Query gi|254780743|ref|YP_003065156.1| putative uracil-DNA glycosylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 261
No_of_seqs 186 out of 1458
Neff 6.3
Searched_HMMs 39220
Date Sun May 29 19:17:29 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780743.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00758 UDG_fam4 uracil-DNA 100.0 0 0 461.5 14.9 175 87-261 1-182 (185)
2 COG1573 Uracil-DNA glycosylase 100.0 0 0 321.6 17.1 189 73-261 6-202 (202)
3 pfam03167 UDG Uracil DNA glyco 100.0 4E-40 9.8E-45 248.8 13.6 142 101-252 1-147 (147)
4 PRK10201 G/U mismatch-specific 98.7 9.5E-07 2.4E-11 58.5 12.7 140 105-253 7-161 (168)
5 KOG4120 consensus 97.2 0.01 2.6E-07 35.5 11.0 161 97-261 138-318 (426)
6 TIGR00584 mug mismatch-specifi 94.4 0.13 3.2E-06 29.3 5.8 100 98-198 136-252 (347)
7 COG3663 Mug G:T/U mismatch-spe 93.6 0.33 8.5E-06 26.9 6.7 146 102-253 4-162 (169)
8 PRK05333 NAD-dependent deacety 86.7 1.9 4.9E-05 22.6 5.4 10 186-195 214-223 (285)
9 PRK05254 uracil-DNA glycosylas 67.3 10 0.00026 18.4 7.9 114 107-240 57-195 (223)
10 PRK06100 DNA polymerase III su 52.8 14 0.00036 17.6 2.9 91 107-251 38-128 (132)
11 COG1391 GlnE Glutamine synthet 52.2 19 0.00048 16.9 5.2 95 97-191 691-803 (963)
12 TIGR01819 F420_cofD LPPG:Fo 2- 49.7 7.7 0.0002 19.1 1.1 33 108-148 265-297 (359)
13 TIGR01236 D1pyr5carbox1 1-pyrr 47.8 11 0.00028 18.3 1.7 50 183-236 247-303 (551)
14 TIGR00639 PurN phosphoribosylg 46.3 19 0.00049 16.9 2.7 58 174-249 82-143 (215)
15 pfam03603 DNA_III_psi DNA poly 42.3 27 0.0007 16.0 3.1 90 107-251 36-125 (128)
16 KOG2267 consensus 40.6 15 0.00039 17.5 1.5 37 114-150 374-410 (475)
17 PRK06856 DNA polymerase III su 36.1 34 0.00088 15.4 3.0 91 107-252 35-125 (127)
18 TIGR00416 sms DNA repair prote 31.9 40 0.001 15.0 3.9 89 96-194 91-204 (481)
19 PRK02122 glucosamine-6-phospha 31.5 41 0.001 15.0 5.8 93 141-239 487-600 (660)
20 TIGR00628 ung uracil-DNA glyco 30.3 43 0.0011 14.9 6.5 118 106-242 54-198 (225)
21 TIGR02456 treS_nterm trehalose 30.0 36 0.00093 15.3 2.0 22 9-30 183-205 (560)
22 KOG2611 consensus 28.4 47 0.0012 14.7 3.0 115 132-254 444-605 (698)
23 pfam07799 DUF1643 Protein of u 28.0 47 0.0012 14.6 8.2 79 106-196 11-97 (135)
24 TIGR01950 SoxR redox-sensitive 25.8 15 0.00038 17.5 -0.6 79 13-91 15-113 (142)
25 PRK10602 murein peptide amidas 24.7 55 0.0014 14.3 6.4 89 160-253 127-232 (237)
26 PRK06278 cobyrinic acid a,c-di 21.6 22 0.00057 16.5 -0.3 70 186-260 243-321 (482)
27 KOG1577 consensus 21.1 65 0.0017 13.9 2.9 10 231-240 255-264 (300)
28 PRK13844 recombination protein 20.8 66 0.0017 13.8 1.9 47 72-118 45-92 (200)
29 TIGR01246 dapE_proteo succinyl 20.7 57 0.0014 14.2 1.6 110 92-217 47-186 (383)
30 PRK03604 moaC bifunctional mol 20.4 67 0.0017 13.8 5.7 83 106-211 146-240 (301)
31 pfam06100 Strep_67kDa_ant Stre 20.3 67 0.0017 13.8 4.8 65 96-160 374-445 (500)
32 TIGR02375 pseudoazurin pseudoa 20.2 68 0.0017 13.7 2.3 35 109-143 85-123 (123)
No 1
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4; InterPro: IPR005273 This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The function of these proteins is unknown. .
Probab=100.00 E-value=0 Score=461.51 Aligned_cols=175 Identities=27% Similarity=0.530 Sum_probs=165.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHH-HCCCCCC-CCCEEEEEECCCCCCC
Q ss_conf 0388520028772236788888489985789830011200120700489999998-6098622-2100000001225666
Q gi|254780743|r 87 FHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQ-SIEIMRT-QIHISMISPWHPPGNR 164 (261)
Q Consensus 87 ~~~C~L~~~~~~~v~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~-aigl~r~-~vyitn~vkcrPp~nr 164 (261)
|++|+|++++||+|+|+||.+|+|||||||||.+||++|+||||+||+|||+||+ +|||+|+ +|||||+||||||+||
T Consensus 1 C~~C~L~~~rT~~VpGdG~~~a~i~~VGEAPG~~EDr~G~PFVG~aGkLLd~lL~e~iGl~R~q~vYITNvvKCRPP~NR 80 (185)
T TIGR00758 1 CRKCELHKTRTNAVPGDGNPDAEIMFVGEAPGREEDRKGRPFVGRAGKLLDELLEEAIGLSREQNVYITNVVKCRPPNNR 80 (185)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCC
T ss_conf 98886522377641077756454789854788224207898354005689999999837443786235225654685222
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHCCC---CCCCHHCCCEEEEEE--CCCCCEEEEEEECHHHHHC
Q ss_conf 67788999999999998632297679952559999984465---331011065057664--2897378999708038833
Q gi|254780743|r 165 NLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNND---AQKTYQNLGKWSNLC--TPHSIIPTLATVHPQELIQ 239 (261)
Q Consensus 165 ~p~~~ei~~c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~---~~~i~~~rG~~~~~~--~~~~~i~~~pt~HPs~LLr 239 (261)
.||++|++.|.|||.+||++|+|++||+||++|++.+|+.. ..+|+++||+++.+. .-+..|++++||||||+||
T Consensus 81 ~PT~eE~~~C~pyL~~~i~lI~Pkvi~~lGr~Aa~~~l~~~gl~~~~I~k~rG~vf~~~~k~~~~~i~~~~~YHPA~~Lr 160 (185)
T TIGR00758 81 DPTPEEVEACAPYLVKQIELIRPKVIICLGRTAAQSILGKAGLEFEGITKVRGRVFEYRNKILGTKIKVLATYHPAALLR 160 (185)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEEEEECCEECCCCEEEEEEECCHHHHC
T ss_conf 38989998515788999975098068996027889887652876267301211577314804276047998643436416
Q ss_pred CHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 6598999999999999998609
Q gi|254780743|r 240 YPLIKKNTWHALITLKKALKNL 261 (261)
Q Consensus 240 ~P~~K~~aW~DL~~l~~~L~~l 261 (261)
||.+|+..|+||+.+|..|.||
T Consensus 161 ~P~l~~~~~~Df~~~k~~l~el 182 (185)
T TIGR00758 161 NPQLRRELEEDFKTIKARLKEL 182 (185)
T ss_pred CCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9623205889899999999997
No 2
>COG1573 Uracil-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=321.59 Aligned_cols=189 Identities=28% Similarity=0.528 Sum_probs=178.8
Q ss_pred CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCC-CCCC
Q ss_conf 469989999999600388520028772236788888489985789830011200120700489999998609862-2210
Q gi|254780743|r 73 KACSLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMR-TQIH 151 (261)
Q Consensus 73 ~~~~l~~L~~~~~~~~~C~L~~~~~~~v~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r-~~vy 151 (261)
...++++|++.+.+|+.|++...++++|+|.|+.+|+||||||+||+.||++|+||+|+||++|++||..+|+.+ +++|
T Consensus 6 ~~~~~~~l~~~i~~c~~C~~~~~~~~~v~~~g~~~a~i~iVGeaPG~~~~~tG~pF~g~aG~~L~~~l~~~~~~~~~~~~ 85 (202)
T COG1573 6 AAELLEELREEIEACRRCPLLKDRTPVVPGGGNPTARILIVGEAPGAGEDRTGRPFVGKAGDLLDRILGAIGGLRYEDVY 85 (202)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHCCCCCCCCCCCCCCEEEEECCCCCCHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCEE
T ss_conf 77789999987631877744032388887788887788998379971311059815580489999999985166567667
Q ss_pred EEEEEECC-CCCCC---CCCHHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECC-CCCE
Q ss_conf 00000012-25666---6778899999999999863229767995255999998446533101106505766428-9737
Q gi|254780743|r 152 ISMISPWH-PPGNR---NLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTP-HSII 226 (261)
Q Consensus 152 itn~vkcr-Pp~nr---~p~~~ei~~c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~-~~~i 226 (261)
|||+++|+ ||+|| +|+++|+.+|+|||..||++++|++||+||++|.+++++....+++..||+|+.+... ..++
T Consensus 86 it~~~~~~~~p~~~~~~~p~~~E~~~c~p~l~~~i~l~~pkviv~LG~~A~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~ 165 (202)
T COG1573 86 ITNVVKCRYPPGNRPPGDPTPEEIKACRPFLEAEIALIRPKVILLLGEYAAKSLLGLKGEPITELRGRWGAYRPKGGGGI 165 (202)
T ss_pred EEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCCE
T ss_conf 75243543689999999969889864056799998427988899807899999863156651002542443325678762
Q ss_pred EEEEEECHHHHHCCH--HHHHHHHHHHHHHHHHHHCC
Q ss_conf 899970803883365--98999999999999998609
Q gi|254780743|r 227 PTLATVHPQELIQYP--LIKKNTWHALITLKKALKNL 261 (261)
Q Consensus 227 ~~~pt~HPs~LLr~P--~~K~~aW~DL~~l~~~L~~l 261 (261)
.+|||||||++++++ ..|..+|+||+.+++++.++
T Consensus 166 ~~~p~~HPs~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 202 (202)
T COG1573 166 RVFPTYHPSPLNRNPGKLNKWFFWEDLKKLKALLRQL 202 (202)
T ss_pred EEEEECCCCHHHHCHHHHCHHHHHHHHHHHHHHHHCC
T ss_conf 8986058709873821207599999999999986459
No 3
>pfam03167 UDG Uracil DNA glycosylase superfamily.
