Query psy15222
Match_columns 444
No_of_seqs 340 out of 1831
Neff 6.6
Searched_HMMs 46136
Date Sat Aug 17 00:20:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05667 dnaG DNA primase; Val 100.0 2.1E-77 4.7E-82 641.6 46.3 417 1-439 114-538 (580)
2 TIGR01391 dnaG DNA primase, ca 100.0 1.2E-68 2.5E-73 556.0 35.2 293 1-310 117-415 (415)
3 COG0358 DnaG DNA primase (bact 100.0 8.6E-65 1.9E-69 546.1 32.4 300 1-320 112-415 (568)
4 TIGR00646 MG010 DNA primase-re 100.0 3E-51 6.5E-56 385.7 19.4 190 40-256 23-216 (218)
5 PHA02540 61 DNA primase; Provi 100.0 2.5E-46 5.3E-51 374.8 21.2 203 11-264 123-330 (337)
6 PHA02031 putative DnaG-like pr 100.0 6E-45 1.3E-49 350.4 15.5 171 42-251 85-263 (266)
7 PRK08624 hypothetical protein; 100.0 1.4E-39 3E-44 326.8 19.9 189 17-253 154-358 (373)
8 PF08275 Toprim_N: DNA primase 100.0 1E-36 2.3E-41 268.3 10.0 124 7-142 1-128 (128)
9 TIGR02760 TraI_TIGR conjugativ 99.8 8.4E-20 1.8E-24 218.5 20.9 209 2-268 1670-1889(1960)
10 PHA02415 DNA primase domain-co 99.7 1.2E-17 2.5E-22 179.4 13.9 209 10-259 116-355 (930)
11 PRK04031 DNA primase; Provisio 99.7 1.6E-17 3.4E-22 168.6 11.7 120 134-266 153-274 (408)
12 cd03364 TOPRIM_DnaG_primases T 99.7 2.5E-16 5.4E-21 127.1 11.3 78 149-229 1-78 (79)
13 PF13155 Toprim_2: Toprim-like 99.6 4.8E-16 1E-20 129.3 8.3 89 152-240 1-96 (96)
14 PF13662 Toprim_4: Toprim doma 99.6 5.6E-15 1.2E-19 119.7 8.5 77 149-228 1-80 (81)
15 cd01027 TOPRIM_RNase_M5_like T 99.5 2.9E-14 6.3E-19 115.8 8.9 67 149-215 2-69 (81)
16 cd01029 TOPRIM_primases TOPRIM 99.5 1.5E-13 3.2E-18 110.3 10.8 77 149-228 1-77 (79)
17 PF13362 Toprim_3: Toprim doma 99.3 6.5E-12 1.4E-16 104.8 7.5 91 150-246 1-96 (96)
18 smart00493 TOPRIM topoisomeras 99.3 1E-11 2.2E-16 98.7 7.5 68 149-216 1-72 (76)
19 PRK07078 hypothetical protein; 99.1 1.2E-09 2.6E-14 121.3 14.8 152 92-253 135-298 (759)
20 PF12965 DUF3854: Domain of un 99.0 1.1E-09 2.3E-14 96.9 8.8 100 148-248 10-130 (130)
21 PF10410 DnaB_bind: DnaB-helic 99.0 7.9E-10 1.7E-14 83.9 6.0 59 258-317 1-59 (59)
22 cd00188 TOPRIM Topoisomerase-p 98.7 6.9E-08 1.5E-12 75.7 8.0 68 149-216 1-72 (83)
23 PF01751 Toprim: Toprim domain 98.0 1.4E-05 3E-10 67.1 6.0 69 150-218 1-87 (100)
24 PRK04017 hypothetical protein; 97.9 0.00017 3.7E-09 63.8 11.5 69 147-216 21-90 (132)
25 PF08278 DnaG_DnaB_bind: DNA p 97.8 8.6E-05 1.9E-09 64.9 7.9 93 343-441 1-96 (127)
26 COG1658 Small primase-like pro 97.7 0.00018 3.9E-09 63.3 7.8 69 147-215 8-79 (127)
27 TIGR00334 5S_RNA_mat_M5 ribonu 97.5 0.00078 1.7E-08 62.2 10.3 102 149-257 3-110 (174)
28 smart00766 DnaG_DnaB_bind DNA 97.5 0.0005 1.1E-08 58.0 8.4 93 344-441 1-94 (125)
29 COG4643 Uncharacterized protei 97.1 0.0031 6.7E-08 63.3 9.4 144 87-251 155-309 (366)
30 PRK14719 bifunctional RNAse/5- 96.2 0.016 3.4E-07 59.9 7.8 75 147-225 22-98 (360)
31 KOG2373|consensus 95.1 0.11 2.4E-06 53.0 8.9 136 118-263 95-232 (514)
32 PF00772 DnaB: DnaB-like helic 94.5 0.37 8E-06 39.9 9.4 64 340-406 5-69 (103)
33 PF13154 DUF3991: Protein of u 94.3 0.11 2.5E-06 41.5 5.6 22 91-112 29-50 (77)
34 COG3593 Predicted ATP-dependen 93.9 0.39 8.4E-06 52.5 10.4 84 130-214 378-471 (581)
35 COG4026 Uncharacterized protei 93.5 0.58 1.3E-05 44.8 9.5 82 150-237 9-101 (290)
36 cd01026 TOPRIM_OLD TOPRIM_OLD: 91.8 0.38 8.1E-06 40.0 5.4 59 148-206 3-70 (97)
37 PRK00076 recR recombination pr 90.1 2.1 4.6E-05 40.6 9.2 87 147-236 77-178 (196)
38 cd01025 TOPRIM_recR TOPRIM_rec 90.0 2.6 5.6E-05 36.5 8.9 83 150-235 2-100 (112)
39 TIGR00615 recR recombination p 87.2 5.8 0.00012 37.6 10.0 87 147-236 77-179 (195)
40 COG0353 RecR Recombinational D 87.1 5.4 0.00012 37.7 9.7 87 147-236 78-180 (198)
41 PRK13844 recombination protein 82.1 12 0.00026 35.6 9.7 86 147-236 81-182 (200)
42 PRK06321 replicative DNA helic 67.9 14 0.00029 39.8 6.8 65 339-406 18-83 (472)
43 PRK05748 replicative DNA helic 64.6 15 0.00032 39.1 6.3 64 340-406 13-77 (448)
44 TIGR03600 phage_DnaB phage rep 63.9 13 0.00029 38.9 5.8 62 342-406 3-65 (421)
45 TIGR00665 DnaB replicative DNA 62.4 18 0.00039 38.1 6.4 63 341-406 6-69 (434)
46 PRK08760 replicative DNA helic 60.9 23 0.00049 38.2 6.9 64 340-406 36-100 (476)
47 PRK05595 replicative DNA helic 60.7 21 0.00046 37.9 6.6 65 339-406 10-75 (444)
48 PRK06904 replicative DNA helic 60.2 22 0.00048 38.2 6.7 65 339-406 25-90 (472)
49 PRK08506 replicative DNA helic 60.1 49 0.0011 35.6 9.3 63 341-406 7-70 (472)
50 PRK08840 replicative DNA helic 59.7 21 0.00045 38.4 6.3 64 340-406 23-87 (464)
51 PRK05636 replicative DNA helic 57.2 23 0.0005 38.4 6.2 64 340-406 73-137 (505)
52 PRK09165 replicative DNA helic 54.7 26 0.00057 37.9 6.2 65 339-406 23-88 (497)
53 COG5440 Uncharacterized conser 54.5 56 0.0012 29.8 7.1 59 171-243 56-114 (161)
54 PRK08006 replicative DNA helic 54.3 29 0.00062 37.4 6.3 64 340-406 30-94 (471)
55 PRK07004 replicative DNA helic 53.4 30 0.00065 37.1 6.3 64 340-406 18-82 (460)
56 cd01028 TOPRIM_TopoIA TOPRIM_T 48.7 26 0.00057 31.0 4.2 46 184-232 84-129 (142)
57 PF09664 DUF2399: Protein of u 47.8 61 0.0013 29.4 6.5 83 148-243 18-106 (152)
58 COG0305 DnaB Replicative DNA h 45.9 44 0.00095 35.7 6.0 66 339-406 5-70 (435)
59 PF09133 SANTA: SANTA (SANT As 44.2 18 0.00038 30.1 2.2 29 20-49 62-90 (93)
60 PRK07773 replicative DNA helic 43.5 46 0.001 38.7 6.2 65 339-406 26-91 (886)
61 cd03363 TOPRIM_TopoIA_TopoI TO 43.3 57 0.0012 28.4 5.4 53 182-239 61-116 (123)
62 cd03362 TOPRIM_TopoIA_TopoIII 42.1 32 0.00069 30.8 3.8 46 184-231 92-137 (151)
63 PF07057 TraI: DNA helicase Tr 41.6 32 0.0007 30.3 3.5 48 58-112 66-113 (126)
64 TIGR02109 PQQ_syn_pqqE coenzym 41.0 1.1E+02 0.0023 31.3 7.9 48 155-202 68-117 (358)
65 PRK13745 anaerobic sulfatase-m 40.0 59 0.0013 34.1 5.9 37 167-203 101-137 (412)
66 PRK06749 replicative DNA helic 39.4 63 0.0014 34.3 6.0 60 341-404 6-65 (428)
67 PRK05301 pyrroloquinoline quin 36.9 1.3E+02 0.0028 30.9 7.8 44 157-200 79-124 (378)
68 cd03361 TOPRIM_TopoIA_RevGyr T 35.0 61 0.0013 29.9 4.5 36 181-216 106-144 (170)
69 PF13743 Thioredoxin_5: Thiore 33.9 2.3E+02 0.0049 26.0 8.2 107 212-322 18-125 (176)
70 PF14827 Cache_3: Sensory doma 33.9 39 0.00084 28.7 2.8 18 91-108 90-107 (116)
71 PHA02542 41 41 helicase; Provi 33.0 2E+02 0.0042 31.1 8.6 61 343-406 1-63 (473)
72 cd00223 TOPRIM_TopoIIB_SPO TOP 32.4 67 0.0015 29.0 4.3 61 150-210 2-70 (160)
73 PF08281 Sigma70_r4_2: Sigma-7 32.1 1.5E+02 0.0032 21.1 5.4 20 303-322 29-48 (54)
74 COG0641 AslB Arylsulfatase reg 31.3 1.5E+02 0.0032 31.1 7.1 50 168-217 91-153 (378)
75 PF04391 DUF533: Protein of un 30.5 4.4E+02 0.0096 24.8 9.5 45 273-320 139-183 (188)
76 TIGR03820 lys_2_3_AblA lysine- 28.9 1.7E+02 0.0037 31.1 7.1 99 174-279 199-301 (417)
77 PF08220 HTH_DeoR: DeoR-like h 28.9 62 0.0014 24.0 2.9 21 302-322 16-36 (57)
78 PRK13758 anaerobic sulfatase-m 28.6 90 0.002 31.9 5.0 33 170-202 95-127 (370)
79 cd07983 LPLAT_DUF374-like Lyso 27.1 3.6E+02 0.0079 24.4 8.4 79 148-234 25-107 (189)
80 PF14850 Pro_dh-DNA_bdg: DNA-b 27.1 1.5E+02 0.0032 25.8 5.1 39 263-304 3-41 (114)
81 PF00582 Usp: Universal stress 26.5 2E+02 0.0043 23.3 6.0 35 191-228 2-36 (140)
82 TIGR00646 MG010 DNA primase-re 25.8 87 0.0019 30.3 3.9 39 3-41 10-55 (218)
83 PF09397 Ftsk_gamma: Ftsk gamm 25.5 50 0.0011 25.7 1.8 45 16-71 9-55 (65)
84 COG3444 Phosphotransferase sys 25.1 2.1E+02 0.0046 26.3 6.1 71 148-233 77-148 (159)
85 PF09999 DUF2240: Uncharacteri 25.1 5.2E+02 0.011 23.4 10.1 106 193-318 24-141 (144)
86 TIGR02679 conserved hypothetic 24.7 3.9E+02 0.0084 28.1 8.8 80 150-242 252-337 (385)
87 smart00843 Ftsk_gamma This dom 24.4 77 0.0017 24.6 2.7 44 17-71 9-54 (63)
88 PF13707 RloB: RloB-like prote 24.4 1.3E+02 0.0028 27.3 4.8 11 191-201 60-70 (183)
89 PF06971 Put_DNA-bind_N: Putat 21.7 99 0.0022 22.8 2.7 19 303-321 31-49 (50)
90 PF01418 HTH_6: Helix-turn-hel 21.5 2.9E+02 0.0063 21.6 5.6 22 301-322 35-56 (77)
91 PF13413 HTH_25: Helix-turn-he 21.1 1.3E+02 0.0029 22.8 3.5 29 288-317 34-62 (62)
92 PF04273 DUF442: Putative phos 20.9 2.2E+02 0.0049 24.2 5.2 76 178-261 14-92 (110)
93 PF00949 Peptidase_S7: Peptida 20.9 82 0.0018 28.0 2.5 17 96-112 102-118 (132)
94 smart00351 PAX Paired Box doma 20.4 2.5E+02 0.0053 24.3 5.5 57 303-359 36-96 (125)
No 1
>PRK05667 dnaG DNA primase; Validated
Probab=100.00 E-value=2.1e-77 Score=641.56 Aligned_cols=417 Identities=36% Similarity=0.554 Sum_probs=353.4
Q ss_pred CHHHHHHHHHHhc--CCHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCC
Q psy15222 1 MICASDFYKIQLK--NSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQ 76 (444)
Q Consensus 1 ~~~a~~~y~~~L~--~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~ 76 (444)
|+.|++||+.+|. .++.|++||++||||++||++|+|||+|.+|+.|.++|.+ ++. +.|.++||+..++++
T Consensus 114 ~~~a~~~y~~~L~~~~~~~a~~YL~~RGls~~~i~~f~lGyap~~~~~L~~~l~~~~~~~-~~l~~~GL~~~~~~~---- 188 (580)
T PRK05667 114 MELAAKFYQQQLRTPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSE-KELEEAGLLIKNEDG---- 188 (580)
T ss_pred HHHHHHHHHHHHcCccchHHHHHHHHcCCCHHHHHHhCCccCCChHHHHHHHHHhcCCCH-HHHHHCCceEecCCC----
Confidence 4689999999995 4578999999999999999999999999999999999975 666 889999999876541
Q ss_pred CcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecC
Q psy15222 77 SPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEG 156 (444)
Q Consensus 77 g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG 156 (444)
| .+||+|++||||||+|.+|+||||+||.+ +++.|||+|||||++|+|++.|||+|.|++++++.++||||||
T Consensus 189 ~------~~yd~Fr~RimfPI~d~~G~vigF~GR~l-~~~~pKYlNSpet~iF~K~~~LYgl~~a~~~i~~~~~viivEG 261 (580)
T PRK05667 189 G------GPYDRFRNRIMFPIRDLRGRVIGFGGRVL-GDDKPKYLNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEG 261 (580)
T ss_pred C------CcchhcCCeEEEEEECCCCcEEEEEeeec-CCCCCeeeCCCCCCCccCCccccCccHHHHhcccCCeEEEEee
Confidence 4 58999999999999999999999999999 4678999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCc
Q psy15222 157 YMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDP 236 (444)
Q Consensus 157 ~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDp 236 (444)
|||||+++|+|++||||++||++|.+|+++|++++++||+|||||.||++||+|+++.++++...|+.|+++.+|+|+||
T Consensus 262 ~~Dvisl~q~Gi~naVA~lGtalt~~~~~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~gkDp 341 (580)
T PRK05667 262 YMDVIALHQAGITNAVASLGTALTEEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDP 341 (580)
T ss_pred HHHHHHHHHcCCCcEEEeCCCCCCHHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCCCCCh
Confidence 99999999999999999999999999999999999999999999999999999999997777778999999999999999
Q ss_pred chhhhhhcHHHHHHHHHhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHH
Q psy15222 237 DSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNE 316 (444)
Q Consensus 237 dd~l~~~G~~~~~~~l~~a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~ 316 (444)
|||++++|.++|.++++++.|+++|+++++.+++|++++++|.++++++.++|+.+++ |++|+.|++++|+++|++.+.
T Consensus 342 dd~l~~~G~~~~~~~i~~a~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~-~~~~~~~~~~l~~~~~~~~~~ 420 (580)
T PRK05667 342 DDLVRKEGPEAFRALLEQAIPLSEFLIRRLIPGKDLDTPEGRAALLERAAPLIAKIPD-PTLRDSYRRKLAERLGILDDA 420 (580)
T ss_pred HHHHHHhCHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHHCcCHHH
Confidence 9999999999999999999999999999999999999999999999999999999999 999999999999999999999
Q ss_pred HHHHHhhcccccccccccccCCChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCH
Q psy15222 317 INNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDH 396 (444)
Q Consensus 317 i~~~~~~~~~~~~~~~~~~~~~~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 396 (444)
+.+.+..... + +..+......+|+.+|++|+++|++...+... +... .| +....+..++..+...+...+.
T Consensus 421 l~~~~~~~~~--~---~~~~~~~~~~~~~~ll~~ll~~p~~~~~~~~~-~~~~-~~--~~~~~~~~l~~~~~~~~~~~~~ 491 (580)
T PRK05667 421 QLEQLVPKAQ--E---PQLKAERPRTAERELLALLLQHPELAEEVRDA-LDEE-DF--EGLPLFRALLEAILAQPGLTTG 491 (580)
T ss_pred HHHHHhhccc--c---ccccccccchHHHHHHHHHHhCHHHHHHHHHh-cccc-cc--cCcHHHHHHHHHHHhcCCCCcH
Confidence 9887653111 1 11122345678999999999999999888653 2111 12 1344455555555553556677
Q ss_pred HHHHHHHHhh-hHHHHHHHHHHhcCCCCCH-HHH--HHHHHHHHHhh
Q psy15222 397 SKFIKYLKKI-NKNFESIIVKIQDNFEYSI-EIA--KKTLLDAIYKD 439 (444)
Q Consensus 397 ~~l~~~l~~~-~~~~~~~~~~~~~~~e~~~-e~~--~~~~~~~~~~~ 439 (444)
..|++.+.+. ...+...+..+....+... +.. .+.+.|++...
