Query 048704
Match_columns 220
No_of_seqs 132 out of 1063
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 12:12:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08173 DNA topoisomerase III 100.0 6E-58 1.3E-62 450.9 19.0 189 4-219 2-203 (862)
2 PRK07726 DNA topoisomerase III 100.0 3.5E-56 7.6E-61 429.3 18.7 187 6-219 2-199 (658)
3 PRK14724 DNA topoisomerase III 100.0 8.1E-56 1.8E-60 440.3 18.8 196 4-219 1-211 (987)
4 PRK07220 DNA topoisomerase I; 100.0 1.3E-55 2.8E-60 429.7 19.5 202 6-219 2-204 (740)
5 PRK14973 DNA topoisomerase I; 100.0 1.8E-54 3.9E-59 427.8 19.6 198 6-219 2-203 (936)
6 PRK07219 DNA topoisomerase I; 100.0 3.8E-54 8.2E-59 423.7 20.1 202 6-219 2-204 (822)
7 TIGR01056 topB DNA topoisomera 100.0 1.2E-53 2.6E-58 411.3 19.1 189 6-219 2-204 (660)
8 TIGR01057 topA_arch DNA topois 100.0 1.5E-53 3.3E-58 408.8 18.6 196 9-219 1-199 (618)
9 PRK05776 DNA topoisomerase I; 100.0 1.5E-52 3.2E-57 404.2 20.7 199 5-219 2-202 (670)
10 PRK09401 reverse gyrase; Revie 100.0 8.3E-51 1.8E-55 410.2 20.5 200 4-219 601-821 (1176)
11 TIGR01051 topA_bact DNA topois 100.0 2.7E-51 5.9E-56 392.5 16.1 169 7-219 1-170 (610)
12 PRK06599 DNA topoisomerase I; 100.0 1.1E-50 2.3E-55 392.3 17.0 176 4-219 2-177 (675)
13 COG0550 TopA Topoisomerase IA 100.0 1.3E-50 2.8E-55 383.1 17.1 178 5-219 1-179 (570)
14 PRK05582 DNA topoisomerase I; 100.0 9.9E-51 2.1E-55 391.3 16.0 173 4-219 2-174 (650)
15 TIGR01054 rgy reverse gyrase. 100.0 1.8E-49 4E-54 400.6 19.8 200 4-219 601-821 (1171)
16 PRK06319 DNA topoisomerase I/S 100.0 3.3E-49 7.1E-54 389.7 17.7 174 4-219 2-175 (860)
17 PRK08780 DNA topoisomerase I; 100.0 1.9E-49 4.1E-54 387.9 15.7 177 4-219 2-178 (780)
18 PRK07561 DNA topoisomerase I s 100.0 5.7E-49 1.2E-53 388.3 17.1 177 5-219 2-187 (859)
19 PRK14701 reverse gyrase; Provi 100.0 2.5E-48 5.4E-53 400.1 21.0 200 4-219 580-802 (1638)
20 KOG1956 DNA topoisomerase III 100.0 3E-48 6.5E-53 360.5 10.8 214 4-219 1-217 (758)
21 KOG1957 DNA topoisomerase III 100.0 9.2E-45 2E-49 326.6 11.8 198 4-219 2-199 (555)
22 cd03362 TOPRIM_TopoIA_TopoIII 100.0 4.5E-43 9.8E-48 282.1 14.4 149 5-162 1-151 (151)
23 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 1.9E-41 4.2E-46 269.9 15.4 142 5-162 1-142 (142)
24 PTZ00407 DNA topoisomerase IA; 100.0 3E-39 6.4E-44 313.4 10.4 197 5-219 10-231 (805)
25 cd03361 TOPRIM_TopoIA_RevGyr T 100.0 1E-37 2.2E-42 255.7 15.4 149 5-162 1-170 (170)
26 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 2.2E-37 4.8E-42 241.3 14.0 123 5-162 1-123 (123)
27 COG1110 Reverse gyrase [DNA re 100.0 5.1E-34 1.1E-38 277.1 16.0 199 4-218 617-836 (1187)
28 smart00436 TOP1Bc Bacterial DN 99.9 1.5E-27 3.3E-32 175.8 6.3 71 142-219 1-71 (89)
29 PF01751 Toprim: Toprim domain 99.9 6.1E-27 1.3E-31 175.7 6.7 99 6-150 1-100 (100)
30 smart00493 TOPRIM topoisomeras 98.9 7.2E-09 1.6E-13 73.0 9.1 73 5-133 1-73 (76)
31 cd01025 TOPRIM_recR TOPRIM_rec 98.5 1.1E-06 2.5E-11 67.3 9.2 91 5-147 1-93 (112)
32 cd00188 TOPRIM Topoisomerase-p 98.1 7.7E-05 1.7E-09 51.4 10.2 81 6-146 2-82 (83)
33 PRK00076 recR recombination pr 97.9 0.00025 5.5E-09 59.4 11.7 109 5-164 79-195 (196)
34 cd01027 TOPRIM_RNase_M5_like T 97.4 0.00043 9.3E-09 50.0 6.0 44 96-146 37-80 (81)
35 PRK13844 recombination protein 97.0 0.014 3.1E-07 49.0 11.7 54 106-164 138-199 (200)
36 TIGR00615 recR recombination p 96.9 0.016 3.4E-07 48.6 11.3 53 106-162 134-194 (195)
37 COG0353 RecR Recombinational D 96.7 0.04 8.6E-07 46.1 11.6 108 5-164 80-197 (198)
38 PF13662 Toprim_4: Toprim doma 95.7 0.017 3.6E-07 41.1 4.0 35 107-145 46-80 (81)
39 COG1658 Small primase-like pro 95.1 0.056 1.2E-06 42.4 5.6 67 96-163 45-120 (127)
40 PRK04031 DNA primase; Provisio 95.0 0.042 9.1E-07 50.8 5.1 67 99-168 203-269 (408)
41 PF09664 DUF2399: Protein of u 94.9 0.26 5.7E-06 39.7 9.1 74 5-133 19-92 (152)
42 TIGR00334 5S_RNA_mat_M5 ribonu 94.4 0.19 4.2E-06 41.4 7.2 71 94-165 35-111 (174)
43 COG4026 Uncharacterized protei 92.9 0.19 4.1E-06 43.1 4.8 44 101-148 52-95 (290)
44 PRK04017 hypothetical protein; 90.0 0.38 8.3E-06 37.9 3.5 31 104-134 62-92 (132)
45 cd03364 TOPRIM_DnaG_primases T 82.7 3.1 6.6E-05 29.1 4.7 27 107-133 43-69 (79)
46 cd01029 TOPRIM_primases TOPRIM 81.4 3.5 7.6E-05 28.5 4.6 27 107-133 43-69 (79)
47 PF02044 Bombesin: Bombesin-li 75.7 0.68 1.5E-05 22.2 -0.4 8 55-62 4-11 (14)
48 PF10087 DUF2325: Uncharacteri 73.4 8.6 0.00019 28.0 4.8 56 99-162 41-96 (97)
49 PF13155 Toprim_2: Toprim-like 72.3 7.9 0.00017 27.7 4.4 26 108-133 48-73 (96)
50 cd03365 TOPRIM_TopoIIA TOPRIM_ 69.3 4.4 9.6E-05 31.5 2.5 27 106-132 76-102 (120)
51 cd03366 TOPRIM_TopoIIA_GyrB TO 66.8 5.6 0.00012 30.6 2.6 27 106-132 71-97 (114)
52 PRK07714 hypothetical protein; 66.4 33 0.00071 25.3 6.7 75 94-181 24-98 (100)
53 PRK06683 hypothetical protein; 66.1 29 0.00064 24.8 6.2 55 94-161 17-71 (82)
54 cd01030 TOPRIM_TopoIIA_like TO 66.0 5.5 0.00012 30.7 2.5 27 106-132 72-98 (115)
55 PHA02031 putative DnaG-like pr 64.4 25 0.00055 30.9 6.6 46 107-156 206-252 (266)
56 PRK05667 dnaG DNA primase; Val 63.5 23 0.00051 34.5 6.9 55 95-156 287-345 (580)
57 COG0358 DnaG DNA primase (bact 58.4 14 0.0003 35.9 4.3 35 99-133 282-316 (568)
58 PRK13601 putative L7Ae-like ri 56.9 50 0.0011 23.7 6.0 54 94-160 14-67 (82)
59 TIGR01391 dnaG DNA primase, ca 56.1 42 0.0009 31.2 6.9 55 95-156 291-346 (415)
60 PRK13600 putative ribosomal pr 55.0 26 0.00056 25.4 4.2 53 94-159 19-71 (84)
61 PF13362 Toprim_3: Toprim doma 54.8 34 0.00074 24.5 5.0 27 107-133 41-69 (96)
62 PRK04175 rpl7ae 50S ribosomal 53.4 90 0.0019 24.0 7.3 78 94-183 36-114 (122)
63 PRK07283 hypothetical protein; 50.9 84 0.0018 23.1 6.6 73 94-180 24-96 (98)
64 PRK13602 putative ribosomal pr 50.4 70 0.0015 22.8 5.9 55 94-161 17-71 (82)
65 TIGR00646 MG010 DNA primase-re 48.1 51 0.0011 28.2 5.6 28 106-133 153-180 (218)
66 PRK14719 bifunctional RNAse/5- 44.8 12 0.00026 34.3 1.4 28 106-133 66-93 (360)
67 KOG2004 Mitochondrial ATP-depe 43.9 78 0.0017 32.2 6.8 74 147-220 352-444 (906)
68 PF05368 NmrA: NmrA-like famil 43.8 31 0.00067 28.5 3.7 52 97-154 55-107 (233)
69 PRK11178 uridine phosphorylase 43.8 47 0.001 28.6 4.9 47 4-54 17-63 (251)
70 TIGR03677 rpl7ae 50S ribosomal 42.4 1.1E+02 0.0025 23.2 6.3 78 94-183 32-110 (117)
71 PRK05583 ribosomal protein L7A 41.7 1.5E+02 0.0032 22.1 6.8 74 94-180 23-96 (104)
72 PF00158 Sigma54_activat: Sigm 39.6 1.7E+02 0.0037 23.4 7.4 62 94-159 9-70 (168)
73 PRK01018 50S ribosomal protein 39.1 1.2E+02 0.0026 22.3 5.8 72 94-177 22-94 (99)
74 PF11549 Sec31: Protein transp 38.3 7.9 0.00017 25.3 -0.6 16 7-22 31-46 (51)
75 PRK06423 phosphoribosylformylg 36.6 91 0.002 21.5 4.6 46 116-162 14-59 (73)
76 COG3640 CooC CO dehydrogenase 34.0 58 0.0013 28.5 3.9 44 104-153 153-198 (255)
77 TIGR01059 gyrB DNA gyrase, B s 32.8 33 0.00071 34.0 2.4 26 107-132 485-510 (654)
78 smart00433 TOP2c Topoisomerase 32.6 33 0.00072 33.5 2.4 25 107-131 453-477 (594)
79 TIGR01055 parE_Gneg DNA topois 31.4 36 0.00077 33.6 2.4 57 106-162 480-550 (625)
80 cd00223 TOPRIM_TopoIIB_SPO TOP 31.1 1.2E+02 0.0026 24.0 5.1 62 94-157 40-102 (160)
81 COG0187 GyrB Type IIA topoisom 31.0 42 0.00091 33.1 2.8 82 107-188 490-617 (635)
82 PRK05559 DNA topoisomerase IV 30.9 37 0.00081 33.5 2.5 56 107-162 487-556 (631)
83 TIGR01058 parE_Gpos DNA topois 30.9 37 0.00081 33.6 2.5 58 107-164 491-564 (637)
84 PTZ00109 DNA gyrase subunit b; 30.9 41 0.0009 34.6 2.8 56 107-162 680-761 (903)
85 PRK05644 gyrB DNA gyrase subun 28.9 44 0.00095 33.1 2.6 56 107-162 492-560 (638)
86 PHA02569 39 DNA topoisomerase 26.3 52 0.0011 32.3 2.6 56 107-163 475-545 (602)
87 cd01234 PH_CADPS CADPS (Ca2+-d 26.2 88 0.0019 23.9 3.2 31 104-134 83-113 (117)
88 KOG1220 Phosphoglucomutase/pho 26.2 2E+02 0.0044 28.3 6.4 38 120-162 346-384 (607)
89 PRK05819 deoD purine nucleosid 25.3 1.3E+02 0.0029 25.4 4.7 41 5-47 14-55 (235)
90 COG2820 Udp Uridine phosphoryl 25.3 1.3E+02 0.0028 26.3 4.5 48 5-56 18-65 (248)
91 KOG3432 Vacuolar H+-ATPase V1 24.7 1.3E+02 0.0029 23.1 3.9 37 145-181 40-82 (121)
92 PRK05783 hypothetical protein; 24.2 1.3E+02 0.0029 21.7 3.8 42 116-157 16-58 (84)
93 PTZ00106 60S ribosomal protein 23.5 3.2E+02 0.007 20.5 6.4 72 94-177 31-103 (108)
94 PRK13374 purine nucleoside pho 23.1 1.6E+02 0.0035 25.0 4.7 46 5-54 15-61 (233)
95 TIGR02679 conserved hypothetic 22.8 2.1E+02 0.0046 26.5 5.8 57 94-162 285-341 (385)
96 PRK14939 gyrB DNA gyrase subun 22.3 70 0.0015 32.4 2.6 56 107-162 491-560 (756)
97 PF12163 HobA: DNA replication 21.7 1.3E+02 0.0028 25.0 3.7 32 98-132 35-66 (180)
98 KOG3849 GDP-fucose protein O-f 20.6 1E+02 0.0022 27.7 3.0 27 92-118 282-311 (386)
99 COG1358 RPL8A Ribosomal protei 20.5 1.2E+02 0.0026 23.3 3.0 56 94-161 33-88 (116)
100 COG1445 FrwB Phosphotransferas 20.3 72 0.0016 24.8 1.8 51 103-166 53-106 (122)
No 1
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=6e-58 Score=450.93 Aligned_cols=189 Identities=26% Similarity=0.320 Sum_probs=160.8
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCC----CCCccCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLD 79 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~ 79 (220)
|++||||||||+|++||++||.. +++ +|||+|+ +|+||||+|||++|++|++| +.|+..
T Consensus 2 m~~LiIAEKPs~Ak~Ia~~Lg~~---~k~--------~gy~e~~--~~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~~---- 64 (862)
T PRK08173 2 SKALIIAEKPSVANDIARALGGF---TKH--------DEYFESD--EYVLSSAVGHLLEIAAPEEYEVKRGKWSFA---- 64 (862)
T ss_pred CCEEEEEeCHHHHHHHHHHhCCC---cCC--------CCeEeCC--cEEEEeeccccccCCCchhccccccccccc----
Confidence 57899999999999999999852 232 5788887 89999999999999999987 356542
Q ss_pred CCCCCceec-----cCCCcHHHHHHHHHHh--ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCH
Q 048704 80 LFQAPVHKA-----ESNPKVHICRHLNQEA--RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152 (220)
Q Consensus 80 l~~~p~~~~-----~~~~~~~~~~~lk~~~--~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~ 152 (220)
++|++|. ....+.++++.|++++ +++|+||||||||||||+|+|+|+++++. +++++|+||||+|+
T Consensus 65 --~LPi~p~~f~~~~~~~~~~q~~~ik~l~k~~~~d~Ii~AtD~dREGElI~~~I~~~~~~-----~kpv~Rlw~sslt~ 137 (862)
T PRK08173 65 --HLPVIPPHFDLNPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIAQHAKA-----KKPVKRLWLQSMTP 137 (862)
T ss_pred --ccCCCCccccccccccHHHHHHHHHHHHhhCCCCEEEECCCCChhHHHHHHHHHHHhCC-----CCCeEEEEEccCCH
Confidence 3444432 2334678999999999 46999999999999999999999999986 57999999999999
Q ss_pred HHHHHHHhcCCCCC--cchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 153 KDILKAMGNLVEPN--RNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 153 ~~I~~A~~nl~~~~--~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++|++||+||+|++ .+|++||+||+++|||||||+||++|+..++. ++ ..++|+||||||||.+
T Consensus 138 ~aI~~a~~nl~~~~~~~~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~-g~--~~~lSvGRVQTPtL~l 203 (862)
T PRK08173 138 QAIRDGFANLRSDEDMQPLADAARCRSEADWLVGINGTRAMTAFNSKG-GG--FFLTTVGRVQTPTLSI 203 (862)
T ss_pred HHHHHHHhcCCCchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHhHhhc-CC--ccccccccchhhHHHH
Confidence 99999999999997 49999999999999999999999999865432 21 2479999999999975
No 2
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=3.5e-56 Score=429.35 Aligned_cols=187 Identities=28% Similarity=0.374 Sum_probs=161.2
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCC----CCCccCCCCCCC
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLDLF 81 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~l~ 81 (220)
+||||||||+|++||++||.. +++ +|||+|+ +++|||+.|||++|++|++| +.|+..