Probab=100.00 E-value=4e-40 Score=248.79 Aligned_cols=142 Identities=23% Similarity=0.455 Sum_probs=126.7
Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 36788888489985789830011200120700489999998609862221000000012256666778899999999999
Q gi|254780743|r 101 CATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMR 180 (261)
Q Consensus 101 ~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~c~p~L~~ 180 (261)
+|.|+++|+|||||++||.+|+++|+||+|++|++|++||.++||++++||+||+++|+|+.++.|+..|+..|++||.+
T Consensus 1 ~~~g~~~a~i~ivg~~Pg~~~~~~G~~f~g~~g~~l~~~l~~~gl~~~~~~itn~~~c~~~~~~~~~~~ei~~~~~~L~~ 80 (147)
T pfam03167 1 PGFGPPNAKVLIVGEAPGPGEDATGLPFAGRAGNLLWRILAEAGLAREGVYLTNVVKCPRPVGRKPTRSEIAACWPYLLE 80 (147)
T ss_pred CCCCCCCCCEEEEECCCCHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 99899999999996798756763699675756999999999828875577998532256876799898999998999999
Q ss_pred HHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHH-----HHHHHHHH
Q ss_conf 8632297679952559999984465331011065057664289737899970803883365989-----99999999
Q gi|254780743|r 181 QIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIK-----KNTWHALI 252 (261)
Q Consensus 181 ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K-----~~aW~DL~ 252 (261)
||++++|++||+||+.|.+++++... ..... ...+++++++||||+++|+|..| +.+|+||+
T Consensus 81 ~i~~i~p~viv~lG~~a~~~~~~~~~-~~~~~---------~~~~~~v~~~~HPS~l~~~~~~~~~~~~~~~~~~L~ 147 (147)
T pfam03167 81 ELALLRPKVVVLLGKTAAKAFLGLGK-KESLF---------EGGGIPVLPLPHPSPLNRNPGFKRPEAFREALEDLK 147 (147)
T ss_pred HHHHCCCCEEEEECHHHHHHHHCCCC-CCCEE---------CCCCCEEEEECCCHHHHCCHHHCCHHHHHHHHHHHC
T ss_conf 99855966899988999999847787-65224---------269917999559079741976417478999999729
No 4
>PRK10201 G/U mismatch-specific DNA glycosylase; Provisional
Probab=98.67 E-value=9.5e-07 Score=58.52 Aligned_cols=140 Identities=16% Similarity=0.228 Sum_probs=101.6
Q ss_pred CCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC-------------CCCEEEEEECCC-CCCCCCCHHH
Q ss_conf 88884899857898300112001207004899999986098622-------------210000000122-5666677889
Q gi|254780743|r 105 TEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRT-------------QIHISMISPWHP-PGNRNLSNIE 170 (261)
Q Consensus 105 ~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~-------------~vyitn~vkcrP-p~nr~p~~~e 170 (261)
.++=+|+|||-.||..--..|.+|.++.- .|-+.|...||... .+=+||+|+ || .....-+.+|
T Consensus 7 ~p~L~vlF~GiNPgl~Sa~~g~~fA~pgN-rFW~~L~~aGlt~r~l~p~ed~~Ll~~giG~TnlV~-R~T~~a~eL~~~E 84 (168)
T PRK10201 7 APGLRVVFCGINPGLSSAGTGFPFAHPAN-RFWKVIHQAGFTDRQLKPEEAQHLLDYRCGVTKLVD-RPTVQANEVSKQE 84 (168)
T ss_pred CCCCEEEEEEECCCHHHHHCCCCCCCCCC-CHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCEEECC-CCCCCHHHCCHHH
T ss_conf 89984899974978888853987789986-348999986898866686664138871977203456-7788936669999
Q ss_pred HHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCH-HHHHHHHH
Q ss_conf 99999999998632297679952559999984465331011065057664289737899970803883365-98999999
Q gi|254780743|r 171 MEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYP-LIKKNTWH 249 (261)
Q Consensus 171 i~~c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P-~~K~~aW~ 249 (261)
+.....-|.+-|+-.+|+++..+|..+.+..++...... |. .+...+ +..+++...||-|-|.. ......|.
T Consensus 85 ~~~g~~~L~~ki~~~~P~~vaf~Gk~ay~~~fg~~~~~~----G~-Q~~~ig--~t~vwVlPspSGln~~~~~~l~~~yr 157 (168)
T PRK10201 85 LRSGGRKLIEKIEDYQPQALAILGKQAYEQGFSQRGAQW----GK-QTLTIG--STQIWVLPNPSGLNRVSLEKLVEAYR 157 (168)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHCCCCCCC----CC-CCCCCC--CCEEEEECCCCCCCCCCHHHHHHHHH
T ss_conf 998899999999986997899977999999968998845----45-877778--81289931885002237999999999
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254780743|r 250 ALIT 253 (261)
Q Consensus 250 DL~~ 253 (261)
+|..
T Consensus 158 eL~~ 161 (168)
T PRK10201 158 ELDQ 161 (168)
T ss_pred HHHH
T ss_conf 9999
No 5
>KOG4120 consensus
Probab=97.19 E-value=0.01 Score=35.54 Aligned_cols=161 Identities=19% Similarity=0.245 Sum_probs=109.7
Q ss_pred CCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCC-------------CCCCEEEEEECCCCCC
Q ss_conf 772236788888489985789830011200120700489999998609862-------------2210000000122566
Q gi|254780743|r 97 LSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMR-------------TQIHISMISPWHPPGN 163 (261)
Q Consensus 97 ~~~v~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r-------------~~vyitn~vkcrPp~n 163 (261)
+++|.-.--.+-+|+|||-.||---...|.-|.|+.. -|-|||.-.||.. ..+-+||+|---.+|.