T Consensus 492 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~d~~~~l 538 (580)
T PRK05667 492 SQLLEHLRDAGLEELAALLESLAVWEEISEEDIAALEKELKDALEKL 538 (580)
T ss_pred HHHHHHHHhhcchhHHHHHHHHhccccccchhhhHHHHHHHHHHHHH
Confidence 7999999976 2223333344443344332 222 47777776654
No 2
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=100.00 E-value=1.2e-68 Score=556.02 Aligned_cols=293 Identities=44% Similarity=0.734 Sum_probs=277.3
Q ss_pred CHHHHHHHHHHhcC---CHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc---CCchhHHHHcCCceecccccc
Q psy15222 1 MICASDFYKIQLKN---SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD---YNNINTLASSGLVVDKIINKV 74 (444)
Q Consensus 1 ~~~a~~~y~~~L~~---~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~---~~~~~~l~~~GL~~~~~~~~~ 74 (444)
++.|++||+++|.. ++.|++||++||||+++|+.|+|||+|.+|+.|.+++.+ |+. +.|.++||+..+++
T Consensus 117 ~~~a~~~y~~~L~~~~~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~l~~~l~~k~~~~~-~~l~~~Gl~~~~~~--- 192 (415)
T TIGR01391 117 LELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELGYAPNNWDFLFDFLQNKKGFDL-ELLAEAGLLVKKEN--- 192 (415)
T ss_pred HHHHHHHHHHHhccCccchHHHHHHHHcCCCHHHHHHcCCCCCCCcHHHHHHHHHhccCCCH-HHHHHCCCeEECCC---
Confidence 36789999999987 457899999999999999999999999999999999864 566 89999999998765
Q ss_pred CCCcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEe
Q psy15222 75 NQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLIT 154 (444)
Q Consensus 75 ~~g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIv 154 (444)
| .+||+|++||||||+|.+|+||||+||.+ +++.|||+|||+|++|+|++.|||+|.|++.+++.++||||
T Consensus 193 --g------~~~d~Fr~RiifPi~d~~G~vvgf~gR~~-~~~~pKYlNspet~~f~K~~~lygl~~a~~~~~~~~~viiv 263 (415)
T TIGR01391 193 --G------KYYDRFRNRIMFPIHDPKGRVVGFGGRAL-GDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILV 263 (415)
T ss_pred --C------CeeeecCCeEEEEEECCCCCEEEEEeeec-CCCCCceeCCCCCCCccCCccccCHhHHHHhhccCCcEEEE
Confidence 5 58999999999999999999999999999 47789999999999999999999999999999999999999
Q ss_pred cChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCC
Q psy15222 155 EGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKY 234 (444)
Q Consensus 155 EG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gk 234 (444)
|||||||+++|+|++||||++||++|.+|+++|++++++||+|||+|.||++||.++++.+.+ .|+.++++.+|+||
T Consensus 264 EG~~Daisl~~~G~~~aVA~~Gtalt~~~~~~l~r~~~~vvl~~D~D~aG~~aa~r~~~~l~~---~g~~v~v~~lp~gk 340 (415)
T TIGR01391 264 EGYMDVIALHQAGIKNAVASLGTALTEEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLP---LGINVKVIKLPGGK 340 (415)
T ss_pred ecHHHHHHHHHCCCCcEEECCCCCCcHHHHHHHHhhCCeEEEEeCCCHHHHHHHHHHHHHHHH---cCCeEEEEECCCCC
Confidence 999999999999999999999999999999999999899999999999999999999998875 58999999999999
Q ss_pred CcchhhhhhcHHHHHHHHHhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHh
Q psy15222 235 DPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKII 310 (444)
Q Consensus 235 Dpdd~l~~~G~~~~~~~l~~a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~ 310 (444)
|||||++++|.++|+++|+++.|+++|+++.+.++++++++++|.++++++.++|..+++ +++|+.|++.+|+++
T Consensus 341 Dpdd~l~~~g~~~~~~~l~~a~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 415 (415)
T TIGR01391 341 DPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNYNLDTPEEKAKLVEELLPLIKKIPD-PILRDYYLQKLAQLL 415 (415)
T ss_pred CHHHHHHHhCHHHHHHHHhcCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999999999999999999999 999999999999864
No 3
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.6e-65 Score=546.08 Aligned_cols=300 Identities=40% Similarity=0.662 Sum_probs=280.6
Q ss_pred CHHHHHHHHHHhc-CCHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCCC
Q psy15222 1 MICASDFYKIQLK-NSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQS 77 (444)
Q Consensus 1 ~~~a~~~y~~~L~-~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~g 77 (444)
|+.|+.||+.+|. .+++|+.||++||++.++++.|+|||||++ +.+..+..+ |.. ..+.++|++..++ |
T Consensus 112 ~~~~~~fy~~~L~~~~~~a~~yL~~Rgls~~~i~~f~iG~ap~~-~~~~~~~~k~~~~~-~~l~~~Gl~~~~~------~ 183 (568)
T COG0358 112 KEEAAIFYQSSLDPEGAAALKYLETRGLAAELIAHFRLGYAPPN-DSLLPFLAKKEYRE-EKLEDLGLLKRKE------G 183 (568)
T ss_pred HHHHHHHHHHHHHhchHHHHHHHHHcCCCHHHHHHhCCCCCCCc-hHHHHHHhcCCcCH-HHHHHCCCeecCC------C
Confidence 5789999999999 677899999999999999999999999999 888833333 456 8999999999765 2
Q ss_pred cccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecCh
Q psy15222 78 PVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGY 157 (444)
Q Consensus 78 ~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~ 157 (444)
.+||+|++||||||+|..|+|||||||.++ +..|||+|||||++|+||+.|||++.|++.+++.+.+||||||
T Consensus 184 ------~~ydrFr~RImfPI~d~~g~vigFggR~l~-~~~~KYlNspet~if~Kg~~Lyg~~~a~~~~~~~~~iivVEGy 256 (568)
T COG0358 184 ------KIYDRFRNRIMFPIRDLRGDVIGFGGRVLG-DDKPKYLNSPETELFKKGEELYGLDPARKKIAKADQIIVVEGY 256 (568)
T ss_pred ------ceeehhcCeeEEeccCCCCCEEeeeccccC-CCCCcccCCCCCcCccCcHHhhCHHHHHHhhccCCeEEEEech
Confidence 589999999999999999999999999995 7779999999999999999999999999999999999999999
Q ss_pred hhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcc
Q psy15222 158 MDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPD 237 (444)
Q Consensus 158 ~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpd 237 (444)
||||+++++||.||||+|||++|++|+.+|+|..++||+|||||.||++||+|+++.+++....| ++|+.+|+|+|||
T Consensus 257 mDViaL~~aGi~naVA~lGTalt~ehi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~~~~~~--v~v~~~P~GkDpD 334 (568)
T COG0358 257 MDVIALHKAGIKNAVASLGTALTEEHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLDFVG--VFVILLPDGKDPD 334 (568)
T ss_pred HHHHHHHHcCCcceeecccccCCHHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhhhccCC--eEEEECCCCCChH
Confidence 99999999999999999999999999999999999999999999999999999999888887777 8999999999999
Q ss_pred hhhhhhcHHHHHHHHHh-cCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHH
Q psy15222 238 SYIRKFGYKIFSKKVLE-AMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNE 316 (444)
Q Consensus 238 d~l~~~G~~~~~~~l~~-a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~ 316 (444)
|+++++|.++|.+.+.+ +.++++|+++.+... ++++ ++|.++++++.+.++.+++ +..|..|.+.+++.++++.+.
T Consensus 335 el~~k~g~~al~~~l~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~ 411 (568)
T COG0358 335 ELIRKEGAEALRKKLPNERLPLIEFLIEYLIPS-NLDT-EGKARLVEEAVPLIKVIPD-EVLRDYYLQKLAELLGISDDA 411 (568)
T ss_pred HHHHHhChHHHHHHHHhCCcCHHHHHHHHhccc-CcCc-hHHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHHhCCCHHH
Confidence 99999999999999877 899999999999888 8888 9999999999999999999 999999999999999999988
Q ss_pred HHHH
Q psy15222 317 INNL 320 (444)
Q Consensus 317 i~~~ 320 (444)
+...
T Consensus 412 ~~~~ 415 (568)
T COG0358 412 LLQL 415 (568)
T ss_pred HHHH
Confidence 7653
No 4
>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=100.00 E-value=3e-51 Score=385.67 Aligned_cols=190 Identities=20% Similarity=0.277 Sum_probs=163.7
Q ss_pred ecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCCCcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCC
Q psy15222 40 APNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNE 117 (444)
Q Consensus 40 ap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~ 117 (444)
+|+.|+.|.++|++ |+. ++++++|+ | ..|++|++||||||+|.+|+||||+||++ ++ .
T Consensus 23 ~~~~~~~l~~~l~~~g~~~-~~~~~~G~-----------~------~~y~~~~~RimFPI~d~~G~vvgFgGR~l-~~-~ 82 (218)
T TIGR00646 23 SKSKYRCAMNYLKKRGFNL-QDFLKVGG-----------G------LAYLGEKEWLNLPLYNFDGNLIGFLNRKV-GF-E 82 (218)
T ss_pred CchhHHHHHHHHHHcCCCH-HHHHHcCC-----------C------EEecccCCEEEEEEECCCCCEEEEeccCC-CC-C
Confidence 34556666666542 555 66677764 2 35899999999999999999999999999 43 6
Q ss_pred cccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhcc-CCeEEE
Q psy15222 118 AKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFY-TNSIIF 196 (444)
Q Consensus 118 pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~-~~~Vil 196 (444)
|||+|||||++|+||+.|||++.+ +++.+.+|||||||||||++|+|+.|+||+|||++|++|++.|++. +++|++
T Consensus 83 ~KYlNspet~~f~K~~~Lygl~~~---~~k~~~vilvEGymDVIsl~qaGi~naVAslGTALT~~q~~lLkr~~~~~Iil 159 (218)
T TIGR00646 83 KEFLYLPFNKPPSKSEAFLGLKEL---PIEDNSIYLVEGDFDWLAFRKAGILNCLPLCGLTISDKQMKFFKQKKIEKIFI 159 (218)
T ss_pred CCcccCCCCCCcccchhhcCcchh---hcCCCEEEEEecHHHHHHHHHCCCCeEEEcCchHhHHHHHHHHhccCCCEEEE
Confidence 999999999999999999999754 5688999999999999999999999999999999999999999985 789999
Q ss_pred EeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCC-CCCcchhhhhhcHHHHHHHHHhcC
Q psy15222 197 SFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPD-KYDPDSYIRKFGYKIFSKKVLEAM 256 (444)
Q Consensus 197 ~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~-gkDpdd~l~~~G~~~~~~~l~~a~ 256 (444)
|||||.||++||.|+++.+. ..|+.++++.+|+ +|||||+++.+| +.+.++|+++.
T Consensus 160 ~~D~D~AG~~Aa~r~~~~L~---~~G~~v~vv~lP~~~KDwNEllk~~~-~~w~~~l~~~~ 216 (218)
T TIGR00646 160 CFDNDFAGKNAAANLEEILK---KAGFITKVIEIKAAAKDWNDLFLLNN-KNWAAALRDHL 216 (218)
T ss_pred EeCCCHHHHHHHHHHHHHHH---HCCCeEEEEeCCCcCCChhHHHHHhh-hhHHHHHHhhh
Confidence 99999999999999999875 3699999999986 599999998776 45788877653
No 5
>PHA02540 61 DNA primase; Provisional
Probab=100.00 E-value=2.5e-46 Score=374.84 Aligned_cols=203 Identities=19% Similarity=0.258 Sum_probs=172.8
Q ss_pred HhcCCHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhccCCchhHHHHcCCceeccccccCCCcccccccccccCC
Q psy15222 11 QLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFR 90 (444)
Q Consensus 11 ~L~~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd~F~ 90 (444)
.|..+++|++||++||||+++++. ||+|++|+.|.+++..-+. . ..+| +
T Consensus 123 ~l~~~~~a~~YL~~RGi~~~~~~~---~~~~~~~~~l~~~l~~~~~--------------~------------~~~d--~ 171 (337)
T PHA02540 123 TLPEDHPIIKYVENRCIPKDKWKL---LYFTREWQKLVNSIKPDTY--------------K------------KEKP--E 171 (337)
T ss_pred hCcccHHHHHHHHHcCCCHHHHHh---cCCCccHHHHHHHHhhccC--------------c------------hhcc--C
Confidence 355677899999999999999885 5778899999887643111 0 1134 4
Q ss_pred ceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHHcCCCe
Q psy15222 91 GRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQ 170 (444)
Q Consensus 91 ~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q~Gi~n 170 (444)
+||||||+|.+|+||||+||+++++..||||||| +|+|++.|||++.|+ +.+.+||||||||||+ ++|
T Consensus 172 ~RImFPI~d~~G~vigFgGR~l~~~~~pKYlNSp---~f~K~~~LYGl~~a~----~~~~vilvEGYmDvi~-----i~n 239 (337)
T PHA02540 172 PRLVIPIFNKDGKIESFQGRALRKDAPQKYITIK---ADEEATKIYGLDRID----PGKTVYVVEGPIDSLF-----LPN 239 (337)
T ss_pred CeeEEEEECCCCCEEEEEeEECCCCCCCCeeeCC---cccccccccChhHhc----cCCEEEEEeCCcceee-----ecc
Confidence 9999999999999999999999655789999986 689999999999765 6789999999999997 689
Q ss_pred EEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCC--CCCCcchhhhhhcH--H
Q psy15222 171 TVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLP--DKYDPDSYIRKFGY--K 246 (444)
Q Consensus 171 aVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP--~gkDpdd~l~~~G~--~ 246 (444)
|||+|||++|.+|+ +++++||+||||| ||++||.|+++.++. .|+.|.++..| ++||||||++++|. +
T Consensus 240 aVAtlGTaLT~~~~----~~~~~vvl~~D~D-a~~~at~r~~~~l~~---~g~~v~v~~~~~~~~kDpde~i~~~G~~~~ 311 (337)
T PHA02540 240 SIAITGGDLDLNEV----PFKDTRVWVLDNE-PRHPDTIKRISKLID---AGEKVVIWDKCPWPSKDINDMIMKGGATPE 311 (337)
T ss_pred ceeeCccccCHhHh----CccceEEEEECCc-hhHHHHHHHHHHHHH---CCCeEEEecCCCCCCcCHHHHHHhcCCCHH
Confidence 99999999999997 5788999999999 888999999998764 68887766555 56999999999996 8
Q ss_pred HHHHHHHhc-CCHHHHHHH
Q psy15222 247 IFSKKVLEA-MSLLQFFLE 264 (444)
Q Consensus 247 ~~~~~l~~a-~~~~~f~~~ 264 (444)
.|.++|++. .+.++|.++
T Consensus 312 ~~~~~i~~n~~~gl~ak~~ 330 (337)
T PHA02540 312 DIMEYIKSNTYQGLMAKLR 330 (337)
T ss_pred HHHHHHHHccccHHHHHHH
Confidence 899999876 899999876
No 6
>PHA02031 putative DnaG-like primase
Probab=100.00 E-value=6e-45 Score=350.37 Aligned_cols=171 Identities=20% Similarity=0.307 Sum_probs=149.1
Q ss_pred CCchHHHHHhc--cCCchhHHHHcCCceeccccccCCCcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcc
Q psy15222 42 NEWNALNKVFL--DYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAK 119 (444)
Q Consensus 42 ~~~~~L~~~l~--~~~~~~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pK 119 (444)
+.|+.|.++|. +|+. +.+++.|+ .+||+||+||||||+| ||+||++ ++.+||
T Consensus 85 ~~w~~L~~~L~~kG~~~-~~l~~~~~------------------~~yDrFr~RimFPI~d------gFgGR~l-~~~~PK 138 (266)
T PHA02031 85 DAYQSLYGLLLSKGIDP-NMMEPGLP------------------LEYSERQGRLIFRTDA------GWLGRAT-ADQQPK 138 (266)
T ss_pred ChHHHHHHHHHHCCCCH-HHHHhcCC------------------cceeeeCCEEEEeecc------ccccccC-CCCCCC
Confidence 45789999987 4776 77766432 2589999999999998 9999999 667899
Q ss_pred ccc--CCCCCccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHH---cCCCeEEEcCCccCCHHHHHHHhcc-CCe
Q psy15222 120 YIN--SPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQ---FGFLQTVAILGTACTSTHIKKILFY-TNS 193 (444)
Q Consensus 120 YlN--spet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q---~Gi~naVA~lGtalt~~q~~~L~r~-~~~ 193 (444)
||| ||++ .|||++. ++++.+.+||||||||||++++ +|+.||||+|||+||++|+++|+++ +++
T Consensus 139 YLN~~SP~~-------~l~~~~~---~~~~~~~vIlvEGYmDVI~l~~a~~aG~~naVA~LGTALT~~q~~~L~r~~~~~ 208 (266)
T PHA02031 139 WVGYGYPAP-------DYVGWPP---ELSMPRPVVLTEDYLSALKVRWACNKPEVFAVALLGTRLRDRLAAILLQQTCPR 208 (266)
T ss_pred cCCCCCCcH-------HHhhchh---hhccCCeEEEEcCcHHHHHHHHHHhcCcceEEECCcccCCHHHHHHHHhcCCCC
Confidence 999 7644 4677654 5568999999999999999976 7999999999999999999999998 899
Q ss_pred EEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcchhhhhhcHHHHHHH
Q psy15222 194 IIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKK 251 (444)
Q Consensus 194 Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~G~~~~~~~ 251 (444)
||+|||||.||++||.|+++.+++ .|++++|+.+|+|+|||||+++.|.+++...
T Consensus 209 Vil~fDgD~AG~~Aa~ra~~~l~~---~~~~v~vv~lP~g~DPDd~ir~~i~eal~~~ 263 (266)
T PHA02031 209 VLIFLDGDPAGVDGSAGAMRRLRP---LLIEGQVIITPDGFDPKDLEREQIRELLIGR 263 (266)
T ss_pred EEEEeCCCHHHHHHHHHHHHHHHH---cCCceEEEECCCCCChHHHHHHHHHHHHhcc
Confidence 999999999999999999998875 4889999999999999999999998887654
No 7
>PRK08624 hypothetical protein; Provisional
Probab=100.00 E-value=1.4e-39 Score=326.77 Aligned_cols=189 Identities=21% Similarity=0.271 Sum_probs=147.0
Q ss_pred HHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhccCCchhHHHHcCCceeccccccCCCcccccccccccCCceEEEE
Q psy15222 17 EAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFP 96 (444)
Q Consensus 17 ~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd~F~~RiifP 96 (444)
+++.|+ +||||++|+++|+|||+ ||+|++|||||
T Consensus 154 ~~~~~l-~RGIs~etik~F~lGy~---------------------------------------------~D~Fr~RImFP 187 (373)
T PRK08624 154 PNRKWL-DEGISEKTQKYWEIKFY---------------------------------------------LDVISQRIIIP 187 (373)
T ss_pred cHHHHH-HcCCCHHHHHHhCCCcc---------------------------------------------ccccCCeeEEE
Confidence 344555 69999999999999996 36799999999
Q ss_pred EecCCCCEEEEEeeecCCC--CCcccccCC--CCC-ccccCCcccCcHHHHHHhhccCcEEEecChhhHH---HHHHcCC
Q psy15222 97 IKNTDGQIIGFGGRLIKDS--NEAKYINSP--ETP-LFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVI---GLSQFGF 168 (444)
Q Consensus 97 I~d~~G~vvgf~gR~l~~~--~~pKYlNsp--et~-~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvl---sl~q~Gi 168 (444)
|+|.+|+||||+||+++++ ..|||+|++ +|+ +|+|+++|||+|.|+++|++.+.+|||||||||| +++|+|
T Consensus 188 I~d~~GrvIGFgGR~l~~~~~~~~KY~p~y~Nst~~~F~Kg~~LYGl~~Ak~~irk~~~vIivEGymDVI~~~a~~~~G- 266 (373)
T PRK08624 188 HRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQNKKYIKEKKKVIIVESEKSVLFSDKFYGEG- 266 (373)
T ss_pred EECCCCCEEEEeCeEcCCCccccccccccCCCCcccccccchhhcCHHHHHHHhccCCeEEEEeccHHHHHHHHHhcCC-
Confidence 9999999999999999543 357777542 233 4999999999999999999999999999999999 778999
Q ss_pred CeEEEcCCccCCHHHHHHHhccC-CeEEEEeCC---ChhHHHHHHHHHHHHH--hhcCCCcEEEEEeCCCC--CCcchhh
Q psy15222 169 LQTVAILGTACTSTHIKKILFYT-NSIIFSFDG---DQAGRRAARRALEVCL--LYATDDKIIKFLFLPDK--YDPDSYI 240 (444)
Q Consensus 169 ~naVA~lGtalt~~q~~~L~r~~-~~Vil~~D~---D~AG~~aa~r~~~~l~--~~~~~g~~v~v~~lP~g--kDpdd~l 240 (444)
.||||+|||++|++|+++|+|++ ++|++|||| |.+|.++....-+.+. ..+..-+++..+..|+| ++-|+=.
