSQTLMDRLSGKIKVDFD 144 (160)
T ss_pred HHHHH------------HHHHHHHHHHHHHHHHCCHHHHHHH-HHCCCCCCCCCHHHHHHHHCCCEEECHH
T ss_conf 88888------------7898879999999970887664576-5112224451078999986496441428
No 217
>TIGR01426 MGT glycosyltransferase, MGT family; InterPro: IPR006326 These sequences belong to the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production. ; GO: 0016758 transferase activity transferring hexosyl groups, 0016999 antibiotic metabolic process.
Probab=34.19 E-value=25 Score=13.48 Aligned_cols=103 Identities=14% Similarity=0.097 Sum_probs=52.5
Q ss_pred CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC--EEEEECCCCCCHHHHHHCCCHHH
Q ss_conf 2113432136626789885126818996178866225777888888777536973--06752578888889972036688
Q gi|254780834|r 293 NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNR--VNFVLLSRGEDPDSFIRCYGKTA 370 (648)
Q Consensus 293 n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~--v~vv~LP~G~DPDe~ir~~G~ea 370 (648)
-+..+|||+||..-.++.+-| .+|+. +.. .=|+.+-.+.||++|= .=++.
T Consensus 262 V~liSLGTvFn~~p~~fyr~f------------------~~AF~--------~~~GW~vV~~~g~~vDp~~L~--~~P~N 313 (429)
T TIGR01426 262 VVLISLGTVFNAQPSKFYRTF------------------VEAFR--------DLPGWHVVLSVGKGVDPADLG--ELPKN 313 (429)
T ss_pred EEEEECCHHHCCCHHHHHHHH------------------HHHCC--------CCCCCEEEEEECCCCCHHHHC--CCCCC
T ss_conf 699975614412447999999------------------98608--------998707999726702646616--79887
Q ss_pred HHHHHHHCCCHHHHHH--HHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 9988641499279999--9998530233145799999999988541799899999999999
Q gi|254780834|r 371 FEKLIVESLPLVDMLW--KRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIR 429 (648)
Q Consensus 371 f~~ll~~A~~l~dFl~--~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la 429 (648)
| .+.+..|-.|.|= +.......++|. .+++..-.|++. ||-...+.+..+.++
T Consensus 314 v--~VR~~VPq~evL~~A~lfvTHgGmnSt---~EaL~~gVP~va-~P~~adQ~~~A~R~~ 368 (429)
T TIGR01426 314 V--EVRRWVPQLEVLEKADLFVTHGGMNST---MEALAAGVPLVA-VPQGADQPMTARRIA 368 (429)
T ss_pred E--EEECCCCHHHHHHHHHHHHHCCCCHHH---HHHHHCCCCEEE-ECCCCCCHHHHHHHH
T ss_conf 7--885465627789888888631660158---999964996898-517888013765751
No 218
>PRK09490 metH B12-dependent methionine synthase; Provisional
Probab=33.81 E-value=24 Score=13.63 Aligned_cols=63 Identities=13% Similarity=0.176 Sum_probs=33.8
Q ss_pred ECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 136888878989989885999799999999981---88587768203677-----788999999999999999997
Q gi|254780834|r 64 CFSCHVKGDHLSFLSALLGCSFIESVQRLAAIA---GVPLPVVDPKIEKK-----EKIQTDLIRLIEVATDFFHHS 131 (648)
Q Consensus 64 cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~---gi~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~ 131 (648)
.+.|.-.|+ -++-|++-||.|+.+-..| |-++=+.++....+ .......++++..+++.-+..
T Consensus 48 ~~~~~l~g~-----~e~Lnlt~Pd~I~~IH~~YleAGaDiIeTNTFgan~~~l~~ygle~~v~ein~~aa~lAr~a 118 (1229)
T PRK09490 48 DWPCDLKGN-----NDLLVLTQPDVIEAIHRAYLEAGADIIETNTFNATTIAQADYGMESLVYELNVEAARLAREA 118 (1229)
T ss_pred CCCCCCCCC-----CCHHHCCCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 475435698-----20523588899999999999836999983699888424544593778999999999999999
No 219
>pfam03393 Pneumo_matrix Pneumovirus matrix protein.
Probab=33.70 E-value=16 Score=15.34 Aligned_cols=16 Identities=13% Similarity=0.169 Sum_probs=7.3
Q ss_pred CCCCHHHHHHHCCCEE
Q ss_conf 5997345232012100
Q gi|254780834|r 176 KGFSEEKIIEAGLLID 191 (648)
Q Consensus 176 ~~~~~~~~~~~gl~~~ 191 (648)
.|.+....++..|+-+
T Consensus 10 ~GvpYTAAVQ~~lvEK 25 (252)
T pfam03393 10 EGSPYTAAVQYNVLEK 25 (252)
T ss_pred CCCCCEEEEEEEEEEC
T ss_conf 5875013788513413
No 220
>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members.
Probab=33.62 E-value=16 Score=15.26 Aligned_cols=12 Identities=42% Similarity=0.255 Sum_probs=4.8
Q ss_pred CCHHHHHHHHHC
Q ss_conf 662678988512
Q gi|254780834|r 302 LTEYQLRLLWKL 313 (648)
Q Consensus 302 lt~~~~~~l~r~ 313 (648)
|+++.+.-+...
T Consensus 253 Lneev~~~~~v~ 264 (391)
T TIGR03287 253 LSEEVLENLKVL 264 (391)
T ss_pred CCHHHHHHHCCC
T ss_conf 699999860575
No 221
>PTZ00124 adenosine deaminase; Provisional
Probab=33.54 E-value=25 Score=13.40 Aligned_cols=125 Identities=10% Similarity=0.028 Sum_probs=64.8
Q ss_pred EECCCCEEEECCCCCCCCHHHHHHHH---------CCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH---HHHHHHHHHHH
Q ss_conf 81789746713688887898998988---------5999799999999981885877682036777---88999999999
Q gi|254780834|r 55 CNDSKGFYYCFSCHVKGDHLSFLSAL---------LGCSFIESVQRLAAIAGVPLPVVDPKIEKKE---KIQTDLIRLIE 122 (648)
Q Consensus 55 v~~~~~~~~cf~c~~~gd~~~f~~~~---------~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~---~~~~~~~~~~~ 122 (648)
|-|.-.+---|+|=..-+++.|+.++ +|-=-++.+..||.+.|++++.........- ..-..+.+.++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~k~LPKvELH~HLdGslrp~tl~eLA~~~~i~~~~~~~e~~~~~~~~~~~~sL~~fL~ 89 (362)
T PTZ00124 10 VLPKDELNIDLSKMGKKERYKIWKRMPKCELHCHLDICFSVDFFIDIIRKYNEQPNLSDEEILDYYLFNKKGKSLVEFVE 89 (362)
T ss_pred HCCCCCCCCCHHHCCHHHHHHHHHHCHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCHHHHHH
T ss_conf 33201157326556627899999859247877076288899999999998198999996999999871467687999999
Q ss_pred HHHHHHHHHHCCCCC--HHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCC
Q ss_conf 999999997326777--578999985068853510124422567741034554205997345232012
Q gi|254780834|r 123 VATDFFHHSLKNARD--KRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGL 188 (648)
Q Consensus 123 ~~~~~~~~~l~~~~~--~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl 188 (648)
. ..+-...|.+.+. ..|.+|+.. ...+=+....+-|+|.- +..+.|++.++.+++-+
T Consensus 90 ~-f~~~~~vl~~~e~l~r~a~e~~~d--~~~dgV~Y~EiRf~P~~------~~~~~g~s~~~v~~av~ 148 (362)
T PTZ00124 90 K-ARMICDIFADYSVLEDLAKHAVFN--KYKEGVVLMEFRYSPAF------LAFKCNLDYDLIHNAIV 148 (362)
T ss_pred H-HHHHHHHHCCHHHHHHHHHHHHHH--HHHCCCEEEEEEECCCC------CCCCCCCCHHHHHHHHH
T ss_conf 9-999999974999999999999999--99739828999757320------26678998899999999
No 222
>pfam04392 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Probab=33.41 E-value=26 Score=13.38 Aligned_cols=81 Identities=17% Similarity=0.134 Sum_probs=52.8
Q ss_pred EEEECCHHHHHH------HHHCCCCCCHHHHHCCCCHHHHHHHHHCC---CEEEEEECCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 899714388999------87435542113432136626789885126---818996178866225777888888777536
Q gi|254780834|r 274 IILVEGYMDVLS------LCQAGVQNVVSSLGTALTEYQLRLLWKLS---PRIVLCFDGDDPGLRAAYKAIDLVLCHLIP 344 (648)
Q Consensus 274 ~i~vEGy~Dvi~------l~~~G~~n~va~~Gtalt~~~~~~l~r~~---~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~ 344 (648)
-||.-+..|-+. +.+-| .|+-...-......|+.+++++. ++|.+.||.++++-.+..+.+....+ +.
T Consensus 82 PIVf~~v~dPv~aglv~s~~~pg-~NvTGvs~~~~~~~~l~ll~~l~P~~k~igviyn~~e~~s~~~~~~~~~~a~--~~ 158 (292)
T pfam04392 82 PIVFAAVTDPVGAKLVPSKEQPG-ENVTGVSDLVDVEQTIELIKKLLPNVKSIGVYYSPSEANSVSLVEEIKKYAK--KS 158 (292)
T ss_pred CEEEEEECCHHHHCCCCCCCCCC-CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHH--HC
T ss_conf 98999726856606644566899-8267852774799999999986889858999957998657999999999999--76
Q ss_pred CCCEEEEECCCCC
Q ss_conf 9730675257888
Q gi|254780834|r 345 GNRVNFVLLSRGE 357 (648)
Q Consensus 345 g~~v~vv~LP~G~ 357 (648)
|+++..+..+...
T Consensus 159 gi~l~~~~v~~~~ 171 (292)
T pfam04392 159 GIKVVEASVPSSN 171 (292)
T ss_pred CCEEEEEECCCHH
T ss_conf 9989999668866
No 223
>KOG3214 consensus
Probab=33.39 E-value=23 Score=13.75 Aligned_cols=54 Identities=20% Similarity=0.268 Sum_probs=28.8
Q ss_pred EEEECCCCC-CCCCCEEEE--CCCCEEEECCCCCCC-CHHHHHHHHCCC----CHHHHHHHHHH
Q ss_conf 575345888-858787981--789746713688887-898998988599----97999999999
Q gi|254780834|r 39 YWACCPFHD-EKTPSFHCN--DSKGFYYCFSCHVKG-DHLSFLSALLGC----SFIESVQRLAA 94 (648)
Q Consensus 39 ~~~~cPfh~-ektpsf~v~--~~~~~~~cf~c~~~g-d~~~f~~~~~~~----~f~ea~~~la~ 94 (648)
-+=-|||.+ ||.-|.++. ...|+-+|=-|+++- --|+.+. +.+ ++.+|++....
T Consensus 22 t~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~Ls--epIDVYSdWiDaCe~vn~ 83 (109)
T KOG3214 22 TQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALS--EPIDVYSDWIDACEAVNN 83 (109)
T ss_pred EEECCCCCCCCCCEEEEEHHHCCCCEEEEEEHHHHHCCCHHHHC--CCHHHHHHHHHHHHHHHC
T ss_conf 16516743551110244113217562644405445255267645--544788999999998613
No 224
>cd03372 TPP_ComE Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.
Probab=32.80 E-value=26 Score=13.30 Aligned_cols=59 Identities=25% Similarity=0.232 Sum_probs=30.9
Q ss_pred CHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 1134321366267898851268189961788662257778888887775369730675257888
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE 357 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~ 357 (648)
.+.+||-++.-.--..+.+ ++-|+|+|||.+=+- ...+++..-.....++.++.|.++.
T Consensus 40 ~lGtMG~~~p~aiGaa~a~--p~kVi~i~GDGs~lM---~~geL~Ti~~~~~~n~~~ivlnN~~ 98 (179)
T cd03372 40 MLGSMGLASSIGLGLALAQ--PRKVIVIDGDGSLLM---NLGALATIAAEKPKNLIIVVLDNGA 98 (179)
T ss_pred EECHHHHHHHHHHHHHHCC--CCCEEEEECCHHHHH---HHHHHHHHHHHCCCCEEEEEEECCC
T ss_conf 3134450889999998657--996899967804654---3669999997268978999983887
No 225
>pfam05566 Pox_vIL-18BP Orthopoxvirus interleukin 18 binding protein. Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections.
Probab=32.78 E-value=24 Score=13.60 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=24.2
Q ss_pred EECCCCC---CCCCCEEEECCCCEEEECCCCCCCCHHH
Q ss_conf 5345888---8587879817897467136888878989
Q gi|254780834|r 41 ACCPFHD---EKTPSFHCNDSKGFYYCFSCHVKGDHLS 75 (648)
Q Consensus 41 ~~cPfh~---ektpsf~v~~~~~~~~cf~c~~~gd~~~ 75 (648)
+.-|+-+ -|-|.+.+....|-|||-||-+.---|+
T Consensus 13 cvh~yvna~e~kcpnl~ivtssgef~csgcv~~mp~fs 50 (126)
T pfam05566 13 CVHPYVNADEIKCPNLDIVTSSGEFRCSGCVEFMPKFS 50 (126)
T ss_pred CCCCCCCCCCCCCCCCCEEECCCCEEEEEHHHHCCCCH
T ss_conf 67531261002489832680468288611454385611
No 226
>TIGR00357 TIGR00357 methionine-R-sulfoxide reductase; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine . It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set , . The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A . The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N-terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity.
Probab=32.76 E-value=21 Score=14.09 Aligned_cols=15 Identities=27% Similarity=0.525 Sum_probs=11.7
Q ss_pred EECCCCEEEECCCCC
Q ss_conf 817897467136888
Q gi|254780834|r 55 CNDSKGFYYCFSCHV 69 (648)
Q Consensus 55 v~~~~~~~~cf~c~~ 69 (648)
-+-+.|+|+|-.||+
T Consensus 34 ~~~~~GiY~di~~g~ 48 (135)
T TIGR00357 34 DNKEDGIYVDITCGE 48 (135)
T ss_pred CCCCCCCEEEECCCC
T ss_conf 124787427621688
No 227
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=32.60 E-value=26 Score=13.28 Aligned_cols=65 Identities=25% Similarity=0.297 Sum_probs=37.3
Q ss_pred CCCCCCCCCHHHHHHHCC--CCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEEC
Q ss_conf 422567741034554205--9973452320121003465410000167168889707785888501001465530010
Q gi|254780834|r 159 LGYAPDSRYSLREHLRQK--GFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYL 234 (648)
Q Consensus 159 lG~ap~~~~~l~~~l~~~--~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYl 234 (648)
=|||+ -+.|...+.+. ..+.+.+ -+++..++++. |-.+ + .-|+-.+|.-|-..=+ +.+++.|++|
T Consensus 57 ~Gwa~--i~~l~~~~~k~~~~~~~~~l--~~iV~~d~K~R--f~l~-~---~~IRA~yGHSi~V~l~-~~~~~~p~~L 123 (211)
T COG1859 57 EGWAD--IDELLEGLRKAGRWLTRELL--LAVVATDDKGR--FELK-E---GKIRARYGHSIPVDLR-LPEAEPPAVL 123 (211)
T ss_pred CCCHH--HHHHHHHHHHHCCCCCHHHH--HHHHHCCCCCE--EEEC-C---CCEEECCCCCEEEECC-CCCCCCCCEE
T ss_conf 66561--99999888762467799999--99984288750--6841-6---6266404753577514-7777898677
No 228
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=32.45 E-value=26 Score=13.26 Aligned_cols=11 Identities=27% Similarity=0.211 Sum_probs=4.0
Q ss_pred CHHHHHHHHHH
Q ss_conf 14579999999
Q gi|254780834|r 397 TPDERAELEIH 407 (648)
Q Consensus 397 spe~ka~~~~~ 407 (648)
|.++.+.++.+
T Consensus 189 s~~e~~~~i~~ 199 (377)
T COG3454 189 SDEEFAEFIEE 199 (377)
T ss_pred CHHHHHHHHHH
T ss_conf 99999999999
No 229
>KOG0257 consensus
Probab=32.41 E-value=26 Score=13.25 Aligned_cols=104 Identities=15% Similarity=0.154 Sum_probs=56.1
Q ss_pred HHHHHCCCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCC----HHHHHHCCC
Q ss_conf 134321366267898851268--1899617886622577788888877753697-306752578888----889972036
Q gi|254780834|r 295 VSSLGTALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFVLLSRGED----PDSFIRCYG 367 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv~LP~G~D----PDe~ir~~G 367 (648)
=-|.|+.+|++++..|-++|. .+++.+|. +-+. ++-+|. -+|++.||+=.+ --|+-+..|
T Consensus 182 hNPtGkvfsReeLe~ia~l~~k~~~lvisDe----------vYe~---~v~d~~~h~r~aslPgm~ertitvgS~gKtf~ 248 (420)
T KOG0257 182 HNPTGKVFSREELERIAELCKKHGLLVISDE----------VYEW---LVYDGNKHIRIASLPGMYERTITVGSFGKTFG 248 (420)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCEEEEEHH----------HHHH---HHHCCCCCEEEECCCCHHHEEEEECCCCCEEE
T ss_conf 9986730579999999999987897999825----------7478---82178765146227762244788514521000
Q ss_pred HHHHHHH-HHHCCCHHHHHHHHHHH--HCCCCCHHHHHHHHHHHHHHH
Q ss_conf 6889988-64149927999999985--302331457999999999885
Q gi|254780834|r 368 KTAFEKL-IVESLPLVDMLWKRETE--NRSFNTPDERAELEIHLKNCI 412 (648)
Q Consensus 368 ~eaf~~l-l~~A~~l~dFl~~~l~~--~~dl~spe~ka~~~~~l~~~I 412 (648)
.-+|+-= +--...+.... ..... .+...||-+.|.+...-.++.
T Consensus 249 ~TGWrlGW~igp~~L~~~~-~~vh~~~~~~~~Tp~q~A~a~a~~~~~~ 295 (420)
T KOG0257 249 VTGWRLGWAIGPKHLYSAL-FPVHQNFVFTCPTPIQEASAAAFALELA 295 (420)
T ss_pred EEEEEEEEEECHHHHHHHH-HHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 0345653464548764647-8786455202680778999998740020
No 230
>LOAD_USPA consensus
Probab=32.37 E-value=26 Score=13.25 Aligned_cols=38 Identities=21% Similarity=0.311 Sum_probs=29.6
Q ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf 81899617886622577788888877753697306752578
Q gi|254780834|r 315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR 355 (648)
Q Consensus 315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~ 355 (648)
++|+++.|+.+...+|...|++++... +-.+.++..=+
T Consensus 1 k~Ilv~vd~s~~s~~a~~~A~~la~~~---~a~l~~lhV~~ 38 (135)
T LOAD_USPA 1 KKILVAIDGSPESEKALRWAVDLAKRR---GAELILLHVIP 38 (135)
T ss_pred CEEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEEEEC
T ss_conf 989999869989999999999999874---99899999962
No 231
>PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed
Probab=32.05 E-value=27 Score=13.21 Aligned_cols=78 Identities=17% Similarity=0.123 Sum_probs=39.0
Q ss_pred HHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE--E----EEEECCCCCCHHHHH-HHHHHHHHHHHCCCCEEE-EECCCC
Q ss_conf 98743554211343213662678988512681--8----996178866225777-888888777536973067-525788
Q gi|254780834|r 285 SLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR--I----VLCFDGDDPGLRAAY-KAIDLVLCHLIPGNRVNF-VLLSRG 356 (648)
Q Consensus 285 ~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~--v----vl~fDgD~AG~kAa~-Ra~e~~l~~l~~g~~v~v-v~LP~G 356 (648)
.+...|..-+=..||| |++||+.|.+-.+. + ..-=..-........ +.-..+...+..++.|-| +..|.|
T Consensus 259 ~~~~~Ga~iIGGCCGT--TPeHIraia~al~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~vEldpP~~ 336 (608)
T PRK08645 259 EFVEEGVRLIGGCCGT--TPEHIRAMKEALRGLKPVVEKEVIPIPKKEPFHPKPSKVKSSLLEKVKKKFTVIVELDPPKG 336 (608)
T ss_pred HHHHCCCCEEEECCCC--CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCEEEEEECCCCC
T ss_conf 9998599799757799--99999999998447899775555666666667887766777589996379679999549999
Q ss_pred CCHHHHHH
Q ss_conf 88889972
Q gi|254780834|r 357 EDPDSFIR 364 (648)
Q Consensus 357 ~DPDe~ir 364 (648)
.|++-++.
T Consensus 337 ~d~~~~~~ 344 (608)
T PRK08645 337 LDTDKFLE 344 (608)
T ss_pred CCHHHHHH
T ss_conf 98789999
No 232
>pfam00949 Peptidase_S7 Peptidase S7, Flavivirus NS3 serine protease. The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
Probab=31.95 E-value=27 Score=13.19 Aligned_cols=18 Identities=33% Similarity=0.604 Sum_probs=12.5
Q ss_pred EEEECCCCEEEEECCCCC
Q ss_conf 897077858885010014
Q gi|254780834|r 209 PIRSSRGQVIAFGGRTLS 226 (648)
Q Consensus 209 Pi~~~~g~~i~f~gR~l~ 226 (648)
||.|..|+|+|+.|-.+.
T Consensus 118 pI~N~~g~ivGlYgngl~ 135 (150)
T pfam00949 118 PIFNQNGQIVGLYGNGLV 135 (150)
T ss_pred CEECCCCCEEEEECCEEE
T ss_conf 658689979999536499
No 233
>pfam10911 DUF2717 Protein of unknown function (DUF2717). Members in this family of proteins are annotated as gene 6.5 protein however currently there is no known function.
Probab=31.82 E-value=27 Score=13.18 Aligned_cols=12 Identities=42% Similarity=0.736 Sum_probs=4.1
Q ss_pred HHHHHCCCCCHH
Q ss_conf 455420599734
Q gi|254780834|r 170 REHLRQKGFSEE 181 (648)
Q Consensus 170 ~~~l~~~~~~~~ 181 (648)
++.|+..||++.
T Consensus 41 i~~Lr~aGySE~ 52 (77)
T pfam10911 41 IDDLRAAGYSES 52 (77)
T ss_pred HHHHHHCCCCHH
T ss_conf 999988466299
No 234
>cd00817 ValRS_core This is the catalytic core domain of valine amino-acyl tRNA synthetases (ValRS) . This enzyme is a monomer, which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=31.70 E-value=27 Score=13.16 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=22.0
Q ss_pred CCCCHHHHHHCCCHHHHHHHHHHCCCH
Q ss_conf 888888997203668899886414992
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLIVESLPL 381 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll~~A~~l 381 (648)
+..||++++.++|.|+++-++-.+.|+
T Consensus 331 Nvv~p~~~l~~yg~D~lRy~l~~~~~~ 357 (363)
T cd00817 331 NVIDPLDVIDGYGADALRFTLASAASQ 357 (363)
T ss_pred CCCCHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 866989999877927999999952998
No 235
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=31.67 E-value=27 Score=13.16 Aligned_cols=27 Identities=15% Similarity=0.150 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf 788888899720366889988641499
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVESLP 380 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A~~ 380 (648)
-+..||++.+.++|+|+++-.+..+-.
T Consensus 642 GNvvdP~~ii~~yGADalRl~~as~~~ 668 (966)
T PRK13804 642 GNVVDPQDVIKQSGADILRLWVASVDY 668 (966)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 898998999987292188899984775
No 236
>KOG2361 consensus
Probab=31.62 E-value=24 Score=13.63 Aligned_cols=16 Identities=25% Similarity=0.256 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHHHCC
Q ss_conf 7778888887775369
Q gi|254780834|r 330 AAYKAIDLVLCHLIPG 345 (648)
Q Consensus 330 Aa~Ra~e~~l~~l~~g 345 (648)
+..++++.+..++++|
T Consensus 161 k~~~a~~nl~~llKPG 176 (264)
T KOG2361 161 KMQSVIKNLRTLLKPG 176 (264)
T ss_pred HHHHHHHHHHHHHCCC
T ss_conf 7899999999974888
No 237
>pfam03976 PPK2 Polyphosphate kinase 2 (PPK2). Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases.