T Consensus 138 ~~tvPD~lc~NldiVIVGiNPGl~aayKGHhyagPgN-hFWKcL~~sgL~e~q~t~~~Dh~Lpk~GiGfTNmvaR~t~gs 216 (426)
T KOG4120 138 LQTVPDYLCENLDIVIVGINPGLTAAYKGHHYAGPGN-HFWKCLNKSGLLEAQFTYLNDHDLPKHGIGFTNMVARPTSGS 216 (426)
T ss_pred HHCCCHHHHCCCCEEEEECCCHHHHHHCCCCCCCCCC-HHHHHHHHHCCCHHHHHCCCCCCCCCCCCCHHHEECCCCCCC
T ss_conf 7347456635766799943701555523676789842-599998771012877502355555001565110011478884
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCE-EEEEEC-CCCCEEEEEEECHHHHHC--
Q ss_conf 6677889999999999986322976799525599999844653310110650-576642-897378999708038833--
Q gi|254780743|r 164 RNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGK-WSNLCT-PHSIIPTLATVHPQELIQ-- 239 (261)
Q Consensus 164 r~p~~~ei~~c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~-~~~~~~-~~~~i~~~pt~HPs~LLr-- 239 (261)
...+..|+..-...|..-+.-.+|++-|.-|.--...+-+.- .+ ..--. .|.|.. ......++.-.-||.--|
T Consensus 217 aDL~~kE~~eG~RIL~eKlqryrP~VavFnGK~I~E~fsk~~-~g--~~~K~f~FG~QP~k~~dt~tfv~VmpsSSaRcA 293 (426)
T KOG4120 217 ADLRKKEMQEGARILYEKLQRYRPQVAVFNGKGIWEEFSKML-TG--KLPKTFVFGWQPEKFGDTNTFVGVMPSSSARCA 293 (426)
T ss_pred CCCCHHHHHCCHHHHHHHHHHHCCCEEEECCCCHHHHHHHHH-HC--CCCCEEEECCCCCCCCCCCEEEEECCCCCHHHH
T ss_conf 210188775212899999986286258871726499987776-16--675125733675557986417997147514431
Q ss_pred -CH--HHHHHHHHHHHHHHHHHHCC
Q ss_conf -65--98999999999999998609
Q gi|254780743|r 240 -YP--LIKKNTWHALITLKKALKNL 261 (261)
Q Consensus 240 -~P--~~K~~aW~DL~~l~~~L~~l 261 (261)
-| +.|-..|.-|+.++++|+.+
T Consensus 294 q~pra~dKv~~y~~lk~~rd~l~gi 318 (426)
T KOG4120 294 QYPRAEDKVNLYNLLKEERDRLRGI 318 (426)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 4872543305999999999986331
No 6
>TIGR00584 mug mismatch-specific thymine-DNA glycosylate (mug); InterPro: IPR003310 G:U mismatches resulting from deamination of cytosine are the most common promutagenic lesions occurring in DNA. Uracil is removed in a base-excision repair pathway by uracil DNA-glycosylase (UDG), which excises uracil from both single- and double-stranded DNA. A biochemically distinct family of DNA repair enzymes which excises both uracil and thymine, but only from mispairs with guanine has been identified . Crystal structures of the mismatch-specific uracil DNA-glycosylase (MUG) from Escherichia coli, and of a DNA complex, reveal structural and functional homology to UDG despite low sequence identity .; GO: 0016798 hydrolase activity acting on glycosyl bonds, 0030983 mismatched DNA binding, 0006298 mismatch repair.
Probab=94.44 E-value=0.13 Score=29.29 Aligned_cols=100 Identities=20% Similarity=0.329 Sum_probs=82.4
Q ss_pred CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC----------------CCCEEEEEECCCC
Q ss_conf 722367888884899857898300112001207004899999986098622----------------2100000001225
Q gi|254780743|r 98 STICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRT----------------QIHISMISPWHPP 161 (261)
Q Consensus 98 ~~v~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~----------------~vyitn~vkcrPp 161 (261)
++|+-.=..|..++|||-.||.---..|.-|.|++- -|-|||.--||... -+-|||+|---.|
T Consensus 136 ~~~PD~l~~N~~~vI~G~NPGl~~~~KGH~y~~P~N-~FWK~L~~S~L~EGn~~l~~l~D~~LPG~~G~G~TNl~~R~~~ 214 (347)
T TIGR00584 136 KTLPDILTFNLDIVIVGLNPGLMAAYKGHAYAGPGN-RFWKCLFKSKLSEGNVELNYLDDKDLPGKYGLGITNLVERTTS 214 (347)
T ss_pred CCCCHHHHCCCCEEEEECCHHHHHHHCCCCCCCCCH-HHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCEEECCCCCC
T ss_conf 044123223763799812725675403555798842-5766654235430223543105756874346760000004888
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEE-CHHHH
Q ss_conf 66667788999999999998632297679952-55999
Q gi|254780743|r 162 GNRNLSNIEMEICRPIIMRQIELISPKILLFI-GNKTK 198 (261)
Q Consensus 162 ~nr~p~~~ei~~c~p~L~~ei~li~Pk~ii~l-G~~a~ 198 (261)
+.......|+..-...|.+-+.--+|+|-|.. |.--.
T Consensus 215 ~~~DL~~~E~~~G~RIL~~K~~~Y~P~~~~F~sGK~Iy 252 (347)
T TIGR00584 215 GSKDLSKKEFREGARILVEKLKKYRPRVAVFISGKCIY 252 (347)
T ss_pred CCCCHHHHHHHCCHHHHHHHHHHCCCCEEEEECCCEEE
T ss_conf 61100056532220567888753188057884483211
No 7
>COG3663 Mug G:T/U mismatch-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=93.64 E-value=0.33 Score=26.91 Aligned_cols=146 Identities=12% Similarity=0.023 Sum_probs=80.0
Q ss_pred CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC-CCCCCCEEEEEECCC-----CCCCCCCHHHHHHHH
Q ss_conf 67888884899857898300112001207004899999986098-622210000000122-----566667788999999
Q gi|254780743|r 102 ATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEI-MRTQIHISMISPWHP-----PGNRNLSNIEMEICR 175 (261)
Q Consensus 102 g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl-~r~~vyitn~vkcrP-----p~nr~p~~~ei~~c~ 175 (261)
..-.++++|||+|-.||.+--..|.+|.-+.-+ +-+|+..+++ +++-+-+..--+..+ .....++.+-+..|.
T Consensus 4 ~vl~~~~~vli~Gs~Pg~~S~~~gfyya~P~Nr-FWr~l~~v~~~d~~l~~~~~e~~~~~~~g~l~~~~i~~~~~~~~~~ 82 (169)
T COG3663 4 DVLDPGLRVLILGSFPGEDSRAAGFYYAHPRNR-FWRVLGLVFFTDAQLEPQEYEKLLDYAKGFLKLRGIGLWDVLEVAK 82 (169)
T ss_pred CCCCCCCEEEEEECCCCHHHHHCCCCCCCCHHH-HHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHCCCCCHHHHHHHH
T ss_conf 636998769998369866567506877882124-9999988706831244446665232000156642654035778877
Q ss_pred H-------HHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHHHHHH
Q ss_conf 9-------999986322976799525599999844653310110650576642897378999708038833659899999
Q gi|254780743|r 176 P-------IIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTW 248 (261)
Q Consensus 176 p-------~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K~~aW 248 (261)
. -+.++++-.+|..++.+|. -++.+. ..+-+....-. .+..+...+++.|+..|+.-...-+.+-.+|
T Consensus 83 re~~~~~d~~ie~~e~~d~aall~~~p-~~~~i~-~~g~~a~~~~~---~l~~~~~~~~vlpssSpa~R~~s~e~l~~~~ 157 (169)
T COG3663 83 RELHNSLDKLIEKVEANDLAALLIRGP-QLREIG-FTGGKAGELPQ---TLAGGGTETWVLPSSSPAARGLSLEKLPSAW 157 (169)
T ss_pred HHCCCHHHHHHHHCCCCCHHHHHHHHH-HHHHHH-CCCCCCEECCC---CCCCCCEEEEECCCCCHHHHCCCHHHHHHHH
T ss_conf 753451555555234203889998746-888665-16976504453---2334643467557787021033388889999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780743|r 249 HALIT 253 (261)
Q Consensus 249 ~DL~~ 253 (261)
.-+..
T Consensus 158 r~l~~ 162 (169)
T COG3663 158 RALPQ 162 (169)
T ss_pred HHHHH
T ss_conf 99999
No 8
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=86.67 E-value=1.9 Score=22.57 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=7.8
Q ss_pred CCCEEEEECH
Q ss_conf 9767995255
Q gi|254780743|r 186 SPKILLFIGN 195 (261)
Q Consensus 186 ~Pk~ii~lG~ 195 (261)
+-.++|.+|.
T Consensus 214 ~aDlllviGT 223 (285)
T PRK05333 214 AADAVLVVGS 223 (285)
T ss_pred CCCEEEEECC
T ss_conf 2999999787
No 9
>PRK05254 uracil-DNA glycosylase; Provisional
Probab=67.31 E-value=10 Score=18.45 Aligned_cols=114 Identities=15% Similarity=0.185 Sum_probs=64.2
Q ss_pred CCCEEEEECCCCCC-CCCCCCCCCCCCH----HHHHHHHHHCC----CC-----------CCCCCEEEEEECCCCCCCCC
Q ss_conf 88489985789830-0112001207004----89999998609----86-----------22210000000122566667
Q gi|254780743|r 107 GQDLMIIGYTPSDS-DNISGKPFSGKTG----NMLDKMLQSIE----IM-----------RTQIHISMISPWHPPGNRNL 166 (261)
Q Consensus 107 ~a~imiVgeaPg~~-Ed~~G~pF~G~aG----~lL~~mL~aig----l~-----------r~~vyitn~vkcrPp~nr~p 166 (261)
+-||+|||+-|--. ....|..|+=+.| .=|.+|+.++. +. ++.|.+.|.+-.--.|. |
T Consensus 57 ~vKVVIlGQDPYh~~gqA~GLaFSv~~~~~~PpSL~NI~kEl~~d~~~~~~~~gdL~~Wa~QGVLLLNt~LTv~~g~--~ 134 (223)
T PRK05254 57 DVKVVILGQDPYHGPGQAHGLSFSVPPGVPLPPSLRNIFKELEDDLGFPIPNHGDLTSWAEQGVLLLNTVLTVEAGQ--A 134 (223)
T ss_pred HCEEEEEECCCCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCEEEEECCEEEECCC--C
T ss_conf 83799984789999765588465679999998359999999998608988888868999857978883532455799--9
Q ss_pred CHHHHHH-HHHHHHHHHHH----CCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCC
Q ss_conf 7889999-99999998632----29767995255999998446533101106505766428973789997080388336
Q gi|254780743|r 167 SNIEMEI-CRPIIMRQIEL----ISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQY 240 (261)
Q Consensus 167 ~~~ei~~-c~p~L~~ei~l----i~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~ 240 (261)
.. +... ...|...-|+. -++-+.++.|+.|.+..- .|...+ .-++-+.|||-|-.+
T Consensus 135 ~S-H~~~GWe~ft~~vi~~l~~~~~~~Vf~LWG~~Aq~~~~-----~i~~~~------------h~il~s~HPSPlSa~ 195 (223)
T PRK05254 135 NS-HAGKGWETFTDAVIKALNERREPVVFILWGSHAQKKKA-----LIDTSK------------HLILESPHPSPLSAH 195 (223)
T ss_pred CC-CCCCCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHH-----CCCCCC------------CEEEEECCCCCCCCC
T ss_conf 98-66899799999999999727898099981668999874-----269878------------779961799952346
No 10
>PRK06100 DNA polymerase III subunit psi; Provisional
Probab=52.81 E-value=14 Score=17.60 Aligned_cols=91 Identities=11% Similarity=0.232 Sum_probs=52.2
Q ss_pred CCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 88489985789830011200120700489999998609862221000000012256666778899999999999863229
Q gi|254780743|r 107 GQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELIS 186 (261)
Q Consensus 107 ~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~c~p~L~~ei~li~ 186 (261)
+-+++||.+.+-.+. .--|++++|++++|+.+++|.. +++.++. |..+ .