T Consensus 267 ~naVA~lGTalT~~q~~lL~r~~~~~Vil~~Dgd~~d~~~~~~~~~~~ki~k~~~~~~~~~~~~~~~d~~g~l~~~~~~~ 346 (373)
T PRK08624 267 NFVVAICGSNISEVQAEKLLRLGVEEVTIALDKEYMDVTEEEVYEYIKKLMKPVKTFAPYVNIYILKDEAGLLKYKDSPP 346 (373)
T ss_pred CcEEECChhhCCHHHHHHHHhcCCCcEEEEecCCccccchHHHHHHHHHHHHHHHhcCcceEEEEEecchhhhccCCCCc
Confidence 99999999999999999999984 699999999 6777665544322221 11122356666666655 2222221
Q ss_pred hhhcHHHHHHHHH
Q psy15222 241 RKFGYKIFSKKVL 253 (444)
Q Consensus 241 ~~~G~~~~~~~l~ 253 (444)
-.|.+.|.++.+
T Consensus 347 -~~~~~~~~~l~~ 358 (373)
T PRK08624 347 -DDNKDTLEELMS 358 (373)
T ss_pred -cCCHHHHHHHHH
Confidence 236788888773
No 8
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=100.00 E-value=1e-36 Score=268.30 Aligned_cols=124 Identities=49% Similarity=0.916 Sum_probs=103.4
Q ss_pred HHHHHhcCCHH--HHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCCCccccc
Q psy15222 7 FYKIQLKNSKE--AINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQSPVIEK 82 (444)
Q Consensus 7 ~y~~~L~~~~~--a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~g~~~~~ 82 (444)
|||.+|.+++. |++||++||||+++|+.|+|||||.+|+.|.+++.+ ++. +.|.++||+..+++ |
T Consensus 1 fy~~~L~~~~~~~a~~YL~~Rgl~~e~i~~F~lGyap~~~~~l~~~l~~~~~~~-~~l~~~GL~~~~~~-----~----- 69 (128)
T PF08275_consen 1 FYHKQLKNNPGKEALEYLKKRGLSDETIKKFQLGYAPGNWDSLLEYLKKKGFSL-EELLEAGLIRKNEN-----G----- 69 (128)
T ss_dssp HHHHHCCCGHHHHHHHHHHHTT--HHHHHHTT-EEE-SCSCHHHHHHCCCCHHH-HHHCCTTCEECCTT-----T-----
T ss_pred CchHHHcCCchHHHHHHHHHcCCCHHHHHHhCCCcccCcHHHHHHHHHhccccH-HHHHHCCCcEEcCC-----C-----
Confidence 89999999876 999999999999999999999999999999999985 555 89999999998775 4
Q ss_pred ccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHH
Q psy15222 83 YKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAK 142 (444)
Q Consensus 83 ~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~ 142 (444)
..||+|++||||||+|.+|+||||+||.+++...|||+|||||++|+|+++|||+|.||
T Consensus 70 -~~~d~F~~RiifPI~d~~G~vvgF~gR~l~~~~~pKYlNs~et~if~K~~~Lyg~~~Ak 128 (128)
T PF08275_consen 70 -GYYDFFRGRIIFPIRDERGRVVGFGGRRLDDENPPKYLNSPETPIFKKSRILYGLDQAK 128 (128)
T ss_dssp -EEEETTTTEEEEEEE-TTS-EEEEEEEESSSSSS-SEEE---BTTB-GGG-EETHHHHH
T ss_pred -CcccccCCeEEEEEEcCCCCEEEEecccCCCCCCCceECCCCCccccCCceecCccccC
Confidence 68999999999999999999999999999666789999999999999999999999986
No 9
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=99.83 E-value=8.4e-20 Score=218.46 Aligned_cols=209 Identities=18% Similarity=0.262 Sum_probs=169.8
Q ss_pred HHHHHHHHHHhc-CCHHHHHHH-HHcCCCHHHHHHccceeecCCchHHHHHhccCCchhHHHHcCCceeccccccCCCcc
Q psy15222 2 ICASDFYKIQLK-NSKEAINFL-KKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPV 79 (444)
Q Consensus 2 ~~a~~~y~~~L~-~~~~a~~YL-~~RGis~e~i~~f~lGyap~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~~~~~~g~~ 79 (444)
+.|.++|+..+. .+..|..|| .+|||+. +..|.|||+|..|. . +
T Consensus 1670 ~~A~rl~~~a~pi~gt~A~~YL~~~RGI~~--~~~~~LrfhP~~y~----------~--------------------~-- 1715 (1960)
T TIGR02760 1670 KRAKSLFQGSQELKGTLAEKYLKQHRGLAS--IDNDDIRFHPTVYS----------S--------------------D-- 1715 (1960)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHhcCCCCC--CCccceEECccccc----------C--------------------C--
Confidence 358899999875 466899999 9999976 47799999997431 0 1
Q ss_pred cccccccccCCceEEEEEecCCCCEEEEEeeecCC--CCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecCh
Q psy15222 80 IEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKD--SNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGY 157 (444)
Q Consensus 80 ~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~--~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~ 157 (444)
. ..|.+++||||+|.+|+++||.++.|++ .+++||+|+|++.+++|+..+++++.++ ..+.++||||+
T Consensus 1716 ----~--~~~~Paliapv~D~~G~i~gv~rt~L~p~~g~~~k~l~~~kr~~G~k~g~~v~l~~~~----~~~~liiaEGi 1785 (1960)
T TIGR02760 1716 ----K--KNKHPALIAAARNEKGEITGIQITYLDKDDANKDKDMDNNKRVKGSISGQFVVINKGM----QGDRSYIAEGI 1785 (1960)
T ss_pred ----C--CCcCCeEEEEEECCCCCEEEEEEEEccCCCCCCCccCCCcccccccccCcEEEecCCC----CCCeEEEEcCH
Confidence 1 2467899999999999999999999963 3578999999999999999999987543 45789999999
Q ss_pred hhHHHHHHcCC--CeEEEcCCcc-CCHHHHHHH-hccCCeEEEEeCCC--hh-HHHHHHHHHHHHHhhcCCCcEEEEEeC
Q psy15222 158 MDVIGLSQFGF--LQTVAILGTA-CTSTHIKKI-LFYTNSIIFSFDGD--QA-GRRAARRALEVCLLYATDDKIIKFLFL 230 (444)
Q Consensus 158 ~Dvlsl~q~Gi--~naVA~lGta-lt~~q~~~L-~r~~~~Vil~~D~D--~A-G~~aa~r~~~~l~~~~~~g~~v~v~~l 230 (444)
+|+||+++++. .++||++|++ +. .++ ....++||||+|+| .+ |++|+.++++.+. ..|+.|+++ +
T Consensus 1786 EtaLS~~~a~~~~~~vvA~lg~~~l~----~i~~~~~~~~viI~~D~D~~~a~G~~Aa~k~~~~l~---~~G~~v~i~-~ 1857 (1960)
T TIGR02760 1786 ETGLSIALANPKATVVIAVGGKNNLS----PIIPKFIPKNVVIVLDNDGEEAKSQRAIEKIINKFK---QDNISARIV-F 1857 (1960)
T ss_pred HHHHHHHHhCCCCccEEEECCccccc----cccCCCCCceEEEEeCCCCcccchHHHHHHHHHHHH---hCCCeeEEe-C
Confidence 99999999874 5689999986 21 122 23468999999999 45 9999999999875 468888877 6
Q ss_pred CCCCCcchhhhhhcHHHHHHHHHhcCCHHHHHHHHHHh
Q psy15222 231 PDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIIL 268 (444)
Q Consensus 231 P~gkDpdd~l~~~G~~~~~~~l~~a~~~~~f~~~~~~~ 268 (444)
|+ |.||+ |.++|.+.|..+.+.++|.+..+..
T Consensus 1858 P~--Dfnd~----g~~~~~~~l~~~~~~~~~~~~~~~~ 1889 (1960)
T TIGR02760 1858 PD--DWNDI----GEEELQKQLMRAISSIEDKDIEIPK 1889 (1960)
T ss_pred Cc--hhhhh----hHHHHHHHHHHhhhhHhhhhhcccc
Confidence 64 66665 8899999999999999999987643
No 10
>PHA02415 DNA primase domain-containing protein
Probab=99.74 E-value=1.2e-17 Score=179.44 Aligned_cols=209 Identities=17% Similarity=0.269 Sum_probs=141.7
Q ss_pred HHhcCCHHHHHHHHHcCCCHHHHHH-ccceeec-CCchHHHHHhccCCchhHHHHcCCceeccccccCCCcccccccccc
Q psy15222 10 IQLKNSKEAINFLKKRGLNEEIILR-FNLGYAP-NEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYD 87 (444)
Q Consensus 10 ~~L~~~~~a~~YL~~RGis~e~i~~-f~lGyap-~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd 87 (444)
.++.++..+++||++||||+++|+. |+.|-.- ..|.. +.+. +|.... ||+
T Consensus 116 r~~ad~rrA~AYLK~RGIS~EVI~~cIk~GlIg~~~W~s-----------~rv~-agd~gy-------gg~--------- 167 (930)
T PHA02415 116 RCLAERERVREYLGGRGISAAAIDAAFAARSLGFNTWTS-----------SKVA-AGEVGH-------AGP--------- 167 (930)
T ss_pred hhccchHHHHHHHHhcCCCHHHHHHHHHcCccccccccc-----------cccc-cccccc-------CCC---------
Confidence 3444567899999999999999996 7776542 23321 1122 333311 010
Q ss_pred cCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHHcC
Q psy15222 88 RFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFG 167 (444)
Q Consensus 88 ~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q~G 167 (444)
.--+||| ++.+|.++....|.++.. +.+. ...-|..+...||+..-...+.+.++|+||||.|||||++++|
T Consensus 168 --nAAFIVp-f~rdGtvv~v~~Rg~d~a----fkG~-vKanf~Gs~~G~gW~~p~~~L~~a~eVwIvEGiIDAISL~q~G 239 (930)
T PHA02415 168 --AAAFIVR-EPADGRVVAVDMRYVDPA----LNGG-VKTQTQGDKAGYGWTADARRLDKAKRVFIVESAINALSIDTCA 239 (930)
T ss_pred --ceEEEec-ccCCceEEEeeecccccc----ccCC-ccccCCCCCCCCccCCCccccCCCCEEEEEechHhHHHHHHcC
Confidence 1134789 568999999999977321 1111 1111322344555543222244568999999999999999999
Q ss_pred CC--eEEEcCCcc-CCHHHHHHHhccCCeEEEEeCCChh------------HHHHHHHHHHHHHhhcCCCcEEEEEeCC-
Q psy15222 168 FL--QTVAILGTA-CTSTHIKKILFYTNSIIFSFDGDQA------------GRRAARRALEVCLLYATDDKIIKFLFLP- 231 (444)
Q Consensus 168 i~--naVA~lGta-lt~~q~~~L~r~~~~Vil~~D~D~A------------G~~aa~r~~~~l~~~~~~g~~v~v~~lP- 231 (444)
++ .+||++|.+ .+......+ ..++|++|+|||+| |++||++..+.+.. .|+....|...
T Consensus 240 i~avAaVAL~GLan~~~iD~~~l--~~KrVvlcLDNDea~~~~~~~~g~rpG~eAA~~l~e~lta---~~i~~~lvd~~~ 314 (930)
T PHA02415 240 MPGAAALALRGLANVDAIDFSSL--RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLAS---LNISAVLVDQAG 314 (930)
T ss_pred chhHHHHHHcCcCCCchhhchhh--cCceEEEEecCCccccccCcccccCccHHHHHHHHHHHhh---cCCceEEeehhh
Confidence 98 467889976 554555544 25799999999998 99999999888753 47666665422
Q ss_pred --C-------CC----CcchhhhhhcHHHHHHHHHhcCCHH
Q psy15222 232 --D-------KY----DPDSYIRKFGYKIFSKKVLEAMSLL 259 (444)
Q Consensus 232 --~-------gk----Dpdd~l~~~G~~~~~~~l~~a~~~~ 259 (444)
+ |. |.|||++++|++.+...++.-.||+
T Consensus 315 w~~~~~~~~~~~~~~~d~nd~l~~~g~~~~~~~l~~~~~wl 355 (930)
T PHA02415 315 WLADLADGETKQQPINDVNDYLQLRGPEELARALEQLEPWL 355 (930)
T ss_pred hhhhcccccccccccccHHHHHHHhCHHHHHHHHHhccccc
Confidence 1 44 9999999999999999998777653
No 11
>PRK04031 DNA primase; Provisional
Probab=99.73 E-value=1.6e-17 Score=168.57 Aligned_cols=120 Identities=22% Similarity=0.302 Sum_probs=102.3
Q ss_pred cccCc--HHHHHHhhccCcEEEecChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHH
Q psy15222 134 ELYGL--FEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRA 211 (444)
Q Consensus 134 ~Lygl--~~a~~~i~~~~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~ 211 (444)
+-||- -.|.+.+++.+.+|||||++||++|+++|+.|+||++||+++.++.++ .+ +++|++|||+|.||+.+.+++
T Consensus 153 ~eyg~ekL~Agp~i~k~~~iIVVEG~~DVi~L~~aGi~nvVAt~GT~l~~~i~~l-~k-~~~Vil~~DgD~aGe~I~k~l 230 (408)
T PRK04031 153 TEYGPEKLPAGPNVDDSDAIIVVEGRADVLNLLRYGIKNAIAVEGTNVPETIIEL-SK-KKTVTAFLDGDRGGELILKEL 230 (408)
T ss_pred eeecccccccCcccccCCeEEEEeCHHHHHHHHhcccceEEEeCCcccHHHHHHH-hc-CCCEEEEECCCHHHHHHHHHH
Confidence 45887 578889999999999999999999999999999999999987665554 44 789999999999999887665
Q ss_pred HHHHHhhcCCCcEEEEEeCCCCCCcchhhhhhcHHHHHHHHHhcCCHHHHHHHHH
Q psy15222 212 LEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEI 266 (444)
Q Consensus 212 ~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~G~~~~~~~l~~a~~~~~f~~~~~ 266 (444)
.+ .+...++..+|+|+||+++. .+++.+.|.++.|+.+|+.+.-
T Consensus 231 ~~-------v~~~d~VaraP~G~dVE~ls----~eeI~kAL~~~~p~~~~l~~~~ 274 (408)
T PRK04031 231 LQ-------VADIDYVARAPPGKEVEELT----KKEIAKALRNKVPVEQYLEELG 274 (408)
T ss_pred Hh-------hcceeEEecCCCCCChhhCC----HHHHHHHHHhcCCHHHHHHhhh
Confidence 43 24566788999999999995 6779999999999999987643
No 12
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=99.69 E-value=2.5e-16 Score=127.07 Aligned_cols=78 Identities=42% Similarity=0.585 Sum_probs=71.2
Q ss_pred CcEEEecChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEE
Q psy15222 149 GYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFL 228 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~ 228 (444)
++++||||++|+||+++.|+.++||++|++++++|++.|.++.++|++|+|+|.||++|+.++.+.+.+ .|+.++++
T Consensus 1 ~~v~i~EG~~D~ls~~~~g~~~~va~~G~~~~~~~~~~L~~~~~~vii~~D~D~aG~~a~~~~~~~l~~---~g~~~~~~ 77 (79)
T cd03364 1 KKVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLK---LGLNVRVL 77 (79)
T ss_pred CeEEEEeCHHHHHHHHHcCCCCEEECCCccCcHHHHHHHHhcCCeEEEEECCCHHHHHHHHHHHHHHHH---CCCeEEEE
Confidence 469999999999999999999999999999999999999987689999999999999999999998764 58888876
Q ss_pred e
Q psy15222 229 F 229 (444)
Q Consensus 229 ~ 229 (444)
.
T Consensus 78 ~ 78 (79)
T cd03364 78 T 78 (79)
T ss_pred e
Confidence 5
No 13
>PF13155 Toprim_2: Toprim-like
Probab=99.64 E-value=4.8e-16 Score=129.34 Aligned_cols=89 Identities=26% Similarity=0.323 Sum_probs=72.3
Q ss_pred EEecChhhHHHHHHcCCCe------EEEcCCccCCHHHHHHHhccC-CeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcE
Q psy15222 152 LITEGYMDVIGLSQFGFLQ------TVAILGTACTSTHIKKILFYT-NSIIFSFDGDQAGRRAARRALEVCLLYATDDKI 224 (444)
Q Consensus 152 iIvEG~~Dvlsl~q~Gi~n------aVA~lGtalt~~q~~~L~r~~-~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~ 224 (444)
|||||++|+||++|.+..+ +++++|+..++.+.+.|.+.. ++|++|||||.||++++.++.+.+.........
T Consensus 1 ~v~Eg~iDaLS~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~~~~~~ 80 (96)
T PF13155_consen 1 VVFEGPIDALSYYQLGKENIKDNSLSLAGGGTLSEKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEGFPNIK 80 (96)
T ss_pred cEEeCHHHHHHHHHhCchhcCCceEEEECCchHHHHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhCCCcce
Confidence 6999999999999998775 688888877788888885432 689999999999999999988776532112356
Q ss_pred EEEEeCCCCCCcchhh
Q psy15222 225 IKFLFLPDKYDPDSYI 240 (444)
Q Consensus 225 v~v~~lP~gkDpdd~l 240 (444)
+.+..+|.+||+||+|
T Consensus 81 ~~~~~~~~~KD~Nd~L 96 (96)
T PF13155_consen 81 VRIEDPPDGKDWNDYL 96 (96)
T ss_pred eeecCCCCCcCchhhC
Confidence 6777789999999986
No 14
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=99.58 E-value=5.6e-15 Score=119.74 Aligned_cols=77 Identities=30% Similarity=0.414 Sum_probs=56.7
Q ss_pred CcEEEecChhhHHHHHHcCCCeEEEcCCccC-CHHHHHHHhccC--CeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEE
Q psy15222 149 GYVLITEGYMDVIGLSQFGFLQTVAILGTAC-TSTHIKKILFYT--NSIIFSFDGDQAGRRAARRALEVCLLYATDDKII 225 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi~naVA~lGtal-t~~q~~~L~r~~--~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v 225 (444)
+.++||||++|+++++++|++++|+++|+++ +.+|+....... ++|++|+|+|.+|++++.++.+.+.+ .|++|
T Consensus 1 k~viIvEG~~D~~~l~~~g~~~~v~~~g~~~~~~~~~~~~~~~~~~~~Vii~~D~D~~G~~~a~~i~~~l~~---~gi~v 77 (81)
T PF13662_consen 1 KEVIIVEGEFDAIALEQAGYKNVVAVLGGNLSPLDQILREKLEKKVKEVIIAFDNDKAGEKAAQKIAKKLLP---LGIRV 77 (81)
T ss_dssp --EEEESSHHHHHHHHHTT-TTEEEESSSS---HHHHHHHHHH---SEEEEEEESSHHHHHHHHHHHHHHG---------
T ss_pred CEEEEECCHHHHHHHHHhCCCeEEEECCCCCChHHHhChHhhhccCceEEEEeCcCHHHHHHHHHHHHHHHh---hcccc
Confidence 4699999999999999999999999999998 777877655544 89999999999999999999887753 47766
Q ss_pred EEE
Q psy15222 226 KFL 228 (444)
Q Consensus 226 ~v~ 228 (444)
+++
T Consensus 78 ~~v 80 (81)
T PF13662_consen 78 TRV 80 (81)
T ss_dssp ---
T ss_pred ccC
Confidence 543
No 15
>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=99.54 E-value=2.9e-14 Score=115.84 Aligned_cols=67 Identities=24% Similarity=0.329 Sum_probs=63.5
Q ss_pred CcEEEecChhhHHHHHHcCC-CeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHH
Q psy15222 149 GYVLITEGYMDVIGLSQFGF-LQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVC 215 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi-~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l 215 (444)
+.+|||||++|+++++++|+ .++|++.||++++++++++++..++||+++|+|.+|++++.++.+.+
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~~~~i~t~Gt~~~~~~~~~l~~~~~~VIiltD~D~aG~~i~~~~~~~l 69 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYL 69 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCCccEEEECCCcCCHHHHHHHHHhCCEEEEEECCCHHHHHHHHHHHHHh
Confidence 46899999999999999999 89999999999999999999988999999999999999999988865
No 16
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=99.51 E-value=1.5e-13 Score=110.33 Aligned_cols=77 Identities=40% Similarity=0.623 Sum_probs=67.2
Q ss_pred CcEEEecChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEE
Q psy15222 149 GYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFL 228 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~ 228 (444)
+.++||||++|++|+++.|+.++|+++|++.++.++..+.+..++|++|+|+|.+|++++.++.+.+.. .+..+++.