Probab=31.62 E-value=27 Score=13.15 Aligned_cols=42 Identities=26% Similarity=0.359 Sum_probs=28.4
Q ss_pred CHHHHHCCCCHHHHHHHHHCCCEEEEEECC-CCCCHHHHHHHHH
Q ss_conf 113432136626789885126818996178-8662257778888
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKLSPRIVLCFDG-DDPGLRAAYKAID 336 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~~~~vvl~fDg-D~AG~kAa~Ra~e 336 (648)
.+..|...|..-|-.+-. ....|++.|.| |.||+-.+.+.+-
T Consensus 10 ~~~~L~~~L~~lQ~~l~~-~~~~viIv~eG~daaGKg~~I~~l~ 52 (229)
T pfam03976 10 ELAKLQIELVKLQEWVYA-EGKKLVVIFEGRDAAGKGGAIKRIT 52 (229)
T ss_pred HHHHHHHHHHHHHHHHHH-CCCCEEEEEECCCCCCCHHHHHHHH
T ss_conf 999999999999999997-5994899996657787369999998
No 238
>COG1206 Gid NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]
Probab=31.58 E-value=19 Score=14.54 Aligned_cols=146 Identities=21% Similarity=0.250 Sum_probs=82.4
Q ss_pred CCCEEEEEEEECC---CCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEC
Q ss_conf 1671688897077---8588850100146553001038767653521011081788886433100002356787089971
Q gi|254780834|r 202 FRNRLIFPIRSSR---GQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVE 278 (648)
Q Consensus 202 Fr~Ri~fPi~~~~---g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vE 278 (648)
|.|-+- ||.+.- -.++-|..|- |+++ .-|||-|=| ....+.++.|.-...+.... ...+. ...|
T Consensus 159 FyDAaA-PIi~~dSIdmd~~~~~sRY-dKg~-a~YiNCPmt-----kEey~~F~eaL~~ae~~~~k----~fEk~-~~Fe 225 (439)
T COG1206 159 FYDAAA-PIIEFDSIDMDKAYLKSRY-DKGE-ADYINCPMT-----KEEYLAFYEALIEAEKAPLK----DFEKE-KYFE 225 (439)
T ss_pred EECCCC-CEEECCCCCHHHHHHHHCC-CCCC-CHHHCCCCC-----HHHHHHHHHHHHHCCCCCHH----HHCCC-CCCC
T ss_conf 621247-4332055434777765003-5564-112069888-----99999999999743457834----41256-1214
Q ss_pred CHHHHHHHHHCCCCCC----HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf 4388999874355421----134321366267898851268189961788662257778888887775369730675257
Q gi|254780834|r 279 GYMDVLSLCQAGVQNV----VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLS 354 (648)
Q Consensus 279 Gy~Dvi~l~~~G~~n~----va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP 354 (648)
|-|-.=-+.+-|.+.- .-|.| |+.-+--.-++ .--||=.---|++|.--.+=+.+. .|+-|-+-+|..+=
T Consensus 226 gCmPIE~mA~rG~~Tl~~GPmKPvG--L~~p~~~tgk~-pYAVVQLRqdna~GtLynmVGFQT---~LkwgeQkrVf~mI 299 (439)
T COG1206 226 GCMPIEVMAERGRKTLRFGPMKPVG--LEDPRDPTGKR-PYAVVQLRQDNAAGTLYNMVGFQT---HLKWGEQKRVFRMI 299 (439)
T ss_pred CCCCHHHHHHHCCCHHCCCCCCCCC--CCCCCCCCCCC-CEEEEEEECCCCCCCEEEEEEEEE---CCCHHHHHHHHHHC
T ss_conf 5676999986270001248888757--77887777888-617998520465664465430130---35210255465536
Q ss_pred CCCCHHHHHHCC
Q ss_conf 888888997203
Q gi|254780834|r 355 RGEDPDSFIRCY 366 (648)
Q Consensus 355 ~G~DPDe~ir~~ 366 (648)
.|..-.+|+|-.
T Consensus 300 PgLeNAefvRyG 311 (439)
T COG1206 300 PGLENAEFVRYG 311 (439)
T ss_pred CCCCHHHHHHCC
T ss_conf 783111444203
No 239
>cd03785 GT1_MurG MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=31.43 E-value=27 Score=13.13 Aligned_cols=66 Identities=27% Similarity=0.341 Sum_probs=41.0
Q ss_pred HHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH---HHHHHCCCCCCH----HHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf 01108178888643310000235678708997143889---998743554211----34321366267898851268189
Q gi|254780834|r 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV---LSLCQAGVQNVV----SSLGTALTEYQLRLLWKLSPRIV 318 (648)
Q Consensus 246 ~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv---i~l~~~G~~n~v----a~~Gtalt~~~~~~l~r~~~~vv 318 (648)
+.+.++.++...+++.++ +-+|-+=||.-+ ++.+..|++-++ +.+|.+ -+++.++++.|.
T Consensus 73 ~~~~~~~~~~~~l~~~kP--------d~vi~~GGY~s~P~~laA~~~~iP~~ihEqN~v~G~a-----nr~l~~~a~~i~ 139 (350)
T cd03785 73 KLLKGVLQARKILKKFKP--------DVVVGFGGYVSGPVGLAAKLLGIPLVIHEQNAVPGLA-----NRLLARFADRVA 139 (350)
T ss_pred HHHHHHHHHHHHHHHCCC--------CEEEECCCCHHHHHHHHHHHCCCCCEEECCCCCCCHH-----HHHHCCCCCEEE
T ss_conf 999999999999996499--------9999889810389999999729985565677225713-----233210039899
Q ss_pred EEECCC
Q ss_conf 961788
Q gi|254780834|r 319 LCFDGD 324 (648)
Q Consensus 319 l~fDgD 324 (648)
+.|+..
T Consensus 140 ~~f~~~ 145 (350)
T cd03785 140 LSFPET 145 (350)
T ss_pred ECCHHH
T ss_conf 857565
No 240
>PRK04023 DNA polymerase II large subunit; Validated
Probab=31.42 E-value=26 Score=13.34 Aligned_cols=19 Identities=37% Similarity=0.364 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHHCCCCCC
Q ss_conf 99799999999981885877
Q gi|254780834|r 83 CSFIESVQRLAAIAGVPLPV 102 (648)
Q Consensus 83 ~~f~ea~~~la~~~gi~~~~ 102 (648)
.++-||++ ++..+|+++..
T Consensus 453 ps~eEA~~-iS~~~~vPLHP 471 (1128)
T PRK04023 453 PSQEEALK-LSEEYGVPLHP 471 (1128)
T ss_pred CCHHHHHH-HHHHHCCCCCC
T ss_conf 89999999-99983999899
No 241
>TIGR01943 rnfA electron transport complex, RnfABCDGE type, A subunit; InterPro: IPR011293 The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This entry describes the A subunit.; GO: 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=31.22 E-value=13 Score=16.03 Aligned_cols=13 Identities=8% Similarity=-0.210 Sum_probs=4.2
Q ss_pred CHHHHHHHHHHHH
Q ss_conf 1457999999999
Q gi|254780834|r 397 TPDERAELEIHLK 409 (648)
Q Consensus 397 spe~ka~~~~~l~ 409 (648)
++-|...+.-.+.
T Consensus 37 ~A~GMg~AvtFVm 49 (193)
T TIGR01943 37 TAVGMGLAVTFVM 49 (193)
T ss_pred HHCCCCHHHHHHH
T ss_conf 3216618999999
No 242
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=30.87 E-value=27 Score=13.20 Aligned_cols=42 Identities=19% Similarity=0.301 Sum_probs=23.0
Q ss_pred HCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHH
Q ss_conf 222101588777775575345888858787981789746713688887898998988
Q gi|254780834|r 24 YVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSAL 80 (648)
Q Consensus 24 ~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~ 80 (648)
|--|+..|.- .-...++.+++ +.|+|+|-+||.- .|+--+++
T Consensus 12 y~v~r~~gTE-----~pfsg~y~~~~--------~~G~y~C~~C~~~--LF~s~~Kf 53 (284)
T PRK05550 12 YRVIEDKGTE-----RPFSGEYYDHD--------EKGVYLCKKCGAP--LFRSEDKF 53 (284)
T ss_pred HHHHHHCCCC-----CCCCCCCCCCC--------CCEEEEECCCCCC--CCCCCCCC
T ss_conf 9999736889-----99877554898--------9879994589970--45566514
No 243
>TIGR02918 TIGR02918 conserved hypothetical protein TIGR02918; InterPro: IPR014267 Members of this entry are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus..
Probab=30.86 E-value=17 Score=15.03 Aligned_cols=253 Identities=18% Similarity=0.262 Sum_probs=113.9
Q ss_pred CCCCCCCCCCHHHHHHHC-----CCCCHHHHHHH-CCC--EECC-CCCCCCCCCC-CE---EEEEEEECCCCEEE-----
Q ss_conf 442256774103455420-----59973452320-121--0034-6541000016-71---68889707785888-----
Q gi|254780834|r 158 KLGYAPDSRYSLREHLRQ-----KGFSEEKIIEA-GLL--IDGD-NSATSYDRFR-NR---LIFPIRSSRGQVIA----- 219 (648)
Q Consensus 158 ~lG~ap~~~~~l~~~l~~-----~~~~~~~~~~~-gl~--~~~~-~~~~~~d~Fr-~R---i~fPi~~~~g~~i~----- 219 (648)
.|||--+.==+|++|... ..|+.++|.+. |.- .... +|+..-=.|. +- |+.=..|+.-++|-
T Consensus 54 NiGF~D~eiIWLY~yFTDiKIAPTtYTvd~l~~~l~~~~~~~E~vnGK~~~~ff~l~~~~fv~cyL~~E~~~~VdRvEyV 133 (511)
T TIGR02918 54 NIGFKDDEIIWLYQYFTDIKIAPTTYTVDDLEKELGLEITRREKVNGKVVKLFFNLNDSIFVTCYLKNESKDIVDRVEYV 133 (511)
T ss_pred HCCCCCCCEEEEEECCCCCEECCCCCCHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCEEEEEEEECCCCCCEEEEEEE
T ss_conf 44898775788430246530524544078989751885403510066089999984697399998634888804676777
Q ss_pred EECCCCC-------------------------------CCCC--CEECCCCCCCCCC-CC-HHCCCHHHHHHHHHHHHCC
Q ss_conf 5010014-------------------------------6553--0010387676535-21-0110817888864331000
Q gi|254780834|r 220 FGGRTLS-------------------------------KGES--VKYLNSPETILFH-KG-KNLYNFFGALNYLQKSIRK 264 (648)
Q Consensus 220 f~gR~l~-------------------------------~~~~--~KYlNSpeT~if~-K~-~~Ly~l~~a~~~~~~~~~~ 264 (648)
+.|..+. ++.- --|||.-+..+|+ +- .+||+ |++.-...--
T Consensus 134 ~~G~LiRKDfYSYTr~fsEYYAP~Dn~A~LY~R~FYNEDGSIAY~e~~dqG~~s~F~F~dG~iLYs----K~eliayFl~ 209 (511)
T TIGR02918 134 SNGKLIRKDFYSYTRVFSEYYAPADNKAKLYQRTFYNEDGSIAYEEYVDQGDESVFVFKDGKILYS----KQELIAYFLK 209 (511)
T ss_pred ECCEEEEEECCCCEEEEEEECCCCCCCCEEEECEEECCCCCHHHHHCCCCCCCEEEECCCCCEECC----HHHHHHHHHH
T ss_conf 378224231134132356411776798547101124258834344203798843678379745418----6999999999
Q ss_pred CCCCCCCCEEEEECCHHH--HHHHHHCCCCC-CHHHHHC----------CCCHHHHHHHHHC--------CCEEEEEECC
Q ss_conf 023567870899714388--99987435542-1134321----------3662678988512--------6818996178
Q gi|254780834|r 265 DVRRNSSSFIILVEGYMD--VLSLCQAGVQN-VVSSLGT----------ALTEYQLRLLWKL--------SPRIVLCFDG 323 (648)
Q Consensus 265 ~~~~~~~~~~i~vEGy~D--vi~l~~~G~~n-~va~~Gt----------alt~~~~~~l~r~--------~~~vvl~fDg 323 (648)
+......|-+| +-=-.| -+.-=|+=++| .-|=+|. +.|+.|| ||+- ++.|=+.
T Consensus 210 ~L~LT~~Di~I-lDR~~~dknliiGQ~Vl~Nkg~AklgVVvHAEHf~~~~t~e~~I--LWNNyYEYqF~nA~~iDFF--- 283 (511)
T TIGR02918 210 QLNLTKKDIII-LDRSTGDKNLIIGQAVLENKGPAKLGVVVHAEHFSESATNETYI--LWNNYYEYQFSNADYIDFF--- 283 (511)
T ss_pred HCCCCCCCEEE-EECCCCCCEEEEEEEEEEECCCEEEEEEEEEEECCCCCCCCCCC--CCCCCHHHHCCCCCEEEEE---
T ss_conf 60698566899-97368993058713888750870289999746368886168602--2146525531568665113---
Q ss_pred CCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCCCCHHHHHHC--CCHHHHHHHHHH--C-CCHHHHHHHHHHHHCCCC
Q ss_conf 866225777888888777536--973067525788888899720--366889988641--4-992799999998530233
Q gi|254780834|r 324 DDPGLRAAYKAIDLVLCHLIP--GNRVNFVLLSRGEDPDSFIRC--YGKTAFEKLIVE--S-LPLVDMLWKRETENRSFN 396 (648)
Q Consensus 324 D~AG~kAa~Ra~e~~l~~l~~--g~~v~vv~LP~G~DPDe~ir~--~G~eaf~~ll~~--A-~~l~dFl~~~l~~~~dl~ 396 (648)
.-||..==+++...-+. +.++||.++|=| ==|++-.. ++...|.-+-.+ | .--+|++++...+.+. +
T Consensus 284 ----ItATd~Q~~~l~~QF~kY~~~~P~i~TIPVG-Sl~~L~~p~W~~Rkp~SiiTASRLA~EKHiDWLV~AVv~Ak~-~ 357 (511)
T TIGR02918 284 ----ITATDIQNQILLEQFKKYKNIEPKIYTIPVG-SLDELQYPEWQERKPFSIITASRLAKEKHIDWLVKAVVKAKK-S 357 (511)
T ss_pred ----EECHHHHHHHHHHHHHHHCCCCCEEEEEECC-CHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCC-C
T ss_conf ----4005788999999888747998778885057-543357886346452156777341376712688899999513-3
Q ss_pred CH----------HHHHHH-----HHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 14----------579999-----9999988541799899999999
Q gi|254780834|r 397 TP----------DERAEL-----EIHLKNCINHIKDQKLRYYYSQ 426 (648)
Q Consensus 397 sp----------e~ka~~-----~~~l~~~I~~I~d~~~R~~yl~ 426 (648)
-| .++.++ .+++-..|.......+.+.|.+
T Consensus 358 ~P~l~FDIYG~GgE~~~L~~iI~~n~A~DYI~LkGH~~L~~vY~~ 402 (511)
T TIGR02918 358 VPELTFDIYGEGGEKSKLKKIINENQAEDYIRLKGHKNLSEVYKD 402 (511)
T ss_pred CCCEEEEECCCCHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHCC
T ss_conf 885110003563788999998763120012431154335666232
No 244
>TIGR03329 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
Probab=30.83 E-value=28 Score=13.05 Aligned_cols=19 Identities=5% Similarity=0.209 Sum_probs=8.8
Q ss_pred CEEEE-CCCC-CCCCCCEEEE
Q ss_conf 55753-4588-8858787981
Q gi|254780834|r 38 DYWAC-CPFH-DEKTPSFHCN 56 (648)
Q Consensus 38 ~~~~~-cPfh-~ektpsf~v~ 56 (648)
-|.|| |=.| .+..|+..|-
T Consensus 33 G~tGLstA~~L~~~~pg~~Vv 53 (460)
T TIGR03329 33 GFTGLWTAIMIKQQRPALDVL 53 (460)
T ss_pred CHHHHHHHHHHHHHCCCCCEE
T ss_conf 399999999999748999889
No 245
>TIGR00300 TIGR00300 conserved hypothetical protein TIGR00300; InterPro: IPR005239 This family of conserved hypothetical proteins has no known function..
Probab=30.42 E-value=19 Score=14.46 Aligned_cols=34 Identities=32% Similarity=0.544 Sum_probs=23.7
Q ss_pred CCHHHHHH----HHHCCCCCCHHHHHCCCCH-------------HHHHHHHHC
Q ss_conf 14388999----8743554211343213662-------------678988512
Q gi|254780834|r 278 EGYMDVLS----LCQAGVQNVVSSLGTALTE-------------YQLRLLWKL 313 (648)
Q Consensus 278 EGy~Dvi~----l~~~G~~n~va~~Gtalt~-------------~~~~~l~r~ 313 (648)
+||.|++- |.-|.|+ .|++||+|.- .|++.+...
T Consensus 238 ~GYv~~Ll~GNAlA~HDIE--~~~~GTSLGvD~~~G~~V~gGhrHHl~~In~v 288 (418)
T TIGR00300 238 EGYVDALLAGNALAVHDIE--IALYGTSLGVDIKRGKPVPGGHRHHLKAINKV 288 (418)
T ss_pred HHHHHHHHCCCCHHHHHHH--HHHCCCCCCEECCCCCCCCCCCHHHHHHHHHH
T ss_conf 4478887516701012266--76404423205246855898843688888888
No 246
>KOG2518 consensus
Probab=30.40 E-value=28 Score=12.99 Aligned_cols=27 Identities=19% Similarity=0.203 Sum_probs=14.1
Q ss_pred HHHHHCCCCCCHHHHHCCCCHHHHHHHHHC
Q ss_conf 998743554211343213662678988512
Q gi|254780834|r 284 LSLCQAGVQNVVSSLGTALTEYQLRLLWKL 313 (648)
Q Consensus 284 i~l~~~G~~n~va~~Gtalt~~~~~~l~r~ 313 (648)
--|.-+.+...|.-+|- .. -.++|.+|
T Consensus 219 ciLSGCDYl~slpGvGl--~t-A~k~l~k~ 245 (556)
T KOG2518 219 CILSGCDYLSSLPGVGL--AT-AHKLLSKY 245 (556)
T ss_pred HHHCCCCCCCCCCCCCH--HH-HHHHHHHC
T ss_conf 98427731124765229--99-99999853
No 247
>cd00250 CAS_like Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2
Probab=30.27 E-value=28 Score=12.97 Aligned_cols=62 Identities=18% Similarity=0.234 Sum_probs=29.8
Q ss_pred EEEEEECC-CCEEEEECCCCCCC-CCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 88897077-85888501001465-53001038767653521011081788886433100002356787089971438899
Q gi|254780834|r 207 IFPIRSSR-GQVIAFGGRTLSKG-ESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVL 284 (648)
Q Consensus 207 ~fPi~~~~-g~~i~f~gR~l~~~-~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi 284 (648)
+|++.... -.-++++...|..- +.|-|-..|. + ..|..+..+ ..++.-++|-|+--+-
T Consensus 77 ~~~v~~~~~~~n~AyT~~~L~~HtD~~y~~~~Pg---~---q~LhCl~~~--------------~~GGeS~~vDg~~va~ 136 (262)
T cd00250 77 VVPVPGKENAQNGAYTNTLLPLHTDLAYHEYRPG---L---QILHCLRNT--------------ATGGATLLVDGFRVAL 136 (262)
T ss_pred EEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC---E---EEEEEECCC--------------CCCCCEEEEEHHHHHH
T ss_conf 0797516997664546565454557887779981---6---778703137--------------8899349872999999
Q ss_pred HHHH
Q ss_conf 9874
Q gi|254780834|r 285 SLCQ 288 (648)
Q Consensus 285 ~l~~ 288 (648)
.|-+
T Consensus 137 ~L~~ 140 (262)
T cd00250 137 KLLR 140 (262)
T ss_pred HHHH
T ss_conf 9988
No 248
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=30.15 E-value=23 Score=13.79 Aligned_cols=21 Identities=38% Similarity=0.452 Sum_probs=10.0
Q ss_pred HHHHHHCCCCCHHHHHHHCCCE
Q ss_conf 3455420599734523201210
Q gi|254780834|r 169 LREHLRQKGFSEEKIIEAGLLI 190 (648)
Q Consensus 169 l~~~l~~~~~~~~~~~~~gl~~ 190 (648)
+..+|.++|++ ....-|||-.
T Consensus 242 ~~~~L~s~G~~-A~~YHAGL~~ 262 (607)
T TIGR01389 242 LAERLESQGIS-ALAYHAGLSN 262 (607)
T ss_pred HHHHHHHCCCC-EEECCCCCCH
T ss_conf 99999747962-0403679877
No 249
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=29.93 E-value=22 Score=14.01 Aligned_cols=19 Identities=5% Similarity=-0.055 Sum_probs=7.8
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q ss_conf 7998999999999999988
Q gi|254780834|r 415 IKDQKLRYYYSQAIRDRLQ 433 (648)
Q Consensus 415 I~d~~~R~~yl~~la~~L~ 433 (648)
.+=+.+-+=+++.+++.+.
T Consensus 78 ~~Lp~~aqP~l~~ls~~~~ 96 (252)
T TIGR02431 78 APLPKVAQPLLERLSAQTH 96 (252)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 1589999999999998537
No 250
>cd00762 NAD_bind_malic_enz NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glut
Probab=29.92 E-value=29 Score=12.93 Aligned_cols=39 Identities=15% Similarity=0.082 Sum_probs=17.0
Q ss_pred CEEEECCCCCCC----CHHHHHHHHCCCCHHHHHHH--HHHHHCC
Q ss_conf 746713688887----89899898859997999999--9998188
Q gi|254780834|r 60 GFYYCFSCHVKG----DHLSFLSALLGCSFIESVQR--LAAIAGV 98 (648)
Q Consensus 60 ~~~~cf~c~~~g----d~~~f~~~~~~~~f~ea~~~--la~~~gi 98 (648)
+.+=|||.|..| +.+--.|..+|++-.||.+. +.++.|+
T Consensus 26 ~riv~~GAGsAg~gia~~l~~~~~~~Gl~~~ea~~~i~lvD~~GL 70 (254)
T cd00762 26 HKVLFNGAGAAALGIANLIVXLXVKEGISKEEACKRIWXVDRKGL 70 (254)
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHCCEEEECCCCC
T ss_conf 589998832999999999999864326532433210788537773
No 251
>cd00763 Bacterial_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent phosphofructokinases. These are allosrterically regulated homotetramers; the subunits are of about 320 amino acids.
Probab=29.88 E-value=29 Score=12.92 Aligned_cols=16 Identities=13% Similarity=0.399 Sum_probs=7.5
Q ss_pred EEEEECCCC-CCHHHHH
Q ss_conf 067525788-8888997
Q gi|254780834|r 348 VNFVLLSRG-EDPDSFI 363 (648)
Q Consensus 348 v~vv~LP~G-~DPDe~i 363 (648)
..++.+|+- .|+|+++
T Consensus 185 ad~iliPE~~~~~~~~~ 201 (317)
T cd00763 185 AEFIVIPEAEFDREEVA 201 (317)
T ss_pred CCEEEECCCCCCHHHHH
T ss_conf 98999689999999999
No 252
>PRK06850 hypothetical protein; Provisional
Probab=29.77 E-value=16 Score=15.28 Aligned_cols=15 Identities=40% Similarity=0.605 Sum_probs=6.9
Q ss_pred ECCCCEEE-EECCCCC
Q ss_conf 07785888-5010014
Q gi|254780834|r 212 SSRGQVIA-FGGRTLS 226 (648)
Q Consensus 212 ~~~g~~i~-f~gR~l~ 226 (648)
+..|.+|= .|-|.-.
T Consensus 143 ~~~ge~IlvLGtR~~E 158 (488)
T PRK06850 143 SAFGEVIVVLGTRKAE 158 (488)
T ss_pred HHCCCEEEEEECCHHH
T ss_conf 7539789998545277
No 253
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829 Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=29.58 E-value=25 Score=13.40 Aligned_cols=13 Identities=46% Similarity=0.889 Sum_probs=5.7
Q ss_pred CCCCCHHHHHHHH
Q ss_conf 8866225777888
Q gi|254780834|r 323 GDDPGLRAAYKAI 335 (648)
Q Consensus 323 gD~AG~kAa~Ra~ 335 (648)
||-+|.||..|++
T Consensus 9 GDCPGLNAVIR~v 21 (339)
T TIGR02483 9 GDCPGLNAVIRGV 21 (339)
T ss_pred CCCCHHHHHHHHH
T ss_conf 7741123898787
No 254
>CHL00010 infA translation initiation factor 1
Probab=29.57 E-value=29 Score=12.88 Aligned_cols=19 Identities=26% Similarity=0.656 Sum_probs=12.8
Q ss_pred CCCCCCCCEEEEEEEECCC
Q ss_conf 1000016716888970778
Q gi|254780834|r 197 TSYDRFRNRLIFPIRSSRG 215 (648)
Q Consensus 197 ~~~d~Fr~Ri~fPi~~~~g 215 (648)
++||--+|||+|-.+|..+
T Consensus 58 SpYDltkGRI~~R~k~~~~ 76 (78)
T CHL00010 58 SPYDLTKGRIIYRLRNKDS 76 (78)
T ss_pred CCCCCCCEEEEEEECCCCC
T ss_conf 7567885789999045656
No 255
>COG2957 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]
Probab=29.32 E-value=29 Score=12.85 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=11.6
Q ss_pred EEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 67525788888899720366889988641
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
+|+-|+.|..+|+= ....|.+..++..
T Consensus 199 kvlWL~~Gl~~D~T--DgHiDtlarFv~p 225 (346)
T COG2957 199 KVLWLEYGLKNDDT--DGHIDTLARFVAP 225 (346)
T ss_pred EEEECCCCCCCCCC--CCHHHHHHHHCCC
T ss_conf 78982678767766--5104546654278
No 256
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=29.32 E-value=29 Score=12.85 Aligned_cols=120 Identities=14% Similarity=0.137 Sum_probs=69.9
Q ss_pred CCEEEEECCHHHHHHH-HHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEE---ECCC------CCCHHHHHHHHHHHHH
Q ss_conf 8708997143889998-7435542113432136626789885126818996---1788------6622577788888877
Q gi|254780834|r 271 SSFIILVEGYMDVLSL-CQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLC---FDGD------DPGLRAAYKAIDLVLC 340 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l-~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~---fDgD------~AG~kAa~Ra~e~~l~ 340 (648)
..+.+-.|...|+..+ ...|+.+++-|.|. ++++-+..|..+++-+.+= ++.| .|.-+-.++.++.+..
T Consensus 92 GEP~~q~e~~~~~~~~ake~Gl~~~l~TnG~-~~~~~~~~l~~~~D~v~~DlK~~~~~~yr~~tg~~~~~vl~~~~~l~~ 170 (260)
T COG1180 92 GEPTLQAEFALDLLRAAKERGLHVALDTNGF-LPPEALEELLPLLDAVLLDLKAFDDELYRKLTGADNEPVLENLELLAD 170 (260)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCEEEEECCCC-CCHHHHHHHHHHCCCEEEECCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 6044439999999999998799089976899-882689999974231488406688788898756871688999999861
Q ss_pred HHHCCCCEEEEECCCC-CCHHHHHHCCCHHHHHHHH-HHCCCHHHHHHHHHHHHCC
Q ss_conf 7536973067525788-8888997203668899886-4149927999999985302
Q gi|254780834|r 341 HLIPGNRVNFVLLSRG-EDPDSFIRCYGKTAFEKLI-VESLPLVDMLWKRETENRS 394 (648)
Q Consensus 341 ~l~~g~~v~vv~LP~G-~DPDe~ir~~G~eaf~~ll-~~A~~l~dFl~~~l~~~~d 394 (648)
. ..-..++.+..|.- .|+++. +.- .+.+.++. ..+..+.-|...+..+...