T Consensus 2 ~LiIaEKPs~Ak~Ia~~L~~~---~~~--------~g~~~g~--~~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~------ 62 (658)
T PRK07726 2 RLFIAEKPSVGRDIADVLKPH---KKG--------DGYIEGN--GYIVTWAIGHLLELAEPEAYDERYKRWRLE------ 62 (658)
T ss_pred eEEEEeCHHHHHHHHHHhCCc---cCC--------CCeEeCC--CEEEEechhhhccCCCchhcccccCccccc------
Confidence 799999999999999999852 222 5788887 89999999999999999876 456532
Q ss_pred CCCceec-----cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHH
Q 048704 82 QAPVHKA-----ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDIL 156 (220)
Q Consensus 82 ~~p~~~~-----~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~ 156 (220)
++|+.|. ...++.++++.|++++++||+||||||||||||+|||+|+++++. +++++|+|||++|+++|+
T Consensus 63 ~lpi~p~~~~~~~~~~~~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~-----~~~v~Rl~~sslt~~~I~ 137 (658)
T PRK07726 63 DLPIIPEKWKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCGV-----RKPIKRLWISSLTDKAIK 137 (658)
T ss_pred cCCCCcccceeeeccchHHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhCC-----CCCeEEEEEccCCHHHHH
Confidence 3454442 134567899999999999999999999999999999999999996 579999999999999999
Q ss_pred HHHhcCCCCC--cchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 157 KAMGNLVEPN--RNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 157 ~A~~nl~~~~--~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+||+||+|++ .+|++||+||+++||+||||+||++|+.+++. ++ +.++|+||||||||.+
T Consensus 138 ~A~~nl~~~~~~~~l~~aa~aR~~~D~liG~nlSr~~t~~~~~~--g~-~~~lS~GRVQTPtL~l 199 (658)
T PRK07726 138 RAFANLKPGKETIPLYYSALARSRADWLVGINMTRAYTLLGRKA--GY-NGVLSVGRVQTPTLAL 199 (658)
T ss_pred HHHHhcCCchhhHHHHHHHHHHHHHHHHhhhhHhHHHHHHHhhc--CC-CcceeecccccchhHH
Confidence 9999999985 59999999999999999999999999987643 22 3589999999999975
No 3
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=8.1e-56 Score=440.29 Aligned_cols=196 Identities=27% Similarity=0.332 Sum_probs=160.6
Q ss_pred CceEEEEeChHHHHHHHHHcCC--CCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC----CCccCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSG--GKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ----DWNASNP 77 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~--~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~----~w~~~~p 77 (220)
|++||||||||+|++||++|++ +.+ ++. +|||+|+ +|+||||+|||++|++|++|. .|+..
T Consensus 1 Mk~LiIAEKPSvAk~IA~aL~~~~g~~-~k~--------~gy~eg~--~~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~~-- 67 (987)
T PRK14724 1 TKTLVIAEKPSVAQDIVRALTPVAGKF-EKH--------DEHFESD--SYVVTSAVGHLVEIQAPEEFDVKRGKWSFA-- 67 (987)
T ss_pred CCEEEEEeCHHHHHHHHHHhhhccCCC-cCC--------CceecCC--CEEEEecccccccCCChhhcccccCCcccc--
Confidence 5789999999999999999952 112 222 5788887 899999999999999999873 56543
Q ss_pred CCCCCCCceec-----cCCCcHHHHHHHHHHh--ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCc
Q 048704 78 LDLFQAPVHKA-----ESNPKVHICRHLNQEA--RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSV 150 (220)
Q Consensus 78 ~~l~~~p~~~~-----~~~~~~~~~~~lk~~~--~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~ssl 150 (220)
++|++|. ....+.++++.|++++ +++|+||||||||||||+|+|+|++++++.+.+.+++++|+|||++
T Consensus 68 ----~LPiiP~~f~~~~~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~~~~~kpv~Rlw~ssl 143 (987)
T PRK14724 68 ----NLPVIPPYFDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAKGGLGKPVKRLWLQSM 143 (987)
T ss_pred ----ccccCCccceeeeccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCcccccCCCceEEEEEccC
Confidence 3555543 2344578999999999 4678999999999999999999999998621111379999999999
Q ss_pred CHHHHHHHHhcCCCCCc--chHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 151 TEKDILKAMGNLVEPNR--NEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 151 t~~~I~~A~~nl~~~~~--~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
|+++|++||+||+++++ +|++||+||+++|||||||+||++|+..+.. +++ .++|+||||||||.+
T Consensus 144 T~~aI~~af~nlr~~~~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~-~~~--~~lSvGRVQTPtL~l 211 (987)
T PRK14724 144 TPQAIRDGFDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRD-GGF--FLTTVGRVQTPTLSL 211 (987)
T ss_pred CHHHHHHHHhCCCCchhhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhc-CCc--ceeccccchhHHHHH
Confidence 99999999999999984 9999999999999999999999999854322 221 378999999999975
No 4
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.3e-55 Score=429.66 Aligned_cols=202 Identities=29% Similarity=0.369 Sum_probs=171.8
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcc-cccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLY-TRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~-~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
.||||||||+|++||++||++..+ .+..++++|+|. .+|+ +++|+|+.|||++|++|++|++|..|++..+|+.+
T Consensus 2 ~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~~g~~~y~~~--~~g~--~~~v~~~~GHl~~l~~P~~y~~w~~~~~~~l~~~~ 77 (740)
T PRK07220 2 HLIITEKNIAARRIAQILAPKKPKKTRVSGVDVYRYE--DNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDARDLIDAE 77 (740)
T ss_pred eEEEEeCHHHHHHHHHHhCCCCccccccCCcceeEEe--cCCC--CEEEEEeCcccccCCCCccccccCCCChhHcCCcc
Confidence 599999999999999999854322 234566666553 1455 89999999999999999999889888766676655
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE 164 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~ 164 (220)
+.. ...+.++++.|++++++||+||||||||||||+|||+|+++++..+ +.++++|+|||++|+++|++||+||++
T Consensus 78 ~~~--~~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~~--~~~~~~R~~fs~iT~~~I~~A~~n~~~ 153 (740)
T PRK07220 78 IIT--TPTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVN--PDIKFDRVRYSAITKKEIERAFSNPVE 153 (740)
T ss_pred eEe--cCCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHhcC--CCCceEEEEEccCCHHHHHHHHhCCCC
Confidence 443 2456889999999999999999999999999999999999998642 246999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 165 PNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 165 ~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+|.+|++||+|||++||+||||+||++|+.+++.. +.++|+||||||||.|
T Consensus 154 ~d~~l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~~----~~~lS~GRVQtptL~l 204 (740)
T PRK07220 154 VDFNLADAGHSRQVIDLVWGAALTRYISLAAGRLG----KMFLSVGRVQSPTLAL 204 (740)
T ss_pred CChhHHHHHHHHHHHHHHhchhcCHHHHHHHHhhC----CccccccccchhhhHH
Confidence 99999999999999999999999999999876421 2479999999999975
No 5
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.8e-54 Score=427.83 Aligned_cols=198 Identities=27% Similarity=0.358 Sum_probs=167.5
Q ss_pred eEEEEeChHHHHHHHHHcCCCCc--ccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC--CCCCC
Q 048704 6 VLMVAEKPSIALSIATVLSGGKL--YTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN--PLDLF 81 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~--~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~--p~~l~ 81 (220)
.||||||||+|++||++||++.. .++.+++.+|.| + +.+|||+.|||++|++++.|++|+..+ |..++
T Consensus 2 ~LiIAEKPSvAk~IA~~L~~~~~~~~k~~g~~~~y~~-----~---~~~vt~~~GHLl~l~y~~~yk~W~~~~LPP~~l~ 73 (936)
T PRK14973 2 HLIIAEKNIAANRIAQILAGKTKVQVKKDGGVSTYSF-----D---DTVVVGLRGHVVEVDFEPGYTNWRSEEHTPRSLI 73 (936)
T ss_pred EEEEEcCHHHHHHHHHHhCCCCccccccCCCcceEEe-----C---CCEEEEEcccceecccCcccCCCccccCChhhcc
Confidence 49999999999999999986421 234456655543 3 348999999999999999999998753 34455
Q ss_pred CCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhc
Q 048704 82 QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN 161 (220)
Q Consensus 82 ~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~n 161 (220)
+.++.+ ...+.++++.|++++++||.||||||||||||+|+|+|+++++..+ ++++++|+|||++|+++|++||+|
T Consensus 74 ~~~~~~--~~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~~--~~~~v~R~~fs~iT~~~I~~A~~n 149 (936)
T PRK14973 74 DADTIK--KPTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAVN--PKVPIDRARFSAITKEEIVTAFAE 149 (936)
T ss_pred Ccceee--cCchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhhcc--CCCceEEEEEccCCHHHHHHHHhC
Confidence 555433 2346789999999999999999999999999999999999998643 257999999999999999999999
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 162 LVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 162 l~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+++++.+|++||+||+++||++|||+||++|+.++..+ +.++|+||||||||.|
T Consensus 150 l~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~~~~g~----~~~lS~GRVQTPtL~l 203 (936)
T PRK14973 150 PTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGG----DNILSVGRVQSPTLAM 203 (936)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhcCC----CcceeeccccchHHHH
Confidence 99999999999999999999999999999999876321 3589999999999976
No 6
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=3.8e-54 Score=423.70 Aligned_cols=202 Identities=35% Similarity=0.415 Sum_probs=166.5
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcc-cccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLY-TRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~-~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
+||||||||+|++||++|+++..+ ++..++++|+|.+ +|+ +|+|||+.|||++|++|++|++|+..+|..+++.+
T Consensus 2 ~LiIaEKps~Ak~Ia~~L~~g~~~~~~~~g~~~~~~~~--~g~--~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l~~~~ 77 (822)
T PRK07219 2 ELIIAEKNNAARRIADILSGGKAKKKRVNGVPYYEFER--KGE--KWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDAD 77 (822)
T ss_pred EEEEEeCHHHHHHHHHHhcCCCcccccCCCcceEEecC--CCC--eEEEEEecCcccccCCchhcCCcCcCChhhccccc
Confidence 799999999999999999654332 3445666776632 354 89999999999999999999999876544334333
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE 164 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~ 164 (220)
+.+ ...+.++++.|++++++||+||||||||||||+|||+|++++.... .++++|+|||++|+++|++||+||++
T Consensus 78 ~~~--~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~~---~~~v~R~~fs~iT~~~I~~A~~n~~~ 152 (822)
T PRK07219 78 PVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREVC---QVPVKRARFSSLTKKEIRKAFENPDE 152 (822)
T ss_pred eee--cCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhcC---CCceeEEEEccCCHHHHHHHHhCccc
Confidence 222 2356789999999999999999999999999999966655555321 57999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 165 PNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 165 ~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+|.+|++||+||+++||+||||+||++|+.+++.+. ..++|+||||||||.|
T Consensus 153 ~d~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~---~~~lS~GRVQtPtL~l 204 (822)
T PRK07219 153 IDFNLADAGEARQIIDLYWGAALTRFLSLSVRQLGR---WDFLSVGRVQTPTLAF 204 (822)
T ss_pred CCHHHHHHHHHHHHHHHHhhhhhCHHHHHHHHhccc---cCccccccccchhhHH
Confidence 999999999999999999999999999998864311 2589999999999976
No 7
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=1.2e-53 Score=411.33 Aligned_cols=189 Identities=26% Similarity=0.311 Sum_probs=159.9
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceec-CCcceEEEEccccceecccCCCCC----CCCccCCCCCC
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFL-GSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLDL 80 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~l 80 (220)
.||||||||+|++||++||.+ +++ +|||+ |+ +|+|+|+.|||++|++|++| ++|+..+
T Consensus 2 ~LiIaEKPs~Ak~Ia~~L~~~---~~~--------~gy~e~g~--~~~V~~~~GHl~~L~~p~~~~~~~~~W~~~~---- 64 (660)
T TIGR01056 2 TLVLCEKPSQARDLATVLAKK---KKG--------NGYLEIGV--GGFVTWAVGHLVELAEPEEYDEKYKNWRTYD---- 64 (660)
T ss_pred eEEEEeCHHHHHHHHHHhCCC---cCC--------CCcEEECC--cEEEEeCchhhhcCCChhhcccccCccccCC----
Confidence 699999999999999999863 222 57787 77 89999999999999988754 5676533
Q ss_pred CCCCcee-----ccCCCcHHHHHHHHHHhc--cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHH
Q 048704 81 FQAPVHK-----AESNPKVHICRHLNQEAR--GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEK 153 (220)
Q Consensus 81 ~~~p~~~-----~~~~~~~~~~~~lk~~~~--~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~ 153 (220)
+|+.| .....+.++++.|+++++ +||.||+|||||||||+|||+|+++++.. +..+++|+|||++|++
T Consensus 65 --lp~~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~~---~~~~v~Ri~f~~iT~~ 139 (660)
T TIGR01056 65 --LPLEPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKVT---DKVTIKRLWISSLVDS 139 (660)
T ss_pred --CCcccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCCC---CCCceEEEEeccCCHH
Confidence 33322 123457889999999999 99999999999999999999999999862 1248999999999999
Q ss_pred HHHHHHhcCCCC--CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 154 DILKAMGNLVEP--NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 154 ~I~~A~~nl~~~--~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+|++||+||+++ +.+|++||+||+++||++|||+||++|+.++.. ++ +.++|+||||||||.+
T Consensus 140 ~I~~A~~n~~~~~~~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~--g~-~~~lS~GRVQtptL~l 204 (660)
T TIGR01056 140 SIRKAFKNLRPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREA--GN-DGVLSVGRVQTPTLAM 204 (660)
T ss_pred HHHHHHHcCCCchhhhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhc--CC-CCceecccchhhhhHH
Confidence 999999999997 569999999999999999999999999987643 22 3479999999999975
No 8
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=1.5e-53 Score=408.82 Aligned_cols=196 Identities=25% Similarity=0.277 Sum_probs=159.6
Q ss_pred EEeChHHHHHHHHHcCCCCc-ccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCcee
Q 048704 9 VAEKPSIALSIATVLSGGKL-YTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHK 87 (220)
Q Consensus 9 IaEKPs~Ak~ia~~L~~~~~-~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~~~ 87 (220)
||||||+|++||++||.+.. .++++++++|+|+ ++|+ +++||||.|||++|++|++ .+|..|+ +-.+|+.+
T Consensus 1 iAEKPs~A~~ia~~l~~~~~~~~~~~g~~y~~~~--~~g~--~~~Vt~~~GHl~~l~~p~~-~~~~~w~---~~~lP~~~ 72 (618)
T TIGR01057 1 IAEKPKVAAKIAGALSDGRVLKKSEYGVPYWEVR--RDGK--KIIVASAVGHLFGLHPKSR-GGYPVFD---IEWVPIFE 72 (618)
T ss_pred CCCChHHHHHHHHHhCCCCcccccCCCceEEEEe--cCCC--eEEEEEeccccccCCCccc-cCCCCCC---cccCceee
Confidence 79999999999999987421 1334454455543 2365 8999999999999999986 2333322 22466665
Q ss_pred ccC--CCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCC
Q 048704 88 AES--NPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEP 165 (220)
Q Consensus 88 ~~~--~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~ 165 (220)
... ..+.++++.|++++++||+||||||||||||+|+|+|+++++. .++++|+|||++|+++|++||+||++.
T Consensus 73 ~~~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~-----~~~v~Rl~~~~lt~~~I~~a~~nl~~~ 147 (618)
T TIGR01057 73 FDKGKGYVSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCG-----VERAKRMKFSTLTKQDIRRAYANPEEI 147 (618)
T ss_pred ecCCcccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc-----CCCceEEEEccCCHHHHHHHHhCcccC
Confidence 421 1235899999999999999999999999999999999999975 368999999999999999999999988
Q ss_pred CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 166 NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 166 ~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+.+|++||+||+++||++|||+||++|+.++...+ .+.++|+||||||||.|
T Consensus 148 ~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~--~~~~lS~GRVQtPtL~l 199 (618)
T TIGR01057 148 DYGMVDAGMARHILDWYWGINLSRALMEAIRAAAG--RWVILSAGRVQGPTLAF 199 (618)
T ss_pred CHhHHHHHHHHHHHHHHHhhhhhHHHHHHhhccCC--CcccccccccchhHHHH
Confidence 88999999999999999999999999998764322 13589999999999975
No 9
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.5e-52 Score=404.16 Aligned_cols=199 Identities=25% Similarity=0.288 Sum_probs=159.5
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCC-CCCCcc-CCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPA-YQDWNA-SNPLDLFQ 82 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~-y~~w~~-~~p~~l~~ 82 (220)
++||||||||+|++||++||.+...++.+++.+|+|. ++|+ +|+|+|+.|||++|++|+. |..+.. +.| .|.