T Consensus 38 ~~rLliVa~~~P~~~----------~~ll~~dILrsm~L~~~qv~~l-------------tpeql~~----L~~~----~ 86 (132)
T PRK06100 38 DCKLLLVAPQCPQNE----------TALLFERVLKSMQLELSQARHI-------------EPEQLSM----LGEH----S 86 (132)
T ss_pred HCEEEEECCCCCCCC----------CCHHHHHHHHHCCCCHHHEEEC-------------CHHHHHC----CCCC----C
T ss_conf 255999808986656----------4068999999869999993000-------------9999961----8877----8
Q ss_pred CCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHHHHHHHHH
Q ss_conf 76799525599999844653310110650576642897378999708038833659899999999
Q gi|254780743|r 187 PKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHAL 251 (261)
Q Consensus 187 Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K~~aW~DL 251 (261)
+.-+=.+|..+.. ...| ..+-+..-+-|-.|+..||.-|+-.
T Consensus 87 ~~~~W~lG~~~~~-----------~~~~------------~~L~SP~L~el~~n~~aKRaLWqQI 128 (132)
T PRK06100 87 LEWVWFAGCDSLS-----------HQNA------------KQLQSPLLSDIDGNNEHRRALWQQI 128 (132)
T ss_pred CCEEEECCCCCCC-----------CCCC------------CEEECCCHHHHHCCHHHHHHHHHHH
T ss_conf 8606756876665-----------3458------------7672848898826989999999998
No 11
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=52.22 E-value=19 Score=16.90 Aligned_cols=95 Identities=9% Similarity=0.133 Sum_probs=57.0
Q ss_pred CCCCCCCCCC---------CCCEEEEECCCCCCCCCCCCCCCCC--CHHHHHHHHHHCCCCCCC-CCEEEEEECCCCCCC
Q ss_conf 7722367888---------8848998578983001120012070--048999999860986222-100000001225666
Q gi|254780743|r 97 LSTICATQTE---------GQDLMIIGYTPSDSDNISGKPFSGK--TGNMLDKMLQSIEIMRTQ-IHISMISPWHPPGNR 164 (261)
Q Consensus 97 ~~~v~g~G~~---------~a~imiVgeaPg~~Ed~~G~pF~G~--aG~lL~~mL~aigl~r~~-vyitn~vkcrPp~nr 164 (261)
.=.|.|.|-. +.++||+-++|..-|+--|+|.-+. ...+-.++++...-...+ +-+--=.+-||.|+.
T Consensus 691 ~~aVvg~GKLGg~ELgy~SDlDLvflyd~~~~~~~~~~k~~d~~~~y~rlaqrli~~lsa~T~~G~LYEVD~RLRPsG~~ 770 (963)
T COG1391 691 GFAVVGYGKLGGRELGYGSDLDLVFLYDPDDDVETSGGKPIDAVQFYTRLAQRLISLLSAPTAEGVLYEVDMRLRPSGAA 770 (963)
T ss_pred CEEEEECCCCCCHHCCCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCC
T ss_conf 36999514556412067887646988437510002578875088999999999999964777788722320365868888
Q ss_pred CCCHHHHHHHHH------HHHHHHHHCCCCEEE
Q ss_conf 677889999999------999986322976799
Q gi|254780743|r 165 NLSNIEMEICRP------IIMRQIELISPKILL 191 (261)
Q Consensus 165 ~p~~~ei~~c~p------~L~~ei~li~Pk~ii 191 (261)
-|-...+.++.. |-|.|.+|++.++|.
T Consensus 771 G~lv~s~~AF~kYq~~eAwTWEhqAL~RAR~i~ 803 (963)
T COG1391 771 GPLVTSIDAFAKYQREEAWTWEHQALTRARAIA 803 (963)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 874123799999998620259999998888864
No 12
>TIGR01819 F420_cofD LPPG:Fo 2-phospho-L-lactate transferase; InterPro: IPR010115 This entry represents LPPG:Fo 2-phospho-L-lactate transferase (CofD), which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. .
Probab=49.72 E-value=7.7 Score=19.14 Aligned_cols=33 Identities=24% Similarity=0.538 Sum_probs=22.3
Q ss_pred CCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 84899857898300112001207004899999986098622
Q gi|254780743|r 108 QDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRT 148 (261)
Q Consensus 108 a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~ 148 (261)
+-+=+|+-.|=..| .||.|+|| |.|+|+|++-+
T Consensus 265 a~~kVVavSPIvG~----~~vsGpA~----Klm~A~G~dvs 297 (359)
T TIGR01819 265 ATVKVVAVSPIVGD----KPVSGPAG----KLMAAVGVDVS 297 (359)
T ss_pred CCCCEEEECCCCCC----CCCCCCHH----HCCCCCCCCCC
T ss_conf 69738997164068----88758434----20422343634
No 13
>TIGR01236 D1pyr5carbox1 1-pyrroline-5-carboxylate dehydrogenase; InterPro: IPR005931 The delta(1)-pyrroline-5-carboxylate synthetase (1.5.1.12 from EC) a mitochondrial inner membrane, ATP- and NADPH-dependent, bifunctional enzyme, catalyzes the reduction of glutamate to delta1-pyrroline-5-carboxylate, a critical step in the de novo biosynthesis of proline and ornithine. It is the rate-limiting enzyme in proline biosynthesis and is subject to feedback inhibition by proline. 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase.; GO: 0003842 1-pyrroline-5-carboxylate dehydrogenase activity, 0006561 proline biosynthetic process, 0005759 mitochondrial matrix.
Probab=47.83 E-value=11 Score=18.26 Aligned_cols=50 Identities=20% Similarity=0.337 Sum_probs=21.3
Q ss_pred HHCCCCE--EEEECHHHHHHHHCCCCCCCHH--CCCEEEEE---ECCCCCEEEEEEECHHH
Q ss_conf 3229767--9952559999984465331011--06505766---42897378999708038
Q gi|254780743|r 183 ELISPKI--LLFIGNKTKNFFFNNDAQKTYQ--NLGKWSNL---CTPHSIIPTLATVHPQE 236 (261)
Q Consensus 183 ~li~Pk~--ii~lG~~a~~~ll~~~~~~i~~--~rG~~~~~---~~~~~~i~~~pt~HPs~ 236 (261)
.+..|++ |..-|++..-.-|-+. +.+ -|||+|+| .+.-+| +=|..-|||.
T Consensus 247 Vlad~~lag~~FTGS~~tF~~Lwk~---v~~nl~~GkYh~fPRi~GETGG-KdF~~VHpSA 303 (551)
T TIGR01236 247 VLADPDLAGIHFTGSTSTFKHLWKK---VASNLDRGKYHNFPRIVGETGG-KDFHLVHPSA 303 (551)
T ss_pred EECCCCCCCEEECCCCHHHHHHHHH---HHCCCCCCCCCCCCCEEEECCC-CCCEEECCCC
T ss_conf 6146011020313771478888666---6223435753478702321489-7737874898
No 14
>TIGR00639 PurN phosphoribosylglycinamide formyltransferase; InterPro: IPR004607 This family describes phosphoribosylglycinamide formyltransferase (GAR transformylase), one of several proteins found in formyltransferase. This enzyme uses formyl tetrahydrofolate as a formyl group donor to produce 5'-phosphoribosyl-N-formylglycinamide. PurT, a different GAR transformylase, uses ATP and formate rather than formyl tetrahydrofolate. Experimental proof includes complementation of Escherichia coli purN mutants by orthologs from vertebrates (where it is a domain of a multifunctional protein), Bacillus subtilis, and Arabidopsis thaliana. In phylogenetic analyses, the member from Saccharomyces cerevisiae shows a long branch length but membership in the family, while the formyltetrahydrofolate deformylases form a closely related outgroup. ; GO: 0004644 phosphoribosylglycinamide formyltransferase activity, 0006189 'de novo' IMP biosynthetic process.