T Consensus 171 ~-g~~ve~r~lviPg~~d~~e~i-~~i-~~~i~~~~~~~p~~~l~fhp~~~~~~~p 223 (260)
T COG1180 171 L-GVHVEIRTLVIPGYNDDEEEI-REL-AEFIADLGPEIPIHLLRFHPDYKLKDLP 223 (260)
T ss_pred C-CCEEEEEEEECCCCCCCHHHH-HHH-HHHHHHCCCCCCEEEECCCCCHHCCCCC
T ss_conf 7-983999887338988999999-999-9999730866655875668740113579
No 257
>KOG2168 consensus
Probab=29.31 E-value=24 Score=13.69 Aligned_cols=27 Identities=22% Similarity=-0.002 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999988413267621230
Q gi|254780834|r 618 ISILHEVHIQIHQIESQEAMIEGFGKM 644 (648)
Q Consensus 618 ~~el~elk~~L~~l~~~Eal~e~~~~~ 644 (648)
...++.++.+-+.+-..-+.|+.++++
T Consensus 795 ~~~l~~lr~~a~~i~~~a~~I~yRmps 821 (835)
T KOG2168 795 ETKLDRLRDQARAIVMMAAMIPYRMPS 821 (835)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf 789999999999999999754521873
No 258
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=29.29 E-value=29 Score=12.84 Aligned_cols=36 Identities=19% Similarity=0.222 Sum_probs=28.5
Q ss_pred HHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf 2678988512---68189961788662257778888887
Q gi|254780834|r 304 EYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLVL 339 (648)
Q Consensus 304 ~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~l 339 (648)
...++.|+++ +++|+|+-|.|.-|-.=|+.+.+++.
T Consensus 106 ~k~v~~lk~lak~ad~v~lATD~DREGEaIa~hi~~~l~ 144 (170)
T cd03361 106 LETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALR 144 (170)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf 999999999986089799857998222299999999955
No 259
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative; InterPro: IPR011916 This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II..
Probab=29.04 E-value=29 Score=12.81 Aligned_cols=78 Identities=23% Similarity=0.349 Sum_probs=36.3
Q ss_pred CCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CE
Q ss_conf 78708997143889998743554211343213662678988512681899617886622577788888877753697-30
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RV 348 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v 348 (648)
..+++=+||-.. -+.+|||-..+..+. +-|+.| +.|.+.+.-.. +-++|. +-
T Consensus 133 ~~n~LHtV~~NL-----------s~L~PLGl~~~~~~~--------rCvm~y------~~adw~a~ral--L~eaGv~~~ 185 (347)
T TIGR02201 133 QSNTLHTVEQNL-----------SVLAPLGLDSLAKEA--------RCVMSY------SEADWKAVRAL--LDEAGVSEN 185 (347)
T ss_pred CCCEEEEEEHHH-----------HHHCCCCCCCCCCCC--------EEECCC------CHHHHHHHHHH--HHHCCCCCC
T ss_conf 887234210124-----------664246888565766--------021378------86459999985--232579998
Q ss_pred EEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 67525788888899720366889988641
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
+||.=|.-- -|.|---.+-|..+++-
T Consensus 186 YiVIqPtsR---wfFKCW~~drfsali~A 211 (347)
T TIGR02201 186 YIVIQPTSR---WFFKCWEDDRFSALIDA 211 (347)
T ss_pred CEEECCCCC---CCCCCCHHHHHHHHHHH
T ss_conf 178736736---31016621358999998
No 260
>pfam02969 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
Probab=28.90 E-value=30 Score=12.79 Aligned_cols=48 Identities=23% Similarity=0.324 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 799999999981885-8776820367778899999999999999999732
Q gi|254780834|r 85 FIESVQRLAAIAGVP-LPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK 133 (648)
Q Consensus 85 f~ea~~~la~~~gi~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 133 (648)
-+|+|+..|+..||. ++. +....-...-.-++-++.+.|.+|-++--+
T Consensus 5 ~~esik~iAeS~Gi~~l~d-e~a~~La~dveyRl~eiiqeA~KFMrhskR 53 (66)
T pfam02969 5 PQESMKVIAESLGITNLSD-EAAALLAEDVEYRLKEIVQDAAKFMRHSKR 53 (66)
T ss_pred CHHHHHHHHHHCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 5888999999949888999-999998999999999999999999998675
No 261
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=28.58 E-value=30 Score=12.75 Aligned_cols=73 Identities=10% Similarity=0.078 Sum_probs=44.1
Q ss_pred EECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE
Q ss_conf 971438-89998743554211343213662678988512681------89961788662257778888887775369730
Q gi|254780834|r 276 LVEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV 348 (648)
Q Consensus 276 ~vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v 348 (648)
..||=| |++++-.-.+... +..|..++.++++.+-.++++ +-.+|+||..+--..+|. +..
T Consensus 218 ~a~Gs~RDalslldqai~~~-~~~~~~I~~~~V~~MLGl~Drs~lidL~e~Il~Gd~~kaL~~l~~------iy~----- 285 (507)
T PRK06645 218 KSEGSARDAVSILDQAASMS-AKSDNIISPQVINQMLGLVDLSVIIEFVEYIIERETEKAINLINK------LYG----- 285 (507)
T ss_pred HCCCCHHHHHHHHHHHHHHH-CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHH------HHH-----
T ss_conf 55998678999999999975-489870269999998389985679999999982999999999999------998-----
Q ss_pred EEEECCCCCCHHHHHHCC
Q ss_conf 675257888888997203
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCY 366 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~ 366 (648)
.|-||+.+++.-
T Consensus 286 ------~G~Dp~~iL~DL 297 (507)
T PRK06645 286 ------SSVNLEIFIESV 297 (507)
T ss_pred ------CCCCHHHHHHHH
T ss_conf ------499999999999
No 262
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=28.48 E-value=30 Score=12.73 Aligned_cols=33 Identities=27% Similarity=0.312 Sum_probs=25.4
Q ss_pred HHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 678988512681899617886622577788888
Q gi|254780834|r 305 YQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDL 337 (648)
Q Consensus 305 ~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~ 337 (648)
.+++.+.+-+++||++-|.|.-|..=++...+.
T Consensus 64 ~~ik~l~~~ad~viiAtD~DrEGE~I~~~i~~~ 96 (123)
T cd03363 64 KELKKLAKKADEIYLATDPDREGEAIAWHLAEV 96 (123)
T ss_pred HHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHH
T ss_conf 999999850998998489982479999999999
No 263
>PRK05362 phosphopentomutase; Provisional
Probab=28.27 E-value=30 Score=12.71 Aligned_cols=88 Identities=19% Similarity=0.255 Sum_probs=44.6
Q ss_pred CCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHH-HHHHHHCC-CEEEEE----ECC------CCCCHHHHHHHHHHH
Q ss_conf 870899714388999874355421134321366267-89885126-818996----178------866225777888888
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQ-LRLLWKLS-PRIVLC----FDG------DDPGLRAAYKAIDLV 338 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~-~~~l~r~~-~~vvl~----fDg------D~AG~kAa~Ra~e~~ 338 (648)
...|+.|==--|..+ -.||...+-+.+++=.-++ +..+++-. +-.+++ ||. |.+|...++..++.-
T Consensus 236 g~~V~~IGKi~DIf~--~~Gi~~~~~~~~n~~~~~~~l~~~~~~~~~glif~NlvdfD~lyGHrrD~~gYa~aLe~fD~~ 313 (393)
T PRK05362 236 GGEVIAVGKIADIFA--GQGITEKVKAKSNMDGMDATIEEMKEAGDNGLVFTNLVDFDSLYGHRRDVAGYAKALEEFDRR 313 (393)
T ss_pred CCEEEEECCHHHHHC--CCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 984999815798644--788660116888199999999999746469779985201154405655878999999999998
Q ss_pred HHHHHCCC---CEEEEECCCCCCHH
Q ss_conf 77753697---30675257888888
Q gi|254780834|r 339 LCHLIPGN---RVNFVLLSRGEDPD 360 (648)
Q Consensus 339 l~~l~~g~---~v~vv~LP~G~DPD 360 (648)
|+.+.+.+ ++-|++-..|-||-
T Consensus 314 L~~il~~l~~dDLLIITADHGnDPT 338 (393)
T PRK05362 314 LPELLALLKEDDLLIITADHGNDPT 338 (393)
T ss_pred HHHHHHHCCCCCEEEEECCCCCCCC
T ss_conf 9999984797878999487788999
No 264
>pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243.
Probab=28.24 E-value=24 Score=13.55 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=8.3
Q ss_pred HHHHHHHHHHCCCCCCHHHHHH
Q ss_conf 9999999975388999899998
Q gi|254780834|r 518 LWSFLFSDFVEQKYFLPEEIHQ 539 (648)
Q Consensus 518 L~~~i~~~~~~~~~~~~~~l~~ 539 (648)
|+.-++.....+..++.+.+..
T Consensus 25 l~~~LLr~La~G~PVt~~~LA~ 46 (77)
T pfam12324 25 LFRPLLRMLADGRPVTREDLAG 46 (77)
T ss_pred HHHHHHHHHHCCCCCCHHHHHH
T ss_conf 9999999994799868999998
No 265
>PRK00048 dihydrodipicolinate reductase; Provisional
Probab=28.16 E-value=30 Score=12.69 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=30.0
Q ss_pred CCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEE
Q ss_conf 14388999-874355421134321366267898851268189961
Q gi|254780834|r 278 EGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCF 321 (648)
Q Consensus 278 EGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~f 321 (648)
++-++.+. +.++|++-|++|- -|+++|+..|+++++++-+++
T Consensus 80 ~~~~~~~~~~~~~~~~~ViGTT--G~~~~~~~~i~~~s~~ipil~ 122 (265)
T PRK00048 80 EATLENLEFALEHGKPLVIGTT--GFTEEQLAALREAAKKIPVVI 122 (265)
T ss_pred HHHHHHHHHHHHCCCCEEEEEC--CCCHHHHHHHHHHCCCCCEEE
T ss_conf 9999999999974997799608--999899999997465887899
No 266
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=28.04 E-value=30 Score=12.67 Aligned_cols=31 Identities=23% Similarity=0.258 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHH
Q ss_conf 7888888997203668899886414992799
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDM 384 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dF 384 (648)
-+..||++++.++|+|+++=.+..+.+..|.
T Consensus 544 GNvi~p~eii~~yGADalR~~la~~~~~~d~ 574 (809)
T PRK13208 544 GNVVDPEELLEKYGADAVRYWAANSRLGSDT 574 (809)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHCCCCCCCC
T ss_conf 8968978986533809999999618944465
No 267
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004559 Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins called HemN (IPR004558 from INTERPRO). This family contains a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including Escherichia coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the Escherichia coli hemN family. The member of this family from Bacillus subtilis was shown to complement a hemF/hemN double mutant of Salmonella typhimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize haem de novo. ; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=27.99 E-value=20 Score=14.33 Aligned_cols=39 Identities=28% Similarity=0.401 Sum_probs=19.4
Q ss_pred EEECCHHHHHHH------HHCCCCCCHHHHHC-CCCHHHHHHHHHCCC
Q ss_conf 997143889998------74355421134321-366267898851268
Q gi|254780834|r 275 ILVEGYMDVLSL------CQAGVQNVVSSLGT-ALTEYQLRLLWKLSP 315 (648)
Q Consensus 275 i~vEGy~Dvi~l------~~~G~~n~va~~Gt-alt~~~~~~l~r~~~ 315 (648)
|-||--=|.|+. -.+||.. =+||. +|.++.+..|-|..+
T Consensus 95 it~eANP~~~~ae~~kglk~aGinR--lS~GvQsF~dDkL~~lgR~H~ 140 (371)
T TIGR00539 95 ITVEANPDLVEAEKLKGLKEAGINR--LSLGVQSFEDDKLEKLGRVHK 140 (371)
T ss_pred EEECCCCCHHHHHHHHHHHHCCEEE--EECCCCCCHHHHHHHHHHHCC
T ss_conf 1110782125698863676557023--321334541557888642113
No 268
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=27.62 E-value=31 Score=12.62 Aligned_cols=35 Identities=26% Similarity=0.323 Sum_probs=27.2
Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 18996178866225777888888777536973067525
Q gi|254780834|r 316 RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL 353 (648)
Q Consensus 316 ~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L 353 (648)
+|.++.|++...++|...|++++.. .|-.+.++..
T Consensus 1 ~Ilv~vd~s~~s~~al~~a~~la~~---~~~~l~~v~v 35 (130)
T cd00293 1 RILVAVDGSEESERALRWAARLARR---LGAELVLLHV 35 (130)
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHH---CCCEEEEEEE
T ss_conf 9999989898999999999999987---2997999999
No 269
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558 This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=27.54 E-value=31 Score=12.61 Aligned_cols=12 Identities=33% Similarity=0.263 Sum_probs=7.1
Q ss_pred CCCHHHHHHHHH
Q ss_conf 366267898851
Q gi|254780834|r 301 ALTEYQLRLLWK 312 (648)
Q Consensus 301 alt~~~~~~l~r 312 (648)
=||.+|+..|.+
T Consensus 117 YL~~~Q~~~l~~ 128 (462)
T TIGR00538 117 YLSPEQIEELMK 128 (462)
T ss_pred CCCHHHHHHHHH
T ss_conf 378899999999
No 270
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=27.45 E-value=28 Score=12.97 Aligned_cols=34 Identities=15% Similarity=0.298 Sum_probs=24.2
Q ss_pred HHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 899998506885351012442256774103455420599
Q gi|254780834|r 140 LHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGF 178 (648)
Q Consensus 140 a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~ 178 (648)
-++||..||+|+.||+-|.-- ...+..|+.+.|.
T Consensus 30 Fl~yL~er~~S~~Ti~aY~~d-----L~~F~~fl~~~g~ 63 (361)
T PRK01287 30 FVEWLQERNWSERTLKVQTHH-----TYHFILWCEERGL 63 (361)
T ss_pred HHHHHHHCCCCHHHHHHHHHH-----HHHHHHHHHHCCC
T ss_conf 999999839989999999999-----9999999998489
No 271
>PRK01611 argS arginyl-tRNA synthetase; Reviewed
Probab=27.11 E-value=31 Score=12.55 Aligned_cols=47 Identities=23% Similarity=0.262 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 379999999998477889999844300237998899999999999753
Q gi|254780834|r 481 SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVE 528 (648)
Q Consensus 481 ~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~ 528 (648)
...|+.|+..|..+|+.+....+.+..... ...+..|....-..|..
T Consensus 483 ~~~E~~Li~~l~~fp~vv~~a~~~~~Ph~l-~~YL~~La~~Fn~fY~~ 529 (570)
T PRK01611 483 EEEELELIKKLAEFPEVVESAAEELEPHRI-ANYLYELAGAFHSFYNA 529 (570)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHH-HHHHHHHHHHHHHHHHC
T ss_conf 989999999998879999999996881899-99999999999999851
No 272
>KOG4657 consensus
Probab=26.84 E-value=32 Score=12.51 Aligned_cols=63 Identities=14% Similarity=0.210 Sum_probs=45.4
Q ss_pred CCCCCCEEEEEEEECCCCEEEEECCCCCCCCC-------CEECCCCCCCCCCCCHHCCCHHHHHHHHHHH
Q ss_conf 00016716888970778588850100146553-------0010387676535210110817888864331
Q gi|254780834|r 199 YDRFRNRLIFPIRSSRGQVIAFGGRTLSKGES-------VKYLNSPETILFHKGKNLYNFFGALNYLQKS 261 (648)
Q Consensus 199 ~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~-------~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~ 261 (648)
-++|++++=|-|.-..|.||-|.=--||+.++ .-|=++.++++-+-+-.|||+..|....++.
T Consensus 151 a~wy~dyLGleie~~hgevikfiFTnIdpkdp~~~FsF~vhL~e~~Dy~Vvd~~P~L~gl~~a~s~vr~t 220 (246)
T KOG4657 151 ASWYNDYLGLEIEAGHGEVIKFIFTNIDPKDPTREFSFTVHLGEDIDYQVVDHSPQLQGLTSAISAVRPT 220 (246)
T ss_pred HHHHHHHCCCEEEECCCCEEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf 8899985073455135746889872258888764503687534545765667688763478899875112
No 273
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase; InterPro: IPR002698 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase 6.3.3.2 from EC catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg^2+ . 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin .; GO: 0005524 ATP binding, 0030272 5-formyltetrahydrofolate cyclo-ligase activity, 0009396 folic acid and derivative biosynthetic process.
Probab=26.83 E-value=17 Score=15.08 Aligned_cols=18 Identities=33% Similarity=0.700 Sum_probs=9.2
Q ss_pred EEEEE--EEECCCCEEEEEC
Q ss_conf 16888--9707785888501
Q gi|254780834|r 205 RLIFP--IRSSRGQVIAFGG 222 (648)
Q Consensus 205 Ri~fP--i~~~~g~~i~f~g 222 (648)
=|+.| .+|.+|.=+||||
T Consensus 118 l~~VP~vAfD~~G~RlGyGg 137 (183)
T TIGR02727 118 LIIVPGVAFDRRGYRLGYGG 137 (183)
T ss_pred EEEECCEEECCCCCEEECCC
T ss_conf 68826376889886740568
No 274
>pfam06447 consensus
Probab=26.79 E-value=32 Score=12.50 Aligned_cols=13 Identities=8% Similarity=0.174 Sum_probs=6.0
Q ss_pred CCEEEEECCHHHH
Q ss_conf 8708997143889
Q gi|254780834|r 271 SSFIILVEGYMDV 283 (648)
Q Consensus 271 ~~~~i~vEGy~Dv 283 (648)
+++.|+.++|=|.
T Consensus 253 ~~C~v~~s~~Gdl 265 (407)
T pfam06447 253 RGCFVTGSAWGDL 265 (407)
T ss_pred CCCEEEEEEEEEC
T ss_conf 7748998888632
No 275
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=26.74 E-value=32 Score=12.49 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=17.8
Q ss_pred ECCCCCCCCCCEEEECCCCEEEECCCCCCCC
Q ss_conf 3458888587879817897467136888878
Q gi|254780834|r 42 CCPFHDEKTPSFHCNDSKGFYYCFSCHVKGD 72 (648)
Q Consensus 42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd 72 (648)
.||=.....+. +.....|+|-.||..+|
T Consensus 30 ~C~~Cg~~~~~---~~~~r~~~C~~Cg~~~~ 57 (69)
T pfam07282 30 TCSVCGHKNKE---SLSGRTFKCPNCGFVAD 57 (69)
T ss_pred CCCCCCCCCCC---CCCCCEEECCCCCCEEC
T ss_conf 27999899867---48887898998996899
No 276
>pfam09445 Methyltransf_15 RNA cap guanine-N2 methyltransferase. RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine.
Probab=26.70 E-value=22 Score=13.96 Aligned_cols=15 Identities=20% Similarity=0.549 Sum_probs=11.9
Q ss_pred CCCCCCCCHHHHHHH
Q ss_conf 368888789899898
Q gi|254780834|r 65 FSCHVKGDHLSFLSA 79 (648)
Q Consensus 65 f~c~~~gd~~~f~~~ 79 (648)
-.||.||+.|.|-..
T Consensus 7 ~fcG~Ggn~I~fA~~ 21 (165)
T pfam09445 7 VFCGAGGNTIQFANV 21 (165)
T ss_pred CCCCCCHHHHHHHHH
T ss_conf 377807999999975
No 277
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.69 E-value=32 Score=12.49 Aligned_cols=28 Identities=29% Similarity=0.477 Sum_probs=20.6
Q ss_pred CCCCC-CCCCCEEEE--CCCCEEEECCCCCC
Q ss_conf 45888-858787981--78974671368888
Q gi|254780834|r 43 CPFHD-EKTPSFHCN--DSKGFYYCFSCHVK 70 (648)
Q Consensus 43 cPfh~-ektpsf~v~--~~~~~~~cf~c~~~ 70 (648)
|||.+ |+.-|.+|. ...++-+|=.||..
T Consensus 25 Cp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 25 CPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCCCCCEEEEEEEEEECCCEEEEECCCCCCE
T ss_conf 6855872355788974274568971457553
No 278
>cd05312 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH
Probab=26.64 E-value=32 Score=12.48 Aligned_cols=38 Identities=26% Similarity=0.283 Sum_probs=17.3
Q ss_pred HHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE
Q ss_conf 38899987435542113432136626789885126818
Q gi|254780834|r 280 YMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI 317 (648)
Q Consensus 280 y~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v 317 (648)
-.|||.....-+--.+++.|-+||++.++.+.+.++++
T Consensus 97 L~e~v~~~kp~vlIG~S~~~g~ft~e~v~~Ma~~~e~P 134 (279)
T cd05312 97 LLEVVKAVKPTVLIGLSGVGGAFTEEVVRAMAKSNERP 134 (279)
T ss_pred HHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHCCCCC
T ss_conf 99999724897799806898977999999998459997
No 279
>pfam06945 DUF1289 Protein of unknown function (DUF1289). This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown.
Probab=26.62 E-value=32 Score=12.48 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=9.6
Q ss_pred EECCCCCCCCHHH
Q ss_conf 7136888878989
Q gi|254780834|r 63 YCFSCHVKGDHLS 75 (648)
Q Consensus 63 ~cf~c~~~gd~~~ 75 (648)
+|.||+...+=|.
T Consensus 16 ~C~GC~Rt~~EI~ 28 (56)
T pfam06945 16 ICVGCGRTLDEIA 28 (56)
T ss_pred EEECCCCCHHHHH
T ss_conf 7419999989998
No 280
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704 At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=26.57 E-value=32 Score=12.47 Aligned_cols=12 Identities=33% Similarity=0.540 Sum_probs=4.5
Q ss_pred ECCCCEEEEECC
Q ss_conf 077858885010
Q gi|254780834|r 212 SSRGQVIAFGGR 223 (648)
Q Consensus 212 ~~~g~~i~f~gR 223 (648)
|.+|+|-+..-|
T Consensus 214 daqGrveainqr 225 (658)
T TIGR02329 214 DAQGRVEAINQR 225 (658)
T ss_pred CCCCHHHHHHHH
T ss_conf 144327899888
No 281
>pfam09332 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Probab=26.40 E-value=32 Score=12.45 Aligned_cols=12 Identities=25% Similarity=0.371 Sum_probs=4.6
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999998841326
Q gi|254780834|r 626 IQIHQIESQEAM 637 (648)
Q Consensus 626 ~~L~~l~~~Eal 637 (648)
+....|+.-|.+
T Consensus 229 ~yF~~LekKE~m 240 (346)
T pfam09332 229 EYFNPLEKKEQM 240 (346)
T ss_pred HHHHHHHHHHHH
T ss_conf 998888889999
No 282
>KOG0340 consensus
Probab=26.39 E-value=32 Score=12.44 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=11.8
Q ss_pred CCHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf 888899720366889988641499
Q gi|254780834|r 357 EDPDSFIRCYGKTAFEKLIVESLP 380 (648)
Q Consensus 357 ~DPDe~ir~~G~eaf~~ll~~A~~ 380 (648)
.|||+||..-|..+=.-....|.+
T Consensus 333 r~P~~yiHRvGRtARAGR~G~aiS 356 (442)
T KOG0340 333 RDPKDYIHRVGRTARAGRKGMAIS 356 (442)
T ss_pred CCHHHHHHHHCCHHCCCCCCCEEE
T ss_conf 987888876030120567764289
No 283
>PRK10850 phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr); Provisional
Probab=26.37 E-value=32 Score=12.44 Aligned_cols=62 Identities=21% Similarity=0.336 Sum_probs=39.8
Q ss_pred HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
=++..++|..+|.+.++|..|--|..+..+-+ -...|-.|.|. -+|.|-++-+ +++.+++.+
T Consensus 22 ~v~~a~~f~s~I~l~~~~~~anakSi~~im~L---g~~~G~~i~i~--a~G~De~~Al-----~~l~~ll~e 83 (85)
T PRK10850 22 FVKEAKGFTSEITVTSNGKSASAKSLFKLQTL---GLTQGTVVTIS--AEGEDEQKAV-----EHLVKLMAE 83 (85)
T ss_pred HHHHHHHCCCEEEEEECCEEECHHHHHHHHHC---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHH
T ss_conf 99999628986999989999845849999974---98998999999--9788999999-----999999984
No 284
>pfam07014 Hs1pro-1_C Hs1pro-1 protein C-terminus. This family represents the C-terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance.
Probab=26.35 E-value=29 Score=12.84 Aligned_cols=46 Identities=17% Similarity=0.156 Sum_probs=22.8
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 8888877753697306752578888889972036688998864149927999999
Q gi|254780834|r 334 AIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKR 388 (648)
Q Consensus 334 a~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~ 388 (648)
.+|....++.+-. -|--=+|||||+|-+..-+. +.+.+-..|.+++
T Consensus 91 ~vERiWKLL~~ie-----DlhllMDPdDFlrLK~qL~i----ks~~~~~afCfRS 136 (261)
T pfam07014 91 LLERIWKLLADIE-----DLHLLMDPDDFLRLKKQLSI----KSSPESAAFCFRS 136 (261)
T ss_pred HHHHHHHHHHHHH-----HHHHHCCHHHHHHHHHHHCC----CCCCCCCCCCHHH
T ss_conf 9999999999888-----99861598899989987431----2478886411007
No 285
>KOG0177 consensus
Probab=26.23 E-value=32 Score=12.42 Aligned_cols=48 Identities=17% Similarity=0.238 Sum_probs=26.2
Q ss_pred CCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHH-HHHHHHHHCCCCC
Q ss_conf 8885878798178974671368888789899898859997999-9999998188587
Q gi|254780834|r 46 HDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIES-VQRLAAIAGVPLP 101 (648)
Q Consensus 46 h~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea-~~~la~~~gi~~~ 101 (648)
+.+..--+++-.++..--| ||++||+++|-- |..+ +..---|-|++++
T Consensus 28 ~k~~~dK~~~ls~~~lm~~--~Ge~GDt~qF~e------yi~~Ni~LY~irnGyeLS 76 (200)
T KOG0177 28 LKDDHDKIHRLSDHILMAT--VGEAGDTVQFTE------YIQKNIQLYKIRNGYELS 76 (200)
T ss_pred ECCCCCCEEEECCCEEEEE--ECCCCCEEHHHH------HHHHHHHHHHHHCCCCCC
T ss_conf 7366440267243104553--058865107999------998530576542687678
No 286
>KOG0456 consensus
Probab=26.23 E-value=31 Score=12.57 Aligned_cols=32 Identities=16% Similarity=0.470 Sum_probs=22.5
Q ss_pred HHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHH
Q ss_conf 99998506885351012442256774103455
Q gi|254780834|r 141 HYYLDERGIDSHAIEMFKLGYAPDSRYSLREH 172 (648)
Q Consensus 141 ~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~ 172 (648)
-+||..+|.....++-|.||+..-+|.++-+-
T Consensus 208 aA~lnd~G~kar~~D~~~I~~~~~d~~t~~d~ 239 (559)
T KOG0456 208 AAYLNDIGHKARQYDAFEIGFITTDDFTNDDI 239 (559)
T ss_pred HHHHHHCCCCCEEECHHHEECCCCCCCCCHHH
T ss_conf 99987328532351143420332433343247
No 287
>PRK00380 panC pantoate--beta-alanine ligase; Reviewed
Probab=25.96 E-value=33 Score=12.38 Aligned_cols=59 Identities=22% Similarity=0.365 Sum_probs=32.6
Q ss_pred CHHHHHCCCCHHHHHHHHHC---CCEEEEE-------ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf 11343213662678988512---6818996-------17886622577788888877753697306752578
Q gi|254780834|r 294 VVSSLGTALTEYQLRLLWKL---SPRIVLC-------FDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR 355 (648)
Q Consensus 294 ~va~~Gtalt~~~~~~l~r~---~~~vvl~-------fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~ 355 (648)
-|.||| ||-+.|+.++++- ++.+|.. |...+ -.+.==|.++.-+.+++ ...|.+++.|.