T Consensus 1 ~~v~i~EG~~Dals~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~vii~~D~D~~G~~~~~~~~~~~~~---~~~~~~i~ 77 (79)
T cd01029 1 DEVIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLA---LGGRVRVP 77 (79)
T ss_pred CEEEEEeCHHHHHHHHHcCCCCEEECCCccCcHHHHHHHHhcCCEEEEEECCCHHHHHHHHHHHHHHHH---CCCEEEEe
Confidence 368999999999999999998899999999988889988876689999999999999999999888764 36666543
No 17
>PF13362 Toprim_3: Toprim domain
Probab=99.29 E-value=6.5e-12 Score=104.80 Aligned_cols=91 Identities=23% Similarity=0.289 Sum_probs=72.6
Q ss_pred cEEEecChhhHHHH-HHcCCCeEEEcCCcc-CCHHHHHHHhccCCeEEEEeCCChh--HHHHHHHHHHHHHhhcCCCcEE
Q psy15222 150 YVLITEGYMDVIGL-SQFGFLQTVAILGTA-CTSTHIKKILFYTNSIIFSFDGDQA--GRRAARRALEVCLLYATDDKII 225 (444)
Q Consensus 150 ~viIvEG~~Dvlsl-~q~Gi~naVA~lGta-lt~~q~~~L~r~~~~Vil~~D~D~A--G~~aa~r~~~~l~~~~~~g~~v 225 (444)
+++||||+.|++|+ ++..-..+|+++|++ +..-... ...++|++|.|+|.+ |++++.++.+.+. ..|+.+
T Consensus 1 tl~i~EG~etals~~~~~~~~~~~a~~~~~nl~~~~~~---~~~~~vii~~D~D~~~~G~~~a~~~~~~~~---~~g~~~ 74 (96)
T PF13362_consen 1 TLIIAEGIETALSIAQQATGVPVVAALGAGNLKNVAIP---EPGRRVIIAADNDKANEGQKAAEKAAERLE---AAGIAV 74 (96)
T ss_pred CEEEEEhHHHHHHHHHhcCCCeEEEEEChhhhhhhcCC---CCCCeEEEEECCCCchhhHHHHHHHHHHHH---hCCCeE
Confidence 48999999999999 554434588888874 4311111 356899999999999 9999999988875 369999
Q ss_pred EEEeC-CCCCCcchhhhhhcHH
Q psy15222 226 KFLFL-PDKYDPDSYIRKFGYK 246 (444)
Q Consensus 226 ~v~~l-P~gkDpdd~l~~~G~~ 246 (444)
.++.. |+|+|+||++++.|.|
T Consensus 75 ~~~~p~~~g~D~ND~l~~~G~e 96 (96)
T PF13362_consen 75 SIVEPGPEGKDWNDLLQARGKE 96 (96)
T ss_pred EEECCCCCCchHHHHHHhhCCC
Confidence 98877 7889999999999864
No 18
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=99.28 E-value=1e-11 Score=98.68 Aligned_cols=68 Identities=26% Similarity=0.322 Sum_probs=59.7
Q ss_pred CcEEEecChhhHHHHHHcCCC--eEEEcCCccCCHHHHHHHhccC--CeEEEEeCCChhHHHHHHHHHHHHH
Q psy15222 149 GYVLITEGYMDVIGLSQFGFL--QTVAILGTACTSTHIKKILFYT--NSIIFSFDGDQAGRRAARRALEVCL 216 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi~--naVA~lGtalt~~q~~~L~r~~--~~Vil~~D~D~AG~~aa~r~~~~l~ 216 (444)
++++||||++|+++++++|.. .+++++|+..+.++++.|++.. ++|++|+|+|.+|+++++++.+.+.
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~~i~~~l~ 72 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKLAELLK 72 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCCEEEEEEeeeecHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHHHHHHHhh
Confidence 368999999999999999983 6889999988889999998865 5799999999999999999887654
No 19
>PRK07078 hypothetical protein; Validated
Probab=99.09 E-value=1.2e-09 Score=121.34 Aligned_cols=152 Identities=18% Similarity=0.168 Sum_probs=107.4
Q ss_pred eEEEEEecCCCCEEEEEeeecCCCCCcc-c--ccCCCCC-ccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHHcC
Q psy15222 92 RIMFPIKNTDGQIIGFGGRLIKDSNEAK-Y--INSPETP-LFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFG 167 (444)
Q Consensus 92 RiifPI~d~~G~vvgf~gR~l~~~~~pK-Y--lNspet~-~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q~G 167 (444)
-..+|++|.+|++++.-.|.-.+ +.-| | ++..... .-.+...|||++... +...|+||||+-||.+|.+.|
T Consensus 135 ~~~~~Y~D~~G~~~~~v~R~~~~-~~~K~fr~~~g~~~~~~~~~~~pLy~lp~l~----~a~~V~lvEGEk~adal~~~g 209 (759)
T PRK07078 135 TAKWDYLDAAGKLIAVVYRYDPP-GRRKEFRPWDAKRRKMAPPEPRPLYNQPGLL----SAEQVVLVEGEKCAQALIDAG 209 (759)
T ss_pred eeEEEEECCCCCEEEEEEeecCC-CCCceeecccCCcceecCCCCcCCcCchhhh----cCCeEEEEeChHHHHHHHhcC
Confidence 35699999999999998887632 2222 1 2322211 112456789997654 457899999999999999999
Q ss_pred CCeEEEcCCccCC--HHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeC-----CCCCCcchhh
Q psy15222 168 FLQTVAILGTACT--STHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFL-----PDKYDPDSYI 240 (444)
Q Consensus 168 i~naVA~lGtalt--~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~l-----P~gkDpdd~l 240 (444)
+..+.++.|+... .....-|.. .+|+|+.|+|++|.++|.++.+.+.. .|..+.++.+ |+|.|..|.+
T Consensus 210 ~~att~~~Ga~~~~~~~d~~~L~g--~~VvI~pD~D~~G~~~a~~va~~l~~---~g~~~~~v~~p~~~~~~~~D~aD~~ 284 (759)
T PRK07078 210 VVATTAMHGANAPVDKTDWSPLAG--KAVLIWPDRDKPGWEYADRAAQAILS---AGASSCAVLLPPEDLPEGWDAADAI 284 (759)
T ss_pred CeEEecCCCCCCCcccccccccCC--CEEEEEcCCChHHHHHHHHHHHHHHh---cCCeEEEEEecCcccCcCCCHHHHH
Confidence 9745556676433 232333543 69999999999999999999888764 4666655544 4689999999
Q ss_pred hhh-cHHHHHHHHH
Q psy15222 241 RKF-GYKIFSKKVL 253 (444)
Q Consensus 241 ~~~-G~~~~~~~l~ 253 (444)
... +.+.|..+.+
T Consensus 285 ~~G~~~~~~~~~~~ 298 (759)
T PRK07078 285 AEGFDVAGFLAHGE 298 (759)
T ss_pred HcCCCHHHHHhhcc
Confidence 864 5666766654
No 20
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=99.02 E-value=1.1e-09 Score=96.93 Aligned_cols=100 Identities=20% Similarity=0.237 Sum_probs=72.3
Q ss_pred cCcEEEecChhhHHHHHHcCCCeEEEcCCccCCH----------------HHHHHHhccCCeEEEEeCCC--hhHHHHHH
Q psy15222 148 SGYVLITEGYMDVIGLSQFGFLQTVAILGTACTS----------------THIKKILFYTNSIIFSFDGD--QAGRRAAR 209 (444)
Q Consensus 148 ~~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~----------------~q~~~L~r~~~~Vil~~D~D--~AG~~aa~ 209 (444)
.-+|+||||..-+.++.++|+. +||+.|..-.. .++..+....++|++|||.| ..-...+.
T Consensus 10 ~~pi~ItEG~kKA~al~s~G~~-aIalpGV~~~~~~~~~~~~~~~~~~L~p~L~~~~~~gr~v~iaFD~D~~~~Tn~~V~ 88 (130)
T PF12965_consen 10 NIPIWITEGAKKAGALLSQGYP-AIALPGVNNGYRWPKDEGDKIGKRRLIPELAKLAKPGREVYIAFDADTKPKTNKNVR 88 (130)
T ss_pred CccEEEEechHHHHHHHcCCce-EEEeCceeccccccccccccccchhcchhHHHhccCCceEEEEecCCCccchhHHHH
Confidence 4579999999999999999985 99999864221 13333333357999999999 33333333
Q ss_pred HHHHHHHhhc-CCCcEEEEEeCC--CCCCcchhhhhhcHHHH
Q psy15222 210 RALEVCLLYA-TDDKIIKFLFLP--DKYDPDSYIRKFGYKIF 248 (444)
Q Consensus 210 r~~~~l~~~~-~~g~~v~v~~lP--~gkDpdd~l~~~G~~~~ 248 (444)
+++..+..++ ..|+.|+++.+| .+|-.|||+.++|.++|
T Consensus 89 ~a~~~l~~~L~~~G~~v~~~~w~~~~~KGiDD~l~~~G~~~f 130 (130)
T PF12965_consen 89 RAIKRLGKLLKEAGCKVKIITWPPGEGKGIDDLLAAKGPDAF 130 (130)
T ss_pred HHHHHHHHHHHHCCCEEEEEEeCCCCCCCHhHHHHhcCcccC
Confidence 3333332222 369999999999 57999999999999876
No 21
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=98.99 E-value=7.9e-10 Score=83.86 Aligned_cols=59 Identities=22% Similarity=0.274 Sum_probs=51.9
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHHH
Q psy15222 258 LLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEI 317 (444)
Q Consensus 258 ~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~i 317 (444)
+++|+++++.+++|+++|++|.++++++.|+|+.+++ |++|+.|++++|+++|+++++|
T Consensus 1 L~ef~~~~l~~~~dl~~~egk~~~~~~~~~~i~~i~~-~i~r~~y~~~la~~~~i~~~~L 59 (59)
T PF10410_consen 1 LSEFLIERLSKGYDLDTPEGKAEAVREAAPLIAQIPD-PIERELYIRELAERLGISEDAL 59 (59)
T ss_dssp HHHHHHHHHGGGS-TTSHHHHHHHHHHHHHHHTT--S-HHHHHHHHHHHHHHCT-SSTT-
T ss_pred CHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHhCcCcccC
Confidence 5899999999999999999999999999999999999 9999999999999999997653
No 22
>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=98.69 E-value=6.9e-08 Score=75.69 Aligned_cols=68 Identities=32% Similarity=0.373 Sum_probs=56.3
Q ss_pred CcEEEecChhhHHHHHHcCC--CeEEEcCCccC--CHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHH
Q psy15222 149 GYVLITEGYMDVIGLSQFGF--LQTVAILGTAC--TSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCL 216 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi--~naVA~lGtal--t~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~ 216 (444)
+.++||||..|++++.+.+. ..++++.|+.. +..++..+.+...+|++|+|+|.+|..++.+..+...
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~ 72 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK 72 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcHHHHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHH
Confidence 36899999999999999987 36888888876 4666777766568999999999999988887777654
No 23
>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=97.98 E-value=1.4e-05 Score=67.13 Aligned_cols=69 Identities=20% Similarity=0.154 Sum_probs=54.6
Q ss_pred cEEEecChhhHHHHHHcCC---CeEEEcCCccCCHH------------HHHHHhc---cCCeEEEEeCCChhHHHHHHHH
Q psy15222 150 YVLITEGYMDVIGLSQFGF---LQTVAILGTACTST------------HIKKILF---YTNSIIFSFDGDQAGRRAARRA 211 (444)
Q Consensus 150 ~viIvEG~~Dvlsl~q~Gi---~naVA~lGtalt~~------------q~~~L~r---~~~~Vil~~D~D~AG~~aa~r~ 211 (444)
++|||||+.|+.++.++.- ..++++.|..++.. +++.|++ .+++||+|.|.|..|+..++.+
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i 80 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEI 80 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHH
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccccccccccccccccchhhHHHhhhccEeeecCCCChHHHHHHHHH
Confidence 4899999999999999865 46889999765332 2666654 3789999999999999999999
Q ss_pred HHHHHhh
Q psy15222 212 LEVCLLY 218 (444)
Q Consensus 212 ~~~l~~~ 218 (444)
++.+...
T Consensus 81 ~~~~~~~ 87 (100)
T PF01751_consen 81 IELLGKN 87 (100)
T ss_dssp HHHHHHH
T ss_pred HHHHhHh
Confidence 9877643
No 24
>PRK04017 hypothetical protein; Provisional
Probab=97.90 E-value=0.00017 Score=63.77 Aligned_cols=69 Identities=23% Similarity=0.272 Sum_probs=58.1
Q ss_pred ccCcEEEecChhhHHHHHHcCCC-eEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFL-QTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCL 216 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~-naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~ 216 (444)
..+.+|||||--|.-++.++|+. +.+.+-|.+++... +.+....+.||+..|.|.+|.+-+.+..+.+.
T Consensus 21 ~~g~vIVVEGk~D~~~L~~lGv~~~iI~t~g~~~~~~~-e~ia~~~r~VIILTD~D~~GekIr~~l~~~l~ 90 (132)
T PRK04017 21 EAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIA-ELIASRGKEVIILTDFDRKGEELAKKLSEYLQ 90 (132)
T ss_pred CCCCEEEEeCccHHHHHHHcCCCccEEEECCeecchHH-HHHHhcCCeEEEEECCCcchHHHHHHHHHHHH
Confidence 34578999999999999999995 77888898887766 66665678999999999999999988776653
No 25
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=97.79 E-value=8.6e-05 Score=64.89 Aligned_cols=93 Identities=13% Similarity=0.266 Sum_probs=70.1
Q ss_pred HHHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh--hHHHHHHHHHHhcC
Q psy15222 343 IEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI--NKNFESIIVKIQDN 420 (444)
Q Consensus 343 ~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~ 420 (444)
.+|.+|++|++||.+...+.. ...+..+.++..+++..+++.++. ++..+.+.++++++++ ...+.+++. .+
T Consensus 1 P~R~~i~lLLq~P~La~~~~d--~~~l~~~~~~~~~lL~~li~~~~~-~p~~~~a~lle~~r~~~~~~~l~~La~---~e 74 (127)
T PF08278_consen 1 PMRRAIALLLQHPQLAQRVPD--LLALEDFQDPGIRLLRELIELIRE-NPNISTAQLLEYWRGTPHGETLAQLAA---WE 74 (127)
T ss_dssp HHHHHHHHHHH-GGGGGGS-----TTSHCCCSTTHHHHHHHHHHHHH-STT--HHHHHHTTTTCTTHHHHHHHHC---HC
T ss_pred CHHHHHHHHHHCHHHHhhCCC--ccchhhccChHHHHHHHHHHHHcc-CCCCCHHHHHHHHhCCCcHHHHHHHHh---Cc
Confidence 368999999999999999983 234556778899999999999999 8999999999999987 344455444 23
Q ss_pred CCC-CHHHHHHHHHHHHHhhhh
Q psy15222 421 FEY-SIEIAKKTLLDAIYKDRK 441 (444)
Q Consensus 421 ~e~-~~e~~~~~~~~~~~~~~~ 441 (444)
... +.++.+..|.|++.+...
T Consensus 75 ~~~~~~~~~~~ef~d~l~~L~~ 96 (127)
T PF08278_consen 75 HLIEDEEDIEQEFQDALARLQE 96 (127)
T ss_dssp CCC-HHHHHHHHHHHHHHHHHH
T ss_pred ccccCchhHHHHHHHHHHHHHH
Confidence 445 778999999999987654
No 26
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=97.66 E-value=0.00018 Score=63.26 Aligned_cols=69 Identities=23% Similarity=0.256 Sum_probs=59.5
Q ss_pred ccCcEEEecChhhHHHHHHcCCCeEEEcCCccCC-HHHHHHHhc--cCCeEEEEeCCChhHHHHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFLQTVAILGTACT-STHIKKILF--YTNSIIFSFDGDQAGRRAARRALEVC 215 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt-~~q~~~L~r--~~~~Vil~~D~D~AG~~aa~r~~~~l 215 (444)
+.+.||||||--|..++.+.|...++-++|.+++ .+-++.|++ ..+.||+..|.|..|.+-..+..+.+
T Consensus 8 ~~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~l~~~l 79 (127)
T COG1658 8 ELKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKKLKEYL 79 (127)
T ss_pred hcCceEEEeCCcHHHHHHHhcCCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCCcchHHHHHHHHHHh
Confidence 3478999999999999999999889999999877 677888877 57789999999999999887765543
No 27
>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=97.52 E-value=0.00078 Score=62.22 Aligned_cols=102 Identities=15% Similarity=0.118 Sum_probs=70.6
Q ss_pred CcEEEecChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhcc--CCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEE
Q psy15222 149 GYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFY--TNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIK 226 (444)
Q Consensus 149 ~~viIvEG~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~--~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~ 226 (444)
+.||||||=-|...+.++---.++.+.|++++.+-++.|+.. .+.||++.|+|.+|.+--....+. .| + ++
T Consensus 3 kevIVVEGK~D~~~lk~~~d~~~I~T~Gs~i~~~~i~~i~~~~~~rgVIIfTDpD~~GekIRk~i~~~-vp----~--~k 75 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQH-LP----G--YE 75 (174)
T ss_pred CeEEEEecchHHHHHHHhcCceEEEECCCccCHHHHHHHHHHhhcCCEEEEeCCCCchHHHHHHHHHH-CC----C--Ce
Confidence 579999999999999887544799999999999888887653 457999999999998876554443 23 2 33
Q ss_pred EEeCCC--CCC-cchhhhhh-cHHHHHHHHHhcCC
Q psy15222 227 FLFLPD--KYD-PDSYIRKF-GYKIFSKKVLEAMS 257 (444)
Q Consensus 227 v~~lP~--gkD-pdd~l~~~-G~~~~~~~l~~a~~ 257 (444)
.+.+|. ... -.+.=..+ .++++.+.|+++..
T Consensus 76 hafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~ 110 (174)
T TIGR00334 76 NCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHE 110 (174)
T ss_pred EEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhcc
Confidence 444552 111 01222222 36677777776654
No 28
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.
Probab=97.50 E-value=0.0005 Score=58.05 Aligned_cols=93 Identities=13% Similarity=0.230 Sum_probs=70.0
Q ss_pred HHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhHHHHHHHHHHhcC-CC
Q psy15222 344 EYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDN-FE 422 (444)
Q Consensus 344 E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~-~e 422 (444)
|+.+|++|+++|++...+.... ....|.++..+.+..++..+.. ++..+...+++.+.+. .++++++++... ..