Probab=46.34 E-value=19 Score=16.87 Aligned_cols=58 Identities=14% Similarity=0.221 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCE-EEEEECCCCCEEEEEEECHHHHHCCHH-H--HHHHHH
Q ss_conf 999999986322976799525599999844653310110650-576642897378999708038833659-8--999999
Q gi|254780743|r 174 CRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGK-WSNLCTPHSIIPTLATVHPQELIQYPL-I--KKNTWH 249 (261)
Q Consensus 174 c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~-~~~~~~~~~~i~~~pt~HPs~LLr~P~-~--K~~aW~ 249 (261)
+-.-|-+++..-.|.+||+=|= ..+|+..+ +.+..|+ ..++ |||-|=..|. . -+.||+
T Consensus 82 ~d~~i~~~l~~~~vdlvvlAGf---MRIL~~~F--l~~f~grP~lNI-------------HPSLLP~F~Gt~ha~~qAl~ 143 (215)
T TIGR00639 82 FDQAIAEELKAAEVDLVVLAGF---MRILGPTF--LSAFAGRPILNI-------------HPSLLPAFPGTLHAVEQALE 143 (215)
T ss_pred HHHHHHHHHHHHCCCEEEECCH---HHHCCHHH--HHHHCCCCEEEE-------------CCCCCCCCCCCHHHHHHHHH
T ss_conf 9999999999609969998461---44416688--986279984750-------------75446677775578999998
No 15
>pfam03603 DNA_III_psi DNA polymerase III psi subunit.
Probab=42.27 E-value=27 Score=15.99 Aligned_cols=90 Identities=13% Similarity=0.206 Sum_probs=50.1
Q ss_pred CCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 88489985789830011200120700489999998609862221000000012256666778899999999999863229
Q gi|254780743|r 107 GQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELIS 186 (261)
Q Consensus 107 ~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~c~p~L~~ei~li~ 186 (261)
+-|++||.+.+-. +... ||.++|++++|+.+++|.. +++.+.. |. .-.
T Consensus 36 ~~rLliVa~~~p~----------~~~~-L~~dILrsl~L~~~q~~~l-------------t~eql~~----L~----~~~ 83 (128)
T pfam03603 36 HIRLLLVANELPQ----------LDDP-LFQDILRSLKLTLSQALCL-------------TPEQLAM----LP----EQH 83 (128)
T ss_pred CCEEEEECCCCCC----------CCCC-HHHHHHHHCCCCHHHCCCC-------------CHHHHHC----CC----CCC
T ss_conf 4669998189877----------5561-8999999869999993010-------------9999940----77----677
Q ss_pred CCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHHHHHHHHH
Q ss_conf 76799525599999844653310110650576642897378999708038833659899999999
Q gi|254780743|r 187 PKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHAL 251 (261)
Q Consensus 187 Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K~~aW~DL 251 (261)
+-.+ +++|.+.... ..|+ .+-+-.-+-|-.|+..||.-|+-.
T Consensus 84 ~~~~---------W~lG~~~~~~--~~~~------------~l~SP~L~~l~~n~~aKRaLWqQI 125 (128)
T pfam03603 84 LCWY---------WFLGCEQQLI--LAGK------------QLQSPSLSDLDGNAQAKRALWQQI 125 (128)
T ss_pred CCEE---------EECCCCCCCC--CCCC------------EECCCCHHHHHCCHHHHHHHHHHH
T ss_conf 7716---------8756876641--3574------------215939998814879999999997
No 16
>KOG2267 consensus
Probab=40.63 E-value=15 Score=17.45 Aligned_cols=37 Identities=27% Similarity=0.362 Sum_probs=28.6
Q ss_pred ECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 5789830011200120700489999998609862221
Q gi|254780743|r 114 GYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQI 150 (261)
Q Consensus 114 geaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~v 150 (261)
.-.|--.+|..|-||.+-+-+.|..-|+++|++.+++
T Consensus 374 ~~~~p~~gd~hgCPFr~~~~e~L~qkL~s~~i~~~~I 410 (475)
T KOG2267 374 LMNPPSEGDYHGCPFRHSDPEHLKQKLKSMGIDIEQI 410 (475)
T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 3798997766799977898899999988636698888
No 17
>PRK06856 DNA polymerase III subunit psi; Validated
Probab=36.06 E-value=34 Score=15.42 Aligned_cols=91 Identities=14% Similarity=0.188 Sum_probs=51.7
Q ss_pred CCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 88489985789830011200120700489999998609862221000000012256666778899999999999863229
Q gi|254780743|r 107 GQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELIS 186 (261)
Q Consensus 107 ~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~c~p~L~~ei~li~ 186 (261)
+-+++||.+.+-... +. ||..+|++++|+.+++|.. +++.+.. | ..-.
T Consensus 35 ~~rLliVa~~~p~~~----------~~-L~~dVLrsl~L~~~q~~~l-------------t~eq~~~----L----~~~~ 82 (127)
T PRK06856 35 HIRLVIVAEELPALT----------DP-LLSDILRSLTLSPDQVLCL-------------TPEQVAM----L----PQGH 82 (127)
T ss_pred HCEEEEEECCCCCCC----------CH-HHHHHHHHCCCCHHHEEEE-------------CHHHHHH----C----CCCC
T ss_conf 316999828986543----------76-9999999858999991000-------------8999963----7----7677
Q ss_pred CCEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHHHHHHHHHH
Q ss_conf 767995255999998446533101106505766428973789997080388336598999999999
Q gi|254780743|r 187 PKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHALI 252 (261)
Q Consensus 187 Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K~~aW~DL~ 252 (261)
+..+=.+|..... ..-| ..+-|-.-+-|-.|+..||..|+-..
T Consensus 83 ~~~~W~lG~~~~~-----------~~~~------------~~l~Sp~L~~L~~n~~aKRaLWqQIc 125 (127)
T PRK06856 83 RCNSWLLGTDEPL-----------CLAG------------AQVQSPALTELRANPTAKRALWQQIC 125 (127)
T ss_pred CCEEEECCCCCCC-----------CCCC------------CEECCCCHHHHHCCHHHHHHHHHHHH
T ss_conf 6648981565455-----------0348------------76758189988369799999999984
No 18
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=31.89 E-value=40 Score=15.02 Aligned_cols=89 Identities=17% Similarity=0.181 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEE-----EEECCCC--C-CCCCC
Q ss_conf 87722367888884899857898300112001207004899999986098622210000-----0001225--6-66677
Q gi|254780743|r 96 SLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISM-----ISPWHPP--G-NRNLS 167 (261)
Q Consensus 96 ~~~~v~g~G~~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn-----~vkcrPp--~-nr~p~ 167 (261)
.-+.|.|-|-..--+.+||-.|| +|+|--||.-+..=.+-...-.|+|- =+|-|.. | ...++
T Consensus 91 ElDrVLGGGivpGsliLiGG~PG----------~GKSTLLLqV~~~LA~~~~~~LYVsGEES~~Q~klRA~RLGit~~~~ 160 (481)
T TIGR00416 91 ELDRVLGGGIVPGSLILIGGDPG----------IGKSTLLLQVACQLAKNSMKVLYVSGEESLQQIKLRATRLGITDLVE 160 (481)
T ss_pred CCCEEECCCCCCCCEEEECCCCC----------CCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCCCCCCCC
T ss_conf 10011067222441698468899----------63567899999998404881689972301677888875455324787
Q ss_pred H----HHHH-------------HHHHHHHHHHHHCCCCEEEEEC
Q ss_conf 8----8999-------------9999999986322976799525
Q gi|254780743|r 168 N----IEME-------------ICRPIIMRQIELISPKILLFIG 194 (261)
Q Consensus 168 ~----~ei~-------------~c~p~L~~ei~li~Pk~ii~lG 194 (261)
+ +-|+ .-.+++...|+-.+|+++|.=.