T Consensus 25 ~VPTMG-aLH~GHlsLI~~A~~~~d~vvVSIFVNP~QF~~~e-D~~~YPr~~e~D~~~l~-~~gvD~vF~P~ 93 (283)
T PRK00380 25 FVPTMG-NLHEGHLSLVREARAEADVVVVSIFVNPLQFGPNE-DLDRYPRTLEADLAKLE-AAGVDLVFAPS 93 (283)
T ss_pred EECCCC-HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCC-CCCCCCCCHHHHHHHHH-HCCCCEEECCC
T ss_conf 985872-27589999999999749929999850601059875-40128987899999999-86998997887
No 288
>cd01816 Raf_RBD The Raf serine/threonine kinases are composed of three conserved regions, CR1, CR2 and CR3. CR1 has two Ras binding domains (RBD and CRD), CR2 is a serine/threonine rich domain and CR3 is the catalytic kinase domain. The RBD of Raf is structurally similar to ubiquitin with little of no sequence similarity.The Raf signalling pathway plays an important role in the proliferation and survival of tumor cells.
Probab=25.92 E-value=21 Score=14.14 Aligned_cols=33 Identities=21% Similarity=0.210 Sum_probs=24.8
Q ss_pred HHHHCCCCHHHHCCCCCCC-----CCCCCCHHHHHHHC
Q ss_conf 9985068853510124422-----56774103455420
Q gi|254780834|r 143 YLDERGIDSHAIEMFKLGY-----APDSRYSLREHLRQ 175 (648)
Q Consensus 143 yl~~Rg~~~~~~~~f~lG~-----ap~~~~~l~~~l~~ 175 (648)
-|+.|||++|...-|.+|- .|-+|+.....|..
T Consensus 29 alk~R~L~pe~C~V~~~~~~~~t~~~i~WdTd~~~L~g 66 (74)
T cd01816 29 ALKVRGLQPECCAVFRLGDGSSKKLRIDWDTDISSLIG 66 (74)
T ss_pred HHHHCCCCHHHEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99874998658599975688777853575465531015
No 289
>cd00807 Gln_GluRS_non_core Glutaminyl-tRNA synthetase (GlnRS) and non-descriminating Glutamyl-tRNA synthetase (GluRS) cataytic core domain. These enzymes attach Gln or Glu, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the "non-descriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme.
Probab=25.86 E-value=33 Score=12.37 Aligned_cols=25 Identities=16% Similarity=-0.013 Sum_probs=10.4
Q ss_pred CCCCCCHHHH-HCCCCHHHHHHHHHC
Q ss_conf 3554211343-213662678988512
Q gi|254780834|r 289 AGVQNVVSSL-GTALTEYQLRLLWKL 313 (648)
Q Consensus 289 ~G~~n~va~~-Gtalt~~~~~~l~r~ 313 (648)
-||+.||=.. -..-|+-|+.+...+
T Consensus 120 ~gITHViRG~D~l~nt~~q~~l~~aL 145 (238)
T cd00807 120 EGITHSLRTKEFQDRREKYDWLYEYL 145 (238)
T ss_pred CCCCEEEECCCCCCCCHHHHHHHHHC
T ss_conf 78876887621013879999999984
No 290
>COG4230 Delta 1-pyrroline-5-carboxylate dehydrogenase [Energy production and conversion]
Probab=25.83 E-value=27 Score=13.10 Aligned_cols=16 Identities=25% Similarity=0.194 Sum_probs=7.4
Q ss_pred CCHHHHHCCCCHHHHH
Q ss_conf 2113432136626789
Q gi|254780834|r 293 NVVSSLGTALTEYQLR 308 (648)
Q Consensus 293 n~va~~Gtalt~~~~~ 308 (648)
|+.-.=-|||++.-+.
T Consensus 353 NAMIVDSsAL~EQVv~ 368 (769)
T COG4230 353 NAMIVDSSALAEQVVA 368 (769)
T ss_pred CEEEEECHHHHHHHHH
T ss_conf 3388622010899999
No 291
>pfam00944 Peptidase_S3 Alphavirus core protein. Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.
Probab=25.74 E-value=33 Score=12.35 Aligned_cols=23 Identities=35% Similarity=0.583 Sum_probs=15.3
Q ss_pred HCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEE
Q ss_conf 01210034654100001671688897077858885
Q gi|254780834|r 186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAF 220 (648)
Q Consensus 186 ~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f 220 (648)
+|.-.+.+.|+ ||.|-+|+|||.
T Consensus 100 ~g~g~~GDSGR------------pi~DN~GrVVaI 122 (157)
T pfam00944 100 KGVGGKGDSGR------------PILDNTGRVVAI 122 (157)
T ss_pred CCCCCCCCCCC------------CCCCCCCCEEEE
T ss_conf 46778888898------------116588878999
No 292
>PRK09040 hypothetical protein; Provisional
Probab=25.65 E-value=28 Score=13.07 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=16.2
Q ss_pred CCCEEEEECCHHHHHHHHHC--CCC
Q ss_conf 78708997143889998743--554
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQA--GVQ 292 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~--G~~ 292 (648)
..+.+|.||||+|-...+.. .|+
T Consensus 121 ~~~~~i~V~GhTD~~pi~~~~~~f~ 145 (215)
T PRK09040 121 ARDEILMVSGFTDDQPVRAGNRRFA 145 (215)
T ss_pred CCCCEEEEEECCCCCCCCCCCCCCC
T ss_conf 7986599873489976767788889
No 293
>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.
Probab=25.59 E-value=33 Score=12.33 Aligned_cols=56 Identities=14% Similarity=0.097 Sum_probs=24.7
Q ss_pred CCCCCCHH-HHHCCCCHHHH-HHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CEEEE
Q ss_conf 35542113-43213662678-988512681899617886622577788888877753697-30675
Q gi|254780834|r 289 AGVQNVVS-SLGTALTEYQL-RLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN-RVNFV 351 (648)
Q Consensus 289 ~G~~n~va-~~Gtalt~~~~-~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~-~v~vv 351 (648)
.-|++++- |+++ | +.++ ..+-+ .+.+|++||.. .++..+.+|++.+ .+.|. +|+++
T Consensus 25 gHI~gA~niP~~~-l-e~~~~~~~p~-kd~~Ivvyc~~-g~~~~s~~Aa~~L---~~~Gy~~V~~L 83 (92)
T cd01532 25 SHPLWAANLPLSR-L-ELDAWVRIPR-RDTPIVVYGEG-GGEDLAPRAARRL---SELGYTDVALL 83 (92)
T ss_pred CCCCCCCCCCHHH-H-HHHHHHHCCC-CCCEEEEEECC-CCCHHHHHHHHHH---HHCCCCCEEEC
T ss_conf 8885677298889-8-7767763879-99829999699-9962999999999---98699686885
No 294
>COG1915 Uncharacterized conserved protein [Function unknown]
Probab=25.51 E-value=15 Score=15.56 Aligned_cols=25 Identities=32% Similarity=0.530 Sum_probs=13.0
Q ss_pred CCHHHHHHH----HHCCCCCCHHHHHCCCCH
Q ss_conf 143889998----743554211343213662
Q gi|254780834|r 278 EGYMDVLSL----CQAGVQNVVSSLGTALTE 304 (648)
Q Consensus 278 EGy~Dvi~l----~~~G~~n~va~~Gtalt~ 304 (648)
|||.|++-. .-+.|+ .|.+||+|.-
T Consensus 226 ~GyV~~L~~GNAlA~HDIE--~~l~GTSLGv 254 (415)
T COG1915 226 EGYVDALLAGNALAVHDIE--QALMGTSLGV 254 (415)
T ss_pred HHHHHHHHCCCCEEECHHH--HHHHCCCCCE
T ss_conf 3058876557701320467--8761353021
No 295
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=25.49 E-value=33 Score=12.32 Aligned_cols=83 Identities=19% Similarity=0.159 Sum_probs=52.8
Q ss_pred EEEECCHHHHHHH------HHCCCCCCHHHHHCCCCHHHHHHHHHCC---CEEEEEECCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 8997143889998------7435542113432136626789885126---818996178866225777888888777536
Q gi|254780834|r 274 IILVEGYMDVLSL------CQAGVQNVVSSLGTALTEYQLRLLWKLS---PRIVLCFDGDDPGLRAAYKAIDLVLCHLIP 344 (648)
Q Consensus 274 ~i~vEGy~Dvi~l------~~~G~~n~va~~Gtalt~~~~~~l~r~~---~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~ 344 (648)
-||.-+..|-+.. .+-| .|+....-..-...|+++++++. ++|-+.||..+++-.+..+.++.+. -+.
T Consensus 83 PIVF~~V~dPv~aglv~s~~~pg-~NvTGvs~~~~~~~~l~l~~~l~P~~k~igvlyn~~e~ns~~~~~~~~~~a--~~~ 159 (281)
T cd06325 83 PIVFTAVTDPVGAGLVKSLEKPG-GNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAA--AKL 159 (281)
T ss_pred CEEEEECCCHHHCCCCCCCCCCC-CCEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHH--HHC
T ss_conf 98999516866627543567899-957998787478999999998588985899995799865699999999999--976
Q ss_pred CCCEEEEECCCCCCHHHH
Q ss_conf 973067525788888899
Q gi|254780834|r 345 GNRVNFVLLSRGEDPDSF 362 (648)
Q Consensus 345 g~~v~vv~LP~G~DPDe~ 362 (648)
|+++..+..+ ++.|+
T Consensus 160 Gi~v~~~~v~---~~~ei 174 (281)
T cd06325 160 GIEVVEATVS---SSNDV 174 (281)
T ss_pred CCEEEEEECC---CHHHH
T ss_conf 9889999459---88899
No 296
>KOG0164 consensus
Probab=25.44 E-value=33 Score=12.31 Aligned_cols=61 Identities=20% Similarity=0.326 Sum_probs=29.1
Q ss_pred CCCCEEEEECCHHHHHHHHH----CCCCCCHHHHHCCCCHHHHHHHHHCC------CEEEEEECCCCCCHHHH
Q ss_conf 67870899714388999874----35542113432136626789885126------81899617886622577
Q gi|254780834|r 269 NSSSFIILVEGYMDVLSLCQ----AGVQNVVSSLGTALTEYQLRLLWKLS------PRIVLCFDGDDPGLRAA 331 (648)
Q Consensus 269 ~~~~~~i~vEGy~Dvi~l~~----~G~~n~va~~Gtalt~~~~~~l~r~~------~~vvl~fDgD~AG~kAa 331 (648)
+...+.++.-|-++|.+.+. .++.++..+.| |+++-+..+|+.. .+|-+.=+.|..|+.+.
T Consensus 223 ~~~~Y~ylnqg~~~v~sinD~~dfk~V~~Am~vIg--Fs~eEVe~v~~iiAavLhLGNv~f~~~ed~~~~~~~ 293 (1001)
T KOG0164 223 NPQSYNYLNQGSAKVSSINDASDFKAVQKAMRVIG--FSEEEVESVLSIIAAVLHLGNVEFADNEDSSGIVNG 293 (1001)
T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHH
T ss_conf 75300222000233046551777999998888738--888999999999999985066688514765454005
No 297
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=25.40 E-value=33 Score=12.35 Aligned_cols=17 Identities=18% Similarity=0.337 Sum_probs=11.5
Q ss_pred ECCCCCCCCHHHHHHHH
Q ss_conf 13688887898998988
Q gi|254780834|r 64 CFSCHVKGDHLSFLSAL 80 (648)
Q Consensus 64 cf~c~~~gd~~~f~~~~ 80 (648)
.+|||.|+..+....++
T Consensus 5 DiGCG~G~~~~~LA~~~ 21 (224)
T smart00828 5 DFGCGYGSDLIDLAERH 21 (224)
T ss_pred EEECCCCHHHHHHHHHC
T ss_conf 98366888899999977
No 298
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases including those similar to IntD, a putative integrase-like protein, a component of the vanD glycopeptide resistance cluster in Enterococcus faecium BM4339. Members of this CD are predominantly bacterial in origin.
Probab=25.38 E-value=33 Score=12.40 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=13.5
Q ss_pred HHHHHHCCCCHHHHCCCC
Q ss_conf 999985068853510124
Q gi|254780834|r 141 HYYLDERGIDSHAIEMFK 158 (648)
Q Consensus 141 ~~yl~~Rg~~~~~~~~f~ 158 (648)
.+||.+||+|+.||+.|.
T Consensus 2 ~~yL~e~g~S~~Ti~sY~ 19 (263)
T cd01196 2 EEYLYKNNLSKNTVSSYL 19 (263)
T ss_pred HHHHHHCCCCHHHHHHHH
T ss_conf 587967697899999999
No 299
>pfam05480 Staph_haemo Staphylococcus haemolytic protein. This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus. Gonococcal growth inhibitor from Staphylococcus act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death.
Probab=25.38 E-value=30 Score=12.77 Aligned_cols=25 Identities=28% Similarity=0.546 Sum_probs=16.4
Q ss_pred CCHHHHHH-HHHCCCCCCHHHHHCCC
Q ss_conf 14388999-87435542113432136
Q gi|254780834|r 278 EGYMDVLS-LCQAGVQNVVSSLGTAL 302 (648)
Q Consensus 278 EGy~Dvi~-l~~~G~~n~va~~Gtal 302 (648)
||.+++|+ ..++|+.+-=|.|||++
T Consensus 2 ~~l~eAI~n~V~Ag~~~DwaklGtSI 27 (43)
T pfam05480 2 SGLFEAIKNAVQAGIAQDWAKLGTSI 27 (43)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHCCHH
T ss_conf 17999999999986026389842069
No 300
>COG3673 Uncharacterized conserved protein [Function unknown]
Probab=25.37 E-value=33 Score=12.30 Aligned_cols=23 Identities=22% Similarity=0.600 Sum_probs=14.7
Q ss_pred CCCCCCCCCCEEEECCCCEEEECC
Q ss_conf 458888587879817897467136
Q gi|254780834|r 43 CPFHDEKTPSFHCNDSKGFYYCFS 66 (648)
Q Consensus 43 cPfh~ektpsf~v~~~~~~~~cf~ 66 (648)
|-|...- |+..-+.-|++-.||-
T Consensus 16 ~g~~s~~-~~~~~ds~k~lV~CfD 38 (423)
T COG3673 16 CGFTSDL-NLLAEDSMKRLVFCFD 38 (423)
T ss_pred CCCCCCC-CCCCCCCCCEEEEEEC
T ss_conf 6788887-5332357642899963
No 301
>KOG2730 consensus
Probab=25.21 E-value=34 Score=12.28 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=9.3
Q ss_pred EEECCHHHHHHHHHCC
Q ss_conf 9971438899987435
Q gi|254780834|r 275 ILVEGYMDVLSLCQAG 290 (648)
Q Consensus 275 i~vEGy~Dvi~l~~~G 290 (648)
.++--+.|+.+-.|+.
T Consensus 147 FI~GD~ld~~~~lq~~ 162 (263)
T KOG2730 147 FICGDFLDLASKLKAD 162 (263)
T ss_pred EEECHHHHHHHHHHHH
T ss_conf 8833099999988641
No 302
>KOG4672 consensus
Probab=25.10 E-value=34 Score=12.26 Aligned_cols=14 Identities=14% Similarity=0.197 Sum_probs=5.8
Q ss_pred CHHHHHHHCCCCCH
Q ss_conf 10345542059973
Q gi|254780834|r 167 YSLREHLRQKGFSE 180 (648)
Q Consensus 167 ~~l~~~l~~~~~~~ 180 (648)
-..+.+|+++-+..
T Consensus 102 p~~~~~L~r~evey 115 (487)
T KOG4672 102 PVMFSHLQRREVEY 115 (487)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 07889999876666
No 303
>pfam03811 Ins_element1 Insertion element protein.
Probab=25.08 E-value=34 Score=12.26 Aligned_cols=28 Identities=18% Similarity=0.443 Sum_probs=17.9
Q ss_pred ECCCCCCCCCCE----EEECCCCEEEECCCCCC
Q ss_conf 345888858787----98178974671368888
Q gi|254780834|r 42 CCPFHDEKTPSF----HCNDSKGFYYCFSCHVK 70 (648)
Q Consensus 42 ~cPfh~ektpsf----~v~~~~~~~~cf~c~~~ 70 (648)
.|||.+... +- .-...+|.|.|..|+..
T Consensus 7 ~Cp~C~s~~-~V~KnG~~~~G~QRYrC~~C~r~ 38 (88)
T pfam03811 7 HCPRCSSTE-GVYRHGQSTAGHQRYRCRHCRRT 38 (88)
T ss_pred ECCCCCCCC-CEEECCCCCCCCCCEEECCCCCE
T ss_conf 797888987-67718968999857772778955
No 304
>pfam06819 Arc_PepC Archaeal Peptidase A24 C-terminal Domain. This region is of unknown function but is found in some archaeal pfam01478. It is predicted to be of mixed alpha/beta secondary structure by JPred.
Probab=25.05 E-value=27 Score=13.08 Aligned_cols=24 Identities=38% Similarity=0.435 Sum_probs=17.8
Q ss_pred CCCHHHHHCCCCHHHHHHHHHCCC
Q ss_conf 421134321366267898851268
Q gi|254780834|r 292 QNVVSSLGTALTEYQLRLLWKLSP 315 (648)
Q Consensus 292 ~n~va~~Gtalt~~~~~~l~r~~~ 315 (648)
+.++.|.|--||++|+..|+++..
T Consensus 78 ~~i~~~~~EGLs~E~IE~LkkLv~ 101 (111)
T pfam06819 78 EEVAGTSGEGLTEEQIEKLKKLVS 101 (111)
T ss_pred CEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 757515645677989999999997
No 305
>cd00687 Terpene_cyclase_nonplant_C1 NonPlant Terpene Cyclases, Class 1 (C1). This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are foun
Probab=24.97 E-value=34 Score=12.24 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=18.2
Q ss_pred HHHHHCCCCCCHHHHHCCCCHHHHHHHHHCC
Q ss_conf 9987435542113432136626789885126
Q gi|254780834|r 284 LSLCQAGVQNVVSSLGTALTEYQLRLLWKLS 314 (648)
Q Consensus 284 i~l~~~G~~n~va~~Gtalt~~~~~~l~r~~ 314 (648)
-.+...++...+|-+----+.+++.++..+.
T Consensus 36 ~~~~~~~~~~~~a~~~P~a~~e~L~l~~~~~ 66 (303)
T cd00687 36 KRFLSADFGDLAALFYPDADDERLMLAADLM 66 (303)
T ss_pred HHHHCCCHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 9987499998898868999989999999999
No 306
>PRK00443 nagB glucosamine-6-phosphate deaminase; Provisional
Probab=24.93 E-value=34 Score=12.23 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=8.7
Q ss_pred CCCEEEEEECCCCCCH
Q ss_conf 2681899617886622
Q gi|254780834|r 313 LSPRIVLCFDGDDPGL 328 (648)
Q Consensus 313 ~~~~vvl~fDgD~AG~ 328 (648)
..+++++..|-++|..
T Consensus 231 ~H~~~~~~lD~~AAs~ 246 (264)
T PRK00443 231 LHPNATVVLDEEAASE 246 (264)
T ss_pred CCCCEEEEECHHHHHC
T ss_conf 4998899988899806
No 307
>PRK08174 DNA topoisomerase III; Validated
Probab=24.91 E-value=34 Score=12.23 Aligned_cols=13 Identities=23% Similarity=0.378 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 3799999999984
Q gi|254780834|r 481 SLREAALLLTLIN 493 (648)
Q Consensus 481 ~~~E~~LL~llI~ 493 (648)
...|..|+..|-+
T Consensus 487 ryTEasLi~~M~~ 499 (670)
T PRK08174 487 PYTEGTLIKAMKN 499 (670)
T ss_pred CCCHHHHHHHHHH
T ss_conf 9898999999986
No 308
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=24.86 E-value=34 Score=12.22 Aligned_cols=77 Identities=19% Similarity=0.284 Sum_probs=44.8
Q ss_pred ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE------EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 71438-89998743554211343213662678988512681------899617886622577788888877753697306
Q gi|254780834|r 277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPR------IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVN 349 (648)
Q Consensus 277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~------vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~ 349 (648)
-||=| |++++-. .+++-.|..+|.+++..+...++. +--++++|.+ +++..++. ++
T Consensus 210 a~GsmRDAlsiLd----Q~~s~~~~~i~~~~v~~~lG~~~~~~~~~l~~~i~~~d~~---~~l~~~~~---~~------- 272 (563)
T PRK06674 210 ADGGMRDALSLLD----QAISFSDERVTTEDVLAVTGAVSQQYLGNLVECIRENDVS---RALRIIDE---MM------- 272 (563)
T ss_pred CCCCHHHHHHHHH----HHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHH---HHHHHHHH---HH-------
T ss_conf 6997889999999----9997159976899999986899889999999999848999---99999999---99-------
Q ss_pred EEECCCCCCHHHHHHCCCHHHHHHHH
Q ss_conf 75257888888997203668899886
Q gi|254780834|r 350 FVLLSRGEDPDSFIRCYGKTAFEKLI 375 (648)
Q Consensus 350 vv~LP~G~DPDe~ir~~G~eaf~~ll 375 (648)
-.|+||.-|+..- ..-|++++
T Consensus 273 ----~~G~d~~~~~~dl-~~~~r~~l 293 (563)
T PRK06674 273 ----GQGKDPVRLMEDF-IYYYRDML 293 (563)
T ss_pred ----HCCCCHHHHHHHH-HHHHHHHH
T ss_conf ----8799999999999-99999988
No 309
>pfam09393 DUF2001 Protein of unknown function (DUF2001). This family includes phage-like element PBSX protein whose structure adopts a beta barrel flanked with alpha helical regions.
Probab=24.85 E-value=30 Score=12.72 Aligned_cols=35 Identities=26% Similarity=0.447 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf 25777888888777536973067525788888899
Q gi|254780834|r 328 LRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF 362 (648)
Q Consensus 328 ~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ 362 (648)
.+-+-|..++....++.|..++|-..-...||+++
T Consensus 66 ~kvtS~~~~~~~~~ik~G~~~~f~Ii~~l~DP~s~ 100 (141)
T pfam09393 66 YKVTSRFRKLMIDYIKTGKDPYFEIISKLEDPDSY 100 (141)
T ss_pred EEECHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
T ss_conf 98568999999999964998228999990799766
No 310
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.82 E-value=34 Score=12.22 Aligned_cols=10 Identities=20% Similarity=0.478 Sum_probs=5.2
Q ss_pred HCCCCCCHHH
Q ss_conf 4355421134
Q gi|254780834|r 288 QAGVQNVVSS 297 (648)
Q Consensus 288 ~~G~~n~va~ 297 (648)
++|+.-+..|
T Consensus 190 ~~Gf~e~~~P 199 (429)
T COG0172 190 KHGFTEVLPP 199 (429)
T ss_pred HCCCEEEECC
T ss_conf 7696586576
No 311
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.68 E-value=34 Score=12.20 Aligned_cols=20 Identities=20% Similarity=0.275 Sum_probs=9.8
Q ss_pred CCHHHHHCCCCHHHHHHHHH
Q ss_conf 21134321366267898851
Q gi|254780834|r 293 NVVSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 293 n~va~~Gtalt~~~~~~l~r 312 (648)
.-|+.+.-.+|+.+-...|+
T Consensus 240 ~~v~v~HS~ls~~eR~~~w~ 259 (699)
T PRK05580 240 ARVAVLHSGLSDGERYRAWL 259 (699)
T ss_pred CCEEEECCCCCHHHHHHHHH
T ss_conf 95799648898579999999
No 312
>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]
Probab=24.66 E-value=34 Score=12.19 Aligned_cols=31 Identities=13% Similarity=0.003 Sum_probs=17.9
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHH
Q ss_conf 78888889972036688998864149927999
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVESLPLVDML 385 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl 385 (648)
|.--+|+.+. ..+.+++..+++...+.++|+
T Consensus 191 ~a~~~~~~~~-d~~~~~~~~Ll~~~~~~~~~v 221 (366)
T COG4963 191 AAPTELAKNY-DLKTGAVERLLDLLRGSFDFV 221 (366)
T ss_pred CCCCCHHHHC-CCCCCHHHHHHHHHHCCCCEE
T ss_conf 3774456521-533126999999764028838
No 313
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235 This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=24.66 E-value=18 Score=14.77 Aligned_cols=40 Identities=30% Similarity=0.444 Sum_probs=25.7
Q ss_pred HCCCCEEEEECCCCCC-HHHH---HHCCCHHHHHHHHHHCC-CHHHHH
Q ss_conf 3697306752578888-8899---72036688998864149-927999
Q gi|254780834|r 343 IPGNRVNFVLLSRGED-PDSF---IRCYGKTAFEKLIVESL-PLVDML 385 (648)
Q Consensus 343 ~~g~~v~vv~LP~G~D-PDe~---ir~~G~eaf~~ll~~A~-~l~dFl 385 (648)
+-|++|||| ++.| |++| |+.+-+--|.+-|.|.. ...||-
T Consensus 119 rlGIevrFv---d~dd~pe~~~k~id~nTKAvf~EtIgNP~~~v~Die 163 (434)
T TIGR01326 119 RLGIEVRFV---DGDDDPEELEKAIDENTKAVFAETIGNPALNVPDIE 163 (434)
T ss_pred HCCEEEEEE---CCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCCCHH
T ss_conf 448148872---788887899976066751898401238776767858
No 314
>PRK09401 reverse gyrase; Reviewed
Probab=24.66 E-value=34 Score=12.19 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=28.3
Q ss_pred HHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf 678988512---6818996178866225777888888777
Q gi|254780834|r 305 YQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLVLCH 341 (648)
Q Consensus 305 ~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~l~~ 341 (648)
+-++.|+++ +++|+|+-|.|.=|-+=||...+.+.+.