T Consensus 1 ~r~lL~lll~~P~l~~~v~~~~--~~~~f~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~~~--~~~~~l~~l~~~~~~ 75 (125)
T smart00766 1 MRELIRLLLQNPELASLVPDLL--TLEDFTHPGLALLAELLATCRG-NPGLTTGQLLEHWRDT--PYEELLSELAVWDHL 75 (125)
T ss_pred CHHHHHHHHHCHHHHhhCCCch--hhhhcccccHHHHHHHHHHHHc-CCCCcHHHHHHHHcCC--hHHHHHHHHHhcccc
Confidence 4789999999999999986541 2234556777888888887776 5666889999999754 578888888863 44
Q ss_pred CCHHHHHHHHHHHHHhhhh
Q psy15222 423 YSIEIAKKTLLDAIYKDRK 441 (444)
Q Consensus 423 ~~~e~~~~~~~~~~~~~~~ 441 (444)
.+.+...+.+.||+...++
T Consensus 76 ~~~~~~~~~~~~~l~~l~~ 94 (125)
T smart00766 76 IDEENLEEEFLDTLARLRK 94 (125)
T ss_pred CCchHHHHHHHHHHHHHHH
Confidence 5567888899999887644
No 29
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.06 E-value=0.0031 Score=63.34 Aligned_cols=144 Identities=20% Similarity=0.297 Sum_probs=87.5
Q ss_pred ccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCC-CccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHH
Q psy15222 87 DRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPET-PLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQ 165 (444)
Q Consensus 87 d~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet-~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q 165 (444)
+.|+..-++|..|..|+.++..- +.+++.-|++..... ..|.-=. |.+ ....++||+|||--++++.|
T Consensus 155 ~~~~~~slip~~d~~Gel~~lq~--I~~dG~Krf~~Ggr~kg~f~p~~---g~~------~~aa~lvi~EGyATal~i~~ 223 (366)
T COG4643 155 VQLRDGSLIPLRDADGELTGLQL--IQPDGTKRFLKGGRVKGCFIPLG---GLA------GPAARLVIAEGYATALSISQ 223 (366)
T ss_pred ccccccceEEEEcCCCCEeeeEE--EcCCccceeccCCcccceeeecC---CCc------ccccceEEeechhHHHHHHH
Confidence 56777777799999999998754 445555565543221 1111111 121 13456999999999999998
Q ss_pred c-CCCeEEEcCCccCCHHHHHHH-hcc-CCeEEEEeCCCh-----hHHHHHHHHHHHHHhhcCCCcEEEEEeCCC-C-CC
Q psy15222 166 F-GFLQTVAILGTACTSTHIKKI-LFY-TNSIIFSFDGDQ-----AGRRAARRALEVCLLYATDDKIIKFLFLPD-K-YD 235 (444)
Q Consensus 166 ~-Gi~naVA~lGtalt~~q~~~L-~r~-~~~Vil~~D~D~-----AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~-g-kD 235 (444)
+ |..-++|.--+.|..- ...| +++ ...||||-|+|. +|+..+..+.... .| . +.+|. + -|
T Consensus 224 ~~ga~v~aAi~agNll~V-A~al~~~~Pda~iIIaAD~D~~~~nnpG~t~A~eaA~Av-----ng-~---~~lP~~~~ad 293 (366)
T COG4643 224 ATGAPVAAAIDAGNLLAV-ASALRKKFPDAQIIIAADDDINTANNPGLTKAEEAAQAV-----NG-T---VALPPFGPAD 293 (366)
T ss_pred HhhhhHHhhhhcccHHHH-HHHHHHhCCCcceEEEeccccccCCCcchHHHHHHHHhh-----Cc-e---eecCCCCCCc
Confidence 5 5442333332333221 2223 333 348999999997 7888888776543 12 2 23443 2 59
Q ss_pred cchhhhhhcHHHHHHH
Q psy15222 236 PDSYIRKFGYKIFSKK 251 (444)
Q Consensus 236 pdd~l~~~G~~~~~~~ 251 (444)
++|+....|..+-+..
T Consensus 294 wpD~~tq~n~la~r~~ 309 (366)
T COG4643 294 WPDGFTQFNDLATRCA 309 (366)
T ss_pred Ccchhhhcchhhhhhh
Confidence 9999988886554433
No 30
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=96.15 E-value=0.016 Score=59.90 Aligned_cols=75 Identities=19% Similarity=0.271 Sum_probs=56.6
Q ss_pred ccCcEEEecChhhHHHHHHcCCC-eEEEcCCccCCHHHHHHHh-ccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcE
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFL-QTVAILGTACTSTHIKKIL-FYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKI 224 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~-naVA~lGtalt~~q~~~L~-r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~ 224 (444)
+.+.+|||||--|..||...|++ +.+-+-+..++. -...|- ...++||+++|-|.+|+..+.+.++.|. ..|+.
T Consensus 22 ~~~~~ilveg~~d~~~l~~lgi~g~~i~~s~~p~~~-cad~ii~~gi~rVVi~~D~d~~G~~~~~~~~~~L~---~aGi~ 97 (360)
T PRK14719 22 EKGIPILVEGPNDILSLKNLKINANFITVSNTPVFQ-IADDLIAENISEVILLTDFDRAGRVYAKNIMEEFQ---SRGIK 97 (360)
T ss_pred hCCCEEEEEcchHHHHHHHcCCCCcEEEEeCCchHH-HHHHHHHcCCCEEEEEECCCCCCCccchHHHHHHH---HCCCE
Confidence 44689999999999999999996 555544444443 334443 3457999999999999998888888775 36887
Q ss_pred E
Q psy15222 225 I 225 (444)
Q Consensus 225 v 225 (444)
|
T Consensus 98 V 98 (360)
T PRK14719 98 V 98 (360)
T ss_pred E
Confidence 7
No 31
>KOG2373|consensus
Probab=95.07 E-value=0.11 Score=53.05 Aligned_cols=136 Identities=15% Similarity=0.099 Sum_probs=89.4
Q ss_pred cccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecChhhHHHHHHc-CCCeEEEcCCccCCH-HHHHHHhccCCeEE
Q psy15222 118 AKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQF-GFLQTVAILGTACTS-THIKKILFYTNSII 195 (444)
Q Consensus 118 pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~q~-Gi~naVA~lGtalt~-~q~~~L~r~~~~Vi 195 (444)
.-|=-..++++=++-+.+||+|.+- +....||||-...|+|+++++ |+....-+-|+.+-+ .-+..|.+ .++||
T Consensus 95 ~~ye~~~~~~~r~a~~~~fGL~l~~---rrd~~vVltsne~D~lal~~~t~~~t~~LP~g~~~lP~~~LPyLE~-F~~i~ 170 (514)
T KOG2373|consen 95 ENYELPDETSVRQAFNGVFGLHLAT---RRDRSVVLTSNERDALALYEATKALTFALPHGEILLPQLVLPYLEE-FDKIY 170 (514)
T ss_pred ccCCCCcccchhhhhcceeceeecc---cccceEEEeecchhHHHHhhhcCceEEEcccccccCcHHHHHHHHh-hheEE
Confidence 3444444566777778899999875 367889999999999999986 566333366776544 56677776 58999
Q ss_pred EEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcchhhhhhcHHHHHHHHHhcCCHHHHHH
Q psy15222 196 FSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFL 263 (444)
Q Consensus 196 l~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~G~~~~~~~l~~a~~~~~f~~ 263 (444)
+++--|...-.||.-.+..+ .-..|-.+ -|+..-|.-...-.+.-.+..++..|.|+-+--+
T Consensus 171 fWl~~d~~sw~aAk~fa~kL-----n~~rClLv-rp~e~~p~p~~al~~rlnl~~il~~a~p~~hk~i 232 (514)
T KOG2373|consen 171 FWLPVDHVSWSAAKDFASKL-----NTLRCLLV-RPEERPPEPVRALDHRLNLNSILNSAVPMRHKGI 232 (514)
T ss_pred EEecccccchHHHHHHHhhc-----CcceEEEE-CCCCCCcchhhhhcccccHHHHHhhhchhhhhhh
Confidence 99988887667765544433 23334332 3554444444333444556777888887655433
No 32
>PF00772 DnaB: DnaB-like helicase N terminal domain; InterPro: IPR007693 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1B79_D 1JWE_A 3GXV_C 3BGW_C 2R6D_B 2R6C_D 2R6E_B 2R6A_A 2VYE_A 2VYF_B ....
Probab=94.46 E-value=0.37 Score=39.92 Aligned_cols=64 Identities=17% Similarity=0.191 Sum_probs=45.6
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..|+.+|+.+..+... + .-+.|..+ ++.++..+.+.+++ +..+|+..+...+.+.
T Consensus 5 ~~~aE~~lL~~lL~~~~~~~~i~~~-L-~~e~F~~~~h~~If~~i~~l~~~-~~~id~~~v~~~l~~~ 69 (103)
T PF00772_consen 5 DIEAEKALLGALLNDPEAIDEIIDK-L-SPEDFYDPAHRRIFEAILELYRE-GEPIDPITVAEELSDE 69 (103)
T ss_dssp HHHHHHHHHHHHHHSCCHHHHHHTT---SGGGSSSHHHHHHHHHHHHHHHT-TS--SHHHHHHHHHHT
T ss_pred cHHHHHHHHHHHHcChHHHHHHhcc-C-CHHHhCCHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHC
Confidence 4578999999999999998877532 1 11234444 56667777777777 8999999999999765
No 33
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=94.27 E-value=0.11 Score=41.51 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=20.1
Q ss_pred ceEEEEEecCCCCEEEEEeeec
Q psy15222 91 GRIMFPIKNTDGQIIGFGGRLI 112 (444)
Q Consensus 91 ~RiifPI~d~~G~vvgf~gR~l 112 (444)
+-++||.+|..|+++|+.-|-.
T Consensus 29 ~N~vF~~~d~~g~~~ga~~rGt 50 (77)
T PF13154_consen 29 GNVVFVGYDENGKPVGAELRGT 50 (77)
T ss_pred ccEEEEEECCCCCEEEEEEECC
Confidence 3689999999999999999987
No 34
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=93.86 E-value=0.39 Score=52.52 Aligned_cols=84 Identities=21% Similarity=0.235 Sum_probs=57.8
Q ss_pred ccCCcccCcHHHHHHhhccCcEEEecChhhHHHHH----HcCCC---e---EEEcCCccCCHHHHHHHhccCCeEEEEeC
Q psy15222 130 HKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLS----QFGFL---Q---TVAILGTACTSTHIKKILFYTNSIIFSFD 199 (444)
Q Consensus 130 ~K~~~Lygl~~a~~~i~~~~~viIvEG~~Dvlsl~----q~Gi~---n---aVA~lGtalt~~q~~~L~r~~~~Vil~~D 199 (444)
.|...-|.++.+|..+--.+.||+|||.-+++-+. ++|+. + +|..-|+++ +.-++.-..+..++.+..|
T Consensus 378 ~~r~i~r~l~~trs~~lFAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs~~-k~f~kf~~~~gI~~~vitD 456 (581)
T COG3593 378 DKRRIKRHLDATRSSLLFARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGL-KPFIKFAEAMGIRVHVITD 456 (581)
T ss_pred chhhhhhhcccccchhhhhceeEEEeccchhhhHHHHHHHhccccccCcEEEEeecccCc-HHHHHHhhccCceEEEEec
Confidence 34556677777777666678999999999999765 56653 2 333344444 3334422334569999999
Q ss_pred CChhHHHHHHHHHHH
Q psy15222 200 GDQAGRRAARRALEV 214 (444)
Q Consensus 200 ~D~AG~~aa~r~~~~ 214 (444)
+|++|.++..+.-.+
T Consensus 457 ~D~~g~~~~~~~~~l 471 (581)
T COG3593 457 GDEAGKKYEATVRDL 471 (581)
T ss_pred CCcccchhhhhhhhc
Confidence 999999998775543
No 35
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=93.49 E-value=0.58 Score=44.84 Aligned_cols=82 Identities=22% Similarity=0.226 Sum_probs=53.5
Q ss_pred cEEEecChhhHHHHHHc------CCC--eEEEcCCccCCHHHHHHHhc---cCCeEEEEeCCChhHHHHHHHHHHHHHhh
Q psy15222 150 YVLITEGYMDVIGLSQF------GFL--QTVAILGTACTSTHIKKILF---YTNSIIFSFDGDQAGRRAARRALEVCLLY 218 (444)
Q Consensus 150 ~viIvEG~~Dvlsl~q~------Gi~--naVA~lGtalt~~q~~~L~r---~~~~Vil~~D~D~AG~~aa~r~~~~l~~~ 218 (444)
-=|||||--||=+...+ |-. -+|++. +...++..-++ -++-|+++.|.|..|++-|.+..+.+..+
T Consensus 9 VRIiVEGAsDvE~iSkalQr~aLG~eYnITisSI---iPTT~~eIA~raaeGADlvlIATDaD~~GReLA~kf~eeLrg~ 85 (290)
T COG4026 9 VRIIVEGASDVEVISKALQRLALGSEYNITISSI---IPTTNVEIAKRAAEGADLVLIATDADRVGRELAEKFFEELRGM 85 (290)
T ss_pred EEEEeeccchHHHHHHHHHHhhhcccceeEEEee---ccCchHHHHHHhhccCCEEEEeecCcchhHHHHHHHHHHHHHh
Confidence 45899999998765443 322 233322 11223333333 46789999999999999999988887643
Q ss_pred cCCCcEEEEEeCCCCCCcc
Q psy15222 219 ATDDKIIKFLFLPDKYDPD 237 (444)
Q Consensus 219 ~~~g~~v~v~~lP~gkDpd 237 (444)
. | .+..+.+|-|.|..
T Consensus 86 V--G-hiERmK~PiGHDvE 101 (290)
T COG4026 86 V--G-HIERMKIPIGHDVE 101 (290)
T ss_pred h--h-hhheeccCCCCCcc
Confidence 2 3 24456789888764
No 36
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=91.84 E-value=0.38 Score=39.97 Aligned_cols=59 Identities=19% Similarity=0.165 Sum_probs=39.0
Q ss_pred cCcEEEecChhhHHHHHHc----CCC-----eEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHH
Q psy15222 148 SGYVLITEGYMDVIGLSQF----GFL-----QTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRR 206 (444)
Q Consensus 148 ~~~viIvEG~~Dvlsl~q~----Gi~-----naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~ 206 (444)
.+.+|+|||..|.+.+... |.. -+|-.+|..--..-+.+|.....++++.+|+|..+..
T Consensus 3 a~~vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~~~~~~~~ll~~~~i~~~vi~D~D~~~~~ 70 (97)
T cd01026 3 ADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGKNFKPFIKLLNALGIPVAVLTDLDAKRNE 70 (97)
T ss_pred CCeEEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCcchHHHHHHHHHcCCCEEEEEeCCCCCCc
Confidence 3579999999999986553 211 1333444442223356666667799999999998754
No 37
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.08 E-value=2.1 Score=40.57 Aligned_cols=87 Identities=13% Similarity=0.144 Sum_probs=57.1
Q ss_pred ccCcEEEecChhhHHHHHHcCCCeEE-EcCCccCC------HHH------HHHHhccCCeEEEEeCCChhHHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFLQTV-AILGTACT------STH------IKKILFYTNSIIFSFDGDQAGRRAARRALE 213 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~naV-A~lGtalt------~~q------~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~ 213 (444)
..+.+.|||-.-|++++.+.|.-+.+ -++|..++ +++ ++.+....++||+|++.+--|+.-|.-..+
T Consensus 77 d~~~icVVE~~~Dv~aiE~s~~y~G~YhVL~G~ispl~gi~p~~l~i~~L~~ri~~~v~EVIlA~~pt~EGe~Ta~yi~~ 156 (196)
T PRK00076 77 DQSLICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGIGPEDLNIDELLERLDGEVKEVILATNPTVEGEATAHYIAR 156 (196)
T ss_pred CCCEEEEECCHHHHHHHHhhCcCceEEEEecCCcCCCCCCCccccCHHHHHHHHhCCCCEEEEeCCCCchHHHHHHHHHH
Confidence 45679999999999999998754333 24443332 232 222322377999999999999998888776
Q ss_pred HHHhhcCCCcEEEEE--eCCCCCCc
Q psy15222 214 VCLLYATDDKIIKFL--FLPDKYDP 236 (444)
Q Consensus 214 ~l~~~~~~g~~v~v~--~lP~gkDp 236 (444)
.+.+ .+.+|..+ =+|-|-+.
T Consensus 157 ~lk~---~~ikvtRiA~GiP~G~~l 178 (196)
T PRK00076 157 LLKP---LGVKVTRLAHGVPVGGEL 178 (196)
T ss_pred HHHH---cCCCeeeeeeCCCCCcce
Confidence 6543 25544433 26766443
No 38
>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=90.01 E-value=2.6 Score=36.47 Aligned_cols=83 Identities=17% Similarity=0.169 Sum_probs=53.6
Q ss_pred cEEEecChhhHHHHHHcCCCeEE-EcCCccCC------HH--HHHHHhc-----cCCeEEEEeCCChhHHHHHHHHHHHH
Q psy15222 150 YVLITEGYMDVIGLSQFGFLQTV-AILGTACT------ST--HIKKILF-----YTNSIIFSFDGDQAGRRAARRALEVC 215 (444)
Q Consensus 150 ~viIvEG~~Dvlsl~q~Gi~naV-A~lGtalt------~~--q~~~L~r-----~~~~Vil~~D~D~AG~~aa~r~~~~l 215 (444)
.+.|||-.-|++++.+.|.-+.. -++|..++ ++ .+..|.+ ..++||+|+|.|--|+.-++-..+.+
T Consensus 2 ~lcVVE~~~Dv~~iE~~~~y~G~Y~VL~G~ispl~gi~p~~l~i~~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l 81 (112)
T cd01025 2 KLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKLL 81 (112)
T ss_pred EEEEECCHHHHHHHHhhCccceEEEEeCCCcCCCCCCCccccCHHHHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHH
Confidence 57899999999999998743322 23343333 22 2333322 24789999999999999998877765
Q ss_pred HhhcCCCcEEEEE--eCCCCCC
Q psy15222 216 LLYATDDKIIKFL--FLPDKYD 235 (444)
Q Consensus 216 ~~~~~~g~~v~v~--~lP~gkD 235 (444)
.. .+.++..+ -+|-|-+
T Consensus 82 ~~---~~~kvsRlA~GiP~G~~ 100 (112)
T cd01025 82 KD---FGVKVTRLAQGIPVGGE 100 (112)
T ss_pred hH---cCCCeEEEEEcCCCCcc
Confidence 43 24444433 2676643
No 39
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.21 E-value=5.8 Score=37.63 Aligned_cols=87 Identities=14% Similarity=0.094 Sum_probs=56.7
Q ss_pred ccCcEEEecChhhHHHHHHcCCCeEE-EcCCcc------CCHHHH--HHH-hc----cCCeEEEEeCCChhHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFLQTV-AILGTA------CTSTHI--KKI-LF----YTNSIIFSFDGDQAGRRAARRAL 212 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~naV-A~lGta------lt~~q~--~~L-~r----~~~~Vil~~D~D~AG~~aa~r~~ 212 (444)
....+-|||..-|++++.+.|.-+.+ -++|.. .+++++ ..| .| ..++||+|++.+--|+.-|.-..
T Consensus 77 d~~~iCVVE~~~Dv~aiE~~~~y~G~YhVL~G~iSPldgigp~~l~i~~L~~Ri~~~~v~EVIlAt~~tvEGe~Ta~yi~ 156 (195)
T TIGR00615 77 DNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIA 156 (195)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCchHHHHHHHHH
Confidence 45678899999999999999864333 244432 344442 222 22 26799999999999999888766
Q ss_pred HHHHhhcCCCcEEEEE--eCCCCCCc
Q psy15222 213 EVCLLYATDDKIIKFL--FLPDKYDP 236 (444)
Q Consensus 213 ~~l~~~~~~g~~v~v~--~lP~gkDp 236 (444)
+.+.+ .+++|..+ =+|-|-|.
T Consensus 157 ~~lk~---~~ikvtRlA~GiP~G~~l 179 (195)
T TIGR00615 157 RLLQP---FGVKVTRIASGLPVGGDL 179 (195)
T ss_pred HHhhh---cCCcEEeeeecCCCCcce
Confidence 65542 25444432 25766443
No 40
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=87.12 E-value=5.4 Score=37.72 Aligned_cols=87 Identities=15% Similarity=0.116 Sum_probs=56.9
Q ss_pred ccCcEEEecChhhHHHHHHcCCCeEE-EcCCcc------CCHHH--HHHH-hc---cCC-eEEEEeCCChhHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFLQTV-AILGTA------CTSTH--IKKI-LF---YTN-SIIFSFDGDQAGRRAARRAL 212 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~naV-A~lGta------lt~~q--~~~L-~r---~~~-~Vil~~D~D~AG~~aa~r~~ 212 (444)
+...+.|||..-|++++.+.|.-+.. -++|.. ..+++ +..| .| ... +||+|.+.--.|+.-|.-..