T Consensus 2 ~~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~g~~~~e~~--~~g~--~~~V~~~~GHl~~L~~~~~~~~~~~~~~~p--~~~ 75 (670)
T PRK05776 2 YILVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVK--RDGK--KIVVAPAAGHLFGLHTKSKGFPVFDYEWKP--LYE 75 (670)
T ss_pred CEEEEEcCHHHHHHHHHHhCCCccccccCCCceEEEe--cCCC--CEEEEEecccCccCCCcccCCCCCCcCccc--ceE
Confidence 5899999999999999999853323343455555552 2355 8999999999999998874 321110 011 111
Q ss_pred CCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 83 APVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 83 ~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
+.+. ...++++++.|++++++||+||||||||||||+|||||+++++. .++++|+|||++|+++|++||+|+
T Consensus 76 --~~~~-~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~-----~~~v~R~~fs~iT~~~I~~A~~n~ 147 (670)
T PRK05776 76 --IDKG-SKYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLGD-----PKKAKRMKFSALTKSDIRRAFRNL 147 (670)
T ss_pred --eccC-cccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhCC-----CCCeeEEEEccCCHHHHHHHHhCc
Confidence 1110 12245899999999999999999999999999999999999984 468999999999999999999999
Q ss_pred CCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 163 VEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 163 ~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+++|.+|++||+||+++|||+|||+||++|+.+++..+ ...++|+||||||||.|
T Consensus 148 ~~~d~~l~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~g--~~~~lS~GRVQsptL~l 202 (670)
T PRK05776 148 ETLDYEMINAGIARHELDWLWGINVSRALMSSVRDASG--KRVILSAGRVQSPTLKY 202 (670)
T ss_pred cccchhHHHHHHHHHHHHHHHhHHHhHHHHHHhhhhcC--CccceecceecCchhhH
Confidence 99999999999999999999999999999998864332 13479999999999975
No 10
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=8.3e-51 Score=410.23 Aligned_cols=200 Identities=23% Similarity=0.258 Sum_probs=164.6
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-CC-CCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-PL-DLF 81 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-p~-~l~ 81 (220)
+++||||||||+|++||++||.++ .++.+++++|++.. |+ ..++|||+.|||++|..|++|.+|...+ |+ +.+
T Consensus 601 k~~LiIaEkPskAk~IA~~lg~~~-~r~~g~~~~ye~~~---~~-~~~~Vt~s~GHl~dL~~~~~y~g~~~~~~p~~P~y 675 (1176)
T PRK09401 601 KTTLLIVESPTKARTIANFFGRPS-RRRIGGLVVYETVT---GD-RILTITASKGHVYDLTTEIGYYGVLVKDGGFVPVY 675 (1176)
T ss_pred CCEEEEEcCHHHHHHHHHHhCCCc-cccCCCceeEEEec---CC-cEEEEEEeccccccCCCccccCcccccCCccccee
Confidence 579999999999999999998642 33456666666422 33 1348999999999999999998897643 21 111
Q ss_pred C------------------CCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704 82 Q------------------APVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV 142 (220)
Q Consensus 82 ~------------------~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v 142 (220)
. +|...+. ..++.++++.|++++++||+||||||||||||+|||+|+++++.. ++++
T Consensus 676 ~~~k~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~~----~~~i 751 (1176)
T PRK09401 676 DTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSPY----NSNI 751 (1176)
T ss_pred eeeccccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhccc----CCCE
Confidence 0 1111100 145678999999999999999999999999999999999999953 5789
Q ss_pred EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+|+|||++|+++|++||+|++++|.+|++||.||+++||++|||+||++|+.++ +..+|+||||||||.+
T Consensus 752 ~R~~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~-------~~~lSaGRVQTPtL~~ 821 (1176)
T PRK09401 752 KRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFG-------KRNLSAGRVQTPVLGW 821 (1176)
T ss_pred EEEEeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------ccCccccccccchhhh
Confidence 999999999999999999999999999999999999999999999999998764 2359999999999975
No 11
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=100.00 E-value=2.7e-51 Score=392.51 Aligned_cols=169 Identities=25% Similarity=0.278 Sum_probs=147.6
Q ss_pred EEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCce
Q 048704 7 LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVH 86 (220)
Q Consensus 7 LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~~ 86 (220)
||||||||+|++||++||. +++||||.|||++|+.|+.+..|+.. | .| .
T Consensus 1 LiIaEkps~a~~Ia~~lg~------------------------~~~Vt~~~GHl~~l~~~~~~~~~~~~-----~-~~-~ 49 (610)
T TIGR01051 1 LVIVESPAKAKTIKKYLGD------------------------EYEVEASMGHIRDLPKSRLGVDIEKD-----F-EP-E 49 (610)
T ss_pred CEEEeChHHHHHHHHHhCC------------------------CCEEEeccCeeccCCCcccCCChhhc-----C-ce-e
Confidence 7999999999999999974 57899999999999888666667531 2 12 1
Q ss_pred eccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE-EEEEecCcCHHHHHHHHhcCCCC
Q 048704 87 KAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV-HRARFSSVTEKDILKAMGNLVEP 165 (220)
Q Consensus 87 ~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v-~R~~~sslt~~~I~~A~~nl~~~ 165 (220)
.....++.++++.|++++++||+||||||||||||+|+|+|+++++. .+++ +|+|||++|+++|++||+||+++
T Consensus 50 ~~~~~~~~~~~~~i~~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~-----~~~~~~Rl~~s~lt~~~I~~a~~~l~~~ 124 (610)
T TIGR01051 50 YVVSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKP-----KDPVYKRIVFNEITKKAIRAALKNPREI 124 (610)
T ss_pred EEEcccHHHHHHHHHHHHhcCCEEEECCCCCcchhHHHHHHHHHhCC-----CCCCceEEEEccCCHHHHHHHHhCcccc
Confidence 12234678899999999999999999999999999999999999996 3455 99999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 166 NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 166 ~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+.+|++||.||+++||++|||+||++|+.++ ..+|+||||||||.|
T Consensus 125 ~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~~--------~~lSvGRVQtPtL~l 170 (610)
T TIGR01051 125 DMNLVNAQQARRILDRLVGYTLSPLLWKKVA--------KGLSAGRVQSVALRL 170 (610)
T ss_pred chhHHHHHHHHHHHHHHHhHhhhHHHHHhhc--------CCCCcceehHHHHHH
Confidence 9999999999999999999999999998542 249999999999975
No 12
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.1e-50 Score=392.31 Aligned_cols=176 Identities=24% Similarity=0.242 Sum_probs=148.5
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA 83 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~ 83 (220)
|++||||||||+|++||++||. +|+|+||.|||++|..| +..|...+ .|.
T Consensus 2 ~~~LiIaEKPs~ak~Ia~~lg~------------------------~~~V~~~~GHl~~l~~~--~~~~~~~~---~~~- 51 (675)
T PRK06599 2 AKKLVIVESPAKAKTIKKYLGK------------------------DYKVLASFGHVRDLPKK--KGGVDPDN---DFA- 51 (675)
T ss_pred CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEecccchhcCCcc--ccCCCccc---CCC-
Confidence 3789999999999999999974 67899999999999543 33554322 222
Q ss_pred CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
+.....+++.++++.|++++++||+||||||||||||+|||+|+++++... ...++++|+|||++|+++|++||+|++
T Consensus 52 -~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~-~~~~~v~Rl~~s~lt~~~I~~a~~n~~ 129 (675)
T PRK06599 52 -PKYEIIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEAK-LKDKNVKRVVFNEITKKAVQEAIENPR 129 (675)
T ss_pred -ceEEECCcHHHHHHHHHHHHhhCCEEEECCCCCcchHHHHHHHHHHHHhhc-CCCCCeeEEEEccCCHHHHHHHHhCcc
Confidence 111223457889999999999999999999999999999999999995100 015789999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+++.+|++||+||+++||++|||+||++|+.++ ..+|+||||||||.+
T Consensus 130 ~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~lS~GRVQtPtL~l 177 (675)
T PRK06599 130 DIDMDLVDAQQARRALDYLVGFKLSPLLWKKVR--------RGLSAGRVQSVALRL 177 (675)
T ss_pred cCCHHHHHHHHHHHHHHHHhhhhhCHHHHHhcc--------CCCccceeHHHHhHH
Confidence 999999999999999999999999999998763 249999999999975
No 13
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.3e-50 Score=383.08 Aligned_cols=178 Identities=30% Similarity=0.355 Sum_probs=154.3
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
+.|||||||++||+||++||. +|+|+|+.|||++|.+|++++.|...+.. .|...
T Consensus 1 ~~LiIvEsPskAk~Ia~~Lg~------------------------~~~V~as~GHi~dl~~~~~~~~~~~~~~~-~~~~~ 55 (570)
T COG0550 1 KRLIIVESPSKAKTIAKYLGK------------------------GYVVTASVGHLRDLPFPEEYKGWVDVDLP-IFEPK 55 (570)
T ss_pred CeEEEEeCHHHHHHHHHhcCC------------------------CcEEEEcccccccCCChhhccCCcCCccc-ccccc
Confidence 469999999999999999986 58999999999999999998888764311 11111
Q ss_pred ceeccCCC-cHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 85 VHKAESNP-KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 85 ~~~~~~~~-~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
+. .... +.++++.|+.++++||.||||||||||||+|||||+++++..+ ..+++|||||++|+++|++||+|++
T Consensus 56 ~~--~~~~~k~~~v~~lk~~ak~ad~v~lAtD~DREGE~I~~~i~~~l~~~~---~~~~~R~~F~eiT~~aI~~A~~~p~ 130 (570)
T COG0550 56 YI--IKPGKKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKN---PSKVKRVVFSEITKKAILSAFKNPR 130 (570)
T ss_pred ee--ccchhhHHHHHHHHHHhccCCEEEECCCCCcchHHHHHHHHHHhCccC---CCceeEEEEecCCHHHHHHHHhCch
Confidence 11 1122 6888999999999999999999999999999999999999842 1479999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
..|.+|++|++||+++|||+|+|+||++|+.+++ .++|+||||||||.+
T Consensus 131 ~id~~lv~A~~aR~~lD~lvG~~lSr~l~~~~~~-------~~LSaGRVQSpaL~l 179 (570)
T COG0550 131 EIDMNLVDAQLARRILDRLVGYNLSRLLWKKLKR-------GVLSAGRVQSPALRL 179 (570)
T ss_pred hhchHHHHHHHHHHHHHHHhhhhhhHHHHHhhcc-------CCCCCccccchhhhh
Confidence 9999999999999999999999999999998753 179999999999975
No 14
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=9.9e-51 Score=391.28 Aligned_cols=173 Identities=23% Similarity=0.273 Sum_probs=146.3
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA 83 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~ 83 (220)
|++||||||||+|++||++||. +|+|+||.|||++|..| .+. .+|.+.+.
T Consensus 2 m~~LiIaEkps~a~~ia~~lg~------------------------~~~V~~~~GHl~~l~~~-~~~----~~~~~~~~- 51 (650)
T PRK05582 2 MKKLVIVESPAKAKTIEKYLGK------------------------NYKVVASMGHIRDLPKS-QLG----IDIENNFE- 51 (650)
T ss_pred CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCchhcCCCc-cCC----CCcccCCc-
Confidence 4789999999999999999964 68999999999999865 210 11111111
Q ss_pred CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
|.. .....+.++++.|++++++||+||||||||||||+|||+|+++++.. .++++|+|||++|+++|++||+||+
T Consensus 52 ~~~-~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~----~~~~~R~~~s~lt~~~I~~a~~nl~ 126 (650)
T PRK05582 52 PKY-ITIRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGLD----EKEKNRIVFNEITKDAIKNAFKNPR 126 (650)
T ss_pred eee-EECCcHHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhCCC----CCCceEEEEcccCHHHHHHHHhCcc
Confidence 110 11235678999999999999999999999999999999999999862 3678999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+++.+|++||+||+++||++|||+||++|+.++ ..+|+||||||||.+
T Consensus 127 ~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~ls~GRVQtPtL~l 174 (650)
T PRK05582 127 KIDMNLVDAQQARRILDRLVGYKLSPLLWKKVK--------KGLSAGRVQSVALKL 174 (650)
T ss_pred cccHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------CCCccccchHhHHHH
Confidence 999999999999999999999999999998653 249999999999975
No 15
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=100.00 E-value=1.8e-49 Score=400.63 Aligned_cols=200 Identities=23% Similarity=0.254 Sum_probs=163.4
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-CC-CC-
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-PL-DL- 80 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-p~-~l- 80 (220)
+++|||||||++|++||++||.++ .++.+++.+|+|.+ |+ ..++|||+.|||++|..|+.|.+|...+ |+ +.
T Consensus 601 k~~LiIvEsP~kAk~Ia~~lg~~~-~r~~~g~~~yE~~~---g~-~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y 675 (1171)
T TIGR01054 601 KTALLVVESPNKARTIARFFGKPS-VRKIGGSVVYEVPV---GD-LILMITASGGHVFDLVTDKGFHGVLVENGRYVPVY 675 (1171)
T ss_pred CceEEEEcChHHHHHHHHHhCCCc-ccccCCcceEEEec---CC-eeEEEEEeCceeeeCCCccccCcccccCCcccccc
Confidence 579999999999999999998743 23336667777643 33 2459999999999999998777776532 11 11
Q ss_pred ------------CC-----CCceec-cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704 81 ------------FQ-----APVHKA-ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV 142 (220)
Q Consensus 81 ------------~~-----~p~~~~-~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v 142 (220)
|+ +|-..+ ...++.++++.|++++++||+||||||||||||+|||+|+++++.. ++++
T Consensus 676 ~~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~~----~~~i 751 (1171)
T TIGR01054 676 TSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPY----NPNV 751 (1171)
T ss_pred cccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhccc----CCCe
Confidence 10 111100 1245688999999999999999999999999999999999999753 5689
Q ss_pred EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+|+|||++|+++|++||+|++++|.+|++||.||+++||++|||+||++|+.++ +..+|+||||||||.+
T Consensus 752 ~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~-------~~~lSaGRVQTPtL~l 821 (1171)
T TIGR01054 752 KRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFN-------KRWLSAGRVQTPVLGW 821 (1171)
T ss_pred EEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhc-------CCCcccceecchhhHH
Confidence 999999999999999999999999999999999999999999999999998653 2469999999999965
No 16
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=3.3e-49 Score=389.71 Aligned_cols=174 Identities=22% Similarity=0.271 Sum_probs=151.3
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA 83 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~ 83 (220)
|+.|||||||++|++|+++||. +|+|+|+.|||++| |+.+.+|...++ |.
T Consensus 2 ~~~LvIvEsP~kak~I~~~Lg~------------------------~~~V~as~GHl~dL--p~~~~~~~~~~~---f~- 51 (860)
T PRK06319 2 KKSLIIVESPAKIKTLQKLLGE------------------------GFIFASSLGHIVDL--PAKEFGIDIEND---FE- 51 (860)
T ss_pred CCeEEEEeCHHHHHHHHHHhCC------------------------CCEEEecccCcccC--CcccCCcCCCCC---CC-
Confidence 3789999999999999999975 68999999999999 666556764322 22
Q ss_pred CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
|.. ....++.++++.|++++++||.||||||||||||+|+|||+++++. +++++|+|||++|+++|++||+|++
T Consensus 52 p~y-~~~~~k~~~~~~ik~~~k~ad~iilAtDpDREGE~I~~~i~~~l~~-----~~~v~Rv~f~~iT~~aI~~A~~~~~ 125 (860)
T PRK06319 52 PDY-QILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLPK-----NTKIQRISFNAITKGAVTEALKHPR 125 (860)
T ss_pred cce-EECccHHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHcCC-----CCCeeEEEEccCCHHHHHHHHhCcc
Confidence 211 1234678999999999999999999999999999999999999975 5799999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++|.+|++|++||+++|||||||+||++|+.++.. ..+|+||||||||.+
T Consensus 126 ~~d~~l~~A~~aR~~lD~lvG~nlSr~l~~~~~~~------~~lSaGRVQsp~L~l 175 (860)
T PRK06319 126 EIDMALVNAQQARRLLDRIVGYKISPILSRKLQRR------SGVSAGRVQSVALKL 175 (860)
T ss_pred ccCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhccC------CCCcCCccchhhhHH
Confidence 99999999999999999999999999999887531 249999999999964
No 17
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.9e-49 Score=387.89 Aligned_cols=177 Identities=23% Similarity=0.210 Sum_probs=149.2
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA 83 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~ 83 (220)
|+.|||||||++|++|+++||. +|+|+|+.|||++|..|+.+- +|...|..
T Consensus 2 ~~~LiIvEsPskAk~I~~~Lg~------------------------~y~V~as~GHi~dL~~~~~~v-----d~~~~f~~ 52 (780)
T PRK08780 2 SKHLVIVESPAKAKTINKYLGK------------------------DFTVLASYGHVRDLVPKEGAV-----DPENGFAM 52 (780)
T ss_pred CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCCcccCCCcccCC-----ChhhCCce
Confidence 3789999999999999999975 689999999999998876541 11111221
Q ss_pred CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
.+. ...++.++++.|++++++||.||+|||||||||+|+|||+++++..+..+.++++|+|||++|+++|++||+|++
T Consensus 53 ~y~--~~~~k~~~~~~lk~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~~~~~~~~v~Ri~f~eiT~~aI~~A~~n~r 130 (780)
T PRK08780 53 RYD--LIDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKDKPMQRVVFTEITPRAIKEAMAKPR 130 (780)
T ss_pred EEE--EcCchHHHHHHHHHHHHhCCEEEECCCCCcccHHHHHHHHHHhcccccCCCCceEEEEEccCCHHHHHHHHhCCC
Confidence 111 124567899999999999999999999999999999999999974211124689999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++|++|++|++||+++|||+|||+||++|..++ ..+|+||||||||.+
T Consensus 131 ~~d~~l~~A~~aRr~lD~lvG~~lSr~l~~~~~--------~~lSaGRVQspaL~l 178 (780)
T PRK08780 131 DIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRM 178 (780)
T ss_pred cCcHhHHHHHHHHHHHHHhcCeeecHHHHHhhC--------CCCcccccHHHHHHH
Confidence 999999999999999999999999999998663 249999999999975
No 18
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=5.7e-49 Score=388.33 Aligned_cols=177 Identities=26% Similarity=0.259 Sum_probs=150.5
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCC-----CCCCccC----
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPA-----YQDWNAS---- 75 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~-----y~~w~~~---- 75 (220)
+.|||||||++|++|+++||. +|+|+|++|||++|..|+. |+.|...