T Consensus 161 ~sqaqdGinnlahdG~L~~L~Et~~e~I~~~~e~~~P~~~ViDS 204 (481)
T TIGR00416 161 PSQAQDGINNLAHDGNLYVLSETNLEQICAEIEELNPQVVVIDS 204 (481)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEC
T ss_conf 02344324543026753215757989999999852994899914
No 19
>PRK02122 glucosamine-6-phosphate deaminase-like protein; Validated
Probab=31.51 E-value=41 Score=14.98 Aligned_cols=93 Identities=14% Similarity=0.294 Sum_probs=57.5
Q ss_pred HHCCCCCCCCCEEEEEECCCCC--CCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECHH---------HHHHHH-------
Q ss_conf 8609862221000000012256--6667788999999999998632297679952559---------999984-------
Q gi|254780743|r 141 QSIEIMRTQIHISMISPWHPPG--NRNLSNIEMEICRPIIMRQIELISPKILLFIGNK---------TKNFFF------- 202 (261)
Q Consensus 141 ~aigl~r~~vyitn~vkcrPp~--nr~p~~~ei~~c~p~L~~ei~li~Pk~ii~lG~~---------a~~~ll------- 202 (261)
.-+|+..++|++.++=++..-. ..+++.++++.- ..-|+-|+|..|.+-|.. ..++++
T Consensus 487 r~~Gl~~~~vhFLdLPFYeTG~i~K~p~~~~Di~i~----~~ll~~vkPhqIyaAGDlaDPhgThrvC~~~i~~al~~lk 562 (660)
T PRK02122 487 RYLGLPDERVHFLDLPFYETGLVRKNPIGEADVEIV----KDLLREIKPHQIFVAGDLADPHGTHRVCLDAVFAALDELK 562 (660)
T ss_pred HHCCCCHHHCEECCCCCCCCCCCCCCCCCHHHHHHH----HHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 871997787310478853578411699998899999----9999855977798736667987625999999999999850
Q ss_pred CCCC---CCCHHCCCEEEEEECCCCCEEEEEEECHHHHHC
Q ss_conf 4653---310110650576642897378999708038833
Q gi|254780743|r 203 NNDA---QKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQ 239 (261)
Q Consensus 203 ~~~~---~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr 239 (261)
+... .-+--.||-|++|.... |...+-..|.-++|
T Consensus 563 ~~~~~~dc~vWlYRGaw~Ew~i~e--iemaVP~Sp~ev~~ 600 (660)
T PRK02122 563 EEEWMKDCRVWLYRGAWAEWEIDE--IEMAVPLSPEELRR 600 (660)
T ss_pred HCHHHHCCEEEEEECCCCCCCHHH--EEEECCCCHHHHHH
T ss_conf 100333170787505433468415--24746799899999
No 20
>TIGR00628 ung uracil-DNA glycosylase; InterPro: IPR002043 Uracil-DNA glycosylase 3.2.2 from EC (UNG) is a DNA repair enzyme that excises uracil residues from DNA by cleaving the N-glycosylic bond. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. The sequence of uracil-DNA glycosylase is extremely well conserved in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses . In eukaryotic cells, UNG activity is found in both the nucleus and the mitochondria. Human UNG1 protein is transported to both the mitochondria and the nucleus . The N-terminal 77 amino acids of UNG1 seem to be required for mitochondrial localisation , but the presence of a mitochondrial transit peptide has not been directly demonstrated. The most N-terminal conserved region contains an aspartic acid residue which has been proposed, based on X-ray structures , to act as a general base in the catalytic mechanism. ; GO: 0004844 uracil DNA N-glycosylase activity, 0006284 base-excision repair.
Probab=30.25 E-value=43 Score=14.86 Aligned_cols=118 Identities=17% Similarity=0.180 Sum_probs=73.5
Q ss_pred CCCCEEEEECCCCCC-CCCCCCCCCCCCHHH----HHHHHHHCC------CC-----------CCCCCEEEEEECCCCCC
Q ss_conf 888489985789830-011200120700489----999998609------86-----------22210000000122566
Q gi|254780743|r 106 EGQDLMIIGYTPSDS-DNISGKPFSGKTGNM----LDKMLQSIE------IM-----------RTQIHISMISPWHPPGN 163 (261)
Q Consensus 106 ~~a~imiVgeaPg~~-Ed~~G~pF~G~aG~l----L~~mL~aig------l~-----------r~~vyitn~vkcrPp~n 163 (261)
.+=||+|||+-|--. ....|.-|+=+.|.= |.+|++++. .. ++-|-+-|.|----.|.
T Consensus 54 ~dVKVVIlGQDPYH~pGqA~GLAFSV~~~~~~PPSL~NIf~EL~~~~p~~~~~p~hG~L~~WA~QGVLLLNt~LTV~~g~ 133 (225)
T TIGR00628 54 EDVKVVILGQDPYHGPGQAHGLAFSVKRGVPIPPSLKNIFKELEADYPDFFSPPKHGCLESWARQGVLLLNTVLTVRRGQ 133 (225)
T ss_pred CCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHCHHHHCCCCCCCCCC
T ss_conf 23157884035845467734443255864677824678999997210211268888985557851413542201125678
Q ss_pred CCCCHHHH---HHHHHHHHHHH-HHCCC-CEEEEECHHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHH
Q ss_conf 66778899---99999999986-32297-679952559999984465331011065057664289737899970803883
Q gi|254780743|r 164 RNLSNIEM---EICRPIIMRQI-ELISP-KILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELI 238 (261)
Q Consensus 164 r~p~~~ei---~~c~p~L~~ei-~li~P-k~ii~lG~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LL 238 (261)
|..=+- +..-..+.+-| +--++ =|.++-|+.|.+..- .|..-+ .-|+-+-|||-|-
T Consensus 134 --p~SH~~~GWe~Ft~~vi~~Ls~~~~~llVFmLWG~~A~~~~~-----~i~~~~------------HlvL~~~HPSPLS 194 (225)
T TIGR00628 134 --PGSHSGLGWERFTDAVISRLSEKRDGLLVFMLWGAHAQKKKS-----LIDPKK------------HLVLKSPHPSPLS 194 (225)
T ss_pred --CCCHHHCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHC-----CCCCCC------------EEEEECCCCCCCC
T ss_conf --622122147899999999999727998899814067777630-----578876------------0787408887001
Q ss_pred CCHH
Q ss_conf 3659
Q gi|254780743|r 239 QYPL 242 (261)
Q Consensus 239 r~P~ 242 (261)
+++.
T Consensus 195 ~~~G 198 (225)
T TIGR00628 195 ARRG 198 (225)
T ss_pred CCCC
T ss_conf 5887
No 21
>TIGR02456 treS_nterm trehalose synthase; InterPro: IPR012810 Trehalose synthase interconverts maltose and alpha,alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor . More information about this protein can be found at Protein of the Month: alpha-Amylase .; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process.
Probab=29.98 E-value=36 Score=15.28 Aligned_cols=22 Identities=32% Similarity=0.557 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHCCHHHH-HHC
Q ss_conf 9999999999998370788-718
Q gi|254780743|r 9 QEQILTIALFYADSGVYWV-FDE 30 (261)
Q Consensus 9 ~~~l~~ll~~~~e~GVd~~-~~~ 30 (261)
.+++...+-||+|.|||.. +|+
T Consensus 183 ~~e~~~v~RFWLDLGvDGFRlDA 205 (560)
T TIGR02456 183 EEEVLEVMRFWLDLGVDGFRLDA 205 (560)
T ss_pred HHHHHHHHHHHHHHCCCEEEECC
T ss_conf 99999999898750777032233
No 22
>KOG2611 consensus
Probab=28.41 E-value=47 Score=14.67 Aligned_cols=115 Identities=15% Similarity=0.141 Sum_probs=56.3
Q ss_pred CHHHHHHHHHHCCCCCCCCCEEEEEECCC-CC-------CCCCCHHH----------------------HHHHHHHHHHH
Q ss_conf 04899999986098622210000000122-56-------66677889----------------------99999999998
Q gi|254780743|r 132 TGNMLDKMLQSIEIMRTQIHISMISPWHP-PG-------NRNLSNIE----------------------MEICRPIIMRQ 181 (261)
Q Consensus 132 aG~lL~~mL~aigl~r~~vyitn~vkcrP-p~-------nr~p~~~e----------------------i~~c~p~L~~e 181 (261)
.-++++.||.--|+....+|+....--+| ++ +..|++.. ...|..++..-
T Consensus 444 Ved~~r~~L~~~g~esl~~~f~~~~w~lpa~~~~~~~~PD~V~~~~Q~lC~I~mN~~v~~p~~~~rd~~f~~ll~~lie~ 523 (698)
T KOG2611 444 VEDLLRYMLSVKGLESLSSPFLSTCWLLPAERLKRMNEPDPVPTPEQMLCQITMNAEVCKPLAYSRDVAFVELLIKLIER 523 (698)
T ss_pred HHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 98888889874577100046999887267600013568998786899999998656530531014563799999999984
Q ss_pred H-HHCC-CCEEEEECHHHHHHHHCCCCCCC-------HH--------CCCEEEEEECCCCCEEEEEEECHHHHHCCHHHH
Q ss_conf 6-3229-76799525599999844653310-------11--------065057664289737899970803883365989
Q gi|254780743|r 182 I-ELIS-PKILLFIGNKTKNFFFNNDAQKT-------YQ--------NLGKWSNLCTPHSIIPTLATVHPQELIQYPLIK 244 (261)
Q Consensus 182 i-~li~-Pk~ii~lG~~a~~~ll~~~~~~i-------~~--------~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K 244 (261)
+ ++++ |.-+|.+|+.|.-.+|-....+. .. +|--|..|+.+.. -+|..|.-+|+.