T Consensus 707 ~vv~aLR~lA~EvDeVyIATDPDREGEaIAwhl~~~Lk~~ 746 (1176)
T PRK09401 707 EIIEALRELALEVDEVLIATDPDTEGEKIAWDVYLLLSPY 746 (1176)
T ss_pred HHHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHHHHCCC
T ss_conf 9999999998755989987899856389999999983554
No 315
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=24.57 E-value=34 Score=12.18 Aligned_cols=11 Identities=27% Similarity=0.471 Sum_probs=4.1
Q ss_pred HHHHCCCCCCH
Q ss_conf 98743554211
Q gi|254780834|r 285 SLCQAGVQNVV 295 (648)
Q Consensus 285 ~l~~~G~~n~v 295 (648)
.|.+.||+.+|
T Consensus 22 ~L~~~gI~~Ii 32 (139)
T cd00127 22 LLKKLGITHVL 32 (139)
T ss_pred HHHHCCCEEEE
T ss_conf 99878980999
No 316
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=24.54 E-value=34 Score=12.18 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=16.8
Q ss_pred EEEECC-CCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 996178-866225777888888777536973067525788
Q gi|254780834|r 318 VLCFDG-DDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 318 vl~fDg-D~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G 356 (648)
.++|.| |.||+-...+.+.-. +...|..|.+..-|.|
T Consensus 5 fI~iEGiDGaGKTT~~~~L~~~--l~~~g~~v~~trEP~~ 42 (208)
T COG0125 5 FIVIEGIDGAGKTTQAELLKER--LEERGIKVVLTREPGG 42 (208)
T ss_pred EEEEECCCCCCHHHHHHHHHHH--HHHCCCEEEEEECCCC
T ss_conf 9999788889889999999999--9982980799868999
No 317
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.34 E-value=14 Score=15.91 Aligned_cols=18 Identities=22% Similarity=0.724 Sum_probs=9.9
Q ss_pred EEEECCCCC---CCCHHHHHH
Q ss_conf 467136888---878989989
Q gi|254780834|r 61 FYYCFSCHV---KGDHLSFLS 78 (648)
Q Consensus 61 ~~~cf~c~~---~gd~~~f~~ 78 (648)
-|+|..||. .|-.|+|..
T Consensus 6 ewkC~VCg~~iieGqkFTF~~ 26 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK 26 (103)
T ss_pred EEEEEEECCEEEECCEEEEEE
T ss_conf 056764088744155788831
No 318
>pfam10191 COG7 Golgi complex component 7 (COG7). COG7 is a component of the conserved oligomeric Golgi complex which is required for normal Golgi morphology and localisation. Mutation in COG7 causes a congenital disorder of glycosylation.
Probab=24.24 E-value=35 Score=12.13 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=3.4
Q ss_pred CCCCCHHHHH
Q ss_conf 7888888997
Q gi|254780834|r 354 SRGEDPDSFI 363 (648)
Q Consensus 354 P~G~DPDe~i 363 (648)
.+|..-+.++
T Consensus 418 T~g~~~~~Ll 427 (768)
T pfam10191 418 TQGLALCGLI 427 (768)
T ss_pred HCCCCHHHHH
T ss_conf 2763428899
No 319
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein B; InterPro: IPR004435 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , . In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) . The MobB domain is similar to that of the urease accessory protein UreG and the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocentres of their respective target enzymes. It is involved in the final step of molybdenum-cofactor biosynthesis. While its precise function has not been identified it is thought to be involved in the transfer of a guanine dinucleotide moiety to molybdopterin, as it shows GTP-binding and weak GTPase activity . The MobB protein (P32125 from SWISSPROT) from Escherichia coli, which is comprised of this domain, is a homodimer . Each molecule is composed of two distinct regions - an outer region comprised of 6 beta-strands and three alpha helices, and an inner region comprised of a two-strand beta hairpin followed by an alpha helix. These regions require interaction with the second monomer to allow proper folding to occur. The two monomers are intertwined and form an extensive 16-stranded beta-sheet. While the active site could not be positively identified, the presence of highly conserved residues suggests the substrate binding site occurs in the central solvent channel.; GO: 0005525 GTP binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=24.23 E-value=33 Score=12.41 Aligned_cols=25 Identities=36% Similarity=0.445 Sum_probs=14.5
Q ss_pred CHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHH
Q ss_conf 8178888643310000235678708997143889
Q gi|254780834|r 250 NFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDV 283 (648)
Q Consensus 250 ~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dv 283 (648)
.|..+.+...- .+--++|||||=|-
T Consensus 84 ~L~~~l~~~~~---------~~~D~~LvEGfK~~ 108 (165)
T TIGR00176 84 DLEALLKRLAD---------RELDIILVEGFKDS 108 (165)
T ss_pred CHHHHHHHCCC---------CCCCEEEEECCCCC
T ss_conf 87999864285---------52687898524557
No 320
>KOG2185 consensus
Probab=24.22 E-value=35 Score=12.13 Aligned_cols=48 Identities=23% Similarity=0.315 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999998724127989999999999999999999884132676
Q gi|254780834|r 590 LLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIE 639 (648)
Q Consensus 590 ~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~e 639 (648)
.+++.+..++..++. ..+|......+...+++.+++|..+.++|+-+.
T Consensus 424 rlkrdm~klkq~l~R--N~gd~v~s~~lqe~L~ev~~~Lasl~aqea~ls 471 (486)
T KOG2185 424 RLKRDMLKLKQMLNR--NKGDLVVSEALQERLKEVRKALASLLAQEAALS 471 (486)
T ss_pred HHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999862--453178999999999999999999999998876
No 321
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=24.20 E-value=35 Score=12.13 Aligned_cols=60 Identities=18% Similarity=0.220 Sum_probs=36.8
Q ss_pred CCCCHHHHHHCCCHHHHHHHHHHCCC---HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 88888899720366889988641499---2799999998530233145799999999988541
Q gi|254780834|r 355 RGEDPDSFIRCYGKTAFEKLIVESLP---LVDMLWKRETENRSFNTPDERAELEIHLKNCINH 414 (648)
Q Consensus 355 ~G~DPDe~ir~~G~eaf~~ll~~A~~---l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~ 414 (648)
...||.+++.++|+|+++-++-...| -.+|=|+......+.+-...--.+++++...+.+
T Consensus 306 n~i~~~~~~~~~g~D~lRyyl~~~~~~~~D~dfs~~~f~~r~NsdL~n~lGNl~~R~~~~~~k 368 (644)
T PRK12267 306 NVVDPEELVDRYGLDALRYYLLREVPFGSDGDFSPEAFVERINSDLANDLGNLLNRTVAMINK 368 (644)
T ss_pred CEECHHHHHHHCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 422379998755940436464444887877778999999998899887777899999999887
No 322
>pfam09740 DUF2043 Uncharacterized conserved protein (DUF2043). This is a 100 residue conserved region of a family of proteins found from fungi to humans. This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.
Probab=24.19 E-value=27 Score=13.19 Aligned_cols=15 Identities=27% Similarity=0.793 Sum_probs=5.6
Q ss_pred CCCCEEEEEEEECCCCE
Q ss_conf 01671688897077858
Q gi|254780834|r 201 RFRNRLIFPIRSSRGQV 217 (648)
Q Consensus 201 ~Fr~Ri~fPi~~~~g~~ 217 (648)
-|.|+|| | +|..|++
T Consensus 92 PFHGkII-p-RDd~G~P 106 (111)
T pfam09740 92 PFHGKIV-P-RDDEGRP 106 (111)
T ss_pred CCCCCCC-C-CCCCCCC
T ss_conf 8778644-8-4436897
No 323
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family; InterPro: IPR011288 This entry describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4 , .; GO: 0008270 zinc ion binding, 0016832 aldehyde-lyase activity, 0019512 lactose catabolic process via tagatose-6-phosphate.
Probab=24.17 E-value=30 Score=12.68 Aligned_cols=89 Identities=21% Similarity=0.340 Sum_probs=50.5
Q ss_pred CCCCC-CHHHHHCC---------CCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC----------CE
Q ss_conf 35542-11343213---------662678988512681899617886622577788888877753697----------30
Q gi|254780834|r 289 AGVQN-VVSSLGTA---------LTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN----------RV 348 (648)
Q Consensus 289 ~G~~n-~va~~Gta---------lt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~----------~v 348 (648)
-||.- +||. ||| |-=+-+..|++.++=+..+==+=.=--+-..|++||-..-+--+- .-
T Consensus 165 TGvDSLAvAI-GTAHGlY~~aP~LDF~RL~~IR~~v~vPLVLHGASdvpde~v~~~IeLGi~KvNVATeLKiAFS~AlK~ 243 (282)
T TIGR01858 165 TGVDSLAVAI-GTAHGLYKEAPKLDFDRLAKIREKVDVPLVLHGASDVPDEDVRRTIELGICKVNVATELKIAFSGALKA 243 (282)
T ss_pred CCCHHHHHHH-HHHHHHHHCCCCCCHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHCCCEEECCHHCCHHHHHHHHH
T ss_conf 2754788988-665323212675337899875220377724217778876789999870741341111100368999999
Q ss_pred EEEECCCCCCHHHHHHCCCHHHHHHHHHHCC
Q ss_conf 6752578888889972036688998864149
Q gi|254780834|r 349 NFVLLSRGEDPDSFIRCYGKTAFEKLIVESL 379 (648)
Q Consensus 349 ~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~ 379 (648)
+|+.-|++-||=.|++. |++++++.+++-.
T Consensus 244 Yf~enp~AnDPR~Ym~~-ak~AMk~vv~~kI 273 (282)
T TIGR01858 244 YFLENPEANDPRKYMRP-AKEAMKKVVEKKI 273 (282)
T ss_pred HHHHCCCCCCCHHHHHH-HHHHHHHHHHHHH
T ss_conf 99748899983252366-7999999988664
No 324
>PRK10116 universal stress protein UspC; Provisional
Probab=24.16 E-value=35 Score=12.12 Aligned_cols=43 Identities=14% Similarity=0.306 Sum_probs=34.4
Q ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf 818996178866225777888888777536973067525788888899
Q gi|254780834|r 315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF 362 (648)
Q Consensus 315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ 362 (648)
++|.+.-|+-....++..||++++..+ |-++.++.. ..||+-|
T Consensus 4 khILVAvDlS~~S~~~i~kA~~lA~~~---~AklslihV--~~~~~~y 46 (142)
T PRK10116 4 SNILVAVAVTPESQQLLAKAVSIARPV---NGKISLITL--ASDPEMY 46 (142)
T ss_pred CEEEEEECCCHHHHHHHHHHHHHHHHC---CCEEEEEEE--ECCHHHH
T ss_conf 689999418850699999999999981---998999999--3576665
No 325
>pfam07212 Hyaluronidase_1 Hyaluronidase protein (HylP). This family consists of several phage associated hyaluronidase proteins (EC:3.2.1.35) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon.
Probab=24.15 E-value=35 Score=12.12 Aligned_cols=14 Identities=14% Similarity=0.297 Sum_probs=6.3
Q ss_pred EECCCCEEEEECCC
Q ss_conf 70778588850100
Q gi|254780834|r 211 RSSRGQVIAFGGRT 224 (648)
Q Consensus 211 ~~~~g~~i~f~gR~ 224 (648)
+|..-+.|-++|..
T Consensus 105 f~qsa~fvdy~gkt 118 (273)
T pfam07212 105 FNQSALFVDYKGTT 118 (273)
T ss_pred CCCCEEEEEECCCC
T ss_conf 24412678603764
No 326
>PRK13559 hypothetical protein; Provisional
Probab=24.08 E-value=35 Score=12.11 Aligned_cols=36 Identities=25% Similarity=0.335 Sum_probs=25.4
Q ss_pred CCEECCCCCCCCCCCCCE-EEEEEEECCCCEEEEECCCCCC
Q ss_conf 210034654100001671-6888970778588850100146
Q gi|254780834|r 188 LLIDGDNSATSYDRFRNR-LIFPIRSSRGQVIAFGGRTLSK 227 (648)
Q Consensus 188 l~~~~~~~~~~~d~Fr~R-i~fPi~~~~g~~i~f~gR~l~~ 227 (648)
+...+++|. .|.+. -|=||+|..|+|+.|-|=..|=
T Consensus 123 l~nyrKDGs----~fwn~l~isPV~D~~G~v~~fig~q~Dv 159 (363)
T PRK13559 123 LLNYRKDGS----PFWNALHLGPIYDEDGKLLYFFGSQWDV 159 (363)
T ss_pred EEEECCCCC----EEEEEEEEEEEECCCCCEEEEEEEEEEE
T ss_conf 999826998----2477689888798999799999999851
No 327
>KOG0385 consensus
Probab=24.05 E-value=35 Score=12.10 Aligned_cols=42 Identities=19% Similarity=0.187 Sum_probs=22.4
Q ss_pred CEEEEEECCC---CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHH
Q ss_conf 8189961788---6622577788888877753697306752578888889
Q gi|254780834|r 315 PRIVLCFDGD---DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDS 361 (648)
Q Consensus 315 ~~vvl~fDgD---~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe 361 (648)
--+||.||+| +.-..|..||--+ -+...|+|..|=...--++
T Consensus 559 ADtVIlyDSDWNPQ~DLQAmDRaHRI-----GQ~K~V~V~RLitentVEe 603 (971)
T KOG0385 559 ADTVILYDSDWNPQVDLQAMDRAHRI-----GQKKPVVVYRLITENTVEE 603 (971)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHC-----CCCCCEEEEEEECCCHHHH
T ss_conf 64799966899821437889988860-----7877159999753551899
No 328
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=24.05 E-value=35 Score=12.10 Aligned_cols=96 Identities=23% Similarity=0.299 Sum_probs=56.1
Q ss_pred CCCEEEEECCHHHHHHHHHC------CCCC--CHHHHHCCCCHHHHHHHHHC---CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf 78708997143889998743------5542--11343213662678988512---6818996178866225777888888
Q gi|254780834|r 270 SSSFIILVEGYMDVLSLCQA------GVQN--VVSSLGTALTEYQLRLLWKL---SPRIVLCFDGDDPGLRAAYKAIDLV 338 (648)
Q Consensus 270 ~~~~~i~vEGy~Dvi~l~~~------G~~n--~va~~Gtalt~~~~~~l~r~---~~~vvl~fDgD~AG~kAa~Ra~e~~ 338 (648)
.-+--|+|||--||=+...+ |-+. +|.+. ..-| |+..-+|- ++-|+|+-|.|..|++-|.|..+-+
T Consensus 6 pVDVRIiVEGAsDvE~iSkalQr~aLG~eYnITisSI-iPTT--~~eIA~raaeGADlvlIATDaD~~GReLA~kf~eeL 82 (290)
T COG4026 6 PVDVRIIVEGASDVEVISKALQRLALGSEYNITISSI-IPTT--NVEIAKRAAEGADLVLIATDADRVGRELAEKFFEEL 82 (290)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEEE-CCCC--HHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHH
T ss_conf 6317998606533899999998864056110588862-2675--199998763568779996057604599999999999
Q ss_pred HHHHHCCCCEEEEECCCCCCHH----HHHHCCCHHHH
Q ss_conf 7775369730675257888888----99720366889
Q gi|254780834|r 339 LCHLIPGNRVNFVLLSRGEDPD----SFIRCYGKTAF 371 (648)
Q Consensus 339 l~~l~~g~~v~vv~LP~G~DPD----e~ir~~G~eaf 371 (648)
-.+ -| .+-=+.+|-|+|-. +++++.=..++
T Consensus 83 rg~--VG-hiERmK~PiGHDvEhiD~elvrkEl~nAl 116 (290)
T COG4026 83 RGM--VG-HIERMKIPIGHDVEHIDVELVRKELKNAL 116 (290)
T ss_pred HHH--HH-HHHEECCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 875--30-45112267787722058999999999999
No 329
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=24.02 E-value=31 Score=12.58 Aligned_cols=73 Identities=21% Similarity=0.204 Sum_probs=42.7
Q ss_pred CCEEEEECCCCCCCC--CCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHH---------HH
Q ss_conf 858885010014655--3001038767653521011081788886433100002356787089971438---------89
Q gi|254780834|r 215 GQVIAFGGRTLSKGE--SVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYM---------DV 283 (648)
Q Consensus 215 g~~i~f~gR~l~~~~--~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~---------Dv 283 (648)
|||.=||=-+ |.|. +.+||-+-+-+ -..|+.++--..|....+-..+- |||=|-- =|
T Consensus 1 GrvwkFGDdv-DTD~IIPGrYLR~~~D~----------~eLA~haM~g~~PeF~~kvr~GD-viVAGkNFGcGSSREQA~ 68 (159)
T TIGR02087 1 GRVWKFGDDV-DTDVIIPGRYLRTTDDP----------DELASHAMEGIDPEFAKKVREGD-VIVAGKNFGCGSSREQAA 68 (159)
T ss_pred CCEEECCCCC-CCCEECCCCCCCCCCCH----------HHHHHHCCCCCCCCHHHHCCCCC-EEEECCCCCCCCCHHHHH
T ss_conf 9377606864-67704585225754777----------88998705589963134078997-887141647788778899
Q ss_pred HHHHHCCCCCCHHHHH
Q ss_conf 9987435542113432
Q gi|254780834|r 284 LSLCQAGVQNVVSSLG 299 (648)
Q Consensus 284 i~l~~~G~~n~va~~G 299 (648)
|||-++||..|||=+-
T Consensus 69 ~ALK~aGv~aviA~SF 84 (159)
T TIGR02087 69 LALKAAGVAAVIAESF 84 (159)
T ss_pred HHHHHCCEEEEEEEEC
T ss_conf 9997479048985201
No 330
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=23.95 E-value=35 Score=12.09 Aligned_cols=34 Identities=9% Similarity=0.031 Sum_probs=15.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 78866225777888888777536973067525788
Q gi|254780834|r 322 DGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356 (648)
Q Consensus 322 DgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G 356 (648)
+.|.+=++.++..+..++.+ ...+.++++.++.+
T Consensus 88 S~D~~~R~~~~e~~~kaI~l-A~~LGi~~I~lag~ 121 (283)
T PRK13209 88 SEDDAVRAQGLEIMRKAIQL-AQDLGIRVIQLAGY 121 (283)
T ss_pred CCCHHHHHHHHHHHHHHHHH-HHHCCCCEEEECCC
T ss_conf 97999999999999999999-99809998996887
No 331
>KOG2874 consensus
Probab=23.78 E-value=35 Score=12.06 Aligned_cols=23 Identities=30% Similarity=0.501 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH--HHHCCCCEEEE
Q ss_conf 577788888877--75369730675
Q gi|254780834|r 329 RAAYKAIDLVLC--HLIPGNRVNFV 351 (648)
Q Consensus 329 kAa~Ra~e~~l~--~l~~g~~v~vv 351 (648)
-++++|++++-. .+-+|.+|.++
T Consensus 168 g~TLKAlelLT~CYilVqG~TVsai 192 (356)
T KOG2874 168 GSTLKALELLTNCYILVQGNTVSAI 192 (356)
T ss_pred CHHHHHHHHHHHCEEEEECCEEEEE
T ss_conf 2057999997521798607677763
No 332
>TIGR00791 gntP transporter, gluconate:H+ symporter (GntP) family; InterPro: IPR003474 This is a family of integral membrane permeases that are involved in gluconate uptake. Escherichia coli contains several members of this family including GntU, a low affinity transporter and GntT, a high affinity transporter .; GO: 0015128 gluconate transmembrane transporter activity, 0015725 gluconate transport, 0016020 membrane.
Probab=23.71 E-value=26 Score=13.26 Aligned_cols=15 Identities=20% Similarity=0.162 Sum_probs=5.3
Q ss_pred CHHHHHHHHHHHHHH
Q ss_conf 988999999999997
Q gi|254780834|r 512 NNELQKLWSFLFSDF 526 (648)
Q Consensus 512 ~~~~~~L~~~i~~~~ 526 (648)
||...-+-..++..|
T Consensus 273 np~~Am~IA~lvA~y 287 (458)
T TIGR00791 273 NPITAMLIAVLVAIY 287 (458)
T ss_pred CHHHHHHHHHHHHHH
T ss_conf 858999999999999
No 333
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=23.69 E-value=36 Score=12.05 Aligned_cols=48 Identities=27% Similarity=0.290 Sum_probs=34.5
Q ss_pred ECCHH-HHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEE------EEEECCCCCCH
Q ss_conf 71438-899987435542113432136626789885126818------99617886622
Q gi|254780834|r 277 VEGYM-DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRI------VLCFDGDDPGL 328 (648)
Q Consensus 277 vEGy~-Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~v------vl~fDgD~AG~ 328 (648)
-||=| |++||-. .++|..|..+|.++++.+..++++- -.+++||....
T Consensus 222 a~GS~RDaLSlLD----Qai~~~~~~i~~~~v~~mLGl~d~~~i~~Ll~~i~~Gd~~~a 276 (600)
T PRK09111 222 AEGSVRDGLSLLD----QAIAHGAGEVTAEQVRDMLGLADRARVIDLFEALMRGDVAAA 276 (600)
T ss_pred CCCCCCHHHHHHH----HHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHH
T ss_conf 4898421899999----999727987569999998688767789999999985586889
No 334
>KOG0260 consensus
Probab=23.67 E-value=27 Score=13.11 Aligned_cols=21 Identities=24% Similarity=0.137 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCHHCCCHHHH
Q ss_conf 038767653521011081788
Q gi|254780834|r 234 LNSPETILFHKGKNLYNFFGA 254 (648)
Q Consensus 234 lNSpeT~if~K~~~Ly~l~~a 254 (648)
=||||+.=|-+...|-||+.-
T Consensus 789 dysPesrGfVENSyL~GLtP~ 809 (1605)
T KOG0260 789 DYSPESRGFVENSYLTGLTPQ 809 (1605)
T ss_pred CCCCCCCCEEECCCCCCCCHH
T ss_conf 998210442321202579889
No 335
>pfam00396 Granulin Granulin.
Probab=23.66 E-value=33 Score=12.35 Aligned_cols=10 Identities=40% Similarity=1.434 Sum_probs=7.7
Q ss_pred EEEECCCCCC
Q ss_conf 5753458888
Q gi|254780834|r 39 YWACCPFHDE 48 (648)
Q Consensus 39 ~~~~cPfh~e 48 (648)
=||+|||.+-
T Consensus 9 ~wgCCP~~~A 18 (43)
T pfam00396 9 GWGCCPLPQA 18 (43)
T ss_pred CEECCCCCCC
T ss_conf 8930779988
No 336
>pfam00282 Pyridoxal_deC Pyridoxal-dependent decarboxylase conserved domain.
Probab=23.46 E-value=15 Score=15.49 Aligned_cols=35 Identities=26% Similarity=0.285 Sum_probs=21.2
Q ss_pred CCHHHHHCCCCH--HHHHHHHHCCCE--EEEEECCCCCC
Q ss_conf 211343213662--678988512681--89961788662
Q gi|254780834|r 293 NVVSSLGTALTE--YQLRLLWKLSPR--IVLCFDGDDPG 327 (648)
Q Consensus 293 n~va~~Gtalt~--~~~~~l~r~~~~--vvl~fDgD~AG 327 (648)
-+||+.||.-|- +-+..|..++.+ +.+=-||--+|
T Consensus 196 ~VvataGTT~tGaiD~l~~i~~i~~~~~lWlHVDaA~GG 234 (370)
T pfam00282 196 FVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDAAYAG 234 (370)
T ss_pred EEEEECCCCCCCCCCCHHHHHHHHHHCCCEEEEEHHHHH
T ss_conf 999863771771347899999999983980884233334
No 337
>pfam11464 Rbsn FYVE-finger-containing Rab5 effector protein rabenosyn-5. Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking.
Probab=23.20 E-value=36 Score=11.98 Aligned_cols=38 Identities=21% Similarity=0.263 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998724127989999999999999999999
Q gi|254780834|r 593 RQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQ 630 (648)
Q Consensus 593 r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~ 630 (648)
.++..++.-|.++...+.-|....|..-|++++.+.-+
T Consensus 3 qQi~nIk~yI~qAr~a~R~DEV~~Le~NLreLq~e~~~ 40 (42)
T pfam11464 3 QQINNIKGYIRQARQAGRFDEVETLEENLRELQDELYE 40 (42)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 79999999999999854516999999999999999874
No 338
>pfam00365 PFK Phosphofructokinase.