T Consensus 2 ~~LvIvEkP~kak~I~~~Lg~------------------------~~~V~~s~GHi~dL~~~~~~~~~~~k~~~w~~l~i 57 (859)
T PRK07561 2 KSLVIVESPAKAKTINKYLGS------------------------DYVVKASVGHIRDLPTSASSVPAKEKGALWARMGV 57 (859)
T ss_pred CEEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCChhhCCCccccChhhhhhchHhhcCc
Confidence 579999999999999999974 6899999999999998544 4433311
Q ss_pred CCCCCCCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHH
Q 048704 76 NPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDI 155 (220)
Q Consensus 76 ~p~~l~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I 155 (220)
+|.+.|.. ......+++++++.|++++++||+||||||||||||+|+|||+++++.. +++++|+|||++|+++|
T Consensus 58 ~~~~~f~~--~y~~~~~k~~~~~~lk~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~~----~~~v~Ri~f~~iT~~aI 131 (859)
T PRK07561 58 DPDHDFEA--LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGD----DVPVKRVVFNEITKNAI 131 (859)
T ss_pred CcccCcce--eEEECccHHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhCCC----CCCeEEEEEccCCHHHH
Confidence 12222221 1122346789999999999999999999999999999999999999842 57999999999999999
Q ss_pred HHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 156 LKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 156 ~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++||+|++++|.+|++|++||+++|||||||+||++|..++ ..+|+||||||||.+
T Consensus 132 ~~A~~n~~~~~~~l~~A~~aRr~lD~lvG~~lS~~l~~~~~--------~~lSaGRVQsp~L~l 187 (859)
T PRK07561 132 QEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRL 187 (859)
T ss_pred HHHHhCcccCCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------cCCCcccchhhhhHH
Confidence 99999999999999999999999999999999999998653 249999999999975
No 19
>PRK14701 reverse gyrase; Provisional
Probab=100.00 E-value=2.5e-48 Score=400.07 Aligned_cols=200 Identities=20% Similarity=0.216 Sum_probs=162.5
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-------
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN------- 76 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~------- 76 (220)
+++||||||||+|++||++||.++ .++.+++.+|++.. |+ +.++|||+.|||++|..|++|.+|...+
T Consensus 580 ~~~LiIaEkPs~Ak~IA~~lg~~~-~r~~g~~~~ye~~~---g~-~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y 654 (1638)
T PRK14701 580 KSALMIVESPNKARTIANFFGQPS-VRKIGDLVAYEVSI---GD-HMLIITASGGHVFDLVTNEGFHGVLINNNLFIPIY 654 (1638)
T ss_pred CCeEEEEeChHHHHHHHHHhCCCc-cccCCCcceEEEec---CC-cEEEEEEecceeccCCCccccCccccccCccCCcc
Confidence 579999999999999999998643 33356777776532 32 3689999999999999888775554321
Q ss_pred --------CCCCCCCCc----eec----cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCC
Q 048704 77 --------PLDLFQAPV----HKA----ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARR 140 (220)
Q Consensus 77 --------p~~l~~~p~----~~~----~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~ 140 (220)
+..+|+.+. .|. ...++.++++.|++++++||+||||||||||||+|||+|++++... ++
T Consensus 655 ~~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~~~----~~ 730 (1638)
T PRK14701 655 DSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLAPY----GP 730 (1638)
T ss_pred cccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhccC----CC
Confidence 112222110 110 1134577899999999999999999999999999999999998643 57
Q ss_pred cEEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 141 KVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 141 ~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
+++|+|||++|+++|++||+|++++|++|++||.||+++||++|||+||++|..++ +..+|+||||||||.|
T Consensus 731 ~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~-------~~~lS~GRVQTPtL~~ 802 (1638)
T PRK14701 731 NIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFE-------DRNLSAGRVQTPVLGW 802 (1638)
T ss_pred CeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhcc-------CCceeecccccchhhh
Confidence 89999999999999999999999999999999999999999999999999998753 2359999999999975
No 20
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=100.00 E-value=3e-48 Score=360.46 Aligned_cols=214 Identities=40% Similarity=0.622 Sum_probs=195.9
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCccccc---CCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRK---ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDL 80 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~---~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l 80 (220)
|+.|++|||+|+|+.+|.+|++|+...+. .++.+|+|+..+.|.+++.++|++.|||+++++|.+|..|..++|.++
T Consensus 1 ~~vl~vAekn~~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~l 80 (758)
T KOG1956|consen 1 MRVLCVAEKNSIAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDEL 80 (758)
T ss_pred CCcccccccchhhhhhhhhcCCCCcCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHHH
Confidence 47899999999999999999998765554 477888887666688899999999999999999999999999999899
Q ss_pred CCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHh
Q 048704 81 FQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMG 160 (220)
Q Consensus 81 ~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~ 160 (220)
|+.|+......+.+.+.+.|+++++.||.+|||||||||||+|||||++.|+..++ ...|.|++||+||+.+|+.|.+
T Consensus 81 f~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~~~--~~~V~RA~Fs~it~~~I~sA~~ 158 (758)
T KOG1956|consen 81 FDAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAVKR--LLQVRRARFSEITRSAIKSAAR 158 (758)
T ss_pred hhhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhhCc--cceeehhhhhcccHHHHHHHHh
Confidence 99998877667778899999999999999999999999999999999999998753 5679999999999999999999
Q ss_pred cCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 161 NLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 161 nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
||+++|+.+++|.+||+++|++||..|||++|+.+++++.-+...++|+|+||.|||-|
T Consensus 159 nlreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgf 217 (758)
T KOG1956|consen 159 NLREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGF 217 (758)
T ss_pred CccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceee
Confidence 99999999999999999999999999999999999988764556899999999999987
No 21
>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]
Probab=100.00 E-value=9.2e-45 Score=326.57 Aligned_cols=198 Identities=56% Similarity=0.871 Sum_probs=184.9
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA 83 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~ 83 (220)
+..|+||||||.|..||++|+.|..++++|...+++|+|.|.|.+..+.||++.||++.|++|+.|++|...+|-+||..
T Consensus 2 ~tvlmvaekpsla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf~a 81 (555)
T KOG1957|consen 2 KTVLMVAEKPSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELFSA 81 (555)
T ss_pred CceeEeecCchHHHHHHHHhhCCccccccCceeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHHHHhCC
Confidence 37899999999999999999998888888999999999999999889999999999999999999999999999999999
Q ss_pred CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704 84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~ 163 (220)
|..+++.++|.+..+-|...++.||.+++|.|+|+|||+|.+||++..+...+.....++|++||++|+++|.+|++||.
T Consensus 82 pt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~~~~tyra~fsaitekdi~~am~~lg 161 (555)
T KOG1957|consen 82 PTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRSDFKTYRAHFSAITEKDIKKAMRNLG 161 (555)
T ss_pred cchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhccCcceEEeeeeccccHHHHHHHHHhcC
Confidence 99988888999999999999999999999999999999999999998887665445678999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
.+|+|.+.|.+|||++|+.| + .++.||+|+||||||-|
T Consensus 162 ~p~~nea~svdarqeldlri---------l---------ds~~isygpcqtptlgf 199 (555)
T KOG1957|consen 162 EPDQNEALSVDARQELDLRI---------L---------DSSLISYGPCQTPTLGF 199 (555)
T ss_pred CCCcchhcccchhhhhhhhh---------h---------hhcceeecCCCCCccee
Confidence 99999999999999999988 1 24689999999999987
No 22
>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=100.00 E-value=4.5e-43 Score=282.08 Aligned_cols=149 Identities=38% Similarity=0.539 Sum_probs=120.3
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCC--CCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLD--LFQ 82 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~--l~~ 82 (220)
++||||||||+|++||++||++.. ++++..++ .+++++. +++|||+.|||++|++|++|..|....+.+ +++
T Consensus 1 ~~LiIAEKPs~Ak~ia~~L~~~~~--~~~~~~~~--~~~~~~~--~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~~ 74 (151)
T cd03362 1 MVLIIAEKPSVAKAIAKILGGGSK--KKGKGRYY--EFYGEGG--GYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFP 74 (151)
T ss_pred CEEEEecCHHHHHHHHHHhCCCCc--cCCccccc--ceecCCC--CEEEEEEhhHhhcccChHHhccCCCCCccccCCcC
Confidence 379999999999999999987532 22222233 3466666 899999999999999999998775433322 343
Q ss_pred CCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 83 APVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 83 ~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
.++......+++++++.|++++++||.||+|||||||||+|||+|+++++.. ++++++|||||++|+++|++||+||
T Consensus 75 ~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~---~~~~v~R~~fsslT~~~I~~A~~nl 151 (151)
T cd03362 75 APFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV---KRKPVKRAWFSSLTPKAIRRAFKNL 151 (151)
T ss_pred CceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC---CCCcEEEEEEccCCHHHHHHHHhcC
Confidence 3333333456789999999999999999999999999999999999999974 2579999999999999999999986
No 23
>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=100.00 E-value=1.9e-41 Score=269.95 Aligned_cols=142 Identities=39% Similarity=0.535 Sum_probs=115.7
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
++||||||||+|++||++||.+. .+++ ++++++ +++||||.|||++|++|++|..|....+..++..+
T Consensus 1 ~~LiIaEKPs~a~~ia~~L~~~~--~~~~--------~~~~~~--~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~ 68 (142)
T cd01028 1 KVLIIAEKPSKAKTIAKILGKGS--KKKG--------FYGEGG--GYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFE 68 (142)
T ss_pred CEEEEEeCHHHHHHHHHHhCCCc--ccCC--------ceecCC--CEEEEEEccccccCCCcccccccccCCchhhCCCC
Confidence 47999999999999999998742 2221 245565 89999999999999999999766443222223333
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
+......++.++++.|++++++||+||||||||||||+|||+|+++++.. +++++|+|||++|+++|++||+||
T Consensus 69 ~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~----~~~v~R~~fsslT~~~I~~A~~nl 142 (142)
T cd01028 69 PKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCD----NKPVKRAWFSEITPKAIREAFKNL 142 (142)
T ss_pred ceEEeCCcHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCCC----CCCeEEEEEccCCHHHHHHHHhCc
Confidence 33233456789999999999999999999999999999999999999972 579999999999999999999986
No 24
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=100.00 E-value=3e-39 Score=313.43 Aligned_cols=197 Identities=19% Similarity=0.208 Sum_probs=146.9
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeee-cceec---CCcceEEEEccccceecccCCCCCCCCccCC--CC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEF-DGMFL---GSHAYIKVTSVVGHVFRLDFPPAYQDWNASN--PL 78 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~-~~~~~---g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~--p~ 78 (220)
..|+|+|+|++.-++...|+.++ -+|-|.| ++.+. -+.+..+..++.||+|.|++- .|+.-. |.
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ 79 (805)
T PTZ00407 10 EKLVIVESPNKVIKVEGLLSDPK------VIPDWSFKQSHLRRIGTGAEKAVAMATTGHFMALKEI----TWSPQASSPA 79 (805)
T ss_pred hheeEEecCCceEEEeecccCCC------cCCCcccccccceeeccchHHHHHHhhcccceeehhe----ecccCCCCCc
Confidence 46999999999999999998742 3445555 23332 123467888999999998643 243211 10
Q ss_pred -------CCCCC-----Ccee--ccCCCcH--HHHH-HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCc
Q 048704 79 -------DLFQA-----PVHK--AESNPKV--HICR-HLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRK 141 (220)
Q Consensus 79 -------~l~~~-----p~~~--~~~~~~~--~~~~-~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~ 141 (220)
+-|+. .+.+ .....+. +++. .|++.+++||+||+|||||||||+|+|||+++++..+...+++
T Consensus 80 ~~~~~~~~~~~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~~~~~k~ 159 (805)
T PTZ00407 80 SVVGAGDEPFPSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLYPKLKVP 159 (805)
T ss_pred ccCCCCCCCCCCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhccccCCc
Confidence 11110 0011 1122233 5565 6999999999999999999999999999999998542212468
Q ss_pred EEEEEecCcCHHHHHHHHhcC--CCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 142 VHRARFSSVTEKDILKAMGNL--VEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 142 v~R~~~sslt~~~I~~A~~nl--~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++|+|||++|+++|++||+|+ ...+.+|++|++||+++|||||||+||++|... ...+|+||||||||.|
T Consensus 160 v~Rv~FseITk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~--------~~~lSaGRVQTPtL~L 231 (805)
T PTZ00407 160 FSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAAN--------SQMRSIGRVQTPALIL 231 (805)
T ss_pred ceEEEEccCCHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhc--------cCceeecccchHHHHH
Confidence 999999999999999999996 456779999999999999999999999998732 2469999999999975
No 25
>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=100.00 E-value=1e-37 Score=255.69 Aligned_cols=149 Identities=26% Similarity=0.312 Sum_probs=117.6
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCcc----------
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNA---------- 74 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~---------- 74 (220)
.+||||||||+|++||++||.+. .++.+++++|+|.+ ++ +.++|||+.|||++|++|++|.+|..
T Consensus 1 ~~LiIaEKPs~Ak~Ia~~L~~~~-~~~~~~~~~~e~~~---~~-~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~p~~~ 75 (170)
T cd03361 1 TALMIVESPNKARTIANFFGRPS-VRRLGGLVVYEVST---GD-GVLMITASGGHVYDLVTKEGGHGVVEDDGRYVPVYD 75 (170)
T ss_pred CeEEEEeChHHHHHHHHHhCCCc-ccccCCceeEEEec---CC-eEEEEEeCCCeeecCCCccCccCccccCCcceeeee
Confidence 37999999999999999998642 34446788888743 22 36789999999999999988765322
Q ss_pred ----CCC-CCCCC-----CCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEE
Q 048704 75 ----SNP-LDLFQ-----APVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVH 143 (220)
Q Consensus 75 ----~~p-~~l~~-----~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~ 143 (220)
+.| ..+|+ +|+.... ..+++++++.|+++++++|+||+|||||||||+|+|+|+++++.. +++++
T Consensus 76 ~~~~c~pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~----~~~v~ 151 (170)
T cd03361 76 SIKRCRDCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPY----NKNIK 151 (170)
T ss_pred EeeccCCcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccC----CCCeE
Confidence 111 12332 3333222 245688999999999999999999999999999999999999863 46899
Q ss_pred EEEecCcCHHHHHHHHhcC
Q 048704 144 RARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 144 R~~~sslt~~~I~~A~~nl 162 (220)
|+|||++|+++|++||+||
T Consensus 152 R~~fs~it~~~I~~a~~n~ 170 (170)
T cd03361 152 RAEFHEVTRRAILEALRNP 170 (170)
T ss_pred EEEEecCCHHHHHHHHhCc
Confidence 9999999999999999986
No 26
>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=100.00 E-value=2.2e-37 Score=241.31 Aligned_cols=123 Identities=27% Similarity=0.355 Sum_probs=105.2
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
|+||||||||+|++||++||. +|+||||.|||++|.+|++|..|.. .| +..+
T Consensus 1 ~~LiIaEKp~~a~~ia~~Lg~------------------------~~~v~~~~GHl~~l~~p~~~~~~~~-~~---~~~~ 52 (123)
T cd03363 1 KKLVIVESPAKAKTIKKYLGK------------------------EYEVLASVGHIRDLPKKGLGVDGED-DG---FEPK 52 (123)
T ss_pred CEEEEEeCHHHHHHHHHHhCC------------------------CcEEEeccCccccCCCcccCCChhc-cC---cCce
Confidence 369999999999999999974 5789999999999999999865432 12 1111
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
+ ....++.++++.|+++++++|+||+|||||||||+|+++|+++++. +.+++|+|||++|+++|++||+||
T Consensus 53 ~--~~~~~~~~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~~-----~~~v~Rl~~sslt~~~I~~A~~n~ 123 (123)
T cd03363 53 Y--VVIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLKL-----KKNVKRVVFNEITKEAIKEALKNP 123 (123)
T ss_pred E--EECccHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcCC-----CCCeEEEEEccCCHHHHHHHHhCc
Confidence 1 1234567899999999999999999999999999999999999986 578999999999999999999986
No 27
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.1e-34 Score=277.10 Aligned_cols=199 Identities=23% Similarity=0.250 Sum_probs=160.5
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC-------CC----
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ-------DW---- 72 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~-------~w---- 72 (220)
+..|+|+|+|++|++||+++|.++ .++-++..+|+-.- |+ .-.+||++.||+++|...+.+- +|
T Consensus 617 kt~L~IVESPnKARTIA~FFgrPS-~R~~~~~~vYEv~~---gD-~vL~ItAS~GHv~DLvt~~g~hGvl~~~~~~vPvY 691 (1187)
T COG1110 617 KTALMIVESPNKARTIASFFGRPS-VRRLGGGVVYEVAI---GD-LVLTITASGGHVFDLVTEPGVHGVLVKDGKYVPVY 691 (1187)
T ss_pred hceEEEEeCChHHHHHHHHhCCcc-eeeeCCeeEEEEec---CC-eEEEEEecCCeeEEeecccccceeeccCCceEehH
Confidence 468999999999999999999753 23337777776521 33 2468999999999997665431 11
Q ss_pred ---ccCC-CCCC-----CCCCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704 73 ---NASN-PLDL-----FQAPVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV 142 (220)
Q Consensus 73 ---~~~~-p~~l-----~~~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v 142 (220)
+.|. -... ..+|.+... ..++...++.|++++-.+|+|+||||||.|||-|||+|..++... +..+
T Consensus 692 ~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~Py----~~ni 767 (1187)
T COG1110 692 DTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRPY----NPNV 767 (1187)
T ss_pred HHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCcC----CCce
Confidence 0110 0000 124544432 356788999999999999999999999999999999999999975 6789
Q ss_pred EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceecc
Q 048704 143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLIC 218 (220)
Q Consensus 143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~ 218 (220)
+|+.|+++|+.+|.+|++|+++.|+||+.|+..|++.|+.|||.||+.++..+. +..+|+||||||+|-
T Consensus 768 kR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~-------~~nLsAGRVQTPVLG 836 (1187)
T COG1110 768 KRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFN-------NKNLSAGRVQTPVLG 836 (1187)
T ss_pred eEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhC-------ccCccccccccccce
Confidence 999999999999999999999999999999999999999999999999998763 456999999999984
No 28
>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Probab=99.94 E-value=1.5e-27 Score=175.80 Aligned_cols=71 Identities=25% Similarity=0.257 Sum_probs=66.3
Q ss_pred EEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704 142 VHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF 219 (220)
Q Consensus 142 v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~ 219 (220)
++|+|||++|+++|++||+|++|.+.+|++||+||+++||++|||+||++|+.+++ .++|+||||||||.+
T Consensus 1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~-------~~ls~GRVQtptL~l 71 (89)
T smart00436 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRK-------GVLSAGRVQTPTLGL 71 (89)
T ss_pred CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCC-------CCcceecchHHHHHH
Confidence 57999999999999999999999888999999999999999999999999998752 379999999999975
No 29
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair 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 2.7.7.6 from EC 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.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=99.94 E-value=6.1e-27 Score=175.69 Aligned_cols=99 Identities=34% Similarity=0.499 Sum_probs=85.6
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCc
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPV 85 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~ 85 (220)
+|||+|||++|++|+++|++ . ++.|+|+.||++++..|+.|..