T Consensus 78 d~~~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl~gigpe~l~i~~L~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI~ 157 (198)
T COG0353 78 DKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGIGPEDLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIA 157 (198)
T ss_pred CCceEEEEcchHHHHHHHHhcccCeeEEEecCccCcccCCCcccccHHHHHHHHhcCCCceEEEecCCCccchHHHHHHH
Confidence 55679999999999999999843332 233322 23443 3333 33 222 99999999999999998877
Q ss_pred HHHHhhcCCCcEEEEE--eCCCCCCc
Q psy15222 213 EVCLLYATDDKIIKFL--FLPDKYDP 236 (444)
Q Consensus 213 ~~l~~~~~~g~~v~v~--~lP~gkDp 236 (444)
+.+.+ .+++|..+ =+|-|-|.
T Consensus 158 ~~l~~---~~ikvtRlA~GiPvGg~l 180 (198)
T COG0353 158 RLLKP---LGLKVTRLAQGVPVGGEL 180 (198)
T ss_pred HHHhh---cCCeEEEEeecCccCCce
Confidence 77654 25555433 25765443
No 41
>PRK13844 recombination protein RecR; Provisional
Probab=82.07 E-value=12 Score=35.63 Aligned_cols=86 Identities=14% Similarity=0.194 Sum_probs=56.2
Q ss_pred ccCcEEEecChhhHHHHHHcCCCeEE-EcCCccC------CHHHH--HHH-hc----cCCeEEEEeCCChhHHHHHHHHH
Q psy15222 147 KSGYVLITEGYMDVIGLSQFGFLQTV-AILGTAC------TSTHI--KKI-LF----YTNSIIFSFDGDQAGRRAARRAL 212 (444)
Q Consensus 147 ~~~~viIvEG~~Dvlsl~q~Gi~naV-A~lGtal------t~~q~--~~L-~r----~~~~Vil~~D~D~AG~~aa~r~~ 212 (444)
..+.+-|||..-|++++.+.|.-+.+ -++|..+ +++++ ..| .| ..++||+|+..+--|+.-|.-..
T Consensus 81 d~~~iCVVE~~~Dv~aiE~t~~y~G~YhVL~G~ispl~gi~p~~l~i~~L~~Ri~~~~v~EVIlAt~~t~EGe~Ta~yi~ 160 (200)
T PRK13844 81 DDTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGIGPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHFIS 160 (200)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCccHHHHHHHHH
Confidence 45678899999999999999864443 2444433 34443 222 22 26799999999999998887766
Q ss_pred HHHHhhcCCCcEEEEE--eCCCCCCc
Q psy15222 213 EVCLLYATDDKIIKFL--FLPDKYDP 236 (444)
Q Consensus 213 ~~l~~~~~~g~~v~v~--~lP~gkDp 236 (444)
+.+ +.+.+|..+ =+|-|-|.
T Consensus 161 ~~l----k~~vkvtRlA~GiP~G~~l 182 (200)
T PRK13844 161 QMI----AKDIKISRIGFGVPFGGEL 182 (200)
T ss_pred HHh----cCCCcEEeeeecCcCCcce
Confidence 554 235555433 25766443
No 42
>PRK06321 replicative DNA helicase; Provisional
Probab=67.87 E-value=14 Score=39.83 Aligned_cols=65 Identities=14% Similarity=0.046 Sum_probs=46.0
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|..+|..||.+|+.+..+... + .-+.|..+ +..+|..+.+.+.+ +..+|+-.+.+.|.+.
T Consensus 18 ~~~eaE~avLG~lL~~~~~~~~v~~~-L-~~e~Fy~~~h~~If~ai~~l~~~-~~~iD~vtv~~~L~~~ 83 (472)
T PRK06321 18 NSKESEMIVLGCMLTSVNYLNLAANQ-L-QEDDFYFLEHKIIFRVLQDAFKS-DKPIDVHLAGEELKRR 83 (472)
T ss_pred CCHHHHHHHHHHHHcCHhHHHHHHhh-C-CHHHCCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHhhc
Confidence 34679999999999999988776432 1 11124344 55566667676666 8999999999888754
No 43
>PRK05748 replicative DNA helicase; Provisional
Probab=64.59 E-value=15 Score=39.09 Aligned_cols=64 Identities=11% Similarity=0.097 Sum_probs=45.8
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..||.+|+.+..+... + .-++|. +.+..+|..+.+.+.+ +..+|+..+.+.|.+.
T Consensus 13 ~~eaE~~VLGalL~~~~~~~~v~~~-L-~~edF~~~~h~~If~ai~~l~~~-g~~iD~~tl~~~L~~~ 77 (448)
T PRK05748 13 SIEAEQAVLGAIFLDPDALITVSEY-L-SPDDFYRHAHRLIFRAMLKLSDR-GEPIDVVTVTEILDDQ 77 (448)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHcCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHHHhc
Confidence 4679999999999999998765432 1 111233 4455666667777776 8899999999888754
No 44
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=63.88 E-value=13 Score=38.91 Aligned_cols=62 Identities=13% Similarity=0.106 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 342 CIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 342 ~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
.+|+.+|..||.+|+.+..+... + .-++|. +.+..+|..+.+.+.+ +..+|+..+.+.|.+.
T Consensus 3 eaE~avLG~lL~~~~~~~~i~~~-L-~~edFy~~~h~~If~ai~~L~~~-~~~iD~~tv~~~L~~~ 65 (421)
T TIGR03600 3 EAEQAVLGGLLLDNDFIERVMAI-L-KPEHFYSQDHRIIFEAMLDMFAE-NRPVDPLTLADKLEAE 65 (421)
T ss_pred HHHHHHHHHHHcCHHHHHHHHhh-C-CHHHCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHHhhc
Confidence 57999999999999998775322 1 111233 4466667777777776 8899999888888654
No 45
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=62.35 E-value=18 Score=38.05 Aligned_cols=63 Identities=14% Similarity=0.116 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 341 ICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 341 ~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
..+|+.+|..||.+|+.+..+... + .-+.|. +.+..+|..+.+.+.+ +..+|+..+...|.+.
T Consensus 6 ~eaE~~vLgalL~~~~~~~~v~~~-L-~~edF~~~~h~~If~ai~~l~~~-g~~iD~~tl~~~l~~~ 69 (434)
T TIGR00665 6 IEAEQAVLGAILLDNEAIDDVAEI-L-KPEDFYRPAHQLIFQAILDLYEK-GEPIDLVTVKEELEKD 69 (434)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHhh-C-CHHHCCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHHhc
Confidence 568999999999999988765321 1 011233 4466667777776666 8889999888888754
No 46
>PRK08760 replicative DNA helicase; Provisional
Probab=60.89 E-value=23 Score=38.18 Aligned_cols=64 Identities=8% Similarity=0.151 Sum_probs=45.6
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..||.+|+.+..+... + .-+.|..+ +..+|..+.+.+.+ +..+|+-.+.+.|...
T Consensus 36 ~~eaEqaVLGalL~~~~~~~~v~~~-L-~~edFy~~~H~~If~ai~~L~~~-~~~iD~vtv~~~L~~~ 100 (476)
T PRK08760 36 SVEAEQAVLGGLMLAPDALDRVNDQ-L-TENDFYRRDHRLIYRAIRELSEK-DRPFDAVTLGEWFESQ 100 (476)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHhCCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHHhc
Confidence 4679999999999999998876432 1 11234344 55566666666666 8899999998888754
No 47
>PRK05595 replicative DNA helicase; Provisional
Probab=60.66 E-value=21 Score=37.87 Aligned_cols=65 Identities=17% Similarity=0.153 Sum_probs=45.3
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|+.+|..||.+|+.+..+... +. -++|. +.+..+|..+.+.+.+ +..+|+..+.+.|.+.
T Consensus 10 ~~~eaE~~VLG~lL~~~~~~~~v~~~-L~-~edFy~~~H~~IF~aI~~L~~~-g~~iD~vtl~~~L~~~ 75 (444)
T PRK05595 10 QSIEAEQSVLGAMIIDKTSIAEAAEV-LK-SEDFYRDSHKVIFSAIIELYQK-DIAVDMLTLTENLKST 75 (444)
T ss_pred CCHHHHHHHHHHHHcCHhHHHHHHhh-CC-HHHcCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHHhcc
Confidence 34679999999999999998765432 11 11233 4455566666676666 8899999888888753
No 48
>PRK06904 replicative DNA helicase; Validated
Probab=60.18 E-value=22 Score=38.21 Aligned_cols=65 Identities=12% Similarity=0.047 Sum_probs=45.4
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|+.+|..||.+|+.+..+... + .-++|..+ +..+|..+.+.+.+ +..+|+..+.+.|.+.
T Consensus 25 ~~~eaE~aVLGalL~~~~~~~~v~~~-L-~~edFy~~~H~~IF~ai~~L~~~-g~~iD~vtl~~~L~~~ 90 (472)
T PRK06904 25 HSIEAEQAVLGGIMLDNRHWDSVAER-V-IADDFYTFEHRIIFQEMELLFRQ-NTPIDLLTLDQALKTK 90 (472)
T ss_pred CCHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHcCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHHhc
Confidence 34679999999999999988765432 1 11123344 55566666666666 8899999998888754
No 49
>PRK08506 replicative DNA helicase; Provisional
Probab=60.14 E-value=49 Score=35.57 Aligned_cols=63 Identities=19% Similarity=0.170 Sum_probs=45.1
Q ss_pred hHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 341 ICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 341 ~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
..+|..+|..||.+|+.+..+... + .-+.|. +.+..+|..+.+.+.+ +..+|+..+.+.|...
T Consensus 7 ~eaE~~vLGalL~~~~~~~~v~~~-L-~~e~Fy~~~h~~If~ai~~l~~~-~~~iD~vtv~~~L~~~ 70 (472)
T PRK08506 7 LDIERAVLSSILFSPDKFEEIASV-L-EPKDFYLPAHQDIFEAMLKLHNE-DEPIDEEFIRKKLPKD 70 (472)
T ss_pred HHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHcCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHhhc
Confidence 578999999999999998765432 1 111243 4466667777777776 8899998888888653
No 50
>PRK08840 replicative DNA helicase; Provisional
Probab=59.65 E-value=21 Score=38.37 Aligned_cols=64 Identities=9% Similarity=0.086 Sum_probs=45.1
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..||.+|+.+..+... +. -++|. +.+..+|..+.+.+.+ +..+|+-.+.+.|.+.
T Consensus 23 ~~eaEqavLGalL~~~~~~~~v~~~-L~-~edFy~~~Hq~If~ai~~L~~~-g~~iD~vtv~~~L~~~ 87 (464)
T PRK08840 23 SLEAEQSVIGGLLLDNERWDTVAEK-VV-ASDFYSRPHRLIFEGVKSILEA-GKPLDLITLSEHLERR 87 (464)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-CC-HHHCCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHHhc
Confidence 3679999999999999998765432 11 11233 4455566666666666 8899999999888754
No 51
>PRK05636 replicative DNA helicase; Provisional
Probab=57.25 E-value=23 Score=38.45 Aligned_cols=64 Identities=14% Similarity=0.135 Sum_probs=45.4
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..||.+|+.+.++... + .-++|..+ +..+|..+.+.+.+ +..+|+..+.+.|.+.
T Consensus 73 ~~eAEqaVLGalL~~p~~i~ev~~~-L-~~edFy~~~Hq~IF~Ai~~L~~~-g~pID~vtV~~~L~~~ 137 (505)
T PRK05636 73 DNEAEQGVLGAMLLSPDTVIDIVEV-L-TPEDFYRPAHQLIFQAIIDLFSD-NKEIDPVIVAGRLDRT 137 (505)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHcCCHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHhhc
Confidence 3679999999999999998775432 1 11124344 55566667777766 8899999888888754
No 52
>PRK09165 replicative DNA helicase; Provisional
Probab=54.66 E-value=26 Score=37.88 Aligned_cols=65 Identities=6% Similarity=0.072 Sum_probs=45.4
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|..+|..||.+|+.+..+... + .-++|..+ +..+|..+.+.+.+ +..+|+..+.++|.+.
T Consensus 23 ~~~eaEqaVLGalL~~~~~~~~v~~~-L-~~edFy~~~H~~IF~ai~~L~~~-g~piD~vtv~~~L~~~ 88 (497)
T PRK09165 23 HNIEAEQALLGAILINNRALDRVSDF-L-KPEHFFEPLHQRIYEAIAKIIRK-GKLATPVTLKTFLEND 88 (497)
T ss_pred CCHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHCCCHHHHHHHHHHHHHHhC-CCCcCHHHHHHHHhhc
Confidence 34689999999999999988775432 1 01123344 55566666676666 8899999999888653
No 53
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=54.47 E-value=56 Score=29.78 Aligned_cols=59 Identities=17% Similarity=0.216 Sum_probs=43.4
Q ss_pred EEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcchhhhhh
Q psy15222 171 TVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243 (444)
Q Consensus 171 aVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~ 243 (444)
++-.+|++++++|.+.|... |-++-.+.+++....++. -| |.+..+|..+||+.+....
T Consensus 56 viVA~gi~ls~eH~~al~aL---------~~e~R~efi~~l~~dLlr---~~--v~F~~~Pn~~~pqsiqvsr 114 (161)
T COG5440 56 VIVAIGIALSQEHRRALMAL---------NPEKREEFIWKLRRDLLR---LG--VDFQALPNPRDPQSIQVSR 114 (161)
T ss_pred EEEEEeeccCHHHHHHHHhc---------ChHHHHHHHHHHHHHHHh---cC--CceEecCCccCCceeEeeh
Confidence 34457999999999999876 445566677776665553 24 7778889999999987653
No 54
>PRK08006 replicative DNA helicase; Provisional
Probab=54.30 E-value=29 Score=37.36 Aligned_cols=64 Identities=11% Similarity=0.121 Sum_probs=45.4
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccC-ccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCS-QNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|..+|..||.+|+.+..+... +. -++|. +.+..+|..+.+.+.+ +..+|+-.+.+.|.+.
T Consensus 30 ~~eaEqavLGalL~~~~~~~~v~~~-L~-~edFy~~~H~~If~ai~~L~~~-g~~iD~vtv~~~L~~~ 94 (471)
T PRK08006 30 SIEAEQSVLGGLMLDNERWDDVAER-VV-ADDFYTRPHRHIFTEMARLQES-GSPIDLITLAESLERQ 94 (471)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-CC-HHHcCCHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHhc
Confidence 3579999999999999987765432 11 11233 4466666667777766 8999999999888754
No 55
>PRK07004 replicative DNA helicase; Provisional
Probab=53.36 E-value=30 Score=37.06 Aligned_cols=64 Identities=14% Similarity=0.023 Sum_probs=44.9
Q ss_pred hhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 340 PICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 340 ~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
...+|+.+|..||.+|+.+.++... + .-+.|..+ +..+|..+.+.+.+ +..+|.-.+.+.|.+.
T Consensus 18 ~~eaEqaVLGalL~~~~~~~~v~~~-L-~~edFy~~~H~~If~ai~~L~~~-g~~iD~vtl~~~L~~~ 82 (460)
T PRK07004 18 SIEAEQSVLGGLLLDNAAWDRIADF-L-SQSDFYRYDHRIIFEHIGRLIAA-TRPADVITVYEALTTS 82 (460)
T ss_pred CHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHcCCHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHHhc
Confidence 3579999999999999998765432 1 11123344 55566666676666 8899998888888754
No 56
>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=48.74 E-value=26 Score=31.02 Aligned_cols=46 Identities=28% Similarity=0.393 Sum_probs=31.9
Q ss_pred HHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCC
Q psy15222 184 IKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPD 232 (444)
Q Consensus 184 ~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~ 232 (444)
++.+.+.+++||+|.|.|.-|+.=++.+++.+.. ....++.+.+..
T Consensus 84 ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~---~~~~v~R~~fss 129 (142)
T cd01028 84 LKKLAKKADEIVLATDPDREGELIAWEILEVLKC---DNKPVKRAWFSE 129 (142)
T ss_pred HHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCC---CCCCeEEEEEcc
Confidence 3444445789999999999999999988876531 134555555543
No 57
>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=47.82 E-value=61 Score=29.39 Aligned_cols=83 Identities=22% Similarity=0.235 Sum_probs=53.4
Q ss_pred cCcEEEecChhhHHHHHHc-CCC--eEEEcCCccCCHHHHHHH---hccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCC
Q psy15222 148 SGYVLITEGYMDVIGLSQF-GFL--QTVAILGTACTSTHIKKI---LFYTNSIIFSFDGDQAGRRAARRALEVCLLYATD 221 (444)
Q Consensus 148 ~~~viIvEG~~Dvlsl~q~-Gi~--naVA~lGtalt~~q~~~L---~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~ 221 (444)
.++|+|||-..=.=++.+. |.. --|++-|. .+.....+| ....-++...-|-|.+|..-|.+..+..
T Consensus 18 ~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt~G~-p~~A~~~LL~~L~~~g~~l~y~GDfDp~Gl~IA~~l~~r~------ 90 (152)
T PF09664_consen 18 SGRVYVVENPAVFSALADELGASCPPLVCTSGQ-PSAAARRLLDRLAAAGARLYYSGDFDPEGLRIANRLIQRY------ 90 (152)
T ss_pred CCEEEEEecHHHHHHHHHhcCCCCCeEEEcCCc-HHHHHHHHHHHHHhCCCEEEEecCCCHHHHHHHHHHHHHh------
Confidence 3459999987655555544 322 24666664 333333444 3334589999999999999888876653
Q ss_pred CcEEEEEeCCCCCCcchhhhhh
Q psy15222 222 DKIIKFLFLPDKYDPDSYIRKF 243 (444)
Q Consensus 222 g~~v~v~~lP~gkDpdd~l~~~ 243 (444)
| ..|..+|++||....
T Consensus 91 ~------~~~Wrm~~~dY~~~~ 106 (152)
T PF09664_consen 91 G------ARPWRMDAEDYLAAL 106 (152)
T ss_pred C------CccccCCHHHHHHhc
Confidence 2 124678999995543
No 58
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=45.89 E-value=44 Score=35.65 Aligned_cols=66 Identities=14% Similarity=0.099 Sum_probs=47.9
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|+.+|-.|+.+|+.+..+... +..-..+.+++..+|..+.+.+++ +..+|.-.+.++|.+.
T Consensus 5 ~~~eAE~~vLG~il~~~~~~~~v~~~-l~~~dFy~~~H~~IF~a~~~l~~~-~~~id~vtv~~~l~~~ 70 (435)
T COG0305 5 QDIEAEQAVLGGILLDPDAIERVSER-LRPEDFYRPAHRLIYQAILDLYGQ-GEPIDLVTVSEELSDR 70 (435)
T ss_pred CCHHHHHHHhhhhhcCHHHHHHHHHh-cChhhcCcHHHHHHHHHHHHHHhc-CCCCcHhHHHHHHhhc
Confidence 34678999999999999998776443 111112335566677777777777 8899999998888765
No 59
>PF09133 SANTA: SANTA (SANT Associated); InterPro: IPR015216 The SANTA domain (SANT associated) is approximately 90 amino acids in length and is conserved in eukaryotes. It is sometimes found in association with the SANT domain (IPR001005 from INTERPRO, also known as the Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha-helices. Many conserved hydrophobic residues are present which implies a possible role in protein-protein interactions.