Probab=23.19 E-value=36 Score=11.97 Aligned_cols=14 Identities=0% Similarity=0.154 Sum_probs=5.5
Q ss_pred EEECCC-CCCHHHHH
Q ss_conf 752578-88888997
Q gi|254780834|r 350 FVLLSR-GEDPDSFI 363 (648)
Q Consensus 350 vv~LP~-G~DPDe~i 363 (648)
++.+|+ ..|+++++
T Consensus 188 ~iliPE~~~~~~~~~ 202 (279)
T pfam00365 188 YIFIPEAPFWEEELC 202 (279)
T ss_pred EEEECCCCCCHHHHH
T ss_conf 999679887589999
No 339
>COG2380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.98 E-value=17 Score=14.91 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf 24422567741034554205997
Q gi|254780834|r 157 FKLGYAPDSRYSLREHLRQKGFS 179 (648)
Q Consensus 157 f~lG~ap~~~~~l~~~l~~~~~~ 179 (648)
|+|-++|.--+.|-.|+..+-|.
T Consensus 1 ~RI~~d~w~~~~le~hv~~~~f~ 23 (327)
T COG2380 1 MRIELDEWIEDELEEHVGDKPFA 23 (327)
T ss_pred CCEECCCCHHHHHHHHHCCCCCC
T ss_conf 91003522466777552356422
No 340
>TIGR00036 dapB dihydrodipicolinate reductase; InterPro: IPR011770 Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants which is involved in the biosynthesis of diaminopimelic acid, a component of bacterial cell walls, and the essential amino acid L-lysine. It catalyses the the reduced pyridine nucleotide-dependent reduction of the alpha,beta-unsaturated cyclic imine, dihydrodipicolinate, to generate tetrahydrodipicolinate as shown below : 2,3-dihydrodipicolinate + NAD(P)H = 2,3,4,5-tetrahydrodipicolinate + NAD(P)(+) As this enzyme is not found in mammals it is a potential target for the development of novel antibacterial and herbicidal compounds. The structures of the Escherichia coli (P04036 from SWISSPROT) and Mycobacterium tuberculosis (P72024 from SWISSPROT) enzymes have been determined , . The enzyme is a homotetramer where each monomer is composed of two domains, an N-terminal NAD(P)H-binding domain which forms a Rossman fold, and a C-terminal substrate-binding domain that forms an open, mixed alpha-beta sandwich.Tetramerisation occurs exclusively through interactions between C-terminal domain residues. Both enzymes show relatively little preference for either NADH or NADPH as cofactor. Conformational changes upon substrate binding bring the cofactor and substrate into close proximity and allow catalysis to occur. ; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0005737 cytoplasm.
Probab=22.93 E-value=37 Score=11.93 Aligned_cols=94 Identities=22% Similarity=0.299 Sum_probs=57.8
Q ss_pred ECCHHHHHH-HHHCCCCCCHHHHHCCCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 714388999-8743554211343213662678988512681--8996178866225777888888777536973067525
Q gi|254780834|r 277 VEGYMDVLS-LCQAGVQNVVSSLGTALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL 353 (648)
Q Consensus 277 vEGy~Dvi~-l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L 353 (648)
=||-++-+. +.++|..=||.| |-||+++.+.|..++.+ |=+. ..+++.|
T Consensus 85 p~g~~~~~~~a~~~Gv~~V~GT--TGf~e~~~~~~~~~a~~~~~~~v---------------------~A~NFa~----- 136 (281)
T TIGR00036 85 PEGVVENVKIALENGVRLVVGT--TGFSEEDLQELRDLAEKKGVAAV---------------------IAPNFAI----- 136 (281)
T ss_pred CHHHHHHHHHHHHCCCEEEECC--CCCCHHHHHHHHHHHHHCCCCEE---------------------EECCCHH-----
T ss_conf 0567899999996688557716--68998999999999986499789---------------------8465068-----
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHC-CCHHHH----HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 7888888997203668899886414-992799----9999985302331457999999999885417
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKLIVES-LPLVDM----LWKRETENRSFNTPDERAELEIHLKNCINHI 415 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~ll~~A-~~l~dF----l~~~l~~~~dl~spe~ka~~~~~l~~~I~~I 415 (648)
|..=|.++++.| +-+-|+ +++. =.++-.|.|.|-|-- +.+.|+..
T Consensus 137 -------------GV~~~~K~~~~aA~~l~D~~DiEIIE~-HHr~K~DAPSGTAL~---~~E~i~~~ 186 (281)
T TIGR00036 137 -------------GVNLMFKLLEKAAKYLGDYTDIEIIEL-HHRHKKDAPSGTALK---LAEIIAEA 186 (281)
T ss_pred -------------HHHHHHHHHHHHHHHHCCCCCEEEEEC-HHCCCCCCCCHHHHH---HHHHHHHH
T ss_conf -------------999999999999876245655454412-002589997078999---99999987
No 341
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=22.85 E-value=37 Score=11.92 Aligned_cols=11 Identities=27% Similarity=0.404 Sum_probs=4.3
Q ss_pred EECCCCCCCCC
Q ss_conf 01038767653
Q gi|254780834|r 232 KYLNSPETILF 242 (648)
Q Consensus 232 KYlNSpeT~if 242 (648)
+|+|...++++
T Consensus 194 ~~~~~~~~~~~ 204 (594)
T smart00433 194 ELLNKNKELLS 204 (594)
T ss_pred HHHCCCCCCCC
T ss_conf 98538987678
No 342
>KOG1818 consensus
Probab=22.83 E-value=34 Score=12.25 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=26.0
Q ss_pred CCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCC
Q ss_conf 0016716888970778588850100146553001038767
Q gi|254780834|r 200 DRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPET 239 (648)
Q Consensus 200 d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT 239 (648)
+..|=|..|-..+..+....-| |+.-..-..|++-=|-.
T Consensus 167 ~C~rCr~~F~~~~rkHHCr~CG-~vFC~qcss~s~~lP~~ 205 (634)
T KOG1818 167 ECLRCRVKFGLTNRKHHCRNCG-QVFCGQCSSKSLTLPKL 205 (634)
T ss_pred CCCEEEEEEEECCCCCCCCCCC-HHHCCCCCCCCCCCCCC
T ss_conf 0111234410015653430021-02225744133676533
No 343
>PRK09846 recT recombination and repair protein RecT; Reviewed
Probab=22.67 E-value=37 Score=11.89 Aligned_cols=79 Identities=16% Similarity=0.230 Sum_probs=34.8
Q ss_pred CHHHHHHHH----HCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCC-CCCE-EEEEE
Q ss_conf 757899998----50688535101244225677410345542059973452320121003465410000-1671-68889
Q gi|254780834|r 137 DKRLHYYLD----ERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDR-FRNR-LIFPI 210 (648)
Q Consensus 137 ~~~a~~yl~----~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~-Fr~R-i~fPi 210 (648)
+..+..||- ++.-+...-.+|+||| .++++-+...|-= .-+.|..+..+|.- -|+. ...+ .--|-
T Consensus 85 ~~LG~AYlVPy~nk~~~~g~~eaQfqiGY-----kG~IqLA~RSGqi--~~I~A~~Vye~D~F--~y~~Gl~~~l~h~p~ 155 (270)
T PRK09846 85 SALGHAYLLPFGNKNEKSGKKEAQLIIGY-----RGMIDLARRSGQI--ASISARVVYENDEF--EFEYGLEEKLVHRPG 155 (270)
T ss_pred CCCCEEEEEECCCCCCCCCCEEEEEEEEH-----HHHHHHHHHCCCE--EEEEEEEEECCCEE--EEECCCCCEEEECCC
T ss_conf 75543899743665566775259999607-----8999999857773--58999999659735--562588743664677
Q ss_pred EECCCCEEEEECCC
Q ss_conf 70778588850100
Q gi|254780834|r 211 RSSRGQVIAFGGRT 224 (648)
Q Consensus 211 ~~~~g~~i~f~gR~ 224 (648)
.+..|.+||+.+=.
T Consensus 156 ~~~~geiigyYA~~ 169 (270)
T PRK09846 156 ENGDGPVTHVYAVA 169 (270)
T ss_pred CCCCCCEEEEEEEE
T ss_conf 68888778999999
No 344
>pfam03194 LUC7 LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP).
Probab=22.58 E-value=37 Score=11.88 Aligned_cols=42 Identities=12% Similarity=0.288 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999872412798999999999999999999988
Q gi|254780834|r 591 LSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIE 632 (648)
Q Consensus 591 L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~ 632 (648)
|..++..+-.++.++...|+.+.+..++.++.+++.+..++.
T Consensus 128 l~~~I~~ll~e~E~LGe~G~VdeA~~~~~~~e~Lk~er~~l~ 169 (252)
T pfam03194 128 LDEEIGKLLAEAEALGEEGKVDEAMKLMKEVEELKAKKKELE 169 (252)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999867999999999999999999999998
No 345
>TIGR03183 DNA_S_dndC putative sulfurtransferase DndC. Members of this protein family are the DndC protein from the dnd (degradation during electrophoresis) operon. The dnd phenotype reflects a sulfur-containing modification to DNA. This operon is sparsely and sporadically distributed among bactera; among the first eight examples are members from the Actinobacteria, Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is suggested to be a sulfurtransferase.
Probab=22.58 E-value=26 Score=13.26 Aligned_cols=15 Identities=33% Similarity=0.618 Sum_probs=7.2
Q ss_pred ECCCCEE-EEECCCCC
Q ss_conf 0778588-85010014
Q gi|254780834|r 212 SSRGQVI-AFGGRTLS 226 (648)
Q Consensus 212 ~~~g~~i-~f~gR~l~ 226 (648)
+..|.+| -.|-|.-.
T Consensus 135 ~~~ge~ilvLGtR~~E 150 (447)
T TIGR03183 135 AANGEVILVLGTRKNE 150 (447)
T ss_pred HCCCCEEEEEECCHHH
T ss_conf 2149689999565277
No 346
>pfam00098 zf-CCHC Zinc knuckle. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Probab=22.54 E-value=31 Score=12.58 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=7.2
Q ss_pred EECCCCCCCCH
Q ss_conf 71368888789
Q gi|254780834|r 63 YCFSCHVKGDH 73 (648)
Q Consensus 63 ~cf~c~~~gd~ 73 (648)
.||-||..|-+
T Consensus 2 ~C~nCG~~GH~ 12 (26)
T pfam00098 2 KCYNCGKEGHL 12 (26)
T ss_pred CCCCCCCCCCC
T ss_conf 32136865411
No 347
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=22.53 E-value=37 Score=11.87 Aligned_cols=13 Identities=8% Similarity=0.135 Sum_probs=8.9
Q ss_pred HCCCHHHHHHHHH
Q ss_conf 1108178888643
Q gi|254780834|r 247 NLYNFFGALNYLQ 259 (648)
Q Consensus 247 ~Ly~l~~a~~~~~ 259 (648)
-=|||...|+.|-
T Consensus 323 dHyGL~~vKeRil 335 (784)
T PRK10787 323 DHYGLERVKDRIL 335 (784)
T ss_pred HHCCHHHHHHHHH
T ss_conf 4306577999999
No 348
>TIGR02410 carnitine_TMLD trimethyllysine dioxygenase; InterPro: IPR012776 Members of this family with known function act as trimethyllysine dioxygenase, an enzyme in the pathway for carnitine biosynthesis from lysine. This enzyme is homologous to gamma-butyrobetaine,2-oxoglutarate dioxygenase, which catalyzes the last step in carnitine biosynthesis. Members of this family appear to be eukaryotic only.; GO: 0005506 iron ion binding, 0031418 L-ascorbic acid binding, 0050353 trimethyllysine dioxygenase activity, 0045329 carnitine biosynthetic process.
Probab=22.52 E-value=37 Score=11.87 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=11.3
Q ss_pred ECCCCEEEECC-CC-CCC-----CHHHHHHHH
Q ss_conf 17897467136-88-887-----898998988
Q gi|254780834|r 56 NDSKGFYYCFS-CH-VKG-----DHLSFLSAL 80 (648)
Q Consensus 56 ~~~~~~~~cf~-c~-~~g-----d~~~f~~~~ 80 (648)
.|.-|.|||.- -| .|| |+|.-+.+.
T Consensus 216 tPGlQlFHlL~H~GG~GG~T~LVD~f~~a~~l 247 (397)
T TIGR02410 216 TPGLQLFHLLKHDGGTGGETLLVDGFYAAEQL 247 (397)
T ss_pred CCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHH
T ss_conf 77452000205688989850100489999999
No 349
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=22.50 E-value=37 Score=11.87 Aligned_cols=62 Identities=19% Similarity=0.335 Sum_probs=36.9
Q ss_pred HHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH
Q ss_conf 789885126818996178866225777888888777536973067525788888899720366889988641
Q gi|254780834|r 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE 377 (648)
Q Consensus 306 ~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~ 377 (648)
=++...+|...|.+.+||-.|--|..+..+-+ -...|-.|.|. -+|.|-++.+ +++.+++++
T Consensus 22 lv~~a~~f~s~I~i~~~~k~~naKSi~~lm~L---g~~~G~~i~i~--a~G~De~~A~-----~~l~~~l~~ 83 (88)
T PRK13780 22 LVQTASKFDSDITLEYNGKSVNLKSIMGVMSL---GVGQGADITIS--AEGADEADAI-----AAIEETMKK 83 (88)
T ss_pred HHHHHHHCCCEEEEEECCEEECCHHHHHHHHH---CCCCCCEEEEE--EECCCHHHHH-----HHHHHHHHH
T ss_conf 99999738977999989999821749999961---78898999999--9788999999-----999999987
No 350
>pfam04055 Radical_SAM Radical SAM superfamily. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Probab=22.43 E-value=37 Score=11.86 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=10.4
Q ss_pred HCCCC--EEEEECCCCCCHHHHH
Q ss_conf 36973--0675257888888997
Q gi|254780834|r 343 IPGNR--VNFVLLSRGEDPDSFI 363 (648)
Q Consensus 343 ~~g~~--v~vv~LP~G~DPDe~i 363 (648)
+.|.. +.++....|+.++++.
T Consensus 137 ~~gi~~~~~~i~~~~~e~~~~~~ 159 (165)
T pfam04055 137 EAGIPVVVDNIVGLPGENDEDLE 159 (165)
T ss_pred HCCCCEEEEEEEECCCCCHHHHH
T ss_conf 87997889999979999999999
No 351
>TIGR02029 AcsF magnesium-protoporphyrin IX monomethyl ester aerobic oxidative cyclase; InterPro: IPR008434 This family represents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions . This enzyme is believed to utilise a binuclear iron centre and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacteria, which are differentially regulated based on the levels of copper and oxygen , . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria. CRD1 (AcsF) is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (-Cu) and oxygen-deficient (-O(2)) Chlamydomonas reinhardtii cells and is localised to the thylakoid membrane. The family also contains the Rhodocyclus gelatinosus (Rhodopseudomonas gelatinosa) AcsF protein .; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process.
Probab=22.35 E-value=23 Score=13.71 Aligned_cols=30 Identities=10% Similarity=0.244 Sum_probs=16.0
Q ss_pred HHCHHH----HHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 847788----999984430023799889999999999
Q gi|254780834|r 492 INHPAI----LQEQYQELADIRYDNNELQKLWSFLFS 524 (648)
Q Consensus 492 I~~P~l----~~~~~e~l~~~~f~~~~~~~L~~~i~~ 524 (648)
=.||++ +-.+.+.-++.++.| +.++..|..
T Consensus 183 ~~nPe~qfyPIF~yFe~WC~DE~~H---Gd~F~~Lmk 216 (344)
T TIGR02029 183 EENPENQFYPIFKYFEEWCQDENRH---GDAFALLMK 216 (344)
T ss_pred CCCCCCCCCCCCHHHHHHCCHHHHH---HHHHHHHHC
T ss_conf 0188875446514465320221015---899999840
No 352
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.35 E-value=37 Score=11.84 Aligned_cols=19 Identities=26% Similarity=0.531 Sum_probs=13.4
Q ss_pred CCCCCCCCEEEEEEEECCC
Q ss_conf 1000016716888970778
Q gi|254780834|r 197 TSYDRFRNRLIFPIRSSRG 215 (648)
Q Consensus 197 ~~~d~Fr~Ri~fPi~~~~g 215 (648)
++||--+|||+|=.+|..+
T Consensus 58 SpYDltkGRIvyR~k~~~~ 76 (87)
T PRK12442 58 SPYDLTKGRINFRHKDERS 76 (87)
T ss_pred CCCCCCCEEEEEEECCCCC
T ss_conf 8777887489988478889
No 353
>pfam05028 PARG_cat Poly (ADP-ribose) glycohydrolase (PARG). Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death.
Probab=22.28 E-value=35 Score=12.14 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=12.0
Q ss_pred CCCHHHHHHCCCHHHHHHHHHHC
Q ss_conf 88888997203668899886414
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEKLIVES 378 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~ll~~A 378 (648)
-++++|-+.-.|.+.|..+-.-+
T Consensus 200 ~l~dnE~i~i~G~~r~s~y~GY~ 222 (339)
T pfam05028 200 VLEDNEAIIIVGAERFSSYTGYA 222 (339)
T ss_pred CCCCCCEEEEECCEEEEEECCCC
T ss_conf 56888379997502356401242
No 354
>COG3313 Predicted Fe-S protein [General function prediction only]
Probab=22.27 E-value=38 Score=11.83 Aligned_cols=25 Identities=28% Similarity=0.582 Sum_probs=14.3
Q ss_pred CCCCEEEE--CCCCEEEECCCCCCCCHHH
Q ss_conf 58787981--7897467136888878989
Q gi|254780834|r 49 KTPSFHCN--DSKGFYYCFSCHVKGDHLS 75 (648)
Q Consensus 49 ktpsf~v~--~~~~~~~cf~c~~~gd~~~ 75 (648)
++|--.|= ++++ +|+||+..-|=|.
T Consensus 7 ~SPCv~vCs~D~~~--~C~GC~Rt~~Ei~ 33 (74)
T COG3313 7 KSPCVGVCSTDEKD--FCRGCGRTRDEIF 33 (74)
T ss_pred CCCEEEEEEECCCC--HHHCCCCCHHHHH
T ss_conf 99801234455765--2014454489998
No 355
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=22.23 E-value=37 Score=11.90 Aligned_cols=22 Identities=18% Similarity=0.223 Sum_probs=12.4
Q ss_pred EEEEECCCCCCHHHHHHCCCHH
Q ss_conf 0675257888888997203668
Q gi|254780834|r 348 VNFVLLSRGEDPDSFIRCYGKT 369 (648)
Q Consensus 348 v~vv~LP~G~DPDe~ir~~G~e 369 (648)
.|-..||+|.||+++.-.-+.+
T Consensus 57 ~R~~~LP~~vd~~~v~s~Ls~d 78 (87)
T cd06481 57 VREAQLPEHVDPEAVTCSLSPS 78 (87)
T ss_pred EEEEECCCCCCHHHCEEEECCC
T ss_conf 9986788996976809963799
No 356
>KOG4506 consensus
Probab=22.20 E-value=38 Score=11.82 Aligned_cols=103 Identities=20% Similarity=0.217 Sum_probs=62.2
Q ss_pred HHHHHHHHCCCCCCHHHHHC----------CCCHHHHHHHHHCCCEEEEE----------ECCCCCCHHHHHHHHHHHHH
Q ss_conf 88999874355421134321----------36626789885126818996----------17886622577788888877
Q gi|254780834|r 281 MDVLSLCQAGVQNVVSSLGT----------ALTEYQLRLLWKLSPRIVLC----------FDGDDPGLRAAYKAIDLVLC 340 (648)
Q Consensus 281 ~Dvi~l~~~G~~n~va~~Gt----------alt~~~~~~l~r~~~~vvl~----------fDgD~AG~kAa~Ra~e~~l~ 340 (648)
.|-|.+..+.|+..||+.|. +||..--..|+...+--.+- ..||..|.+-. -+++++.
T Consensus 249 lddiildeha~pepVaa~gr~g~~adgleESFTI~iGaQLKsMHNlcLlraDrl~DfCk~~egd~sgvk~~--RLemA~k 326 (598)
T KOG4506 249 LDDIILDEHAFPEPVAAIGRIGEEADGLEESFTIHIGAQLKSMHNLCLLRADRLLDFCKHKEGDRSGVKLH--RLEMALK 326 (598)
T ss_pred HHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHCCCEEEHHHHHHHHHHHCCCCCCCHHH--HHHHHHH
T ss_conf 55541482106635888752344431443027873175677554202022778889876421773310079--9999999
Q ss_pred HHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 7536973067525788888899720366889988641499279999999853
Q gi|254780834|r 341 HLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETEN 392 (648)
Q Consensus 341 ~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~ 392 (648)
+...++.=-++..| .||..++.. +-.|...-++.. ||-|+++.++
T Consensus 327 LYSrnL~G~tLLV~--~d~mmhi~~--krDF~kiCee~T---DfHFdriaEQ 371 (598)
T KOG4506 327 LYSRNLCGLTLLVD--NDIMMHIGI--KRDFAKICEECT---DFHFDRIAEQ 371 (598)
T ss_pred HHHHCCCCEEEEEC--CCCHHHCCC--HHHHHHHHHHHC---CCCCHHHHHH
T ss_conf 98514445279845--860543051--148999988730---4473679999
No 357
>PRK10903 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional
Probab=22.16 E-value=38 Score=11.82 Aligned_cols=14 Identities=36% Similarity=0.463 Sum_probs=9.4
Q ss_pred EEECCHHHHHHHHHC
Q ss_conf 997143889998743
Q gi|254780834|r 275 ILVEGYMDVLSLCQA 289 (648)
Q Consensus 275 i~vEGy~Dvi~l~~~ 289 (648)
-|+|| |||+--...
T Consensus 151 ~VveG-mdVvdkI~~ 164 (190)
T PRK10903 151 KVVKG-MDVADKISQ 164 (190)
T ss_pred EEECC-HHHHHHHHC
T ss_conf 99127-799999973
No 358
>TIGR00456 argS arginyl-tRNA synthetase; InterPro: IPR001278 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Arginyl-tRNA synthetase (6.1.1.19 from EC) has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available . ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=22.16 E-value=38 Score=11.81 Aligned_cols=54 Identities=22% Similarity=0.202 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHH
Q ss_conf 3799999999984778899998443002379988999999999997538899989
Q gi|254780834|r 481 SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPE 535 (648)
Q Consensus 481 ~~~E~~LL~llI~~P~l~~~~~e~l~~~~f~~~~~~~L~~~i~~~~~~~~~~~~~ 535 (648)
...|+.|+..+..+|+++....+....- .....+..|...+-.+|...+..+..
T Consensus 513 ~~~E~~L~~~L~~fp~~~~~~~~~~~p~-~l~~Yly~LA~~F~sfY~~~~v~~~~ 566 (600)
T TIGR00456 513 EEKEKELLKLLLQFPEVIEEAAEEREPH-VLTNYLYELAKLFSSFYKACPVLDAE 566 (600)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 8889999999856489999999854718-88999999977642366417788986
No 359
>KOG1177 consensus
Probab=22.15 E-value=13 Score=16.10 Aligned_cols=71 Identities=8% Similarity=0.019 Sum_probs=29.5
Q ss_pred CCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 78798178974671368888789899898859997999999999818858776820367778899999999999999999
Q gi|254780834|r 51 PSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHH 130 (648)
Q Consensus 51 psf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (648)
+++.+| .+ |--||..- .| .+-+-++-++..+++++...-..-.....+..-.+-..++...|+-|++-
T Consensus 30 ~~~~~~-~~---~~~g~~~i----pl----~~~Tigq~l~~~t~~v~dkea~Vf~~eg~R~Tf~~~~~ev~slAaGll~l 97 (596)
T KOG1177 30 WVLLSS-HR---YVHGCSQI----PL----DSETIGQLLETTTERVPDKEAAVFDHEGIRLTFSEFVSEVESLAAGLLSL 97 (596)
T ss_pred CEECCC-CC---CCCCCCCC----CC----CCCCHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 412023-43---01798777----74----31527889877765067514789961341234999999999997568863
Q ss_pred HHC
Q ss_conf 732
Q gi|254780834|r 131 SLK 133 (648)
Q Consensus 131 ~l~ 133 (648)
-|+
T Consensus 98 GL~ 100 (596)
T KOG1177 98 GLK 100 (596)
T ss_pred CCC
T ss_conf 477
No 360
>pfam02330 MAM33 Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions.
Probab=22.09 E-value=38 Score=11.80 Aligned_cols=34 Identities=12% Similarity=0.151 Sum_probs=17.7
Q ss_pred EECCCCCCHHHHHHCCCHHHHHHHHHH-CC--CHHHHHHHH
Q ss_conf 525788888899720366889988641-49--927999999
Q gi|254780834|r 351 VLLSRGEDPDSFIRCYGKTAFEKLIVE-SL--PLVDMLWKR 388 (648)
Q Consensus 351 v~LP~G~DPDe~ir~~G~eaf~~ll~~-A~--~l~dFl~~~ 388 (648)
..=|...+=|+-++ ++|..+|+. .. .+.+|+-++
T Consensus 147 y~gp~f~~Ld~~lq----~~~~~yLe~rGi~~~~~~fl~~~ 183 (203)
T pfam02330 147 YYGPSFKNLDPELQ----DLFHRYLEERGVDATFAKFLVAY 183 (203)
T ss_pred CCCCCCCCCCHHHH----HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 46988141499999----99999999949998999999999
No 361
>TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=22.09 E-value=35 Score=12.16 Aligned_cols=32 Identities=22% Similarity=0.225 Sum_probs=16.2
Q ss_pred CCCEEEEECCCCCCHHHHHHCCCH-HHHHHHHHHC
Q ss_conf 973067525788888899720366-8899886414
Q gi|254780834|r 345 GNRVNFVLLSRGEDPDSFIRCYGK-TAFEKLIVES 378 (648)
Q Consensus 345 g~~v~vv~LP~G~DPDe~ir~~G~-eaf~~ll~~A 378 (648)
-+++.|+- .-.|||+|=.+.-. ..++=|.+.+
T Consensus 101 vk~~ev~g--~a~~p~~YPl~~K~Ghs~efLr~~~ 133 (495)
T TIGR00457 101 VKKIEVVG--EAEDPDDYPLQKKEGHSLEFLRDIA 133 (495)
T ss_pred CEEEEEEE--ECCCCCCCCCCCCCCCCHHHHHCCC
T ss_conf 31468877--4178877776422368767763276
No 362
>pfam02614 UxaC Glucuronate isomerase. This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyses the reactions: D-glucuronate <= D-fructuronate and D-galacturonate <= D-tagaturonate. It is not however clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference.