T Consensus 1 ~liIvE~ps~a~~i~~~l~~---------------------~--~~~v~~~~Ghl~~~~~~~~~~~-------------- 43 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGG---------------------E--EYIVIATSGHLLELAKPEDYDP-------------- 43 (100)
T ss_dssp EEEEESSHHHHHHHHHHSST---------------------T--TEEEEEESSSSEESTTSSHHHC--------------
T ss_pred CEEEEeCHHHHHHHHHHcCC---------------------C--CEEEEEeCCccccccccccccc--------------
Confidence 58999999999999999973 1 5899999999999999988632
Q ss_pred eeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCc-EEEEEecCc
Q 048704 86 HKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRK-VHRARFSSV 150 (220)
Q Consensus 86 ~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~-v~R~~~ssl 150 (220)
..+.+.++.|+++++++|+||+|||||||||.|+++|+++++... .. ++|+|||++
T Consensus 44 -----~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~~----~~~~~R~~~~~i 100 (100)
T PF01751_consen 44 -----KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKNN----PKLIKRVWFSSI 100 (100)
T ss_dssp -----HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHHS----HHHTTEEEEESS
T ss_pred -----ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHhC----CCcCCEEEEecC
Confidence 245788999999999999999999999999999999999999852 22 699999985
No 30
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.95 E-value=7.2e-09 Score=73.03 Aligned_cols=73 Identities=29% Similarity=0.376 Sum_probs=57.0
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
+.|+|+|.|.-|..+.++++. +..+.++.||+..
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~------------------------~~~~~~~~G~~~~---------------------- 34 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGF------------------------GGNVVALGGHLLK---------------------- 34 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCC------------------------CEEEEEEeeeecH----------------------
Confidence 469999999999999998642 3567777899721
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
.+.++.|++.... ++||+|+|+|+||+.+++++.+++..
T Consensus 35 ---------~~~~~~l~~~~~~-~~Iii~~D~D~~G~~~~~~i~~~l~~ 73 (76)
T smart00493 35 ---------KEIIKLLKRLAKK-KEVILATDPDREGEAIAWKLAELLKP 73 (76)
T ss_pred ---------HHHHHHHHHHhcC-CEEEEEcCCChhHHHHHHHHHHHhhh
Confidence 2244455555544 78999999999999999999999875
No 31
>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=98.49 E-value=1.1e-06 Score=67.31 Aligned_cols=91 Identities=23% Similarity=0.185 Sum_probs=61.7
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
+.|||+|.|....+|.+. + .|+| .|.|. .||+--++. ..|. +
T Consensus 1 ~~lcVVE~~~Dv~~iE~~---~----------------~y~G---~Y~VL--~G~ispl~g---------i~p~---~-- 42 (112)
T cd01025 1 NKLCVVEEPRDVLAIEES---G----------------EYRG---LYHVL--GGLISPLDG---------IGPD---D-- 42 (112)
T ss_pred CEEEEECCHHHHHHHHhh---C----------------ccce---EEEEe--CCCcCCCCC---------CCcc---c--
Confidence 369999999999999885 2 1222 45555 677644321 1111 1
Q ss_pred ceeccCCCcHHHHHHHHHHhc--cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe
Q 048704 85 VHKAESNPKVHICRHLNQEAR--GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF 147 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~--~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~ 147 (220)
-.++.|.+.++ +.++||+||||++|||.+++.|.+.++.. ..++.|+-+
T Consensus 43 ----------l~i~~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~----~~kvsRlA~ 93 (112)
T cd01025 43 ----------LNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKLLKDF----GVKVTRLAQ 93 (112)
T ss_pred ----------cCHHHHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHHhHc----CCCeEEEEE
Confidence 11233444443 46899999999999999999999999974 567888754
No 32
>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=98.06 E-value=7.7e-05 Score=51.40 Aligned_cols=81 Identities=27% Similarity=0.293 Sum_probs=56.7
Q ss_pred eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCc
Q 048704 6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPV 85 (220)
Q Consensus 6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~ 85 (220)
.+||+|.++-+..+.+.... +..++++.||... |
T Consensus 2 ~viivEg~~d~~~l~~~~~~------------------------~~~~~~~~G~~~~---------~------------- 35 (83)
T cd00188 2 KLIIVEGPSDALALAQAGGY------------------------GGAVVALGGHALN---------K------------- 35 (83)
T ss_pred EEEEEecHHHHHHHHHHcCC------------------------CEEEEEEccEEcH---------H-------------
Confidence 68999999999999988532 2456677777653 0
Q ss_pred eeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE
Q 048704 86 HKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR 146 (220)
Q Consensus 86 ~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~ 146 (220)
....+....+....|++++|+|.+|+.+.+.+.+..... ...+.|++
T Consensus 36 ----------~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~~~----~~~~~~~~ 82 (83)
T cd00188 36 ----------TRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSL----GKKVRRLL 82 (83)
T ss_pred ----------HHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHHhc----CCceEEee
Confidence 011222333336899999999999999999999988752 34555554
No 33
>PRK00076 recR recombination protein RecR; Reviewed
Probab=97.88 E-value=0.00025 Score=59.44 Aligned_cols=109 Identities=22% Similarity=0.225 Sum_probs=72.9
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
.+|||+|.|.-..+|.+. + .|+| .|-|.. |||--++. ..|. ++.
T Consensus 79 ~~icVVE~~~Dv~aiE~s---~----------------~y~G---~YhVL~--G~ispl~g---------i~p~---~l~ 122 (196)
T PRK00076 79 SLICVVESPADVLAIERT---G----------------EYRG---LYHVLG--GLLSPLDG---------IGPE---DLN 122 (196)
T ss_pred CEEEEECCHHHHHHHHhh---C----------------cCce---EEEEec--CCcCCCCC---------CCcc---ccC
Confidence 579999999999999885 2 1222 455543 66643321 1121 111
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHHHH
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKDIL 156 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~I~ 156 (220)
-.+.++.+ + .++++||+||+|+.|||..+..|.+.++.. ..+|.|+-. .-+++..+.
T Consensus 123 --------i~~L~~ri-~--~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~----~ikvtRiA~GiP~G~~ley~D~~TL~ 187 (196)
T PRK00076 123 --------IDELLERL-D--GEVKEVILATNPTVEGEATAHYIARLLKPL----GVKVTRLAHGVPVGGELEYVDEGTLS 187 (196)
T ss_pred --------HHHHHHHH-h--CCCCEEEEeCCCCchHHHHHHHHHHHHHHc----CCCeeeeeeCCCCCcceeeCCHHHHH
Confidence 13344444 1 568999999999999999999999999863 467888643 345677788
Q ss_pred HHHhcCCC
Q 048704 157 KAMGNLVE 164 (220)
Q Consensus 157 ~A~~nl~~ 164 (220)
+||++.+.
T Consensus 188 ~Al~~R~~ 195 (196)
T PRK00076 188 RALEGRRE 195 (196)
T ss_pred HHHHhCcC
Confidence 88877653
No 34
>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=97.44 E-value=0.00043 Score=50.03 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=33.3
Q ss_pred HHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE
Q 048704 96 ICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR 146 (220)
Q Consensus 96 ~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~ 146 (220)
.++.|++. .+.||++||+|+.|+.|.+.+.++++.. ...++|+.
T Consensus 37 ~~~~l~~~---~~~VIiltD~D~aG~~i~~~~~~~l~~~----~~~~~~~~ 80 (81)
T cd01027 37 TIELIKKA---YRGVIILTDPDRKGEKIRKKLSEYLSGP----VPEIKRAF 80 (81)
T ss_pred HHHHHHHh---CCEEEEEECCCHHHHHHHHHHHHHhccc----CCCeeecc
Confidence 34444443 6899999999999999999999999762 34466653
No 35
>PRK13844 recombination protein RecR; Provisional
Probab=97.01 E-value=0.014 Score=49.05 Aligned_cols=54 Identities=15% Similarity=0.202 Sum_probs=43.5
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE--------ecCcCHHHHHHHHhcCCC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR--------FSSVTEKDILKAMGNLVE 164 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~--------~sslt~~~I~~A~~nl~~ 164 (220)
++++||+||.|+-|||.-+..|.+.++. ..+|.|+= +.=+++..+.+||++.+.
T Consensus 138 ~v~EVIlAt~~t~EGe~Ta~yi~~~lk~-----~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~~ 199 (200)
T PRK13844 138 KIDEVILAISPTVEGETTAHFISQMIAK-----DIKISRIGFGVPFGGELEYLDQQTLLHAFNARTN 199 (200)
T ss_pred CCcEEEEeCCCCccHHHHHHHHHHHhcC-----CCcEEeeeecCcCCcceeecCHHHHHHHHHhCcC
Confidence 6899999999999999999999999985 35677763 234567788888887654
No 36
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.94 E-value=0.016 Score=48.65 Aligned_cols=53 Identities=17% Similarity=0.109 Sum_probs=41.8
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHHHHHHHhcC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKDILKAMGNL 162 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~I~~A~~nl 162 (220)
++.+||+||+|+-|||.-+..|.+.++.. ..++.|+=. .-.++..+.+||++.
T Consensus 134 ~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~----~ikvtRlA~GiP~G~~ley~D~~TL~~Al~~R 194 (195)
T TIGR00615 134 SVKEVILATNPTVEGEATALYIARLLQPF----GVKVTRIASGLPVGGDLEYADEVTLARALEGR 194 (195)
T ss_pred CCcEEEEeCCCCchHHHHHHHHHHHhhhc----CCcEEeeeecCCCCcceeecCHHHHHHHHHcC
Confidence 58999999999999999999999999853 467877642 334577777777654
No 37
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=96.67 E-value=0.04 Score=46.14 Aligned_cols=108 Identities=23% Similarity=0.192 Sum_probs=69.0
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
.+|+|+|-|.-..++.+. +. |+| .|-|. .|||--|+. ..|.
T Consensus 80 ~~icVVe~p~Dv~a~E~~---~~------------f~G-------~YhVL--~G~lspl~g---------igpe------ 120 (198)
T COG0353 80 SQLCVVEEPKDVLALEKT---GE------------FRG-------LYHVL--GGLLSPLDG---------IGPE------ 120 (198)
T ss_pred ceEEEEcchHHHHHHHHh---cc------------cCe-------eEEEe--cCccCcccC---------CCcc------
Confidence 579999999999999886 21 122 35553 456532211 1111
Q ss_pred ceeccCCCcHHHHHHHHHHhccC--CeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHH
Q 048704 85 VHKAESNPKVHICRHLNQEARGC--GHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKD 154 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~a--d~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~ 154 (220)
.--++.|.+.+.+- ++||+||+|--|||.-+..|.+.++.. ..+|.|+=. -=+++-.
T Consensus 121 ---------~l~i~~L~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI~~~l~~~----~ikvtRlA~GiPvGg~lEyvD~~T 187 (198)
T COG0353 121 ---------DLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIARLLKPL----GLKVTRLAQGVPVGGELEYVDEGT 187 (198)
T ss_pred ---------cccHHHHHHHHhcCCCceEEEecCCCccchHHHHHHHHHHhhc----CCeEEEEeecCccCCceecccHHH
Confidence 01123343434333 399999999999999999999999975 467888642 2245666
Q ss_pred HHHHHhcCCC
Q 048704 155 ILKAMGNLVE 164 (220)
Q Consensus 155 I~~A~~nl~~ 164 (220)
+.+||.+.++
T Consensus 188 L~~Al~~R~~ 197 (198)
T COG0353 188 LSRALEGRRK 197 (198)
T ss_pred HHHHHhcCcC
Confidence 7777766553
No 38
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=95.66 E-value=0.017 Score=41.13 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=23.7
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEE
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRA 145 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~ 145 (220)
..+||+|+|+|.+|+..+.++.+.+... ..+++|+
T Consensus 46 ~~~Vii~~D~D~~G~~~a~~i~~~l~~~----gi~v~~v 80 (81)
T PF13662_consen 46 VKEVIIAFDNDKAGEKAAQKIAKKLLPL----GIRVTRV 80 (81)
T ss_dssp -SEEEEEEESSHHHHHHHHHHHHHHG-------------
T ss_pred CceEEEEeCcCHHHHHHHHHHHHHHHhh----ccccccC
Confidence 5789999999999999999999987642 3456654
No 39
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=95.13 E-value=0.056 Score=42.38 Aligned_cols=67 Identities=15% Similarity=0.129 Sum_probs=45.0
Q ss_pred HHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC-cccCCC----Cc---EEE-EEecCcCHHHHHHHHhcCC
Q 048704 96 ICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF-QVNDAR----RK---VHR-ARFSSVTEKDILKAMGNLV 163 (220)
Q Consensus 96 ~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~-~~~~~~----~~---v~R-~~~sslt~~~I~~A~~nl~ 163 (220)
.++.|++.. +-..||+-||||+.||-|...+.+++.. .+.... .+ ..| .-+-++....+++|+++..
T Consensus 45 ~ie~i~~~~-~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~ 120 (127)
T COG1658 45 TIELIKKAQ-KYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP 120 (127)
T ss_pred HHHHHHHhh-ccCCEEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence 344454432 3457999999999999999999999987 211100 01 222 2344777888899988877
No 40
>PRK04031 DNA primase; Provisional
Probab=94.97 E-value=0.042 Score=50.78 Aligned_cols=67 Identities=25% Similarity=0.311 Sum_probs=47.6
Q ss_pred HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCcc
Q 048704 99 HLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRN 168 (220)
Q Consensus 99 ~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~~ 168 (220)
.++++++ .+.||+++|+|+-|+.|.+++++.++... -.+.| .-.-.-++++++|.+||.+..|..+-
T Consensus 203 ~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d~-VaraP-~G~dVE~ls~eeI~kAL~~~~p~~~~ 269 (408)
T PRK04031 203 TIIELSK-KKTVTAFLDGDRGGELILKELLQVADIDY-VARAP-PGKEVEELTKKEIAKALRNKVPVEQY 269 (408)
T ss_pred HHHHHhc-CCCEEEEECCCHHHHHHHHHHHhhcceeE-EecCC-CCCChhhCCHHHHHHHHHhcCCHHHH
Confidence 4556655 78999999999999999999998543110 00111 11235578899999999999987653
No 41
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=94.89 E-value=0.26 Score=39.68 Aligned_cols=74 Identities=22% Similarity=0.222 Sum_probs=50.8
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP 84 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p 84 (220)
..++|+|.|++-..+++.++.. ..-++++.|+.-.
T Consensus 19 ~~V~VvENp~Vf~~~~~~~~~~-----------------------~~pLVCt~G~p~~---------------------- 53 (152)
T PF09664_consen 19 GRVYVVENPAVFSALADELGAS-----------------------CPPLVCTSGQPSA---------------------- 53 (152)
T ss_pred CEEEEEecHHHHHHHHHhcCCC-----------------------CCeEEEcCCcHHH----------------------
Confidence 4599999999999999998652 2233444555311
Q ss_pred ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
.....++.| ...--.+..++|.|.||=.|+..+.+..+.
T Consensus 54 -------A~~~LL~~L---~~~g~~l~y~GDfDp~Gl~IA~~l~~r~~~ 92 (152)
T PF09664_consen 54 -------AARRLLDRL---AAAGARLYYSGDFDPEGLRIANRLIQRYGA 92 (152)
T ss_pred -------HHHHHHHHH---HhCCCEEEEecCCCHHHHHHHHHHHHHhCC
Confidence 012223333 232337999999999999999999998875
No 42
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. 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=94.38 E-value=0.19 Score=41.42 Aligned_cols=71 Identities=13% Similarity=0.100 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcc-----cCCCCc-EEEEEecCcCHHHHHHHHhcCCCC
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQV-----NDARRK-VHRARFSSVTEKDILKAMGNLVEP 165 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~-----~~~~~~-v~R~~~sslt~~~I~~A~~nl~~~ 165 (220)
.+.++.|+.+. +-.-||+-||||.-||-|=..|.+++.... +....+ -.-+=+-..++++|++|++++...
T Consensus 35 ~~~i~~i~~~~-~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~~ 111 (174)
T TIGR00334 35 DETINLIKKAQ-KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHEE 111 (174)
T ss_pred HHHHHHHHHHh-hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhccc
Confidence 45566666654 345699999999999999999999876321 000000 001345567899999999999753
No 43
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=92.91 E-value=0.19 Score=43.07 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=37.3
Q ss_pred HHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEec
Q 048704 101 NQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFS 148 (220)
Q Consensus 101 k~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~s 148 (220)
+..+..||-|+||||+||-|--++....+.+... -..+.||.+.
T Consensus 52 ~raaeGADlvlIATDaD~~GReLA~kf~eeLrg~----VGhiERmK~P 95 (290)
T COG4026 52 KRAAEGADLVLIATDADRVGRELAEKFFEELRGM----VGHIERMKIP 95 (290)
T ss_pred HHhhccCCEEEEeecCcchhHHHHHHHHHHHHHh----hhhhheeccC
Confidence 4556799999999999999999999998888764 5688888874
No 44
>PRK04017 hypothetical protein; Provisional
Probab=89.96 E-value=0.38 Score=37.94 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=26.8
Q ss_pred hccCCeEEEecCCChhHhHHHHHHHHHhCCc
Q 048704 104 ARGCGHLVLWLDCDREGENICFEVIECTGFQ 134 (220)
Q Consensus 104 ~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~ 134 (220)
+.+...||+.||+|.-||-|...+.+.+...