T Consensus 524 lpelvdt~drli~~an~ailglLl~~l~S~~~v~Q~~~s~~~y~qAtI~FL~da~~~~es-------nD~taLvvS~aY- 595 (698)
T KOG2611 524 LPELVDTEDRLIFLANDAILGLLLKVLSSLRKVKQNDFSICRYIQATIRFLWDAYNIDES-------NDPTALVVSIAY- 595 (698)
T ss_pred CHHHHCCCCCEEEEHHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHHHHCCCCC-------CCCCEEEEEHHH-
T ss_conf 667527876666313189999999998600444328865899999999999986413445-------897127951544-
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q gi|254780743|r 245 KNTWHALITL 254 (261)
Q Consensus 245 ~~aW~DL~~l 254 (261)
+-.|.||..+
T Consensus 596 kG~WsDLsEL 605 (698)
T KOG2611 596 KGYWSDLSEL 605 (698)
T ss_pred HHHHHHHHHH
T ss_conf 2136518999
No 23
>pfam07799 DUF1643 Protein of unknown function (DUF1643). The members of this family are all sequences found within hypothetical proteins expressed by various bacterial species. The region concerned is approximately 150 residues long.
Probab=27.97 E-value=47 Score=14.62 Aligned_cols=79 Identities=16% Similarity=0.287 Sum_probs=49.1
Q ss_pred CCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHH--------HHHH
Q ss_conf 88848998578983001120012070048999999860986222100000001225666677889999--------9999
Q gi|254780743|r 106 EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEI--------CRPI 177 (261)
Q Consensus 106 ~~a~imiVgeaPg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~--------c~p~ 177 (261)
....++|||-.|+..+... .++.=+.+.+.-..-|+ ..+++.|+..+|.+ .+.++.. -..+
T Consensus 11 ~~~~~~fIglNPStAd~~~----~DpTi~r~~~fa~~~Gy--gg~~~~NLfa~rst-----~P~~L~~~~dpig~~Nd~~ 79 (135)
T pfam07799 11 SGPTLLFIGLNPSTADAEV----DDPTVRRCIRFARAWGY--GGLVVVNLFAWRAT-----DPKDLRRAADPVGPENDAH 79 (135)
T ss_pred CCCEEEEEEECCCCCCCCC----CCHHHHHHHHHHHHCCC--CEEEEEECCCCCCC-----CHHHHHHCCCCCCHHHHHH
T ss_conf 9985999984488788655----68489999999987799--84999851312169-----9899975648878769999
Q ss_pred HHHHHHHCCCCEEEEECHH
Q ss_conf 9998632297679952559
Q gi|254780743|r 178 IMRQIELISPKILLFIGNK 196 (261)
Q Consensus 178 L~~ei~li~Pk~ii~lG~~ 196 (261)
|.+.++.. ..+|++-|+.
T Consensus 80 i~~~~~~a-~~vv~aWG~~ 97 (135)
T pfam07799 80 LLRAAKWA-DDVVLAWGNH 97 (135)
T ss_pred HHHHHHHC-CEEEEECCCC
T ss_conf 99998713-9299971477
No 24
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211 SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=25.84 E-value=15 Score=17.51 Aligned_cols=79 Identities=15% Similarity=0.253 Sum_probs=41.2
Q ss_pred HHHHHHHHHCCHHHHHHCC--CCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------------------CHHHCC
Q ss_conf 9999999983707887188--20000022244567655567766655567642111------------------023002
Q gi|254780743|r 13 LTIALFYADSGVYWVFDEP--NNEATYESQRKEKSIDSAIQPITNIRHIHSPLVQQ------------------ADSIAQ 72 (261)
Q Consensus 13 ~~ll~~~~e~GVd~~~~~p--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~a~ 72 (261)
-|.|+||..-|.=.-...- +++..-+..+..+.+..++.-.-+..++..+...- ...+.+
T Consensus 15 VSALHFYE~KGLI~S~Rn~GnQRRy~Rd~LRRVa~Ik~AQ~vGipL~~I~~ALa~LP~grtPt~~DW~rlS~~W~~~Lde 94 (142)
T TIGR01950 15 VSALHFYESKGLIHSVRNAGNQRRYKRDVLRRVAVIKVAQRVGIPLAEIAEALAELPEGRTPTADDWARLSSQWKEELDE 94 (142)
T ss_pred HHHHHHHHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 88776541035610113688834232001115674332332589888999999734688998888899998850188899
Q ss_pred CCCCHHHHHHHHHCCCCCC
Q ss_conf 4699899999996003885
Q gi|254780743|r 73 KACSLHELKSLLRSFHDCH 91 (261)
Q Consensus 73 ~~~~l~~L~~~~~~~~~C~ 91 (261)
....|..|++.+..|=+|.
T Consensus 95 RI~~L~~LRD~LdgCIGCG 113 (142)
T TIGR01950 95 RIEQLNALRDQLDGCIGCG 113 (142)
T ss_pred HHHHHHHHHHHCCCCCCCC
T ss_conf 9999976776416862367
No 25
>PRK10602 murein peptide amidase A; Provisional
Probab=24.69 E-value=55 Score=14.27 Aligned_cols=89 Identities=10% Similarity=0.105 Sum_probs=46.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECH-----------HHHHHHHCCCCCCCHH-----CCCEEEEEECCC
Q ss_conf 256666778899999999999863229767995255-----------9999984465331011-----065057664289
Q gi|254780743|r 160 PPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGN-----------KTKNFFFNNDAQKTYQ-----NLGKWSNLCTPH 223 (261)
Q Consensus 160 Pp~nr~p~~~ei~~c~p~L~~ei~li~Pk~ii~lG~-----------~a~~~ll~~~~~~i~~-----~rG~~~~~~~~~ 223 (261)
.||+..-+.-| ..+|.++|+..+|+.||.+-. .-.+++++.....+.. .=|.+-.|.. .
T Consensus 127 ~pG~~p~SEPE----t~aL~~lI~~~~P~~VVS~HaPla~iddp~~s~lg~~l~~~f~LPLv~~vgy~tPGSfGtwc~-~ 201 (237)
T PRK10602 127 LTGDKPGSEPE----TQALCQLIHRLQPAWVVSFHDPLACIEDPRHSELGEWLAQAFELPLVTSVGYETPGSFGSWCA-D 201 (237)
T ss_pred CCCCCCCCCHH----HHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHC-C
T ss_conf 78987667723----899999999729987999605622004898875688888761886131358657860331102-4
Q ss_pred CCEEEEEEE-CHHHHHCCHHHHHHHHHHHHH
Q ss_conf 737899970-803883365989999999999
Q gi|254780743|r 224 SIIPTLATV-HPQELIQYPLIKKNTWHALIT 253 (261)
Q Consensus 224 ~~i~~~pt~-HPs~LLr~P~~K~~aW~DL~~ 253 (261)
..+||+..- -|....-..+.-..+|.||+.
T Consensus 202 r~lpcIT~ElP~~s~d~~~e~~~~~~~dLL~ 232 (237)
T PRK10602 202 LNLHCITAEFPPISADEASEKYLFAMINLLR 232 (237)
T ss_pred CCCCEEEEECCCCCCCCCHHHHHHHHHHHHH
T ss_conf 7885699867833356416899999999972
No 26
>PRK06278 cobyrinic acid a,c-diamide synthase; Validated
Probab=21.58 E-value=22 Score=16.48 Aligned_cols=70 Identities=14% Similarity=0.181 Sum_probs=45.3
Q ss_pred CCCEEEEEC--HHHHHHHHCCCCCCCHHCCCEEEEEECCCCCEEEEEEECHHHHHCCHHHHHHH-------HHHHHHHHH
Q ss_conf 976799525--59999984465331011065057664289737899970803883365989999-------999999999
Q gi|254780743|r 186 SPKILLFIG--NKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNT-------WHALITLKK 256 (261)
Q Consensus 186 ~Pk~ii~lG--~~a~~~ll~~~~~~i~~~rG~~~~~~~~~~~i~~~pt~HPs~LLr~P~~K~~a-------W~DL~~l~~ 256 (261)
.|+-|++|| +.+.+.||... -...+||+.+-...+.....++|. -||+|-|-.|-.. |-|+..+.+
T Consensus 243 ~kkgiiLl~TgS~SGKTFl~T~--i~~kL~~kvfv~KiGpDvRDIVPs---LYllrE~M~ky~SIkI~~rGW~~~~efle 317 (482)
T PRK06278 243 VKKGIILLATGSESGKTFLSTS--IVSKLRGKTFVSKIGPDVRDIVPS---LYLLREPMEKYSSIKISDRGWMEPSEFLE 317 (482)
T ss_pred CCCEEEEEECCCCCCCEEHHHH--HHHHHCCCEEEEECCCCHHHCCHH---HHHCCCHHHHCCCEEECCCCCCCHHHHHH
T ss_conf 9965999843787774311677--888750648998608866652524---63104212204616854678768999999
Q ss_pred HHHC
Q ss_conf 9860
Q gi|254780743|r 257 ALKN 260 (261)
Q Consensus 257 ~L~~ 260 (261)
.+++
T Consensus 318 ~vk~ 321 (482)
T PRK06278 318 FVKN 321 (482)
T ss_pred HHHC
T ss_conf 9734
No 27
>KOG1577 consensus
Probab=21.08 E-value=65 Score=13.85 Aligned_cols=10 Identities=10% Similarity=0.414 Sum_probs=3.9
Q ss_pred EECHHHHHCC
Q ss_conf 7080388336
Q gi|254780743|r 231 TVHPQELIQY 240 (261)
Q Consensus 231 t~HPs~LLr~ 240 (261)
+..|..+.-|
T Consensus 255 S~~~~Ri~eN 264 (300)
T KOG1577 255 SSNPERIKEN 264 (300)
T ss_pred CCCHHHHHHH
T ss_conf 6998999987
No 28
>PRK13844 recombination protein RecR; Provisional
Probab=20.76 E-value=66 Score=13.81 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf 24699899999996003885-200287722367888884899857898
Q gi|254780743|r 72 QKACSLHELKSLLRSFHDCH-LCSTSLSTICATQTEGQDLMIIGYTPS 118 (261)
Q Consensus 72 ~~~~~l~~L~~~~~~~~~C~-L~~~~~~~v~g~G~~~a~imiVgeaPg 118 (261)
.-+..+.++++.+..|..|. +.....-.+..+-+.+..++-|-|.|.