Probab=22.06 E-value=38 Score=11.80 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=7.1
Q ss_pred HHHHHHCCCCCHHHH
Q ss_conf 345542059973452
Q gi|254780834|r 169 LREHLRQKGFSEEKI 183 (648)
Q Consensus 169 l~~~l~~~~~~~~~~ 183 (648)
.++.+...|++++.+
T Consensus 57 kwR~Mra~GV~e~~i 71 (465)
T pfam02614 57 KWRAMRANGVPEDLI 71 (465)
T ss_pred HHHHHHHCCCCHHHC
T ss_conf 999999859988880
No 363
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.98 E-value=16 Score=15.36 Aligned_cols=61 Identities=23% Similarity=0.190 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCC
Q ss_conf 3662678988512681--899617886622577788888877753697306752578888889972036
Q gi|254780834|r 301 ALTEYQLRLLWKLSPR--IVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYG 367 (648)
Q Consensus 301 alt~~~~~~l~r~~~~--vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G 367 (648)
-+..+|+..+--+..+ .|+--.|---|.. |++-..+ --..+.-|||.. .|.||.||.+--|
T Consensus 103 ~l~~EHvlevIeLl~~~tFvlETNG~~~g~d---rslv~el-~nr~nv~vRVsv--KG~dpesF~kIT~ 165 (228)
T COG5014 103 ILGREHVLEVIELLVNNTFVLETNGLMFGFD---RSLVDEL-VNRLNVLVRVSV--KGWDPESFEKITG 165 (228)
T ss_pred CCCHHHHHHHHHHCCCCEEEEEECCEEEECC---HHHHHHH-HCCCCEEEEEEE--CCCCHHHHHHHHC
T ss_conf 4468999999986347649997577688358---8899997-137863999983--5798899898756
No 364
>cd01833 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=21.94 E-value=38 Score=11.78 Aligned_cols=20 Identities=30% Similarity=0.401 Sum_probs=11.5
Q ss_pred HHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHH
Q ss_conf 134321366267898851268189961788662257
Q gi|254780834|r 295 VSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRA 330 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kA 330 (648)
|.++|-++|.- |+|.+|.-.
T Consensus 3 ~~~~gdsit~g----------------d~~n~G~~G 22 (157)
T cd01833 3 IMPLGDSITWG----------------DKDHEGHSG 22 (157)
T ss_pred EEEECCCCCCC----------------CCCCCCCCC
T ss_conf 89822755457----------------899999784
No 365
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=21.93 E-value=38 Score=11.78 Aligned_cols=88 Identities=24% Similarity=0.305 Sum_probs=46.8
Q ss_pred EEEEECCHHHHHHHHHCCCCC---CHHHHHC----CCCHHHHHHHHHCC-CEEEEEECCCCCCHHH--HHHHHHHHHHHH
Q ss_conf 089971438899987435542---1134321----36626789885126-8189961788662257--778888887775
Q gi|254780834|r 273 FIILVEGYMDVLSLCQAGVQN---VVSSLGT----ALTEYQLRLLWKLS-PRIVLCFDGDDPGLRA--AYKAIDLVLCHL 342 (648)
Q Consensus 273 ~~i~vEGy~Dvi~l~~~G~~n---~va~~Gt----alt~~~~~~l~r~~-~~vvl~fDgD~AG~kA--a~Ra~e~~l~~l 342 (648)
.++|||-..=--.|.+.++.+ .|-.-|. -.|..=++.|.... -.|+.++|+|.-|..= +.|.....+++.
T Consensus 2 ~vlVVEK~avf~~L~~~~~~~~~~~iliTgKG~Pd~~TR~fl~~L~~~~~lpv~~l~D~DP~Gi~I~~~Yk~Gs~~~~~~ 81 (160)
T cd00223 2 FVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEELDLPVYILVDGDPYGISILLTYKYGSIKLAYE 81 (160)
T ss_pred EEEEEECHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCCC
T ss_conf 79999649999999974856448889994688887899999999999878988999758866106778886266223124
Q ss_pred HCCC---CEEEEECCCCCCHHHHHH
Q ss_conf 3697---306752578888889972
Q gi|254780834|r 343 IPGN---RVNFVLLSRGEDPDSFIR 364 (648)
Q Consensus 343 ~~g~---~v~vv~LP~G~DPDe~ir 364 (648)
.... .++. -|.-|.++.+
T Consensus 82 ~~~~~~p~i~w----lGl~~sd~~~ 102 (160)
T cd00223 82 SESLATPDLRW----LGLRPSDIIR 102 (160)
T ss_pred CCCCCCCCCEE----EECCHHHHHC
T ss_conf 44455887289----5076999860
No 366
>pfam03949 Malic_M Malic enzyme, NAD binding domain.
Probab=21.92 E-value=38 Score=11.78 Aligned_cols=38 Identities=18% Similarity=0.146 Sum_probs=17.3
Q ss_pred HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEE
Q ss_conf 88999874355421134321366267898851268189
Q gi|254780834|r 281 MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIV 318 (648)
Q Consensus 281 ~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vv 318 (648)
-|||...+-.+--.++..|-+||++.++.+.+.++++|
T Consensus 99 ~e~v~~~kP~vlIG~S~~~g~ft~evv~~Ma~~~~~PI 136 (255)
T pfam03949 99 AEAVKGAKPDVLIGVSGVPGVFTEEIVRAMAEHTERPI 136 (255)
T ss_pred HHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCE
T ss_conf 99986268877998168889889999999981699984
No 367
>TIGR02009 PGMB-YQAB-SF beta-phosphoglucomutase family hydrolase; InterPro: IPR010976 Phosphoglucomutases interconvert D-glucose 1-phosphate and D-glucose 6-phosphate, a reaction which is important for energy metabolism in many organisms and for cell wall biosynthesis in bacteria , . Beta-phosphoglucomutases are monomeric enzymes which interconvert the beta anomers of these compounds using Mg2+ as a cofactor. This entry groups together three clades: the characterised beta-phosphoglucomutases (bPGMs) (including those from Escherichia coli, Bacillus subtilus and Lactococcus lactis, a clade of putative bPGMs from mycobacteria and a clade including the uncharacterised Escherichia coli and Haemophilus influenzae yqaB genes which may prove to be beta-mutases of a related 1-phosphosugar. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the 'variant 3' Glu-Asp version of the third conserved HAD domain. The Lactococcus enzyme has been crystallised and studied in detail . It is composed of two distinct regions, an alpha/beta core domain similar to that found in other HAD family members, and a helical cap domain. The core domain contains a central six-stranded parallel beta sheet surrounded by six alpha helices, while the cap domain consists of an antiparallel four alpha-helix bundle. Overall, the monomer forms a "kidney-bean" shape similar to that observed in other HAD family members such as phosphoserine phosphatase. The active site of the enzyme is located at the interface of the two domains..
Probab=21.76 E-value=38 Score=11.75 Aligned_cols=82 Identities=16% Similarity=0.224 Sum_probs=53.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC--CC-CC-----HHHHHHH
Q ss_conf 9899898859997999999999818858776820367778899999999999999999732--67-77-----5789999
Q gi|254780834|r 73 HLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK--NA-RD-----KRLHYYL 144 (648)
Q Consensus 73 ~~~f~~~~~~~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--~~-~~-----~~a~~yl 144 (648)
..++.....|++-.+.++..-+.+||++|+......-...+ ..++-+.=..+|+..|. .. .. ..-+++|
T Consensus 44 ~~~~~~~l~G~~r~~~~~~il~~~~~~IP~~~~ed~~~~~~---~~~l~~~K~~~y~~ll~qE~~~~~~lp~~~~~l~~l 120 (211)
T TIGR02009 44 EEQYNESLKGLSREDILRAILKLRAVDIPDGSKEDGLSLEK---IEQLAERKNELYRELLRQELTGAEVLPGIENLLKEL 120 (211)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHHHCCCCCHHCCCHHHHHHHH
T ss_conf 99999983899768999999874277699988896889889---999999999999999862267210036558999999
Q ss_pred HHCCCCHHHHCCCCCCCCCCC
Q ss_conf 850688535101244225677
Q gi|254780834|r 145 DERGIDSHAIEMFKLGYAPDS 165 (648)
Q Consensus 145 ~~Rg~~~~~~~~f~lG~ap~~ 165 (648)
++++|. +|-++.+
T Consensus 121 ~~~~i~--------~a~gS~S 133 (211)
T TIGR02009 121 KKKGIA--------VALGSSS 133 (211)
T ss_pred HHCCCC--------EEEEECC
T ss_conf 866985--------7884054
No 368
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=21.74 E-value=38 Score=11.75 Aligned_cols=19 Identities=21% Similarity=0.377 Sum_probs=7.8
Q ss_pred CCCHHHHHHCCCHHHHHHH
Q ss_conf 8888899720366889988
Q gi|254780834|r 356 GEDPDSFIRCYGKTAFEKL 374 (648)
Q Consensus 356 G~DPDe~ir~~G~eaf~~l 374 (648)
|+..-+++.++|-++|+.+
T Consensus 42 g~sI~eIF~~~GE~~FR~~ 60 (172)
T COG0703 42 GMSIAEIFEEEGEEGFRRL 60 (172)
T ss_pred CCCHHHHHHHHHHHHHHHH
T ss_conf 9699999999828999999
No 369
>PRK11460 esterase YpfH; Provisional
Probab=21.74 E-value=38 Score=11.75 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=23.3
Q ss_pred HHCCCCEEEEECC---CCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 5369730675257---8888889972036688998864149927999999985
Q gi|254780834|r 342 LIPGNRVNFVLLS---RGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETE 391 (648)
Q Consensus 342 l~~g~~v~vv~LP---~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~ 391 (648)
.+.|.+|..-..| .+-||+.+ +.-.++|++..|. -.|+.++.
T Consensus 175 ~~~G~~v~~~~~~glGH~I~~egl------~~a~~FLk~~lp~--~~~~~~~~ 219 (230)
T PRK11460 175 IALGGDVTLDIAEDLGHAIDPRLM------QFALDRLRYTVPK--RYWDEALS 219 (230)
T ss_pred HHCCCCEEEEECCCCCCCCCHHHH------HHHHHHHHHHCCH--HHHHHHHC
T ss_conf 987992799862899998899999------9999999873728--67999864
No 370
>KOG1432 consensus
Probab=21.67 E-value=38 Score=11.74 Aligned_cols=37 Identities=19% Similarity=0.267 Sum_probs=21.8
Q ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCH
Q ss_conf 6818996178866225777888888777536973067525788888
Q gi|254780834|r 314 SPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDP 359 (648)
Q Consensus 314 ~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DP 359 (648)
-+++.|||-|- ||.-+=-++. . -..+||+.+-.++|-
T Consensus 318 k~~~wlCygGg-aGyggYg~~g-----w---~Rr~Rv~e~d~~~~~ 354 (379)
T KOG1432 318 KGELWLCYGGG-AGYGGYGIGG-----W---ERRARVFELDLNKDR 354 (379)
T ss_pred CCEEEEEECCC-CCCCCCCCCC-----C---CCCEEEEECCCCCCC
T ss_conf 88079994587-7547767588-----5---440489981456040
No 371
>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional
Probab=21.59 E-value=39 Score=11.73 Aligned_cols=56 Identities=21% Similarity=0.145 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHCCCEEEEEECCCCC--CHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCH
Q ss_conf 6626789885126818996178866--225777888888777536973067525788888
Q gi|254780834|r 302 LTEYQLRLLWKLSPRIVLCFDGDDP--GLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDP 359 (648)
Q Consensus 302 lt~~~~~~l~r~~~~vvl~fDgD~A--G~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DP 359 (648)
+....+....+++++|+++.||--- |--+-.-.-+... -.-|..++|+.-|+|+=|
T Consensus 211 ~vtHdl~~~~~~aDri~vL~~G~iv~~G~p~evl~~e~l~--~~yg~~~~v~~~~~g~~~ 268 (273)
T PRK13547 211 AIVHDPNLAARHADRIAMLADGAIVAHGAPADVMTPEHIA--RCYGFAVKLVDAGDGVPP 268 (273)
T ss_pred EEECCHHHHHHHCCEEEEEECCEEEEECCHHHHCCHHHHH--HHHCCCEEEEECCCCCCC
T ss_conf 9988999999979999999898799984879972989999--982995699998999851
No 372
>PRK04025 S-adenosylmethionine decarboxylase proenzyme; Validated
Probab=21.45 E-value=39 Score=11.70 Aligned_cols=39 Identities=18% Similarity=0.231 Sum_probs=31.5
Q ss_pred CCCCCCEEEECCCCE--EEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf 885878798178974--671368888789899898859997999999999818
Q gi|254780834|r 47 DEKTPSFHCNDSKGF--YYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAG 97 (648)
Q Consensus 47 ~ektpsf~v~~~~~~--~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~g 97 (648)
.|..=|++-+|++++ .-+|.||..- +...|+++|.++.+
T Consensus 61 aESHiSIHTWPE~g~aavDiFTCGd~~------------~P~~A~~~l~~~l~ 101 (139)
T PRK04025 61 AESHISVHTWPEKGYAALDVYTCGETA------------DPEKAVDYILEQFK 101 (139)
T ss_pred EEEEEEEEECCCCCEEEEEEECCCCCC------------CHHHHHHHHHHHHC
T ss_conf 511689996564786999998689989------------99999999999849
No 373
>KOG2578 consensus
Probab=21.36 E-value=31 Score=12.64 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=23.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCC
Q ss_conf 858776820367778899999999999999999732677757899998506885351012
Q gi|254780834|r 98 VPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMF 157 (648)
Q Consensus 98 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f 157 (648)
+.+-..+..+.+-.-+|.++|+|.+.. ++..-+.+||-+.-+++-|
T Consensus 42 vdlvgLddaA~KlgVErRRIYDiVNvl--------------Esig~var~~KnqYsWkGf 87 (388)
T KOG2578 42 VDLVGLDDAARKLGVERRRIYDIVNVL--------------ESIGAVARRGKNQYSWKGF 87 (388)
T ss_pred CCEECHHHHHHHCCCHHHHHHHHHHHH--------------HHHHHHHHCCCCCCCCCCH
T ss_conf 443140667876070477788899999--------------9878998605672011341
No 374
>KOG1409 consensus
Probab=21.35 E-value=39 Score=11.69 Aligned_cols=20 Identities=25% Similarity=0.082 Sum_probs=11.7
Q ss_pred CCCEEEEECCCCCCHHHHHH
Q ss_conf 97306752578888889972
Q gi|254780834|r 345 GNRVNFVLLSRGEDPDSFIR 364 (648)
Q Consensus 345 g~~v~vv~LP~G~DPDe~ir 364 (648)
+++++.+.-|+=+|-|..=+
T Consensus 268 ~mn~~r~etpewl~s~~cQ~ 287 (404)
T KOG1409 268 NMNVKRVETPEWLDSDSCQK 287 (404)
T ss_pred ECCCEEECCCCCCCCCHHHH
T ss_conf 52540561866030640656
No 375
>KOG2150 consensus
Probab=21.30 E-value=39 Score=11.68 Aligned_cols=15 Identities=7% Similarity=0.100 Sum_probs=5.7
Q ss_pred EEEECCCCCCHHHHH
Q ss_conf 996178866225777
Q gi|254780834|r 318 VLCFDGDDPGLRAAY 332 (648)
Q Consensus 318 vl~fDgD~AG~kAa~ 332 (648)
.+.+|.=.+|--|+.
T Consensus 294 ~~~~~~~s~~A~aaA 308 (575)
T KOG2150 294 PIGIDASSSAAPSGA 308 (575)
T ss_pred CCCCCCCCCCCCHHH
T ss_conf 545577765431122
No 376
>TIGR02776 NHEJ_ligase_prk DNA ligase D; InterPro: IPR014143 Members of this entry are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NheJ). The system of the bacterial Ku protein (IPR009187 from INTERPRO) plus this DNA ligase is seen in about 200f bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This entry describes a central and C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs. An additional N-terminal 3 -phosphoesterase (PE) domain (IPR014144 from INTERPRO) is present in some members of this ligase. Most examples of genes for this ligase are adjacent to the gene for Ku..
Probab=21.27 E-value=39 Score=11.67 Aligned_cols=46 Identities=17% Similarity=0.295 Sum_probs=31.5
Q ss_pred HHHHH---CCCCCCHHHHHCCCCHHHHHHHHHCCCEE---EEEECCCCCCHH
Q ss_conf 99874---35542113432136626789885126818---996178866225
Q gi|254780834|r 284 LSLCQ---AGVQNVVSSLGTALTEYQLRLLWKLSPRI---VLCFDGDDPGLR 329 (648)
Q Consensus 284 i~l~~---~G~~n~va~~Gtalt~~~~~~l~r~~~~v---vl~fDgD~AG~k 329 (648)
+++|+ .|--+=|+..||-|+.+-++.|...-+.- -=-|+|-.||.+
T Consensus 224 ~gv~~~~d~G~L~y~G~VgtGF~~~~~~~l~~~L~~~~~~~sPf~~~~~~~~ 275 (645)
T TIGR02776 224 VGVYEQEDGGQLRYAGKVGTGFGADTLKTLLARLKALGAKASPFAGKPAGAK 275 (645)
T ss_pred HHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 7651468889427888602788889999999999987430778778888776
No 377
>pfam06189 5-nucleotidase 5'-nucleotidase. This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (EC:3.1.3.5).
Probab=21.23 E-value=39 Score=11.67 Aligned_cols=67 Identities=21% Similarity=0.324 Sum_probs=38.7
Q ss_pred EEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 89971438899987435542113432136626789885126818996178866225777888888777536973067525
Q gi|254780834|r 274 IILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLL 353 (648)
Q Consensus 274 ~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~L 353 (648)
+.|---..||-..-++|+.-+.-.-.+.-... -.+++=|+||||. |++
T Consensus 85 LFLS~~~~DV~~Ai~~G~aAa~v~~~~~~~~~-------~~~qlRIAFDgDa------------------------VLF- 132 (263)
T pfam06189 85 LFLSANAEDVREALDAGVAAATVLPSTPDDSE-------SDDQLRIAFDGDA------------------------VLF- 132 (263)
T ss_pred EEEECCHHHHHHHHHCCCCEEEEECCCCCCCC-------CCCCEEEEECCCE------------------------EEE-
T ss_conf 68668889999999759971996278867778-------8874589736874------------------------786-
Q ss_pred CCCCCHHHHHHCCCHHHHHHH
Q ss_conf 788888899720366889988
Q gi|254780834|r 354 SRGEDPDSFIRCYGKTAFEKL 374 (648)
Q Consensus 354 P~G~DPDe~ir~~G~eaf~~l 374 (648)
...-....+++|-++|.+-
T Consensus 133 --sDesE~vyq~~GL~aF~~~ 151 (263)
T pfam06189 133 --SDESERVYKAQGLEAFQEH 151 (263)
T ss_pred --CCCHHHHHHHHCHHHHHHH
T ss_conf --5707888986088989986
No 378
>TIGR02434 CobF precorrin-6A synthase (deacetylating); InterPro: IPR012797 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobF precorrin-6A synthase (2.1.1.152 from EC), a pathway-specific enzyme in the aerobic pathway. After precorrin-4 is methylated at C-11 by CobM to produce precorrin-5, the extruded acyl group is then removed in the subsequent step, which also sees a methyl group added at C-1 in a reaction catalysed by CobF. The product of this reaction is precorrin-6A, which is subsequently reduced by an NADH-dependent reductase to precorrin-6B . This entry identifies CobF in high GC Gram-positive, alphaproteobacteria and pseudomonas-related species..
Probab=21.17 E-value=39 Score=11.66 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=14.5
Q ss_pred CCEEEEECCCCCCHHHHHHCCCHHHHHHH
Q ss_conf 73067525788888899720366889988
Q gi|254780834|r 346 NRVNFVLLSRGEDPDSFIRCYGKTAFEKL 374 (648)
Q Consensus 346 ~~v~vv~LP~G~DPDe~ir~~G~eaf~~l 374 (648)
-+|-| .+-.|++=+|++.-. .+=...+
T Consensus 27 adV~f-~~dKG~~KsdL~~lR-r~I~~r~ 53 (259)
T TIGR02434 27 ADVFF-VLDKGEDKSDLVELR-REICERY 53 (259)
T ss_pred CCEEE-EECCCCCHHHHHHHH-HHHHHHH
T ss_conf 83899-975873237999999-9999871
No 379
>PRK13529 malate dehydrogenase; Provisional
Probab=21.16 E-value=39 Score=11.66 Aligned_cols=67 Identities=22% Similarity=0.233 Sum_probs=35.9
Q ss_pred HCCCCCCHHHHHCCC-CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCC---CEEEEECCCCC
Q ss_conf 435542113432136-62678988512681899617886622577788888877753697---30675257888
Q gi|254780834|r 288 QAGVQNVVSSLGTAL-TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGN---RVNFVLLSRGE 357 (648)
Q Consensus 288 ~~G~~n~va~~Gtal-t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~---~v~vv~LP~G~ 357 (648)
+.-+++++-- ---| +.+-.++|.||-++ +.||.-|-=|-.|..=|.-+.- +-..|. +.+||++-.|-
T Consensus 235 ~~~fP~~liq-fEDF~~~nA~~lL~rYr~~-~~~FNDDiQGTaaV~LAgll~A-lri~g~~l~d~riv~~GAGs 305 (563)
T PRK13529 235 KRRFPNALLQ-FEDFAQKNAMRLLERYRDE-ICTFNDDIQGTAAVTLAGLLAA-LKIAGEPLSDQRVVFLGAGS 305 (563)
T ss_pred HHHCCCCEEE-HHCCCCHHHHHHHHHHHHC-CCEECCCCCHHHHHHHHHHHHH-HHHHCCCHHHCEEEEECCCH
T ss_conf 9978982785-0107961389999998650-6422453103779999999999-99829987784799965774
No 380
>KOG0440 consensus
Probab=21.15 E-value=39 Score=11.65 Aligned_cols=29 Identities=28% Similarity=0.394 Sum_probs=20.4
Q ss_pred CCCEEEEECCCCCCHHHHHHCCCHHHHHH
Q ss_conf 97306752578888889972036688998
Q gi|254780834|r 345 GNRVNFVLLSRGEDPDSFIRCYGKTAFEK 373 (648)
Q Consensus 345 g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ 373 (648)
|---.+|.||+|+|-+||+-.+--+-|..
T Consensus 68 g~l~~aV~LP~G~D~nEWlA~nt~~fF~q 96 (243)
T KOG0440 68 GNLREAVKLPEGEDLNEWLAVNTLDFFNQ 96 (243)
T ss_pred CCHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 45999843998776117899847999999
No 381
>pfam04710 Pellino Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase.
Probab=21.12 E-value=39 Score=11.65 Aligned_cols=11 Identities=27% Similarity=0.349 Sum_probs=4.9
Q ss_pred HHHHCCCEEEE
Q ss_conf 88512681899
Q gi|254780834|r 309 LLWKLSPRIVL 319 (648)
Q Consensus 309 ~l~r~~~~vvl 319 (648)
.|.||+=+|++
T Consensus 131 TISRfACRI~~ 141 (416)
T pfam04710 131 TISRFACRIVC 141 (416)
T ss_pred HHHHEEEEEEE
T ss_conf 31010577885
No 382
>COG0585 Uncharacterized conserved protein [Function unknown]
Probab=21.11 E-value=24 Score=13.59 Aligned_cols=45 Identities=24% Similarity=0.372 Sum_probs=37.5
Q ss_pred CEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf 8798178974671368888789899898859997999999999818858
Q gi|254780834|r 52 SFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPL 100 (648)
Q Consensus 52 sf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~~~la~~~gi~~ 100 (648)
-|.|.....+. =+.+|+..-|..+..+++=.+|++.||.+.||+.
T Consensus 31 dF~V~Ei~~~~----~~~~G~~~~~~l~K~~~dT~~a~~~iak~lgv~~ 75 (406)
T COG0585 31 DFIVEEILGYE----PSGDGEYLLFLLRKRGWDTLDAAREIAKRLGVPR 75 (406)
T ss_pred CCEEEEECCCC----CCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCH
T ss_conf 52798624768----7898788999999768876999999999969973
No 383
>pfam05131 Pep3_Vps18 Pep3/Vps18/deep orange family. This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown. The members of this family contain a C-terminal ring finger domain.
Probab=21.11 E-value=39 Score=11.65 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=11.5
Q ss_pred HHHHHCCCCHHHHHHHH
Q ss_conf 13432136626789885
Q gi|254780834|r 295 VSSLGTALTEYQLRLLW 311 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~ 311 (648)
..|.+-+||+.|+-+|.
T Consensus 34 ~~p~si~LTefH~llL~ 50 (147)
T pfam05131 34 SPPKSIALTQFHILLLY 50 (147)
T ss_pred CCCCEEECCHHEEEEEE
T ss_conf 99716870110024575
No 384
>KOG4090 consensus
Probab=21.07 E-value=24 Score=13.62 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=14.1
Q ss_pred CCEEEEECCHHHHHHHHHCC
Q ss_conf 87089971438899987435
Q gi|254780834|r 271 SSFIILVEGYMDVLSLCQAG 290 (648)
Q Consensus 271 ~~~~i~vEGy~Dvi~l~~~G 290 (648)
.+.+-+||||+|++.-.+.-
T Consensus 133 ~~d~slC~~f~e~Lk~Ck~~ 152 (157)
T KOG4090 133 GSDISLCEGYNEMLKQCKKN 152 (157)
T ss_pred CCCHHHHHHHHHHHHHHHHH
T ss_conf 76158889999999999987
No 385
>KOG0402 consensus
Probab=21.05 E-value=31 Score=12.54 Aligned_cols=50 Identities=22% Similarity=0.498 Sum_probs=28.5
Q ss_pred EECCCCCCCCCCEEEECCCCEEEECCCCC---CCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 53458888587879817897467136888---87898998988599979999999998
Q gi|254780834|r 41 ACCPFHDEKTPSFHCNDSKGFYYCFSCHV---KGDHLSFLSALLGCSFIESVQRLAAI 95 (648)
Q Consensus 41 ~~cPfh~ektpsf~v~~~~~~~~cf~c~~---~gd~~~f~~~~~~~~f~ea~~~la~~ 95 (648)
--|+|..-+|-- -..-|+|+|=+|+. ||- +. +----..++.-+++.|-+.