T Consensus 62 a~~~r~VIILTD~D~~GekIr~~l~~~l~~~ 92 (132)
T PRK04017 62 ASRGKEVIILTDFDRKGEELAKKLSEYLQGY 92 (132)
T ss_pred HhcCCeEEEEECCCcchHHHHHHHHHHHHhC
Confidence 3467789999999999999999999988763
No 45
>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=82.67 E-value=3.1 Score=29.12 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=23.7
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
..+||+++|.|..|+.-...+.+.+..
T Consensus 43 ~~~vii~~D~D~aG~~a~~~~~~~l~~ 69 (79)
T cd03364 43 AKEVILAFDGDEAGQKAALRALELLLK 69 (79)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHHHH
Confidence 478999999999999988888887765
No 46
>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=81.38 E-value=3.5 Score=28.48 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=23.1
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
...||++.|.|..|+.....+.+.+..
T Consensus 43 ~~~vii~~D~D~~G~~~~~~~~~~~~~ 69 (79)
T cd01029 43 ARTVILAFDNDEAGKKAAARALELLLA 69 (79)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHH
Confidence 478999999999999888888777764
No 47
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=75.68 E-value=0.68 Score=22.23 Aligned_cols=8 Identities=38% Similarity=0.563 Sum_probs=5.6
Q ss_pred ccccceec
Q 048704 55 SVVGHVFR 62 (220)
Q Consensus 55 ~~~GHl~~ 62 (220)
|++||++.
T Consensus 4 WAvGh~Mg 11 (14)
T PF02044_consen 4 WAVGHFMG 11 (14)
T ss_dssp CHHHCT--
T ss_pred cceeeeec
Confidence 89999985
No 48
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=73.40 E-value=8.6 Score=28.04 Aligned_cols=56 Identities=13% Similarity=0.148 Sum_probs=40.4
Q ss_pred HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 99 HLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 99 ~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
.|.+.+++||.||+-||+=. ....|.+-+.++.. .+|+....- -...+|.++++++
T Consensus 41 ~l~~~i~~aD~VIv~t~~vs--H~~~~~vk~~akk~----~ip~~~~~~--~~~~~l~~~l~~~ 96 (97)
T PF10087_consen 41 RLPSKIKKADLVIVFTDYVS--HNAMWKVKKAAKKY----GIPIIYSRS--RGVSSLERALERL 96 (97)
T ss_pred HHHHhcCCCCEEEEEeCCcC--hHHHHHHHHHHHHc----CCcEEEECC--CCHHHHHHHHHhh
Confidence 45667789999999998754 44568888888864 466664443 4455899888764
No 49
>PF13155 Toprim_2: Toprim-like
Probab=72.28 E-value=7.9 Score=27.68 Aligned_cols=26 Identities=19% Similarity=0.165 Sum_probs=23.7
Q ss_pred CeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 108 GHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 108 d~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
..|++|.|.|..|..-...+.+.+..
T Consensus 48 ~~i~l~~DnD~aG~~~~~~~~~~l~~ 73 (96)
T PF13155_consen 48 KKIVLAFDNDEAGRKAAEKLQKELKE 73 (96)
T ss_pred CcEEEEeCCCHHHHHHHHHHHHHHHh
Confidence 67999999999999999999988875
No 50
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofact
Probab=69.28 E-value=4.4 Score=31.45 Aligned_cols=27 Identities=26% Similarity=0.337 Sum_probs=22.1
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTG 132 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~ 132 (220)
..+.||++||+|..|.+|.--++..+-
T Consensus 76 rY~kiiimtDaD~DG~hI~~Llltff~ 102 (120)
T cd03365 76 RYGRLMIMTDQDHDGSHIKGLLINFIH 102 (120)
T ss_pred CcCeEEEEeCCCCCccHHHHHHHHHHH
Confidence 356899999999999999887766543
No 51
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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 strand joining and as a general acid in strand cleava
Probab=66.82 E-value=5.6 Score=30.62 Aligned_cols=27 Identities=15% Similarity=0.194 Sum_probs=22.3
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTG 132 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~ 132 (220)
.-..||+.||+|..|..|.--++..+-
T Consensus 71 rY~kiiimtDaD~DG~hI~~Llltff~ 97 (114)
T cd03366 71 RYHKIIIMTDADVDGAHIRTLLLTFFF 97 (114)
T ss_pred CcCeEEEEeCCCCCchHHHHHHHHHHH
Confidence 356899999999999999887776543
No 52
>PRK07714 hypothetical protein; Provisional
Probab=66.36 E-value=33 Score=25.30 Aligned_cols=75 Identities=7% Similarity=-0.006 Sum_probs=49.5
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCcchHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAV 173 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~ 173 (220)
.+..+.|++ .++-.||+|.|+... +...+..+|... +.|+.. -.|.+++-.|+-.-...--.+.+.+
T Consensus 24 ~~v~~al~~--g~~~lViiA~D~s~~---~~~ki~~~~~~~----~vp~~~----~~sk~eLG~a~Gk~~~~~vai~d~g 90 (100)
T PRK07714 24 ELVLKEVRS--GKAKLVLLSEDASVN---TTKKITDKCTYY----NVPMRK----VENRQQLGHAIGKDERVVVAVLDEG 90 (100)
T ss_pred HHHHHHHHh--CCceEEEEeCCCCHH---HHHHHHHHHHhc----CCCEEE----eCCHHHHHHHhCCCcceEEEEeCch
Confidence 445566654 468899999999887 456777777653 356532 2578999999985432223566777
Q ss_pred HHHHHHHH
Q 048704 174 DARQEIDL 181 (220)
Q Consensus 174 ~aR~~~D~ 181 (220)
.|+.....
T Consensus 91 ~a~~l~~~ 98 (100)
T PRK07714 91 FAKKLRSM 98 (100)
T ss_pred hHHHHHHH
Confidence 77765543
No 53
>PRK06683 hypothetical protein; Provisional
Probab=66.08 E-value=29 Score=24.82 Aligned_cols=55 Identities=11% Similarity=0.108 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhc
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN 161 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~n 161 (220)
+..++.|++ .++..||+|.|++.. +-..|.++|... ..|+. .+. |..++=+|.--
T Consensus 17 ~~v~kaik~--gkaklViiA~Da~~~---~~~~i~~~~~~~----~Vpv~--~~~--t~~eLG~A~G~ 71 (82)
T PRK06683 17 KRTLEAIKN--GIVKEVVIAEDADMR---LTHVIIRTALQH----NIPIT--KVE--SVRKLGKVAGI 71 (82)
T ss_pred HHHHHHHHc--CCeeEEEEECCCCHH---HHHHHHHHHHhc----CCCEE--EEC--CHHHHHHHhCC
Confidence 556677765 578899999999976 777888888863 45663 222 77888777653
No 54
>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=66.02 E-value=5.5 Score=30.71 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=22.4
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTG 132 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~ 132 (220)
....||+.||+|..|.+|---++..+-
T Consensus 72 rY~kiiimtDaD~DG~hI~~Llltff~ 98 (115)
T cd01030 72 RYGKIIIMTDADVDGSHIRTLLLTFFY 98 (115)
T ss_pred CcCeEEEEeCCCCCccHhHHHHHHHHH
Confidence 356899999999999999887776543
No 55
>PHA02031 putative DnaG-like primase
Probab=64.43 E-value=25 Score=30.94 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=32.8
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe-cCcCHHHHH
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF-SSVTEKDIL 156 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~-sslt~~~I~ 156 (220)
+++||++-|.|.-|..=....++.+... ...++-+.+ ...+|+++.
T Consensus 206 ~~~Vil~fDgD~AG~~Aa~ra~~~l~~~----~~~v~vv~lP~g~DPDd~i 252 (266)
T PHA02031 206 CPRVLIFLDGDPAGVDGSAGAMRRLRPL----LIEGQVIITPDGFDPKDLE 252 (266)
T ss_pred CCCEEEEeCCCHHHHHHHHHHHHHHHHc----CCceEEEECCCCCChHHHH
Confidence 7999999999999998888888877643 233433333 477766654
No 56
>PRK05667 dnaG DNA primase; Validated
Probab=63.49 E-value=23 Score=34.52 Aligned_cols=55 Identities=18% Similarity=0.259 Sum_probs=37.6
Q ss_pred HHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHH---hCCcccCCCCcEEEEEec-CcCHHHHH
Q 048704 95 HICRHLNQEARGCGHLVLWLDCDREGENICFEVIEC---TGFQVNDARRKVHRARFS-SVTEKDIL 156 (220)
Q Consensus 95 ~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~---~~~~~~~~~~~v~R~~~s-slt~~~I~ 156 (220)
+.++.|++ -++.||+|.|.|.-|..-++..++. +... ...++-+.+. ..++.++.
T Consensus 287 ~~~~~L~r---~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~----g~~v~vv~lp~gkDpdd~l 345 (580)
T PRK05667 287 EHLKLLRR---LTDEVILCFDGDKAGRKAALRALELALPLLKD----GRQVRVAFLPDGKDPDDLV 345 (580)
T ss_pred HHHHHHHh---cCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhC----CceEEEEECCCCCChHHHH
Confidence 34444443 3568999999999999999998887 4332 2356555554 67777764
No 57
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=58.35 E-value=14 Score=35.86 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=27.8
Q ss_pred HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 99 HLNQEARGCGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 99 ~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
+++.+.+..+.||+|.|.|+-|+.++|+.++.+..
T Consensus 282 hi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~ 316 (568)
T COG0358 282 HIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLP 316 (568)
T ss_pred HHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhh
Confidence 34444456788999999999999999999885544
No 58
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=56.93 E-value=50 Score=23.68 Aligned_cols=54 Identities=13% Similarity=0.076 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHh
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMG 160 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~ 160 (220)
...++.|++ .++..||+|.|++ +.+-..+.++|... .-|+. ...|..++=+|+-
T Consensus 14 ~~vlkaIk~--gkakLViiA~Da~---~~~~k~i~~~c~~~----~Vpv~----~~~t~~eLG~A~G 67 (82)
T PRK13601 14 KQTLKAITN--CNVLQVYIAKDAE---EHVTKKIKELCEEK----SIKIV----YIDTMKELGVMCG 67 (82)
T ss_pred HHHHHHHHc--CCeeEEEEeCCCC---HHHHHHHHHHHHhC----CCCEE----EeCCHHHHHHHHC
Confidence 556677765 5788999999999 57889999999874 45773 2236777877764
No 59
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=56.14 E-value=42 Score=31.25 Aligned_cols=55 Identities=16% Similarity=0.218 Sum_probs=37.3
Q ss_pred HHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEec-CcCHHHHH
Q 048704 95 HICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFS-SVTEKDIL 156 (220)
Q Consensus 95 ~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~s-slt~~~I~ 156 (220)
..++.|++ .+.+||+|.|.|..|+.-+..+++.+... ...++.+.+. ..++.++.
T Consensus 291 ~~~~~l~r---~~~~vvl~~D~D~aG~~aa~r~~~~l~~~----g~~v~v~~lp~gkDpdd~l 346 (415)
T TIGR01391 291 EHIKLLKR---YADEIILCFDGDKAGRKAALRAIELLLPL----GINVKVIKLPGGKDPDEYL 346 (415)
T ss_pred HHHHHHHh---hCCeEEEEeCCCHHHHHHHHHHHHHHHHc----CCeEEEEECCCCCCHHHHH
Confidence 44444443 35689999999999999998888887653 2345555444 45555553
No 60
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=54.96 E-value=26 Score=25.42 Aligned_cols=53 Identities=13% Similarity=0.142 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAM 159 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~ 159 (220)
++.++.|++ ..+..||+|.|.|.. +-.+|...|... +.|+ .|+. |.+++=+|.
T Consensus 19 kqt~Kai~k--g~~~~v~iA~Da~~~---vv~~l~~lceek----~Ip~--v~V~--s~~~LGkAc 71 (84)
T PRK13600 19 KETLKALKK--DQVTSLIIAEDVEVY---LMTRVLSQINQK----NIPV--SFFK--SKHALGKHV 71 (84)
T ss_pred HHHHHHHhc--CCceEEEEeCCCCHH---HHHHHHHHHHHc----CCCE--EEEC--CHHHHHHHh
Confidence 455666654 457899999999965 447999999874 3444 3344 355566655
No 61
>PF13362 Toprim_3: Toprim domain
Probab=54.83 E-value=34 Score=24.48 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=23.0
Q ss_pred CCeEEEecCCChh--HhHHHHHHHHHhCC
Q 048704 107 CGHLVLWLDCDRE--GENICFEVIECTGF 133 (220)
Q Consensus 107 ad~ii~AtD~DrE--GE~I~~~Il~~~~~ 133 (220)
...||++.|.|.. |+.=+..+.+.+..
T Consensus 41 ~~~vii~~D~D~~~~G~~~a~~~~~~~~~ 69 (96)
T PF13362_consen 41 GRRVIIAADNDKANEGQKAAEKAAERLEA 69 (96)
T ss_pred CCeEEEEECCCCchhhHHHHHHHHHHHHh
Confidence 4568999999999 99988888888875
No 62
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=53.37 E-value=90 Score=24.00 Aligned_cols=78 Identities=18% Similarity=0.060 Sum_probs=51.5
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCc-chHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNR-NEALA 172 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~-~l~~A 172 (220)
...++.|++ +++--||+|.|++.. .+..++..+|... ..|+ +.--|.+++-+|+..-.+..- ...++
T Consensus 36 ~~v~kaikk--gkakLVilA~D~s~~--~i~~~~~~lc~~~----~Vp~----~~~~tk~eLG~a~Gk~~~~svvaI~d~ 103 (122)
T PRK04175 36 NETTKAVER--GIAKLVVIAEDVDPE--EIVAHLPLLCEEK----KIPY----VYVPSKKDLGKAAGLEVGAAAAAIVDA 103 (122)
T ss_pred HHHHHHHHc--CCccEEEEeCCCChH--HHHHHHHHHHHHc----CCCE----EEECCHHHHHHHhCCCCCeEEEEEech
Confidence 345566654 468899999999874 2445667777653 3453 222378999999986544432 56677
Q ss_pred HHHHHHHHHHH
Q 048704 173 VDARQEIDLKV 183 (220)
Q Consensus 173 ~~aR~~~D~li 183 (220)
+.++...|.+.
T Consensus 104 g~a~~~~~~~~ 114 (122)
T PRK04175 104 GKAKELVEDIV 114 (122)
T ss_pred hhhHHHHHHHH
Confidence 88887777654
No 63
>PRK07283 hypothetical protein; Provisional
Probab=50.85 E-value=84 Score=23.07 Aligned_cols=73 Identities=10% Similarity=0.039 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCcchHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAV 173 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~ 173 (220)
.++.+.|++ .++..||+|.|++.++- ..+.+.|... ..|+. .-.|.+++-.|+-..+.. -...+++
T Consensus 24 ~~v~~aik~--gk~~lVi~A~Das~~~~---kk~~~~~~~~----~Vp~~----~~~t~~eLG~a~Gk~~~v-vai~d~g 89 (98)
T PRK07283 24 ELVVKAIQS--GQAKLVFLANDAGPNLT---KKVTDKSNYY----QVEVS----TVFSTLELSAAVGKPRKV-LAVTDAG 89 (98)
T ss_pred HHHHHHHHc--CCccEEEEeCCCCHHHH---HHHHHHHHHc----CCCEE----EeCCHHHHHHHhCCCceE-EEEeChh
Confidence 445566664 46889999999998765 3444444432 34552 223889999999863211 3566888
Q ss_pred HHHHHHH
Q 048704 174 DARQEID 180 (220)
Q Consensus 174 ~aR~~~D 180 (220)
.|+...+
T Consensus 90 ~a~~l~~ 96 (98)
T PRK07283 90 FSKKMRS 96 (98)
T ss_pred HHHHHHH
Confidence 8877654
No 64
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=50.39 E-value=70 Score=22.77 Aligned_cols=55 Identities=18% Similarity=0.160 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhc
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN 161 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~n 161 (220)
...++.|++ .++..||+|.|++. .+-..|..+|... ..|+. .+. |.+++=+|.-.
T Consensus 17 ~~v~kai~~--gkaklViiA~D~~~---~~~~~i~~~c~~~----~Vp~~--~~~--s~~eLG~a~G~ 71 (82)
T PRK13602 17 KQTVKALKR--GSVKEVVVAEDADP---RLTEKVEALANEK----GVPVS--KVD--SMKKLGKACGI 71 (82)
T ss_pred HHHHHHHHc--CCeeEEEEECCCCH---HHHHHHHHHHHHc----CCCEE--EEC--CHHHHHHHHCC
Confidence 456667765 57889999999998 3778888888863 45653 233 67888777643
No 65
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial 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 modelled by this alignment, 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=48.12 E-value=51 Score=28.21 Aligned_cols=28 Identities=18% Similarity=0.175 Sum_probs=25.2
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
.+++||+|.|.|.-|+.-...+++.+..
T Consensus 153 ~~~~Iil~~D~D~AG~~Aa~r~~~~L~~ 180 (218)
T TIGR00646 153 KIEKIFICFDNDFAGKNAAANLEEILKK 180 (218)
T ss_pred CCCEEEEEeCCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988864
No 66
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=44.81 E-value=12 Score=34.34 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=23.5
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTGF 133 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~ 133 (220)
+..+||++||+|+-|+-++..++++++.
T Consensus 66 gi~rVVi~~D~d~~G~~~~~~~~~~L~~ 93 (360)
T PRK14719 66 NISEVILLTDFDRAGRVYAKNIMEEFQS 93 (360)
T ss_pred CCCEEEEEECCCCCCCccchHHHHHHHH
Confidence 5678999999999999989777777765
No 67
>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]
Probab=43.95 E-value=78 Score=32.17 Aligned_cols=74 Identities=18% Similarity=0.188 Sum_probs=45.2
Q ss_pred ecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHH----------HhhhHHHHHHhhcccCC--CCCC---cee---
Q 048704 147 FSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVG----------VAFTRFQTTYFQGKYGN--LDSR---FIS--- 208 (220)
Q Consensus 147 ~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG----------~nlTR~~t~~~~~~~~~--~~~~---~~S--- 208 (220)
+.+---+-+.+-+..|+-.+....+=...|.++||+.- +.+.|+-..+-...|+- ...+ .|.