Probab=44.15 E-value=18 Score=30.15 Aligned_cols=29 Identities=24% Similarity=0.689 Sum_probs=23.4
Q ss_pred HHHHHcCCCHHHHHHccceeecCCchHHHH
Q psy15222 20 NFLKKRGLNEEIILRFNLGYAPNEWNALNK 49 (444)
Q Consensus 20 ~YL~~RGis~e~i~~f~lGyap~~~~~L~~ 49 (444)
...++-|++++.+++|..|| |.+|+.+.+
T Consensus 62 ~~~~~nGfp~~v~~~F~~GF-P~~W~~~~~ 90 (93)
T PF09133_consen 62 SRMRENGFPSEVIKKFMNGF-PENWEEYIN 90 (93)
T ss_pred HhHHHcCCCHHHHHHHhcCC-CHHHHHHHH
Confidence 45567799999999999997 778876543
No 60
>PRK07773 replicative DNA helicase; Validated
Probab=43.47 E-value=46 Score=38.70 Aligned_cols=65 Identities=9% Similarity=0.064 Sum_probs=45.6
Q ss_pred ChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q psy15222 339 QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKNDIDHSKFIKYLKKI 406 (444)
Q Consensus 339 ~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~l~~~ 406 (444)
....+|+.+|..||.+|+.+.++... + .-++|..+ +..+|..+.+.+++ +..+|+..+.+.|.+.
T Consensus 26 ~~~eaEqavLG~lL~~~~~i~~v~~~-L-~~edFy~~~H~~IF~ai~~L~~~-g~piD~vtv~~~L~~~ 91 (886)
T PRK07773 26 QDLAAEQSVLGGMLLSKEAIARVLER-L-RPGAFYRPAHQNIYDAILDLYGR-GEPADLVTVAAELDRR 91 (886)
T ss_pred CCHHHHHHHHHHHHcCHHHHHHHHhh-C-CHHHCCCHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHhc
Confidence 34679999999999999988765332 1 01123344 55566667676666 8899999998888754
No 61
>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=43.31 E-value=57 Score=28.35 Aligned_cols=53 Identities=19% Similarity=0.199 Sum_probs=34.2
Q ss_pred HHHHHHh---ccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcchh
Q psy15222 182 THIKKIL---FYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSY 239 (444)
Q Consensus 182 ~q~~~L~---r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpdd~ 239 (444)
.|++.|+ +.+++||+|.|.|.-|..-++...+.+. .+..++.+.+. ..++.+.
T Consensus 61 ~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~----~~~~v~Rl~~s-slt~~~I 116 (123)
T cd03363 61 KVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLK----LKKNVKRVVFN-EITKEAI 116 (123)
T ss_pred HHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcC----CCCCeEEEEEc-cCCHHHH
Confidence 4554443 4477999999999999999888777542 24455544443 3444443
No 62
>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=42.12 E-value=32 Score=30.85 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=31.3
Q ss_pred HHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCC
Q psy15222 184 IKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLP 231 (444)
Q Consensus 184 ~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP 231 (444)
++.+.+.++.||+|.|.|.-|+.=++.+++.+... ....++.+.+.
T Consensus 92 ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~--~~~~v~R~~fs 137 (151)
T cd03362 92 LKKLAKRADEIVIATDADREGELIGREILEYAKCV--KRKPVKRAWFS 137 (151)
T ss_pred HHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC--CCCcEEEEEEc
Confidence 33444457899999999999999888887765310 13455555544
No 63
>PF07057 TraI: DNA helicase TraI; InterPro: IPR009767 This entry represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [].; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0000746 conjugation; PDB: 3FLD_B.
Probab=41.58 E-value=32 Score=30.27 Aligned_cols=48 Identities=19% Similarity=0.305 Sum_probs=23.8
Q ss_pred hHHHHcCCceeccccccCCCcccccccccccCCceEEEEEecCCCCEEEEEeeec
Q psy15222 58 NTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLI 112 (444)
Q Consensus 58 ~~l~~~GL~~~~~~~~~~~g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l 112 (444)
..|..+||-..... ++||.-.+.| =...++||++|.+|+.-|..-..|
T Consensus 66 a~Lr~~gL~~g~s~-----arfI~~grKY--P~PhvALPv~D~NGK~AGv~L~~L 113 (126)
T PF07057_consen 66 AVLRESGLDPGESM-----ARFIPPGRKY--PQPHVALPVYDRNGKQAGVWLTPL 113 (126)
T ss_dssp HHHHHCT-TTSB--------EEE----SS-----EEEEEEE-TTS-EEEEEEEE-
T ss_pred HHHHHcCCCCCCcc-----eeecCCCCCC--CCcceeceeecCCCceeeeEEeee
Confidence 45777888332221 2222211233 147899999999999998877666
No 64
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E. This model describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.
Probab=40.99 E-value=1.1e+02 Score=31.28 Aligned_cols=48 Identities=13% Similarity=0.312 Sum_probs=36.9
Q ss_pred cChhhHHH-HHHcCCCeEEEcCCccCCHHHHHHHhcc-CCeEEEEeCCCh
Q psy15222 155 EGYMDVIG-LSQFGFLQTVAILGTACTSTHIKKILFY-TNSIIFSFDGDQ 202 (444)
Q Consensus 155 EG~~Dvls-l~q~Gi~naVA~lGtalt~~q~~~L~r~-~~~Vil~~D~D~ 202 (444)
...+|.+. +.+.|+...+.|.|+.+|++.++.|... ...|.+-+|+-.
T Consensus 68 ~~~~~ii~~~~~~g~~~~l~TNG~ll~~e~~~~L~~~g~~~v~iSldg~~ 117 (358)
T TIGR02109 68 PDLVELVAHARRLGLYTNLITSGVGLTEARLDALADAGLDHVQLSFQGVD 117 (358)
T ss_pred ccHHHHHHHHHHcCCeEEEEeCCccCCHHHHHHHHhCCCCEEEEeCcCCC
Confidence 44466664 3456887788999999999999988875 567999999853
No 65
>PRK13745 anaerobic sulfatase-maturase; Provisional
Probab=39.97 E-value=59 Score=34.12 Aligned_cols=37 Identities=19% Similarity=0.046 Sum_probs=31.5
Q ss_pred CCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChh
Q psy15222 167 GFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQA 203 (444)
Q Consensus 167 Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~A 203 (444)
|+.+++-|.||-++++.++.|++..-.|-+.+||.+.
T Consensus 101 ~i~~~i~TNG~ll~~e~~~~l~~~~~~v~ISlDG~~~ 137 (412)
T PRK13745 101 QIDNCIQTNGTLLTDEWCEFFRENNFLVGVSIDGPQE 137 (412)
T ss_pred ceEEEEeecCEeCCHHHHHHHHHcCeEEEEEecCCHH
Confidence 5667889999999999999998865588899999864
No 66
>PRK06749 replicative DNA helicase; Provisional
Probab=39.37 E-value=63 Score=34.29 Aligned_cols=60 Identities=17% Similarity=0.117 Sum_probs=43.3
Q ss_pred hHHHHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q psy15222 341 ICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLK 404 (444)
Q Consensus 341 ~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~l~ 404 (444)
..+|..+|..||.+|+.+.++.-. -+.| +.+.+..+|..+.+.+.+ +..+|+-.+.++|.
T Consensus 6 ~eaE~~vLG~lL~~~~~~~~v~l~-~e~F--~~~~h~~If~ai~~l~~~-~~~iD~~tv~~~l~ 65 (428)
T PRK06749 6 VEAEKTVLGSLLLDGELIKECRLT-EQYF--SMPVHKSIFQLMRKMEDE-GQPIDLVTFTSRVD 65 (428)
T ss_pred HHHHHHHHHHHHcChhhhheeeEC-HHHC--CcHHHHHHHHHHHHHHhC-CCCCCHHHHHHHHh
Confidence 568999999999999998765211 1122 224466667777777776 88999999988886
No 67
>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional
Probab=36.87 E-value=1.3e+02 Score=30.93 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=34.9
Q ss_pred hhhHHHH-HHcCCCeEEEcCCccCCHHHHHHHhcc-CCeEEEEeCC
Q psy15222 157 YMDVIGL-SQFGFLQTVAILGTACTSTHIKKILFY-TNSIIFSFDG 200 (444)
Q Consensus 157 ~~Dvlsl-~q~Gi~naVA~lGtalt~~q~~~L~r~-~~~Vil~~D~ 200 (444)
.++.+.. .+.|+...+.|.|+.+|++.++.|.+. ...|.+-+|+
T Consensus 79 ~~~il~~~~~~g~~~~i~TNG~ll~~~~~~~L~~~g~~~v~iSldg 124 (378)
T PRK05301 79 LEELVAHARELGLYTNLITSGVGLTEARLAALKDAGLDHIQLSFQD 124 (378)
T ss_pred HHHHHHHHHHcCCcEEEECCCccCCHHHHHHHHHcCCCEEEEEecC
Confidence 3555543 446887788999999999999999876 5689999998
No 68
>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=34.98 E-value=61 Score=29.85 Aligned_cols=36 Identities=11% Similarity=0.188 Sum_probs=27.7
Q ss_pred HHHHHHHh---ccCCeEEEEeCCChhHHHHHHHHHHHHH
Q psy15222 181 STHIKKIL---FYTNSIIFSFDGDQAGRRAARRALEVCL 216 (444)
Q Consensus 181 ~~q~~~L~---r~~~~Vil~~D~D~AG~~aa~r~~~~l~ 216 (444)
..|++.|+ +.+++||+|.|.|.-|+.-++.+++.+.
T Consensus 106 ~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~ 144 (170)
T cd03361 106 LETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALR 144 (170)
T ss_pred HHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhc
Confidence 34555444 4578999999999999999988877653
No 69
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=33.94 E-value=2.3e+02 Score=26.02 Aligned_cols=107 Identities=7% Similarity=-0.074 Sum_probs=44.4
Q ss_pred HHHHHhhcCCCcEEEEEeCCCCCCcchhhhhhcHHHHHHHHHh-cCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHh
Q psy15222 212 LEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLE-AMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFK 290 (444)
Q Consensus 212 ~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~G~~~~~~~l~~-a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~ 290 (444)
+..+.......+.++++....-.|.+++....+... ..+.++ ..+...-.+....... ..+..=.+++..+-..+-
T Consensus 18 l~kl~~~~~~~i~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~y~a~la~kAA~~--qg~k~~~~fL~~lQ~a~~ 94 (176)
T PF13743_consen 18 LRKLKEEYGNKIEFRFIPGGLMPDINDFMPRMPING-DFWRNEPRSSSYPACLAYKAAQL--QGKKKARRFLRALQEALF 94 (176)
T ss_dssp HHHHHHHS-TTEEEEEEE--SS-S--SB--H----T-THHHS--BS--HHHHHHHHHHHT--TT-H--HHHHHHHHHHHH
T ss_pred HHHHHHHcCCcEEEEEEEccchHHHHHHHHhcCCCH-HHhcCCCCCCchHHHHHHHHHHH--hChhhHHHHHHHHHHHHH
Confidence 333443334456667666655578888887632211 111222 1122222222222222 222222366666666553
Q ss_pred cCCCCHHHHHHHHHHHHHHhCCCHHHHHHHHh
Q psy15222 291 IIPLSSSLRFKIISSLSKIIKVSFNEINNLFK 322 (444)
Q Consensus 291 ~i~~~~~~r~~~~~~la~~~gi~~~~i~~~~~ 322 (444)
.-.. +.-....+..+|+.+|++.+.+.+.+.
T Consensus 95 ~~~~-~~s~~~~l~~iA~~~gLD~~~F~~d~~ 125 (176)
T PF13743_consen 95 LEGK-NYSDEELLLEIAEELGLDVEMFKEDLH 125 (176)
T ss_dssp TS----TTSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred hcCC-CCCHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3332 233346788999999999998877654
No 70
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=33.90 E-value=39 Score=28.65 Aligned_cols=18 Identities=33% Similarity=0.637 Sum_probs=13.8
Q ss_pred ceEEEEEecCCCCEEEEE
Q psy15222 91 GRIMFPIKNTDGQIIGFG 108 (444)
Q Consensus 91 ~RiifPI~d~~G~vvgf~ 108 (444)
-|...||+|.+|+++|+-
T Consensus 90 ~~~~~PV~d~~g~viG~V 107 (116)
T PF14827_consen 90 LRAFAPVYDSDGKVIGVV 107 (116)
T ss_dssp EEEEEEEE-TTS-EEEEE
T ss_pred EEEEEeeECCCCcEEEEE
Confidence 378999999999999974
No 71
>PHA02542 41 41 helicase; Provisional
Probab=33.01 E-value=2e+02 Score=31.09 Aligned_cols=61 Identities=13% Similarity=0.034 Sum_probs=40.2
Q ss_pred HHHHHHHHHhcCcchhhhcchhhhhhhhccCcc-HHHHHHHHHHHHHhhCCC-CCHHHHHHHHHhh
Q psy15222 343 IEYQIMKLLISYPSLINEINSEDMIIFSKCSQN-YVKMFFQLIDTIHIFKND-IDHSKFIKYLKKI 406 (444)
Q Consensus 343 ~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~-~~~~~l~~~l~~~ 406 (444)
.|+.+|..||.+|+.+..+... +. -+.|..+ +..+|..+.+.+.. +.. .+...+.+.|.+.
T Consensus 1 ~E~~vLg~ll~~~~~~~~v~~~-L~-~e~Fy~~~h~~If~ai~~l~~~-~~~~~~~~tl~~~L~~~ 63 (473)
T PHA02542 1 IEETILSNLIFNEDYFRKVWPY-LK-AEYFESGPEKVIFKLIKKHVNE-YNAIPTIEALSIALENR 63 (473)
T ss_pred CHHHHHHHHHcCHHHHHHHHhh-cC-HHhCCCHHHHHHHHHHHHHHhc-CCCCCcHHHHHHHHHhc
Confidence 3889999999999998765432 11 1234344 55566666676666 666 6777788877653
No 72
>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=32.37 E-value=67 Score=28.99 Aligned_cols=61 Identities=20% Similarity=0.255 Sum_probs=38.0
Q ss_pred cEEEecChhhHHHHHHcCCC---eEEEcCCccCC----HHHHHHHhcc-CCeEEEEeCCChhHHHHHHH
Q psy15222 150 YVLITEGYMDVIGLSQFGFL---QTVAILGTACT----STHIKKILFY-TNSIIFSFDGDQAGRRAARR 210 (444)
Q Consensus 150 ~viIvEG~~Dvlsl~q~Gi~---naVA~lGtalt----~~q~~~L~r~-~~~Vil~~D~D~AG~~aa~r 210 (444)
.|+|||-..=.-.+.+.++. +++-+.|..+. ..-++.|.+. .-.++.+.|.|..|..-+..
T Consensus 2 ~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~P~~~tr~~l~~L~~~~~~~~~~l~D~DP~Gi~I~~~ 70 (160)
T cd00223 2 FVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEELDLPVYILVDGDPYGISILLT 70 (160)
T ss_pred EEEEEecHHHHHHHHHcCccccCCEEEEEcCCcCCHHHHHHHHHHHHhhCCCEEEEECCCcchhhhhHH
Confidence 58899986655567776653 44544455443 2233333322 23689999999999776544
No 73
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=32.15 E-value=1.5e+02 Score=21.14 Aligned_cols=20 Identities=10% Similarity=0.340 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCHHHHHHHHh
Q psy15222 303 ISSLSKIIKVSFNEINNLFK 322 (444)
Q Consensus 303 ~~~la~~~gi~~~~i~~~~~ 322 (444)
.+++|+.+|+++.+++..+.
T Consensus 29 ~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 29 YAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46999999999999987654
No 74
>COG0641 AslB Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]
Probab=31.29 E-value=1.5e+02 Score=31.08 Aligned_cols=50 Identities=16% Similarity=0.070 Sum_probs=39.6
Q ss_pred CCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCCh-------------hHHHHHHHHHHHHHh
Q psy15222 168 FLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQ-------------AGRRAARRALEVCLL 217 (444)
Q Consensus 168 i~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~-------------AG~~aa~r~~~~l~~ 217 (444)
+.+++-|.|+.+|++.++.|++..-.|-+.+||-+ +--.++.++++.+..
T Consensus 91 i~~siqTNg~LL~~e~~e~l~~~~~~IgISiDGp~eihD~~R~~~~GkgTfd~i~~~i~~L~~ 153 (378)
T COG0641 91 ISNALQTNGTLLNDEWAEFLAEHDFLIGISIDGPEEIHDKYRVTKSGKGTFDRVMKGLELLQA 153 (378)
T ss_pred eEEEEEEcccccCHHHHHHHHhcCceEEEeccCchHhccccccCCCCCccHHHHHHHHHHHHH
Confidence 45789999999999999999987669999999953 334567777776653
No 75
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=30.45 E-value=4.4e+02 Score=24.83 Aligned_cols=45 Identities=9% Similarity=0.021 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHHHHHH
Q psy15222 273 KTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNL 320 (444)
Q Consensus 273 ~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~i~~~ 320 (444)
++|+...++..-.. .+-...+ +.+|. |+..||+.+++++..+.++
T Consensus 139 ~~~e~A~evY~aS~-laid~d~-~~Er~-YL~~LA~aL~L~~~lv~~l 183 (188)
T PF04391_consen 139 TDPEQAAEVYLASL-LAIDVDT-FAERA-YLDELAQALGLDPDLVAQL 183 (188)
T ss_pred CCHHHHHHHHHHHH-HHhCCCC-HHHHH-HHHHHHHHhCcCHHHHHHH
Confidence 56777665553332 2233444 77775 9999999999999887653
No 76
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=28.88 E-value=1.7e+02 Score=31.13 Aligned_cols=99 Identities=11% Similarity=0.021 Sum_probs=64.3
Q ss_pred cCCccCCHHHHHHHhccCC-eEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEE--EeCCCCCCcchhhhhhcHHHHHH
Q psy15222 174 ILGTACTSTHIKKILFYTN-SIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKF--LFLPDKYDPDSYIRKFGYKIFSK 250 (444)
Q Consensus 174 ~lGtalt~~q~~~L~r~~~-~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v--~~lP~gkDpdd~l~~~G~~~~~~ 250 (444)
++|+.+|++-++.|+++.. -|.+=||+...-...+.++++.+. ..|+.+.. +.|-.-.|--+.+.+ -+++
T Consensus 199 v~P~RIT~ell~~Lk~~~~~~v~~h~nhp~Eit~~a~~Al~~L~---~aGI~l~nQsVLLkGVND~~~~l~~----L~~~ 271 (417)
T TIGR03820 199 VLPQRITDELVAILKKHHPVWLNTHFNHPREITASSKKALAKLA---DAGIPLGNQSVLLAGVNDCPRIMKK----LVHK 271 (417)
T ss_pred ccccccCHHHHHHHHhcCCeEEEEeCCChHhChHHHHHHHHHHH---HcCCEEEeeceEECCcCCCHHHHHH----HHHH
Confidence 3377799999999988743 355779998777777778887775 46877654 444443444444432 3666
Q ss_pred HHHhc-CCHHHHHHHHHHhhCCCCCHHHHH
Q psy15222 251 KVLEA-MSLLQFFLEEIILNYNLKTIKDIE 279 (444)
Q Consensus 251 ~l~~a-~~~~~f~~~~~~~~~~~~~~~~k~ 279 (444)
++... .|..-|..+.........++..|.
T Consensus 272 L~~~gV~PYYl~~~d~v~G~~hFrv~~~~g 301 (417)
T TIGR03820 272 LVANRVRPYYLYQCDLSEGLSHFRTPVGKG 301 (417)
T ss_pred HHHCCCeeceeeeccCCCCcccccCcHHHH
Confidence 77654 688777777655444556665553
No 77
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=28.85 E-value=62 Score=24.03 Aligned_cols=21 Identities=19% Similarity=0.128 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHh
Q psy15222 302 IISSLSKIIKVSFNEINNLFK 322 (444)
Q Consensus 302 ~~~~la~~~gi~~~~i~~~~~ 322 (444)
-++++|+.||+|+.++++.+.