T Consensus 37 y~CsfCGK~~vK---R~AvGiW~C~~C~kv~agga-~~-~~t~aa~t~rs~irrlre~ 89 (92)
T KOG0402 37 YTCSFCGKKTVK---RKAVGIWKCGSCKKVVAGGA-YT-VTTAAAATVRSTIRRLREL 89 (92)
T ss_pred HHHHHCCHHHHH---HHCEEEEECCCCCEEECCCE-EE-ECCCHHHHHHHHHHHHHHH
T ss_conf 133122605653---23034784167540540524-78-7063368999999999987
No 386
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=21.05 E-value=39 Score=11.64 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 97999999999818858776820367778899999999999999999732
Q gi|254780834|r 84 SFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLK 133 (648)
Q Consensus 84 ~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 133 (648)
.-.|.++..|+..||.--..+....-...-.-++-++.+.|..|.++.-+
T Consensus 3 ~p~esik~iAes~Gi~~l~de~a~~La~dveyRlkei~q~A~Kfm~hskR 52 (65)
T smart00803 3 LPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKR 52 (65)
T ss_pred CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 81788999999859888899999999999999999999999999997576
No 387
>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional
Probab=21.02 E-value=39 Score=11.63 Aligned_cols=59 Identities=17% Similarity=0.184 Sum_probs=32.9
Q ss_pred CHHHHHHHHHCCCEEEEEECCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf 6267898851268189961788--662257778888887775369730675257888888997
Q gi|254780834|r 303 TEYQLRLLWKLSPRIVLCFDGD--DPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI 363 (648)
Q Consensus 303 t~~~~~~l~r~~~~vvl~fDgD--~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i 363 (648)
+...+..+.++|++|+++.+|- +.|--+.+-.-+.+.. --|..++++.=|.+--|=+|+
T Consensus 204 vtHdl~~~~~~aDrv~vl~~G~iv~~G~~~evl~~~~l~~--~yg~~~~v~~~p~~~~~~~~~ 264 (265)
T PRK10575 204 VLHDINMAARYCDYLVALRGGEMIAQGTPAELMRGETLEQ--IYGIPMGILPHPAGAAPVSFV 264 (265)
T ss_pred EECCHHHHHHHCCEEEEEECCEEEEECCHHHHCCHHHHHH--HHCCCCEEEECCCCCCCEEEE
T ss_conf 9388899999699999998996999848899789879999--869965898387879856983
No 388
>pfam09059 TyeA TyeA. Members of this family are composed of two pairs of parallel alpha-helices, and interact with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN.
Probab=20.98 E-value=40 Score=11.63 Aligned_cols=44 Identities=14% Similarity=0.140 Sum_probs=30.5
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHH
Q ss_conf 9999853023314579999999998854179-----9899999999999
Q gi|254780834|r 386 WKRETENRSFNTPDERAELEIHLKNCINHIK-----DQKLRYYYSQAIR 429 (648)
Q Consensus 386 ~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~-----d~~~R~~yl~~la 429 (648)
++.+.....+.+++.+..|..+++.++..|| |+-.|.-.++.+-
T Consensus 26 i~~la~~~~l~d~e~~I~F~~el~~l~R~iP~~vF~d~e~R~~lL~a~Q 74 (81)
T pfam09059 26 IEKLVNALELQDVEKQVLFYQELKRLVRLFPIEVFSDEEQRQNLLQACQ 74 (81)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHH
T ss_conf 9999997079857899899999999999789875589889999999999
No 389
>KOG1253 consensus
Probab=20.89 E-value=40 Score=11.61 Aligned_cols=10 Identities=10% Similarity=0.149 Sum_probs=5.1
Q ss_pred HHHHHHHHHH
Q ss_conf 1788886433
Q gi|254780834|r 251 FFGALNYLQK 260 (648)
Q Consensus 251 l~~a~~~~~~ 260 (648)
||-|.++++.
T Consensus 199 LDsAvqav~~ 208 (525)
T KOG1253 199 LDSAVQAVRD 208 (525)
T ss_pred HHHHHHHHHC
T ss_conf 9999998640
No 390
>pfam04630 Phage_tail Phage major tail protein.
Probab=20.89 E-value=40 Score=11.61 Aligned_cols=20 Identities=15% Similarity=-0.001 Sum_probs=11.2
Q ss_pred HHHCCCEEEEEECCCCCCHH
Q ss_conf 85126818996178866225
Q gi|254780834|r 310 LWKLSPRIVLCFDGDDPGLR 329 (648)
Q Consensus 310 l~r~~~~vvl~fDgD~AG~k 329 (648)
..++..+++-.|.++++|..
T Consensus 163 ~~~~~~~~yk~~~s~d~~Fd 182 (199)
T pfam04630 163 DNAGGNQPYKIFYSGDSGFD 182 (199)
T ss_pred CCCCCCCEEEEEECCCCCCC
T ss_conf 56668951699846998989
No 391
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=20.89 E-value=40 Score=11.61 Aligned_cols=48 Identities=19% Similarity=0.286 Sum_probs=29.1
Q ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCC
Q ss_conf 8189961788662257778888887775369730675257888888997203
Q gi|254780834|r 315 PRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCY 366 (648)
Q Consensus 315 ~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~ 366 (648)
+++.++||.|++-. |.-++.......+..+.+-.++.+.||-..+|+-
T Consensus 135 ~~ftiiYe~~~~L~----rLq~ll~~~~~~~~~i~vr~l~~~~d~r~vLkeI 182 (333)
T cd06394 135 PTASLICAKAECLL----RLEELLRQFLISKETLSVRMLDDSRDPTPLLKEI 182 (333)
T ss_pred CEEEEEEECCHHHH----HHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf 66999970735689----9999987216789807999878899867999999
No 392
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=20.88 E-value=40 Score=11.61 Aligned_cols=37 Identities=14% Similarity=-0.021 Sum_probs=16.7
Q ss_pred CCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHH
Q ss_conf 2113432136626789885126818996178866225
Q gi|254780834|r 293 NVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLR 329 (648)
Q Consensus 293 n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~k 329 (648)
.+++.-|+-.|..|.+++-.-..+.....+.+-++.-
T Consensus 275 ~~~~~~g~~itar~~~~~e~~~~~~~~~~~~~~~~~~ 311 (1449)
T TIGR02013 275 KILLAKGKKITARIKKKLENKSLKRELLLEELLAEDL 311 (1449)
T ss_pred EEEECCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 7984278500489999873131344666688886665
No 393
>TIGR00393 kpsF sugar isomerase, KpsF/GutQ family; InterPro: IPR004800 This is a family of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. The group includes GutQ, a protein of the glucitol operon and KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of Escherichia coli.; GO: 0016853 isomerase activity, 0005975 carbohydrate metabolic process.
Probab=20.85 E-value=31 Score=12.54 Aligned_cols=72 Identities=19% Similarity=0.238 Sum_probs=39.1
Q ss_pred HHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHC--CCEECCCCCCCCCCC----CCEE-EEEE
Q ss_conf 57899998506885351012442256774103455420599734523201--210034654100001----6716-8889
Q gi|254780834|r 138 KRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAG--LLIDGDNSATSYDRF----RNRL-IFPI 210 (648)
Q Consensus 138 ~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~g--l~~~~~~~~~~~d~F----r~Ri-~fPi 210 (648)
+-|..-++.|||++|.=.+|.-|=+ |=+.|.-| ..++.+.+ |-.-... .+..|.. |.|+ |-=|
T Consensus 124 aLa~al~~ArnF~~eDFA~~HPGG~------LG~kLL~k---V~dlm~t~d~lP~v~~t-as~~DAL~e~~~~~LG~~~v 193 (272)
T TIGR00393 124 ALAVALMKARNFSEEDFAKFHPGGA------LGRKLLVK---VKDLMQTDDELPLVAPT-ASFKDALLEMSRKRLGLAVV 193 (272)
T ss_pred HHHHHHHHHCCCCHHHHHCCCCCHH------HHHHHHHH---HHHHHCCCCCCCCEECC-CCCEEEEEEEECCCCCEEEE
T ss_conf 9999998525888424411487046------66788887---67764066567822236-77202102331378617999
Q ss_pred EECCCCEEE
Q ss_conf 707785888
Q gi|254780834|r 211 RSSRGQVIA 219 (648)
Q Consensus 211 ~~~~g~~i~ 219 (648)
.|.+-++.|
T Consensus 194 ~~~~~~~~G 202 (272)
T TIGR00393 194 CDENEQLKG 202 (272)
T ss_pred EECCCCEEE
T ss_conf 715552467
No 394
>pfam04989 CmcI Cephalosporin hydroxylase. Members of this family are about 220 amino acids long. The CmcI protein is presumed to represent the cephalosporin-7--hydroxylase. However this has not been experimentally verified.
Probab=20.78 E-value=40 Score=11.59 Aligned_cols=85 Identities=15% Similarity=0.119 Sum_probs=50.7
Q ss_pred CHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE-----EEEECCCCCCHHH-HHHCCCH-HHHHHHH
Q ss_conf 6267898851268189961788662257778888887775369730-----6752578888889-9720366-8899886
Q gi|254780834|r 303 TEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRV-----NFVLLSRGEDPDS-FIRCYGK-TAFEKLI 375 (648)
Q Consensus 303 t~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v-----~vv~LP~G~DPDe-~ir~~G~-eaf~~ll 375 (648)
+-++++.+.+..+++.++.|+|-. ....++.++..-++++.|-=+ -+=.+|+...|+. +-+.+|+ .|+.++|
T Consensus 95 ~~~~v~~~~~~~~~vlVilDs~Ht-~~hVl~eL~~y~~lv~~GsY~IVeDTii~~~p~~~~~~r~w~~gnnP~~Av~eFL 173 (202)
T pfam04989 95 IIEQVRSLAEPPHPVLVILDSDHT-HEHVLAELRAYAPLVSEGSYLVVEDTIIEDLPESPFPDRPWGKGNNPKTAVTEFL 173 (202)
T ss_pred HHHHHHHHHCCCCCEEEEECCCCC-HHHHHHHHHHHHHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 998899985379858999648865-6889999998752157688999957624317556678886878989799999999
Q ss_pred HHCCCHHHHHHHHHHH
Q ss_conf 4149927999999985
Q gi|254780834|r 376 VESLPLVDMLWKRETE 391 (648)
Q Consensus 376 ~~A~~l~dFl~~~l~~ 391 (648)
++... |.++....
T Consensus 174 ~~~~~---F~iD~~~~ 186 (202)
T pfam04989 174 AEHPE---FEIDTAIE 186 (202)
T ss_pred HHCCC---CEECCCCC
T ss_conf 87899---38653202
No 395
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent pro
Probab=20.73 E-value=36 Score=12.02 Aligned_cols=18 Identities=11% Similarity=0.385 Sum_probs=7.4
Q ss_pred HHHHHCCCCHHHHHHHHH
Q ss_conf 134321366267898851
Q gi|254780834|r 295 VSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 295 va~~Gtalt~~~~~~l~r 312 (648)
|+-.||.||.++++.|.+
T Consensus 46 ~~kvgtGfsd~~l~~l~~ 63 (140)
T cd07968 46 FCKVGSGFSDEELDEIRR 63 (140)
T ss_pred EEEECCCCCHHHHHHHHH
T ss_conf 999856899999999999
No 396
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=20.68 E-value=40 Score=11.58 Aligned_cols=55 Identities=27% Similarity=0.393 Sum_probs=32.9
Q ss_pred HHHHHHHHH---CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf 267898851---26818996178866225777888888777536973067525788888899
Q gi|254780834|r 304 EYQLRLLWK---LSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSF 362 (648)
Q Consensus 304 ~~~~~~l~r---~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ 362 (648)
..|++.|++ -+++||++-|.|.=|..=++..++.+-. ....++=+.+.+ ..|.+.
T Consensus 78 ~~~~~~i~~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~---~~~~v~R~~fss-lT~~~I 135 (142)
T cd01028 78 KKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC---DNKPVKRAWFSE-ITPKAI 135 (142)
T ss_pred HHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEEC-CCHHHH
T ss_conf 9999999999861999998889982279999999999578---899927899835-799999
No 397
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.61 E-value=40 Score=11.57 Aligned_cols=10 Identities=50% Similarity=0.876 Sum_probs=3.6
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999998
Q gi|254780834|r 594 QKEEIEKQIA 603 (648)
Q Consensus 594 ~l~ele~~l~ 603 (648)
++.+++++|.
T Consensus 89 k~~eie~ki~ 98 (107)
T cd04777 89 KKDELEKEIE 98 (107)
T ss_pred HHHHHHHHHH
T ss_conf 9999999999
No 398
>PRK13239 alkylmercury lyase; Provisional
Probab=20.51 E-value=40 Score=11.55 Aligned_cols=38 Identities=29% Similarity=0.515 Sum_probs=21.9
Q ss_pred EEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHH
Q ss_conf 9707785888501001465530010387676535210110817888864
Q gi|254780834|r 210 IRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYL 258 (648)
Q Consensus 210 i~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~ 258 (648)
-+|..|+|||| |=++.+.. -.+. --|+.|| -..|.+++
T Consensus 64 eyD~~G~Iig~-GLTlrpT~-Hrf~--------v~G~~Ly-TWCAlDaL 101 (206)
T PRK13239 64 EYDEDGRIIGY-GLTLRPTP-HRFE--------VDGRQLY-TWCALDTL 101 (206)
T ss_pred EECCCCCEEEE-ECCCCCCC-CEEE--------ECCEEEE-HHHHHHHH
T ss_conf 58589858865-04116668-6789--------8992555-78888876
No 399
>KOG1207 consensus
Probab=20.46 E-value=40 Score=11.54 Aligned_cols=60 Identities=37% Similarity=0.464 Sum_probs=44.9
Q ss_pred CEEEEECCH------HHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf 708997143------8899987435542113432136626789885126818996178866225777888
Q gi|254780834|r 272 SFIILVEGY------MDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAI 335 (648)
Q Consensus 272 ~~~i~vEGy------~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~ 335 (648)
+.+++|-|- -=|.+|+.+|-. |||. |=+++++..|-++++-.|+-.-+|-.|..|..|++
T Consensus 7 G~~vlvTgagaGIG~~~v~~La~aGA~-ViAv---aR~~a~L~sLV~e~p~~I~Pi~~Dls~wea~~~~l 72 (245)
T KOG1207 7 GVIVLVTGAGAGIGKEIVLSLAKAGAQ-VIAV---ARNEANLLSLVKETPSLIIPIVGDLSAWEALFKLL 72 (245)
T ss_pred CEEEEEECCCCCCCHHHHHHHHHCCCE-EEEE---ECCHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHH
T ss_conf 619996056664149999999866887-9999---56988999998529764245575133899999761
No 400
>PRK13551 agmatine deiminase; Provisional
Probab=20.26 E-value=41 Score=11.51 Aligned_cols=54 Identities=11% Similarity=0.142 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHCCC--EEEEEECCCCCCHHH--HHHHHHHHHHH-HHCCCCEEEEECCC
Q ss_conf 66267898851268--189961788662257--77888888777-53697306752578
Q gi|254780834|r 302 LTEYQLRLLWKLSP--RIVLCFDGDDPGLRA--AYKAIDLVLCH-LIPGNRVNFVLLSR 355 (648)
Q Consensus 302 lt~~~~~~l~r~~~--~vvl~fDgD~AG~kA--a~Ra~e~~l~~-l~~g~~v~vv~LP~ 355 (648)
-|..|+-.|.||+. .|+++.-.|..--+. .....+.+... -..|...+++.||-
T Consensus 207 dTdGHID~lARFv~p~~Vl~~~~~d~~d~~~~~~~~~~~~L~~~~da~G~~~~iv~lP~ 265 (360)
T PRK13551 207 ETDGHVDNMCCFVRPGEVALAWTDDENDPQYARSKAALEVLENTTDAKGRKLKVHKLPI 265 (360)
T ss_pred CCCCCEECEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECC
T ss_conf 99987304377438980999944899884679999999999965643698327999369
No 401
>pfam08448 PAS_4 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=20.24 E-value=41 Score=11.50 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=16.6
Q ss_pred CEEEEEEEECCCCEEEEECCCCC
Q ss_conf 71688897077858885010014
Q gi|254780834|r 204 NRLIFPIRSSRGQVIAFGGRTLS 226 (648)
Q Consensus 204 ~Ri~fPi~~~~g~~i~f~gR~l~ 226 (648)
.=.+.||+|..|+++|+-+=..|
T Consensus 82 ~~~~~pi~d~~G~~~g~v~~~~D 104 (110)
T pfam08448 82 ELRLTPLRDPDGEVIGVLVISRD 104 (110)
T ss_pred EEEEEEEECCCCCEEEEEEEEEE
T ss_conf 43576689899999999999998
No 402
>COG3484 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.23 E-value=34 Score=12.26 Aligned_cols=16 Identities=31% Similarity=0.621 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCHHCCC
Q ss_conf 3876765352101108
Q gi|254780834|r 235 NSPETILFHKGKNLYN 250 (648)
Q Consensus 235 NSpeT~if~K~~~Ly~ 250 (648)
-+||||+|+-|..-||
T Consensus 139 aT~etpf~QiGEtKYG 154 (255)
T COG3484 139 ATPETPFLQIGETKYG 154 (255)
T ss_pred CCCCCCEEECCCCCCC
T ss_conf 5899851671431258
No 403
>KOG0415 consensus
Probab=20.16 E-value=14 Score=15.74 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=27.2
Q ss_pred EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 575345888858787981789746713688887898998988599979999
Q gi|254780834|r 39 YWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESV 89 (648)
Q Consensus 39 ~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~~~f~ea~ 89 (648)
|.-.|+||+=.. -|+. |.----|.|.||+-|==+|.-++-.|-||-
T Consensus 36 YYN~clfh~vq~-~f~a----QTGDPtGtG~GG~si~~~lyG~q~rffeaE 81 (479)
T KOG0415 36 YYNFCLFHTVQR-DFTA----QTGDPTGTGDGGESIYGVLYGEQARFFEAE 81 (479)
T ss_pred HCCCCEEEECCC-CCEE----ECCCCCCCCCCCCEEEEECCCCCCHHHHHH
T ss_conf 406450224011-6353----138988778885432000036321011322
No 404
>cd06544 GH18_narbonin Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function. Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity. Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination. This family also includes the VfNOD32 nodulin from Vicia faba.
Probab=20.15 E-value=41 Score=11.49 Aligned_cols=84 Identities=17% Similarity=0.191 Sum_probs=53.4
Q ss_pred CCCHHHHHHHHHCCC--EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-
Q ss_conf 366267898851268--18996178866225777888888777536973067525788888899720366889988641-
Q gi|254780834|r 301 ALTEYQLRLLWKLSP--RIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE- 377 (648)
Q Consensus 301 alt~~~~~~l~r~~~--~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~- 377 (648)
-||+++++.||+..+ +|++..-||..|-. .+.+-|. ..|+|+.+- ...+..+|++
T Consensus 55 ~ltP~~V~~~K~~~pnvKV~iSiGG~~v~~~-------------------~~~f~p~--s~~~WV~NA-v~SL~~iI~~Y 112 (253)
T cd06544 55 NLTPEAVKSIKAQHPNVKVVISIGGRGVQNN-------------------PTPFDPS--NVDSWVSNA-VSSLTSIIQTY 112 (253)
T ss_pred CCCHHHHHHHHHHCCCCEEEEEECCCCCCCC-------------------CEECCCC--HHHHHHHHH-HHHHHHHHHHH
T ss_conf 7499999998852998059999568756687-------------------2111762--077899999-99999999970
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 4992799999998530233145799999999988
Q gi|254780834|r 378 SLPLVDMLWKRETENRSFNTPDERAELEIHLKNC 411 (648)
Q Consensus 378 A~~l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~ 411 (648)
..+.+|.=|++.. .+++.-++.+.+|...
T Consensus 113 ~lDGIDIDyE~f~-----~d~~tF~~cIG~LIt~ 141 (253)
T cd06544 113 NLDGIDIDYEHFP-----ADPDTFVECIGQLITE 141 (253)
T ss_pred CCCCEECCHHHCC-----CCHHHHHHHHHHHHHH
T ss_conf 8886112565446-----8778999999999998
No 405
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.14 E-value=41 Score=11.49 Aligned_cols=36 Identities=14% Similarity=0.291 Sum_probs=24.7
Q ss_pred ECCCCCCCCCCEEEECCCCEEEECCCCC--CCCHHHHHHH
Q ss_conf 3458888587879817897467136888--8789899898
Q gi|254780834|r 42 CCPFHDEKTPSFHCNDSKGFYYCFSCHV--KGDHLSFLSA 79 (648)
Q Consensus 42 ~cPfh~ektpsf~v~~~~~~~~cf~c~~--~gd~~~f~~~ 79 (648)
-||-+. .+.+..++..|.+-|=.||. .-++||-=.+
T Consensus 13 kCp~Cg--~~~ii~D~~~G~~vC~~CG~Vi~e~~ID~~~E 50 (310)
T PRK00423 13 RCPECG--SDKLIYDYERGEIVCADCGYVIEENLIDQGPE 50 (310)
T ss_pred ECCCCC--CCCEEEECCCCCEECCCCCCEEECCCCCCCCC
T ss_conf 898986--98535678998775302887611320236753
No 406
>TIGR02418 acolac_catab acetolactate synthase, catabolic; InterPro: IPR012782 Acetolactate synthase is a thiamin pyrophosphate-dependent enzyme that combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. It exists in two distinct forms that have different properties, though they are clearly related , . The biosynthetic form, found in plants, fungi and bacteria, is involved in the biosynthesis of branched-chain amino acids and contains non-catalytic FAD. The catabolic form is found only in some bacteria, participates in butanediol fermentation, and does not contain FAD. This entry represents the catabolic form of acetolactate synthase, generally found in species that posses acetolactate decarboxylase, which is often encoded in the same operon. The enzyme is thought to be a homotetramer, though this has not conclusively been shown. Each monomer consists of three distinct domains, designated, starting from the N-terminus, as alpha, beta and gamma . The core of the alpha and gamma domains is a six-stranded parallel beta sheet surrounded by alpha helices, while the the beta domain forms a double Rossman fold. The thiamin pyrophosphate cofactor has an unusual conformation that has not been seen in other enzymes using this cofactor, including the biosynthetic form of acetolactate synthase. The active site is located in a funnel at the dimer interface, bordered by residues from all three domains.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding.
Probab=20.12 E-value=26 Score=13.24 Aligned_cols=43 Identities=16% Similarity=0.082 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHHHHHH-------CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3145799999999988541-------7998999999999999988765776
Q gi|254780834|r 396 NTPDERAELEIHLKNCINH-------IKDQKLRYYYSQAIRDRLQQLFQKY 439 (648)
Q Consensus 396 ~spe~ka~~~~~l~~~I~~-------I~d~~~R~~yl~~la~~L~~~~~~~ 439 (648)
.|.++.++++++++..... =.-.+-|++|-+.|+.|++ +|+++
T Consensus 212 aS~~~~~~Av~rll~k~~LPvVeTfQgAG~vsrele~~TFfGRvG-LFrNQ 261 (553)
T TIGR02418 212 ASSQETTEAVRRLLKKTQLPVVETFQGAGVVSRELEDETFFGRVG-LFRNQ 261 (553)
T ss_pred CCCHHHHHHHHHHHCCCCCCCEEEEECCEEECHHCCCCCCEECCC-CCCCC
T ss_conf 888899999999864606882140200513110024565210011-44587
No 407
>pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Probab=20.10 E-value=41 Score=11.48 Aligned_cols=53 Identities=21% Similarity=0.349 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9985899999999999999872412798999999999999999999988413267
Q gi|254780834|r 584 LYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMI 638 (648)
Q Consensus 584 l~~r~~~L~r~l~ele~~l~e~~~~~d~e~~~~l~~el~elk~~L~~l~~~Eal~ 638 (648)
+......+..+...+.+++......+. ....+..+..+++.++..++.+..-+
T Consensus 41 ~~~~~e~L~~~~N~~sk~ig~~~~~~~--~~~~l~~~~~~lk~~i~~le~~~~~~ 93 (108)
T pfam02403 41 LQVELEELQAERNELSKEIGKAKKKKE--DAEALIAEVKELKDELKALEAELREL 93 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999998598999999875774--16889999999999999999999999
No 408
>KOG1597 consensus
Probab=20.07 E-value=41 Score=11.48 Aligned_cols=68 Identities=21% Similarity=0.233 Sum_probs=35.7
Q ss_pred HHCCCCCCHHHHHCCCCHHHHH--HHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH
Q ss_conf 7435542113432136626789--8851268189961788662257778888887775369730675257888888997
Q gi|254780834|r 287 CQAGVQNVVSSLGTALTEYQLR--LLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFI 363 (648)
Q Consensus 287 ~~~G~~n~va~~Gtalt~~~~~--~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~i 363 (648)
|.+|.. +.+.||--+...++. ..||. |-+|.+|..-+ |..+-.-|+|..|.-.-++..|.|.+++..-
T Consensus 17 ~~~gdt-vC~~CGlVl~~r~Id~~sEwrt-------fsnd~~~~DPs-rvG~~sNPlL~~g~L~T~I~~g~g~~s~~~s 86 (308)
T KOG1597 17 HSAGDT-VCSECGLVLEDRIIDEGSEWRT-------FSNDDSDADPS-RVGASSNPLLDGGDLSTFISKGTGTSSSFAS 86 (308)
T ss_pred CCCCCE-ECCCCCEEECCCCCCCCCCCCC-------CCCCCCCCCCC-CCCCCCCCCCCCCCCCEEEECCCCCCHHHHH
T ss_conf 268856-6023772621424256522100-------14677788965-4688889878899854054058887778899
Done!