T Consensus 352 ~P~~v~kv~~eEl~kL~~le~~~sEfnvtrNYLdwlt~LPWgk~S~En~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~k 431 (906)
T KOG2004|consen 352 MPDHVLKVIDEELTKLKLLEPSSSEFNVTRNYLDWLTSLPWGKSSTENLDLARAKEILDEDHYGMEDVKERILEFIAVGK 431 (906)
T ss_pred CcHHHHHHHHHHHHHHhccCccccchhHHHHHHHHHHhCCCCCCChhhhhHHHHHHhhcccccchHHHHHHHHHHHHHHh
Confidence 44444555666667777777666677789999999873 45566655443222320 0000 112
Q ss_pred -eccccceecccC
Q 048704 209 -LVFSSLFLICFH 220 (220)
Q Consensus 209 -~GRvQtp~l~~~ 220 (220)
-|.+|.|.||||
T Consensus 432 Lrgs~qGkIlCf~ 444 (906)
T KOG2004|consen 432 LRGSVQGKILCFV 444 (906)
T ss_pred hcccCCCcEEEEe
Confidence 267899999996
No 68
>PF05368 NmrA: NmrA-like family; InterPro: IPR008030 NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi []. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.; PDB: 2ZCV_A 2ZCU_A 2R6J_B 3C3X_A 2QZZ_B 2QYS_A 2QX7_A 2QW8_A 2R2G_B 3E5M_B ....
Probab=43.85 E-value=31 Score=28.53 Aligned_cols=52 Identities=12% Similarity=-0.056 Sum_probs=36.7
Q ss_pred HHHHHHHhccCCeEEEecCCC-hhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHH
Q 048704 97 CRHLNQEARGCGHLVLWLDCD-REGENICFEVIECTGFQVNDARRKVHRARFSSVTEKD 154 (220)
Q Consensus 97 ~~~lk~~~~~ad~ii~AtD~D-rEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~ 154 (220)
.+.|.+.++++|.||+++... ...-.....+++.+.. .+ |+|..+|++....
T Consensus 55 ~~~l~~al~g~d~v~~~~~~~~~~~~~~~~~li~Aa~~-----ag-Vk~~v~ss~~~~~ 107 (233)
T PF05368_consen 55 PESLVAALKGVDAVFSVTPPSHPSELEQQKNLIDAAKA-----AG-VKHFVPSSFGADY 107 (233)
T ss_dssp HHHHHHHHTTCSEEEEESSCSCCCHHHHHHHHHHHHHH-----HT--SEEEESEESSGT
T ss_pred HHHHHHHHcCCceEEeecCcchhhhhhhhhhHHHhhhc-----cc-cceEEEEEecccc
Confidence 355677778999999999976 3333345678888875 23 9999999886543
No 69
>PRK11178 uridine phosphorylase; Provisional
Probab=43.83 E-value=47 Score=28.64 Aligned_cols=47 Identities=13% Similarity=0.141 Sum_probs=31.8
Q ss_pred CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEE
Q 048704 4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVT 54 (220)
Q Consensus 4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt 54 (220)
|+++||+-=|.-++.|++.|.........+.+++| .|+|+|. .+.|+
T Consensus 17 ~~i~Ii~g~p~e~~~ia~~l~~~~~~~~~~~~~~~--~G~~~g~--~v~v~ 63 (251)
T PRK11178 17 ATLAIVPGDPERVEKIAALMDNPVFLASHREFTSW--RAELDGK--PVIVC 63 (251)
T ss_pred CCEEEECCCHHHHHHHHHHhccchheeeccCeEEE--EEEEcCE--EEEEE
Confidence 68999999999999999999763211123344444 5777765 44443
No 70
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=42.45 E-value=1.1e+02 Score=23.19 Aligned_cols=78 Identities=10% Similarity=-0.017 Sum_probs=51.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCC-cchHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPN-RNEALA 172 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~-~~l~~A 172 (220)
...++.|++ +++.-||+|.|.+... +-.++..+|... +.|+ +...|.+++-+|+..-.+.. -...++
T Consensus 32 ~~v~kaikk--gka~LVilA~D~s~~~--~~~~i~~lc~~~----~Ip~----~~~~sk~eLG~a~Gk~~~~svvaI~d~ 99 (117)
T TIGR03677 32 NEVTKAVER--GIAKLVVIAEDVEPPE--IVAHLPALCEEK----GIPY----VYVKKKEDLGAAAGLEVGAASAAIVDE 99 (117)
T ss_pred HHHHHHHHc--CCccEEEEeCCCCcHH--HHHHHHHHHHHc----CCCE----EEeCCHHHHHHHhCCCCCeEEEEEEch
Confidence 345556654 5688999999997521 345566677653 3453 33448899999998544433 256678
Q ss_pred HHHHHHHHHHH
Q 048704 173 VDARQEIDLKV 183 (220)
Q Consensus 173 ~~aR~~~D~li 183 (220)
+.++...|.+.
T Consensus 100 g~a~~~~~~~~ 110 (117)
T TIGR03677 100 GKAEELLKEII 110 (117)
T ss_pred hhhHHHHHHHH
Confidence 88888888755
No 71
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=41.67 E-value=1.5e+02 Score=22.15 Aligned_cols=74 Identities=5% Similarity=-0.051 Sum_probs=47.3
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCcchHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAV 173 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~ 173 (220)
.++.+.|++ .++--||+|.|+-..+- ..|...|... ..|+. .-.|.+++-.|+-...-.--.+.+.+
T Consensus 23 ~~v~~aik~--gk~~lVI~A~D~s~~~k---kki~~~~~~~----~vp~~----~~~t~~eLg~a~Gk~~~~~iai~d~g 89 (104)
T PRK05583 23 NKCEEAIKK--KKVYLIIISNDISENSK---NKFKNYCNKY----NIPYI----EGYSKEELGNAIGRDEIKILGVKDKN 89 (104)
T ss_pred HHHHHHHHc--CCceEEEEeCCCCHhHH---HHHHHHHHHc----CCCEE----EecCHHHHHHHhCCCCeEEEEEeChH
Confidence 445566665 46889999999976654 6677776652 34542 22688999999975331122555666
Q ss_pred HHHHHHH
Q 048704 174 DARQEID 180 (220)
Q Consensus 174 ~aR~~~D 180 (220)
.++....
T Consensus 90 ~a~~l~~ 96 (104)
T PRK05583 90 MAKKLLK 96 (104)
T ss_pred HHHHHHH
Confidence 6666554
No 72
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=39.63 E-value=1.7e+02 Score=23.45 Aligned_cols=62 Identities=5% Similarity=-0.011 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAM 159 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~ 159 (220)
.+.++.+++.+....-|+|-+.++..=+.+++.|.+..... ..|.-.+-.++++++.+...+
T Consensus 9 ~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~----~~pfi~vnc~~~~~~~~e~~L 70 (168)
T PF00158_consen 9 KRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRK----NGPFISVNCAALPEELLESEL 70 (168)
T ss_dssp HHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTT----TS-EEEEETTTS-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcc----cCCeEEEehhhhhcchhhhhh
Confidence 45667777777666689999999999999999999866642 578999999999998887654
No 73
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=39.11 E-value=1.2e+02 Score=22.31 Aligned_cols=72 Identities=6% Similarity=-0.035 Sum_probs=46.3
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCC-CcchHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEP-NRNEALA 172 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~-~~~l~~A 172 (220)
...++.|++ +++..||+|.|+ ++.+-.++..+|... ..|+. .-.-|.+++=+|.-.-... --...++
T Consensus 22 ~~v~kai~~--gkaklViiA~D~---~~~~~~~i~~~c~~~----~Ip~~---~~~~tk~eLG~a~Gk~~~~~~vaI~D~ 89 (99)
T PRK01018 22 KRTIKAIKL--GKAKLVIVASNC---PKDIKEDIEYYAKLS----GIPVY---EYEGSSVELGTLCGKPFTVSALAIVDP 89 (99)
T ss_pred HHHHHHHHc--CCceEEEEeCCC---CHHHHHHHHHHHHHc----CCCEE---EECCCHHHHHHHhCCCCCEEEEEEecC
Confidence 455667764 578899999997 446778888888763 45653 3334788999988754321 1234445
Q ss_pred HHHHH
Q 048704 173 VDARQ 177 (220)
Q Consensus 173 ~~aR~ 177 (220)
++|+.
T Consensus 90 G~a~~ 94 (99)
T PRK01018 90 GESDI 94 (99)
T ss_pred CHHHH
Confidence 55443
No 74
>PF11549 Sec31: Protein transport protein SEC31; InterPro: IPR021614 Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerisation of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat []. Sec13/31 is a hetero-tetramer which is organised as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron []. ; PDB: 2QTV_D.
Probab=38.30 E-value=7.9 Score=25.28 Aligned_cols=16 Identities=44% Similarity=0.532 Sum_probs=0.5
Q ss_pred EEEEeChHHHHHHHHH
Q 048704 7 LMVAEKPSIALSIATV 22 (220)
Q Consensus 7 LiIaEKPs~Ak~ia~~ 22 (220)
|.|.|||+-||.++-+
T Consensus 31 l~vkEKpsRAKavsva 46 (51)
T PF11549_consen 31 LKVKEKPSRAKAVSVA 46 (51)
T ss_dssp S---------------
T ss_pred hhhhcccccccccccc
Confidence 5689999999987643
No 75
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=36.59 E-value=91 Score=21.54 Aligned_cols=46 Identities=13% Similarity=0.084 Sum_probs=28.9
Q ss_pred CChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 116 CDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 116 ~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
.|.||+.|...+.. ++...-..-...+..++.+.++++++..-+++
T Consensus 14 ~Dp~G~ti~~~l~~-lg~~~v~~Vr~~k~~~l~~~~~~~~~~i~~~l 59 (73)
T PRK06423 14 EDPEALTILKNLNI-LGYNGIKGVSISKVYYFDADSYNEVDEIAGKI 59 (73)
T ss_pred cChHHHHHHHHHHH-cCCCCcceEEEEEEEEEecCCHHHHHHHHHHh
Confidence 48899999998877 45421001234566778777777766644444
No 76
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=34.03 E-value=58 Score=28.46 Aligned_cols=44 Identities=14% Similarity=0.110 Sum_probs=34.8
Q ss_pred hccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEec--CcCHH
Q 048704 104 ARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFS--SVTEK 153 (220)
Q Consensus 104 ~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~s--slt~~ 153 (220)
.+++|.+|.-+||..++=..+..|-+..... . ++|++|- -.+++
T Consensus 153 ~~~vD~vivVvDpS~~sl~taeri~~L~~el-----g-~k~i~~V~NKv~e~ 198 (255)
T COG3640 153 IEGVDLVIVVVDPSYKSLRTAERIKELAEEL-----G-IKRIFVVLNKVDEE 198 (255)
T ss_pred ccCCCEEEEEeCCcHHHHHHHHHHHHHHHHh-----C-CceEEEEEeeccch
Confidence 4589999999999999999999999988863 2 7787663 44443
No 77
>TIGR01059 gyrB DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.
Probab=32.83 E-value=33 Score=33.98 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=21.7
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTG 132 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~ 132 (220)
...|||.||+|..|.+|--.++..+-
T Consensus 485 Y~kiiImtDaD~DG~HI~~Lll~ff~ 510 (654)
T TIGR01059 485 YHKIIIMTDADVDGSHIRTLLLTFFY 510 (654)
T ss_pred cceEEEEeCCCCCcchhHHHHHHHHH
Confidence 45799999999999999987776543
No 78
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=32.59 E-value=33 Score=33.55 Aligned_cols=25 Identities=20% Similarity=0.353 Sum_probs=21.0
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHh
Q 048704 107 CGHLVLWLDCDREGENICFEVIECT 131 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~ 131 (220)
...|||.||+|-.|.+|--.++..+
T Consensus 453 Y~kIiImtDaDvDG~HI~~Llltff 477 (594)
T smart00433 453 YGKIIIMTDADVDGSHIKGLLLTFF 477 (594)
T ss_pred cceEEEEeCCCCCcchhHHHHHHHH
Confidence 4579999999999999987776644
No 79
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer.
Probab=31.45 E-value=36 Score=33.61 Aligned_cols=57 Identities=18% Similarity=0.230 Sum_probs=37.7
Q ss_pred cCCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-----cCcCHHHHHHHHhcC
Q 048704 106 GCGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-----SSVTEKDILKAMGNL 162 (220)
Q Consensus 106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----sslt~~~I~~A~~nl 162 (220)
....|||.||+|-.|.+|--.++..+-...+. -..|++|+.- -++++.+..+.+..+
T Consensus 480 RY~kiiImTDADvDG~HI~~LLltff~r~~p~Li~~G~vy~~~~Pl~kv~~gk~~~y~~~e~e~~~~~~~~ 550 (625)
T TIGR01055 480 RYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKL 550 (625)
T ss_pred ccceEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCCeEEEEeCCEEEEecCCceEEcCCHHHHHHHHHhh
Confidence 35579999999999999988776644321111 1235666543 457888877776543
No 80
>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=31.09 E-value=1.2e+02 Score=24.00 Aligned_cols=62 Identities=16% Similarity=0.130 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccC-CCCcEEEEEecCcCHHHHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVND-ARRKVHRARFSSVTEKDILK 157 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~-~~~~v~R~~~sslt~~~I~~ 157 (220)
+..++.|.+.. --.++..+|.|..|-.|+..+..-....... ....+.++.+-.+.++++.+
T Consensus 40 r~~l~~L~~~~--~~~~~~l~D~DP~Gi~I~~~y~~gs~~~~~~~~~~~~~~l~~~G~~~~d~~~ 102 (160)
T cd00223 40 RRFLRRLHEEL--DLPVYILVDGDPYGISILLTYKYGSIKLAYESESLATPDLRWLGLRPSDIIR 102 (160)
T ss_pred HHHHHHHHHhh--CCCEEEEECCCcchhhhhHHHHhCccccccccccccCCCcEEccCCHHHHhh
Confidence 45556665443 2358999999999999988876522211000 01123477787888888755
No 81
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=31.00 E-value=42 Score=33.12 Aligned_cols=82 Identities=13% Similarity=0.126 Sum_probs=53.3
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-----cCcCHHHHHHHHhcCCC---CC---
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-----SSVTEKDILKAMGNLVE---PN--- 166 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----sslt~~~I~~A~~nl~~---~~--- 166 (220)
...|||.||+|-.|-+|.-.++-.+-...+. .-.|++|+.- -.+++.+..+.++.+.. .+
T Consensus 490 Y~kIiIMTDADvDGaHIrtLLlTfFyr~m~~LIe~G~vyiA~PPLYkv~~~k~~~Y~~~d~E~~~~~~~~~~~~~~~IqR 569 (635)
T COG0187 490 YHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPPLYKVKKGKKTFYAYDDEELEKLLERLGKKKGYEIQR 569 (635)
T ss_pred cCcEEEEecCCCChHHHHHHHHHHHHHHhHHHHHcCcEEEEcCceEEEEcCCceeEeCCHHHHHHHHHHhcccCCceeEe
Confidence 4579999999999999987765433211100 1236777764 45678888888876521 11
Q ss_pred ---------------------c-----chHHHHHHHHHHHHHHHHhhh
Q 048704 167 ---------------------R-----NEALAVDARQEIDLKVGVAFT 188 (220)
Q Consensus 167 ---------------------~-----~l~~A~~aR~~~D~liG~nlT 188 (220)
. .+-+|..|...++.|.|=...
T Consensus 570 yKGLGEMnp~QLwETTmdP~~R~L~~V~i~da~~ad~~f~~LMGd~ve 617 (635)
T COG0187 570 YKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVE 617 (635)
T ss_pred ecccCCCCHHHHHHhccCccceeEEEEEcccHHHHHHHHHHHcCCCch
Confidence 0 245788888888888876643
No 82
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=30.90 E-value=37 Score=33.47 Aligned_cols=56 Identities=16% Similarity=0.208 Sum_probs=36.5
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-----cCcCHHHHHHHHhcC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-----SSVTEKDILKAMGNL 162 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----sslt~~~I~~A~~nl 162 (220)
...|||.||+|-.|.+|--.++..+-...+. ...|++|+.- ..+++++..+..+++
T Consensus 487 Y~kIiImTDaDvDGsHI~~Llltff~~~~p~Li~~G~v~~~~~Pl~kv~~gk~~~y~~~~~e~~~~~~~~ 556 (631)
T PRK05559 487 YGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKL 556 (631)
T ss_pred cCeEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCCeEEEecCCEEEEEcCCceEEecCHHHHHHHHHHh
Confidence 4579999999999999988876644321110 1236667654 355677766665554
No 83
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=30.88 E-value=37 Score=33.57 Aligned_cols=58 Identities=10% Similarity=0.111 Sum_probs=38.1
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-------cCcCHHHHHHHHhcCCC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-------SSVTEKDILKAMGNLVE 164 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-------sslt~~~I~~A~~nl~~ 164 (220)
...|||.||+|-.|.+|--.++..+-...+. ...|++|+.- -..|+++..+..++++.