T Consensus 16 s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred EHHHHHHHHCcCHHHHHHHHH
Confidence 477999999999999998765
No 78
>PRK13758 anaerobic sulfatase-maturase; Provisional
Probab=28.59 E-value=90 Score=31.88 Aligned_cols=33 Identities=18% Similarity=0.142 Sum_probs=27.7
Q ss_pred eEEEcCCccCCHHHHHHHhccCCeEEEEeCCCh
Q psy15222 170 QTVAILGTACTSTHIKKILFYTNSIIFSFDGDQ 202 (444)
Q Consensus 170 naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~ 202 (444)
.++-|.||.++++.++.|......|-+.+||..
T Consensus 95 ~~i~TNG~ll~~~~~~~l~~~~~~v~iSlDg~~ 127 (370)
T PRK13758 95 NSLQTNGTLIDESWAKFLSENKFLVGLSMDGPK 127 (370)
T ss_pred EEEEecCEecCHHHHHHHHHcCceEEEeecCCH
Confidence 468899999999999999876557889999954
No 79
>cd07983 LPLAT_DUF374-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are the uncharacterized DUF374 phospholipid/glycerol acyltransferases and similar proteins.
Probab=27.13 E-value=3.6e+02 Score=24.38 Aligned_cols=79 Identities=15% Similarity=0.054 Sum_probs=40.8
Q ss_pred cCcEEEec---ChhhHHHHHHcCCCeEEEcCCc-cCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCc
Q psy15222 148 SGYVLITE---GYMDVIGLSQFGFLQTVAILGT-ACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDK 223 (444)
Q Consensus 148 ~~~viIvE---G~~Dvlsl~q~Gi~naVA~lGt-alt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~ 223 (444)
.+.+|+|= +++|...+...|.+.. .+.. .....-+..+.+.+..+.+--+++..+.++...+++.+ +.|.
T Consensus 25 ~~~~I~~~~H~s~l~~~~~~~~~~~~~--~v~~~~~~~~~~~~~~~~~g~~~i~r~~~~~~~~~~~~~~~~l----k~g~ 98 (189)
T cd07983 25 GEPVILAFWHGRLLLMPYLFRRRKRIA--ALISRSKDGEIIARVLERLGIRVVRGSSSRGGAAALREMLRAL----KDGY 98 (189)
T ss_pred CCCEEEEEeCchHHHhHHHhccCCCeE--EEEecCcCHHHHHHHHHHhCCCEEEcCCCCcHHHHHHHHHHHH----hCCC
Confidence 44555553 4567767666554422 1222 23233344444444445554445556666666655544 3564
Q ss_pred EEEEEeCCCCC
Q psy15222 224 IIKFLFLPDKY 234 (444)
Q Consensus 224 ~v~v~~lP~gk 234 (444)
.++.+|+|.
T Consensus 99 --~v~ifpeG~ 107 (189)
T cd07983 99 --NIAITPDGP 107 (189)
T ss_pred --EEEEcCCCC
Confidence 346789983
No 80
>PF14850 Pro_dh-DNA_bdg: DNA-binding domain of Proline dehydrogenase; PDB: 2FZM_A 3E2Q_A 3E2S_A 2FZN_A 1K87_A 1TJ2_A 3ITG_B 3E2R_A 1TJ1_A 1TIW_A ....
Probab=27.05 E-value=1.5e+02 Score=25.83 Aligned_cols=39 Identities=10% Similarity=0.244 Sum_probs=28.8
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Q psy15222 263 LEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIIS 304 (444)
Q Consensus 263 ~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~ 304 (444)
++.+.++|+++|.||- ++-.+.+.+-+||| ...++.+++
T Consensus 3 vd~ll~EY~Lss~EGv--aLMcLAEALLRVPD-~~T~d~LI~ 41 (114)
T PF14850_consen 3 VDALLQEYSLSSQEGV--ALMCLAEALLRVPD-AATADALIR 41 (114)
T ss_dssp HHHHHHCTT--HHHHH--HHHHHHHHHHTSSS-HHHHHHHHH
T ss_pred HHHHHHHcCCCcHHHH--HHHHHHHHHHcCCC-HHHHHHHHH
Confidence 5678889999999997 55667788889999 777776553
No 81
>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....
Probab=26.45 E-value=2e+02 Score=23.35 Aligned_cols=35 Identities=34% Similarity=0.470 Sum_probs=26.3
Q ss_pred CCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEE
Q psy15222 191 TNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFL 228 (444)
Q Consensus 191 ~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~ 228 (444)
.++|++|+|++..+..+...++..... .+..+.++
T Consensus 2 ~~~Ilv~~d~~~~~~~al~~a~~la~~---~~~~i~~l 36 (140)
T PF00582_consen 2 YKRILVAIDGSEESRRALRFALELAKR---SGAEITLL 36 (140)
T ss_dssp TSEEEEEESSSHHHHHHHHHHHHHHHH---HTCEEEEE
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHh---hCCeEEEE
Confidence 368999999999999998888876543 24455544
No 82
>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=25.83 E-value=87 Score=30.29 Aligned_cols=39 Identities=41% Similarity=0.531 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcCC-H----HHHHHHHHcCCCHHHHHHcc--ceeec
Q psy15222 3 CASDFYKIQLKNS-K----EAINFLKKRGLNEEIILRFN--LGYAP 41 (444)
Q Consensus 3 ~a~~~y~~~L~~~-~----~a~~YL~~RGis~e~i~~f~--lGyap 41 (444)
+.-=.||+.|++. | ...+||+++|++...+-..+ ++|..
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~g~~~~~~~~~G~~~~y~~ 55 (218)
T TIGR00646 10 ELFFIYHKNLKNQSKSKYRCAMNYLKKRGFNLQDFLKVGGGLAYLG 55 (218)
T ss_pred HHHHHHhhhccccCchhHHHHHHHHHHcCCCHHHHHHcCCCEEecc
Confidence 3444689999863 2 47899999999998887765 45553
No 83
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=25.47 E-value=50 Score=25.73 Aligned_cols=45 Identities=22% Similarity=0.407 Sum_probs=27.8
Q ss_pred HHHHHHHH-HcCCCHH-HHHHccceeecCCchHHHHHhccCCchhHHHHcCCceeccc
Q psy15222 16 KEAINFLK-KRGLNEE-IILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKII 71 (444)
Q Consensus 16 ~~a~~YL~-~RGis~e-~i~~f~lGyap~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~ 71 (444)
..|.+|.. ....|-. .-++|+|||.-.. .| ++.|.+.|++...+.
T Consensus 9 ~~a~~~V~~~~~~S~S~lQR~~rIGynrAa--ri---------id~LE~~GiVs~~~~ 55 (65)
T PF09397_consen 9 EEAVEFVIEEGKASISLLQRKFRIGYNRAA--RI---------IDQLEEEGIVSPANG 55 (65)
T ss_dssp HHHHHHHHHCTCECHHHHHHHHT--HHHHH--HH---------HHHHHHCTSBE---T
T ss_pred HHHHHHHHHcCCccHHHHHHHhCCCHHHHH--HH---------HHHHHHCCCCCCCCC
Confidence 36788874 4566766 4578999997442 22 288999999987654
No 84
>COG3444 Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]
Probab=25.13 E-value=2.1e+02 Score=26.32 Aligned_cols=71 Identities=21% Similarity=0.238 Sum_probs=42.1
Q ss_pred cCcEEEecChhhHHHHHHcCCC-eEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEE
Q psy15222 148 SGYVLITEGYMDVIGLSQFGFL-QTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIK 226 (444)
Q Consensus 148 ~~~viIvEG~~Dvlsl~q~Gi~-naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~ 226 (444)
.+-.+|||...|++.+.+.|.+ ..|-.-|.+.++.-. ..++.| .+|-++. ++ ++.+. ..|..+.
T Consensus 77 ~~v~ll~~~p~d~~~lve~gv~I~~iNVG~m~~~~gk~----~i~k~v--sl~e~D~---~a---f~~L~---~~Gv~~~ 141 (159)
T COG3444 77 QKVFLLFENPQDVLRLVEGGVPIKTINVGGMAFREGKK----QITKAV--SLDEKDI---AA---FKKLK---AKGVEVE 141 (159)
T ss_pred eEEEEEECCHHHHHHHHhcCCCCcEEEEcCccCCCCcE----Eeecce--eeCHHHH---HH---HHHHH---hcCcEEE
Confidence 3568999999999999999976 244444555544311 112222 3332222 22 23232 3588888
Q ss_pred EEeCCCC
Q psy15222 227 FLFLPDK 233 (444)
Q Consensus 227 v~~lP~g 233 (444)
+-.+|..
T Consensus 142 ~r~vP~d 148 (159)
T COG3444 142 VRKVPND 148 (159)
T ss_pred EEECCCC
Confidence 8889974
No 85
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=25.09 E-value=5.2e+02 Score=23.37 Aligned_cols=106 Identities=14% Similarity=0.097 Sum_probs=61.4
Q ss_pred eEEEEeCCChhHHHHHHHHHHHHHhhcCCCc------------EEEEEeCCCCCCcchhhhhhcHHHHHHHHHhcCCHHH
Q psy15222 193 SIIFSFDGDQAGRRAARRALEVCLLYATDDK------------IIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQ 260 (444)
Q Consensus 193 ~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~------------~v~v~~lP~gkDpdd~l~~~G~~~~~~~l~~a~~~~~ 260 (444)
.++++||-+=-.-.-|.+.++.... .|+ ++.-+.+|.|--|++=+ | +..+.++
T Consensus 24 v~~Ls~D~~WmspdqAk~li~~A~~---eGLl~~~~~~l~~~Fd~~~v~iP~~FkP~~~~-------l-----~e~~~fe 88 (144)
T PF09999_consen 24 VFALSFDRKWMSPDQAKRLIDEAIE---EGLLEEEGGYLVPNFDPSEVEIPLGFKPDEEI-------L-----QERDPFE 88 (144)
T ss_pred EeeEeeecCCCCHHHHHHHHHHHHH---CCCeeecCCEEEEecCccccccCCCCCCcHHH-------H-----hcccHHH
Confidence 5788899887666777777776653 232 22234567776665422 1 5567777
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHHHH
Q psy15222 261 FFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEIN 318 (444)
Q Consensus 261 f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~i~ 318 (444)
=+++++.+..+++ |.+++.++...-..+.. -+-.+.-.=.+|.+.|++.+.+.
T Consensus 89 ~ild~ia~~~g~~----~~evv~~in~~q~~~~~-~l~~e~aall~ake~Gvdv~~~~ 141 (144)
T PF09999_consen 89 RILDYIAAKTGIE----KQEVVAEINELQEELGG-LLDPEAAALLYAKEKGVDVSDFA 141 (144)
T ss_pred HHHHHHHHhcCCC----HHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHhCCCHHHHh
Confidence 7888888777665 33444444332222321 12223334467888888877653
No 86
>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=24.72 E-value=3.9e+02 Score=28.12 Aligned_cols=80 Identities=18% Similarity=0.081 Sum_probs=54.2
Q ss_pred cEEEecChhhHHHHHHc-CCC--eEEEcCCccCCHHHHHHHh---ccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCc
Q psy15222 150 YVLITEGYMDVIGLSQF-GFL--QTVAILGTACTSTHIKKIL---FYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDK 223 (444)
Q Consensus 150 ~viIvEG~~Dvlsl~q~-Gi~--naVA~lGtalt~~q~~~L~---r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~ 223 (444)
.|++||-..=.-.+.+. +-. -.|++-|. .+.....+|. ....+++..-|-|..|..-+.+..+.. |
T Consensus 252 ~V~vvENp~vf~~~~~~~~~~~~~lIct~G~-p~~a~~~LL~~L~~~g~~l~YhGDfD~~Gi~Ia~~L~~r~------~- 323 (385)
T TIGR02679 252 RVYVVENPNVLAIALDRLGPRCAPLVCTDGQ-PNAAQIKLLDLLAAAGARLYYHGDFDWPGLRIANGLIRRY------G- 323 (385)
T ss_pred eEEEEecHHHHHHHHHhcCCCCceEEECCCc-chHHHHHHHHHHHhcCCeEEEecCCChhHHHHHHHHHHHh------C-
Confidence 49999998877776663 322 25666664 4444445543 445578888899999998887765542 3
Q ss_pred EEEEEeCCCCCCcchhhhh
Q psy15222 224 IIKFLFLPDKYDPDSYIRK 242 (444)
Q Consensus 224 ~v~v~~lP~gkDpdd~l~~ 242 (444)
.-|..+|+++|.+.
T Consensus 324 -----~~pwrmd~~dY~~a 337 (385)
T TIGR02679 324 -----ARPWRFSAADYRAA 337 (385)
T ss_pred -----CccccCCHHHHHHH
Confidence 23678999999764
No 87
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=24.40 E-value=77 Score=24.57 Aligned_cols=44 Identities=23% Similarity=0.394 Sum_probs=30.3
Q ss_pred HHHHHH-HHcCCCHHH-HHHccceeecCCchHHHHHhccCCchhHHHHcCCceeccc
Q psy15222 17 EAINFL-KKRGLNEEI-ILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKII 71 (444)
Q Consensus 17 ~a~~YL-~~RGis~e~-i~~f~lGyap~~~~~L~~~l~~~~~~~~l~~~GL~~~~~~ 71 (444)
+|.+|. ..+..|-.. -++|+|||.-.. .+ ++.|.+.|++.+.+.
T Consensus 9 ~a~~~V~~~~~~S~S~lQR~~~IGynrAa--ri---------id~lE~~GiV~p~~g 54 (63)
T smart00843 9 EAVELVIETQKASTSLLQRRLRIGYNRAA--RL---------IDQLEEEGIVGPANG 54 (63)
T ss_pred HHHHHHHHhCCCChHHHHHHHhcchhHHH--HH---------HHHHHHCcCCCCCCC
Confidence 577776 445566554 478999997442 22 288999999987654
No 88
>PF13707 RloB: RloB-like protein
Probab=24.39 E-value=1.3e+02 Score=27.33 Aligned_cols=11 Identities=27% Similarity=0.468 Sum_probs=10.1
Q ss_pred CCeEEEEeCCC
Q psy15222 191 TNSIIFSFDGD 201 (444)
Q Consensus 191 ~~~Vil~~D~D 201 (444)
.++|+++||-|
T Consensus 60 ~d~v~~V~D~D 70 (183)
T PF13707_consen 60 YDEVWCVFDRD 70 (183)
T ss_pred CCEEEEEEeCC
Confidence 57999999999
No 89
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=21.75 E-value=99 Score=22.75 Aligned_cols=19 Identities=5% Similarity=0.181 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCHHHHHHHH
Q psy15222 303 ISSLSKIIKVSFNEINNLF 321 (444)
Q Consensus 303 ~~~la~~~gi~~~~i~~~~ 321 (444)
-.+||+.+|+++..|++.+
T Consensus 31 S~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 31 SQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHhcccC
Confidence 5689999999999999876
No 90
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.46 E-value=2.9e+02 Score=21.61 Aligned_cols=22 Identities=32% Similarity=0.223 Sum_probs=16.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHh
Q psy15222 301 KIISSLSKIIKVSFNEINNLFK 322 (444)
Q Consensus 301 ~~~~~la~~~gi~~~~i~~~~~ 322 (444)
.-+.+||+..|+++.+|-++.+
T Consensus 35 ~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 35 MSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp --HHHHHHHCTS-HHHHHHHHH
T ss_pred ccHHHHHHHcCCCHHHHHHHHH
Confidence 4588999999999999988765
No 91
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=21.09 E-value=1.3e+02 Score=22.80 Aligned_cols=29 Identities=10% Similarity=0.233 Sum_probs=22.1
Q ss_pred HHhcCCCCHHHHHHHHHHHHHHhCCCHHHH
Q psy15222 288 LFKIIPLSSSLRFKIISSLSKIIKVSFNEI 317 (444)
Q Consensus 288 ~l~~i~~~~~~r~~~~~~la~~~gi~~~~i 317 (444)
-...+|+ ++.-..|++..|+.+|++++.|
T Consensus 34 ~~~~lp~-~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 34 DFDSLPS-PVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp -GCCSSS-HHHHHHHHHHHHHHTT--HHHH
T ss_pred ChhhCCc-HHHHHHHHHHHHHHhCcCcccC
Confidence 3567888 8887889999999999998764
No 92
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=20.92 E-value=2.2e+02 Score=24.24 Aligned_cols=76 Identities=9% Similarity=0.149 Sum_probs=36.8
Q ss_pred cCCHHHHHHHhccCCeEEEEe--CCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCcchhhhhhcHHHHHHHHHhc
Q psy15222 178 ACTSTHIKKILFYTNSIIFSF--DGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEA 255 (444)
Q Consensus 178 alt~~q~~~L~r~~~~Vil~~--D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDpdd~l~~~G~~~~~~~l~~a 255 (444)
.++++++..|++..=+.|||. |++.+|+-......+.+. ..|+... .+|-. +.. +...-.++|.+.++++
T Consensus 14 Q~~~~d~~~la~~GfktVInlRpd~E~~~qp~~~~~~~~a~---~~Gl~y~--~iPv~--~~~-~~~~~v~~f~~~l~~~ 85 (110)
T PF04273_consen 14 QPSPEDLAQLAAQGFKTVINLRPDGEEPGQPSSAEEAAAAE---ALGLQYV--HIPVD--GGA-ITEEDVEAFADALESL 85 (110)
T ss_dssp S--HHHHHHHHHCT--EEEE-S-TTSTTT-T-HHCHHHHHH---HCT-EEE--E------TTT---HHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHCCCcEEEECCCCCCCCCCCCHHHHHHHHH---HcCCeEE--EeecC--CCC-CCHHHHHHHHHHHHhC
Confidence 689999999988655666665 776776644322222222 2487654 44521 122 2233467788888875
Q ss_pred -CCHHHH
Q psy15222 256 -MSLLQF 261 (444)
Q Consensus 256 -~~~~~f 261 (444)
.|.+-|
T Consensus 86 ~~Pvl~h 92 (110)
T PF04273_consen 86 PKPVLAH 92 (110)
T ss_dssp TTSEEEE
T ss_pred CCCEEEE
Confidence 455444
No 93
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=20.90 E-value=82 Score=28.04 Aligned_cols=17 Identities=41% Similarity=0.782 Sum_probs=15.8
Q ss_pred EEecCCCCEEEEEeeec
Q psy15222 96 PIKNTDGQIIGFGGRLI 112 (444)
Q Consensus 96 PI~d~~G~vvgf~gR~l 112 (444)
||+|.+|+|||+.|-.+
T Consensus 102 pi~n~~g~ivGlYg~g~ 118 (132)
T PF00949_consen 102 PIFNQNGEIVGLYGNGV 118 (132)
T ss_dssp EEEETTSCEEEEEEEEE
T ss_pred ceEcCCCcEEEEEccce
Confidence 89999999999999877
No 94
>smart00351 PAX Paired Box domain.
Probab=20.42 E-value=2.5e+02 Score=24.34 Aligned_cols=57 Identities=12% Similarity=0.135 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCHHHHHHHHhhcccc-cccc-ccc--ccCCChhHHHHHHHHHHhcCcchhh
Q psy15222 303 ISSLSKIIKVSFNEINNLFKINTSS-IKHK-TIE--KKNIQPICIEYQIMKLLISYPSLIN 359 (444)
Q Consensus 303 ~~~la~~~gi~~~~i~~~~~~~~~~-~~~~-~~~--~~~~~~~~~E~~ll~~ll~~p~~~~ 359 (444)
...+|+.|||+..++.+.++..... ...+ +.. .+.......+..++.+.-.+|++..
T Consensus 36 ~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~ 96 (125)
T smart00351 36 PCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFA 96 (125)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCH
Confidence 4588999999999988766532111 0111 110 1111223344556667778888753
Done!