T Consensus 491 Y~kIiImTDADvDGsHIr~LLltff~r~~p~Li~~G~v~~~~~Pl~kv~~~~~~~~~y~~~~~e~~~~~~~~~~ 564 (637)
T TIGR01058 491 YDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDGKKVKYAWSDLELESVKKKLKN 564 (637)
T ss_pred cceEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCCeEEEecCCEEEEEeCCCceEEEeCCHHHHHHHHHhcCC
Confidence 4579999999999999988877644321111 1236666543 34577887777766543
No 84
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=30.85 E-value=41 Score=34.59 Aligned_cols=56 Identities=16% Similarity=0.182 Sum_probs=38.4
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-----------------cCcCHHHHHHHHh
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-----------------SSVTEKDILKAMG 160 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----------------sslt~~~I~~A~~ 160 (220)
-..|||.||+|-.|.+|--.++-.+-...+. ...|++|+.. ...++++..+.++
T Consensus 680 YgKIIIMTDADVDGsHIrtLLLTff~r~~p~Lie~G~vyia~pPLyki~~~~~~~~~~~~~~~k~~~y~~sd~el~~~~~ 759 (903)
T PTZ00109 680 YGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFNVSTKNSKKYIYTWSDEELNVLIK 759 (903)
T ss_pred cCeEEEEeCCCCChhHHHHHHHHHHHHhCHHhhhCCEEEEecCCEEEEEecCcccccccccccceeEEeCCHHHHHHHHH
Confidence 4579999999999999987776543221110 1236777653 4677888888887
Q ss_pred cC
Q 048704 161 NL 162 (220)
Q Consensus 161 nl 162 (220)
.+
T Consensus 760 ~~ 761 (903)
T PTZ00109 760 LL 761 (903)
T ss_pred Hh
Confidence 65
No 85
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=28.95 E-value=44 Score=33.07 Aligned_cols=56 Identities=11% Similarity=0.186 Sum_probs=36.9
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe----cCcCHHHHHHHHhcC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF----SSVTEKDILKAMGNL 162 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~----sslt~~~I~~A~~nl 162 (220)
...|||.||+|-.|.+|--.++..+-..-+. -.-|+.|+.- ...|+.+..+..+.+
T Consensus 492 Y~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~l~~~~~Pl~kv~~gk~~~~~~~~e~~~~~~~~ 560 (638)
T PRK05644 492 YHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKEYAYSDEELDEILAEL 560 (638)
T ss_pred cCeEEEEeCCCCCchHHHHHHHHHHHHhCHHhccCCeEEEecCCEEEEEeCCeEeecCHHHHHHHHHHh
Confidence 4579999999999999988776644321111 1236777654 356667776666544
No 86
>PHA02569 39 DNA topoisomerase II large subunit; Provisional
Probab=26.26 E-value=52 Score=32.32 Aligned_cols=56 Identities=16% Similarity=0.124 Sum_probs=34.9
Q ss_pred CCeEEEecCCChhH-hHHHHHHHHHhCCcccC---------CCCcEEEEEe-----cCcCHHHHHHHHhcCC
Q 048704 107 CGHLVLWLDCDREG-ENICFEVIECTGFQVND---------ARRKVHRARF-----SSVTEKDILKAMGNLV 163 (220)
Q Consensus 107 ad~ii~AtD~DrEG-E~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----sslt~~~I~~A~~nl~ 163 (220)
...|||.||+|-.| .+|--.++..+-. .+. -..|+.|+.- .-.|..+..+..+++.
T Consensus 475 Y~kIiImTDADvDG~sHIr~LLltff~~-~p~Li~~G~v~~~~~Pl~kv~~gk~~~~~~~~~e~~~~~~~~~ 545 (602)
T PHA02569 475 YKNIAIMTDADVDGKGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSLK 545 (602)
T ss_pred cCcEEEEecCCCcchHHHHHHHHHHHHh-chhhccCCeEEEecCCEEEEEcCCeeEEecCHHHHHHHHHhcC
Confidence 45799999999999 9998777765533 211 1235555543 2445666666555543
No 87
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=26.25 E-value=88 Score=23.91 Aligned_cols=31 Identities=16% Similarity=0.094 Sum_probs=25.2
Q ss_pred hccCCeEEEecCCChhHhHHHHHHHHHhCCc
Q 048704 104 ARGCGHLVLWLDCDREGENICFEVIECTGFQ 134 (220)
Q Consensus 104 ~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~ 134 (220)
.+.-|.|+.|||...|-.+=..-++...++.
T Consensus 83 vkegd~~~fa~~de~~r~lwvqa~yratgqs 113 (117)
T cd01234 83 VKEGDELKFATDDENERHLWVQAMYRATGQS 113 (117)
T ss_pred eccCcEEEEeccchHHHHHHHHHHHHHcCcc
Confidence 4678999999999888888777777777764
No 88
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=26.19 E-value=2e+02 Score=28.26 Aligned_cols=38 Identities=13% Similarity=0.197 Sum_probs=24.8
Q ss_pred HhHHHHHHHHHhCCcccCCCCcEEEE-EecCcCHHHHHHHHhcC
Q 048704 120 GENICFEVIECTGFQVNDARRKVHRA-RFSSVTEKDILKAMGNL 162 (220)
Q Consensus 120 GE~I~~~Il~~~~~~~~~~~~~v~R~-~~sslt~~~I~~A~~nl 162 (220)
|-+++|-+++.-+.. .++.-+ .+++.+-+.|.++++..
T Consensus 346 gALl~~~~le~~k~~-----~~~~~~~ml~s~vSs~l~~~ia~~ 384 (607)
T KOG1220|consen 346 GALLSWWVLEEHKGS-----TPVQDVSMLNSTVSSGLTRFIAEI 384 (607)
T ss_pred HHHHHHHHHHhccCC-----CccchhhhhhhHHHHHHHHHHHHH
Confidence 556778888877653 222222 47788888888877765
No 89
>PRK05819 deoD purine nucleoside phosphorylase; Reviewed
Probab=25.34 E-value=1.3e+02 Score=25.40 Aligned_cols=41 Identities=17% Similarity=0.158 Sum_probs=27.1
Q ss_pred ceEEEEeChHHHHHHHH-HcCCCCcccccCCeeeeeecceecCC
Q 048704 5 KVLMVAEKPSIALSIAT-VLSGGKLYTRKASTEVHEFDGMFLGS 47 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~-~L~~~~~~~~~~~~~~~~~~~~~~g~ 47 (220)
+.+|+..-|.-++.||+ .|.........+++..| .|.|+|.
T Consensus 14 ~~vi~~Gdp~r~~~ia~~~l~~~~~~~~~r~~~~~--~G~~~g~ 55 (235)
T PRK05819 14 DTVLMPGDPLRAKYIAETFLEDVVCVNEVRGMLGF--TGTYKGK 55 (235)
T ss_pred CeEEecCCHHHHHHHHHHHhcCcEeeeeeccEEEE--EEEECCE
Confidence 67899999999999998 67653211112333333 6777765
No 90
>COG2820 Udp Uridine phosphorylase [Nucleotide transport and metabolism]
Probab=25.25 E-value=1.3e+02 Score=26.26 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=33.3
Q ss_pred ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEcc
Q 048704 5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSV 56 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~ 56 (220)
..+|+.=-|.-+..||+.|.++..-.....+ -.|.|+|+|. ...||++
T Consensus 18 ~~vilpGdP~R~~~iA~lld~~~~va~~Ref--~~~~g~~~g~--~v~v~St 65 (248)
T COG2820 18 TLVILPGDPERVEKIAKLLDNPVLVASNREF--RTYTGTYNGK--PVTVCST 65 (248)
T ss_pred ceEEecCCHHHHHHHHHHhccchhhhhccce--EEEEEEEcCe--EEEEEec
Confidence 4578888999999999999874321122223 3348999987 7777776
No 91
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=24.69 E-value=1.3e+02 Score=23.06 Aligned_cols=37 Identities=22% Similarity=0.220 Sum_probs=28.7
Q ss_pred EEecCcCHHHHHHHHhcCCCCCc------chHHHHHHHHHHHH
Q 048704 145 ARFSSVTEKDILKAMGNLVEPNR------NEALAVDARQEIDL 181 (220)
Q Consensus 145 ~~~sslt~~~I~~A~~nl~~~~~------~l~~A~~aR~~~D~ 181 (220)
+.=+..|.++|.+||+....-++ |.+.|..-|...|-
T Consensus 40 vv~~~Tt~~eiedaF~~f~~RdDIaIiLInq~~Ae~iR~~vD~ 82 (121)
T KOG3432|consen 40 VVDSKTTVEEIEDAFKSFTARDDIAIILINQFIAEMIRDRVDA 82 (121)
T ss_pred EEeccCCHHHHHHHHHhhccccCeEEEEEhHHHHHHHHHHHHh
Confidence 44568899999999998866443 67788888888774
No 92
>PRK05783 hypothetical protein; Provisional
Probab=24.21 E-value=1.3e+02 Score=21.69 Aligned_cols=42 Identities=26% Similarity=0.203 Sum_probs=21.0
Q ss_pred CChhHhHHHHHHHHH-hCCcccCCCCcEEEEEecCcCHHHHHH
Q 048704 116 CDREGENICFEVIEC-TGFQVNDARRKVHRARFSSVTEKDILK 157 (220)
Q Consensus 116 ~DrEGE~I~~~Il~~-~~~~~~~~~~~v~R~~~sslt~~~I~~ 157 (220)
-|.||+.|-..+... .+....-...++.++.+.+-++++.++
T Consensus 16 lDPqG~aI~~aL~~lg~~~V~~VRvGK~iel~l~~~~~e~a~~ 58 (84)
T PRK05783 16 RDPEGETIQRYVIERYTGNIIEVRAGKYLVFKIEANSPEEAKE 58 (84)
T ss_pred cCchHHHHHHHHHHcCCCCcceEEeeEEEEEEEcCCCHHHHHH
Confidence 366777776655333 221110013456666776666554443
No 93
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=23.46 E-value=3.2e+02 Score=20.46 Aligned_cols=72 Identities=14% Similarity=0.074 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCC-cchHHH
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPN-RNEALA 172 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~-~~l~~A 172 (220)
...++.|++ .++..||+|.|++. .+-..|.++|... ..|+. .-.-|.+++-.|.-...... -...++
T Consensus 31 ~~vlkalk~--gkaklViiA~D~~~---~~kkki~~~~~~~----~Vpv~---~~~~t~~eLG~A~Gk~~r~svvaI~D~ 98 (108)
T PTZ00106 31 KSTLKALRN--GKAKLVIISNNCPP---IRRSEIEYYAMLS----KTGVH---HYAGNNNDLGTACGRHFRVSVMSITDA 98 (108)
T ss_pred HHHHHHHHc--CCeeEEEEeCCCCH---HHHHHHHHHHhhc----CCCEE---EeCCCHHHHHHHhCCccCeEEEEEeCc
Confidence 445566654 57889999999974 4566777777763 45653 22347889999887543332 345555
Q ss_pred HHHHH
Q 048704 173 VDARQ 177 (220)
Q Consensus 173 ~~aR~ 177 (220)
++++.
T Consensus 99 G~a~~ 103 (108)
T PTZ00106 99 GDSDI 103 (108)
T ss_pred chHHH
Confidence 55554
No 94
>PRK13374 purine nucleoside phosphorylase; Provisional
Probab=23.13 E-value=1.6e+02 Score=24.98 Aligned_cols=46 Identities=20% Similarity=0.170 Sum_probs=28.2
Q ss_pred ceEEEEeChHHHHHHHH-HcCCCCcccccCCeeeeeecceecCCcceEEEE
Q 048704 5 KVLMVAEKPSIALSIAT-VLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVT 54 (220)
Q Consensus 5 ~~LiIaEKPs~Ak~ia~-~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt 54 (220)
+.+|++.-|.-++.||+ .|.....-....++.+| .|.|+|. .+.|+
T Consensus 15 ~~vi~~Gdp~R~~~~a~~~~~~~~~~~~~~~~~~~--~G~~~g~--~v~v~ 61 (233)
T PRK13374 15 ETVLMPGDPLRAKYIAETYLEDVVQVTDVRNMFGF--TGTYKGK--KVSVM 61 (233)
T ss_pred CeEEecCCHHHHHHHHHHHhcCceeeecccceEEE--EEEECCE--EEEEE
Confidence 57899999999999996 67553211111233333 5677665 44443
No 95
>TIGR02679 conserved hypothetical protein TIGR02679. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
Probab=22.81 E-value=2.1e+02 Score=26.52 Aligned_cols=57 Identities=23% Similarity=0.148 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl 162 (220)
.....-|..+.+.-..++-.+|.|.||-.|+.++.+..+. .+ +| ++.++.++|+.+.
T Consensus 285 ~a~~~LL~~L~~~g~~l~YhGDfD~~Gi~Ia~~L~~r~~~------~p-wr-----md~~dY~~a~~~~ 341 (385)
T TIGR02679 285 AAQIKLLDLLAAAGARLYYHGDFDWPGLRIANGLIRRYGA------RP-WR-----FSAADYRAAVVGP 341 (385)
T ss_pred HHHHHHHHHHHhcCCeEEEecCCChhHHHHHHHHHHHhCC------cc-cc-----CCHHHHHHHhccC
Confidence 3344444444443334555599999999999999987763 12 33 4666677776643
No 96
>PRK14939 gyrB DNA gyrase subunit B; Provisional
Probab=22.28 E-value=70 Score=32.39 Aligned_cols=56 Identities=13% Similarity=0.141 Sum_probs=36.2
Q ss_pred CCeEEEecCCChhHhHHHHHHHHHhCCcccC---------CCCcEEEEEe-----cCcCHHHHHHHHhcC
Q 048704 107 CGHLVLWLDCDREGENICFEVIECTGFQVND---------ARRKVHRARF-----SSVTEKDILKAMGNL 162 (220)
Q Consensus 107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~---------~~~~v~R~~~-----sslt~~~I~~A~~nl 162 (220)
...|||.||+|-.|.+|--.++..+-...+. ...|++|+.- .-.|+.+..+=+..+
T Consensus 491 Y~kIiIMTDADvDGsHIrtLLltff~r~~p~Lie~G~vyia~pPLykv~~gk~~~y~~~~~e~~~~l~~~ 560 (756)
T PRK14939 491 YHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIEL 560 (756)
T ss_pred cCeEEEEcCCCCCchHHHHHHHHHHHHhChhhccCCeEEEecCcEEEEecCCeeEecCCHHHHHHHHHHh
Confidence 4579999999999999988776644321111 1236777654 345666666666544
No 97
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=21.70 E-value=1.3e+02 Score=25.03 Aligned_cols=32 Identities=19% Similarity=0.174 Sum_probs=19.7
Q ss_pred HHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhC
Q 048704 98 RHLNQEARGCGHLVLWLDCDREGENICFEVIECTG 132 (220)
Q Consensus 98 ~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~ 132 (220)
..|+..+. -..+|+.||.+|| +-...|+..++
T Consensus 35 ~~l~~il~-G~s~iliTD~~R~--WF~~Yil~~IN 66 (180)
T PF12163_consen 35 SALSHILN-GGSFILITDEERE--WFEEYILSNIN 66 (180)
T ss_dssp HHHHHHHT-T-EEEEEE-GGGH--HHHHHHHHHHS
T ss_pred HHHHHHhC-CCeEEEEeCchhH--HHHHHHHHhcC
Confidence 35555554 4579999999997 33445666666
No 98
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.65 E-value=1e+02 Score=27.66 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=20.6
Q ss_pred CcHHHHHHHHHHhc---cCCeEEEecCCCh
Q 048704 92 PKVHICRHLNQEAR---GCGHLVLWLDCDR 118 (220)
Q Consensus 92 ~~~~~~~~lk~~~~---~ad~ii~AtD~Dr 118 (220)
+++.++++|+...+ ++..|++|+|.|.
T Consensus 282 sk~~I~rqik~~v~si~dakSVfVAsDs~h 311 (386)
T KOG3849|consen 282 SKQQILRQIKEKVGSIGDAKSVFVASDSDH 311 (386)
T ss_pred cHHHHHHHHHHHHhhhcccceEEEeccchh
Confidence 45677888876554 6779999999985
No 99
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=20.54 E-value=1.2e+02 Score=23.31 Aligned_cols=56 Identities=13% Similarity=0.119 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhc
Q 048704 94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN 161 (220)
Q Consensus 94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~n 161 (220)
....+.|.+ +++.-||+|.|.|.+ .+..++-..|... +-|+ ..--+.+++=+|+.-
T Consensus 33 ~e~~Kai~~--g~a~LVviA~Dv~P~--~~~~~l~~lc~~~----~vpy----v~V~sk~~LG~a~g~ 88 (116)
T COG1358 33 NEVTKAIER--GKAKLVVIAEDVSPE--ELVKHLPALCEEK----NVPY----VYVGSKKELGKAVGK 88 (116)
T ss_pred HHHHHHHHc--CCCcEEEEecCCCHH--HHHHHHHHHHHhc----CCCE----EEeCCHHHHHHHhCC
Confidence 344555554 578999999999954 3556677777642 2343 223356777777653
No 100
>COG1445 FrwB Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]
Probab=20.27 E-value=72 Score=24.83 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=30.9
Q ss_pred HhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecC---cCHHHHHHHHhcCCCCC
Q 048704 103 EARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSS---VTEKDILKAMGNLVEPN 166 (220)
Q Consensus 103 ~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~ss---lt~~~I~~A~~nl~~~~ 166 (220)
.+..||.||+|+|-+-+++- .+. .+++.|+=... -.++-|.+++++..+..
T Consensus 53 dI~~Ad~VI~AaD~~i~~~~-------ff~------gk~vi~~~~~~aik~~~~li~~a~~~~~~~~ 106 (122)
T COG1445 53 DIAAADVVILAADIEVDLSR-------FFA------GKPVIEVSTKDAIKNPAQLISKALAEAAPPQ 106 (122)
T ss_pred HHHhCCEEEEEecccccHhH-------hhc------CCeEEEecHHHHHhCHHHHHHHHHhcccccc
Confidence 34679999999999988873 221 13555443331 12455666666665543
Done!