T Consensus 45 ~L~~~l~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~iCVVE~~~ 92 (200)
T PRK13844 45 AIANSLLDATANIKKCVYCQALTEDDVCNICSNTNRDDTKLCIIESML 92 (200)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH
T ss_conf 999999999968764788998068887646799998898899983689
No 29
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase; InterPro: IPR005941 The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants . Succinyl-diaminopimelate desuccinylase (3.5.1.18 from EC) hydrolyses N-succinyl-L,L-diaminopimelic acid which is required for the bacterial synthesis of lysine and meso-diaminopimelic acid. This group of bacterial sequences belong to the MEROPS peptidase family M20 (clan MH), subfamily M20A (non-peptidase homologs). ; GO: 0009014 succinyl-diaminopimelate desuccinylase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=20.73 E-value=57 Score=14.18 Aligned_cols=110 Identities=19% Similarity=0.245 Sum_probs=51.6
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEECC----CCCCCCCCC-CCCCC--CCHHHHH-----------HHHHHCCCCCCCCCEE
Q ss_conf 2002877223678888848998578----983001120-01207--0048999-----------9998609862221000
Q gi|254780743|r 92 LCSTSLSTICATQTEGQDLMIIGYT----PSDSDNISG-KPFSG--KTGNMLD-----------KMLQSIEIMRTQIHIS 153 (261)
Q Consensus 92 L~~~~~~~v~g~G~~~a~imiVgea----Pg~~Ed~~G-~pF~G--~aG~lL~-----------~mL~aigl~r~~vyit 153 (261)
|+.++...+|+++.| -|.|+|-. +|..|..+- -||.= +.|.|.- -|+.|.. =|+.
T Consensus 47 ~wa~~g~aif~~~~P--~l~F~GHtDVVP~G~~e~W~~s~PF~p~~~dG~lYGRGAaDMKGs~Aafv~Aae-----rFv~ 119 (383)
T TIGR01246 47 LWATRGTAIFKDGEP--VLAFAGHTDVVPAGPLEQWSSSPPFEPVERDGKLYGRGAADMKGSLAAFVVAAE-----RFVK 119 (383)
T ss_pred HHHHCCEEEECCCCC--EEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCEECCCCCCHHHHHHHHHHHHH-----HHHH
T ss_conf 454557146508876--588746212113888877888769663462121762656214678999999999-----9998
Q ss_pred EEEECCC--CCCCC---CCHH-H------HHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHCCCCCCCHHCCCEEE
Q ss_conf 0000122--56666---7788-9------99999999998632297679952559999984465331011065057
Q gi|254780743|r 154 MISPWHP--PGNRN---LSNI-E------MEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWS 217 (261)
Q Consensus 154 n~vkcrP--p~nr~---p~~~-e------i~~c~p~L~~ei~li~Pk~ii~lG~~a~~~ll~~~~~~i~~~rG~~~ 217 (261)
+ .| +|-|- -|.+ | ...-..||+..=++|. + ..+|+-+..--+|+. .++++ ||.+-
T Consensus 120 ~----~pdhkGa~islLiTSDEEG~A~dGT~~vve~L~~r~~~ID--y-c~VGEPss~k~~GD~-iK~GR-RGSi~ 186 (383)
T TIGR01246 120 K----NPDHKGASISLLITSDEEGEAIDGTKKVVETLMARDELID--Y-CIVGEPSSVKKLGDV-IKNGR-RGSIT 186 (383)
T ss_pred H----CCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC--E-EEEECCCCCCCCCCE-EEECC-CEEEE
T ss_conf 4----7777840534433300013311368899999997258997--8-986065351116886-78423-11354
No 30
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein C/molybdopterin-binding protein; Provisional
Probab=20.37 E-value=67 Score=13.76 Aligned_cols=83 Identities=11% Similarity=0.184 Sum_probs=48.3
Q ss_pred CCCCEEEEECC--CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 88848998578--9830011200120700489999998609862221000000012256666778899999999999863
Q gi|254780743|r 106 EGQDLMIIGYT--PSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIE 183 (261)
Q Consensus 106 ~~a~imiVgea--Pg~~Ed~~G~pF~G~aG~lL~~mL~aigl~r~~vyitn~vkcrPp~nr~p~~~ei~~c~p~L~~ei~ 183 (261)
+.+-|+.+++. -|..||. ||+++..+|...|..-.+.- +| | ...+.|... |.+-++
T Consensus 146 ~~aAViTvSD~~s~G~reD~--------SG~~l~e~L~~~G~~V~~~~---vV----P----Dd~~~I~~~---l~~~~~ 203 (301)
T PRK03604 146 PSAAVLVLSDSIAAGTKEDR--------SGKLLVEGLEEAGCEVSHYQ---II----P----DEPEEIAAA---VQAWIA 203 (301)
T ss_pred CCEEEEEECCCCCCCCCCCC--------HHHHHHHHHHHCCCCCCEEE---EE----C----CCHHHHHHH---HHHHHH
T ss_conf 86699996273137977684--------56999999998698103028---96----8----988999999---999997
Q ss_pred HCCCCEEEEECH----------HHHHHHHCCCCCCCHH
Q ss_conf 229767995255----------9999984465331011
Q gi|254780743|r 184 LISPKILLFIGN----------KTKNFFFNNDAQKTYQ 211 (261)
Q Consensus 184 li~Pk~ii~lG~----------~a~~~ll~~~~~~i~~ 211 (261)
-...+||+.|. .|.+.++....-++..
T Consensus 204 -~~~dlIlTtGGTG~s~RDvTpEAt~~v~ek~ipG~~e 240 (301)
T PRK03604 204 -EGVELIITTGGTGLGPRDVTVETLEPLLERRLPGIEE 240 (301)
T ss_pred -CCCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCCHHH
T ss_conf -7997999708977899978889999877203976999
No 31
>pfam06100 Strep_67kDa_ant Streptococcal 67 kDa myosin-cross-reactive antigen like family. Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis.
Probab=20.33 E-value=67 Score=13.76 Aligned_cols=65 Identities=14% Similarity=0.148 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCCCCEEE-EECCCCCCCCCCCCCCCCCCHH-HHHHHHHHCCCCCCCC-----CEEEEEECCC
Q ss_conf 87722367888884899-8578983001120012070048-9999998609862221-----0000000122
Q gi|254780743|r 96 SLSTICATQTEGQDLMI-IGYTPSDSDNISGKPFSGKTGN-MLDKMLQSIEIMRTQI-----HISMISPWHP 160 (261)
Q Consensus 96 ~~~~v~g~G~~~a~imi-VgeaPg~~Ed~~G~pF~G~aG~-lL~~mL~aigl~r~~v-----yitn~vkcrP 160 (261)
.+|++|...+.+-.|+- -|-.|....|--.+|...-+|+ .|..+|.-+|+..+.+ -.+|.|+|.-
T Consensus 374 ~~QP~F~~Qp~dv~V~WgYgL~pd~~GnyVkKpM~eCtG~EIl~ElL~HLg~p~~~i~~l~~~~~~tIP~~M 445 (500)
T pfam06100 374 NRQPHFKEQPKNETVVWVYGLYSDREGDYIKKPMRECTGEEICQEWLYHLGVPVDEIEELAKDSINTIPVYM 445 (500)
T ss_pred CCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCHHHCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCEECCCC
T ss_conf 489888889998089998743668988855885244887999999998659983367888645664760256
No 32
>TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745 Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding.
Probab=20.19 E-value=68 Score=13.74 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=25.4
Q ss_pred CEEEEECCC----CCCCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf 489985789----83001120012070048999999860
Q gi|254780743|r 109 DLMIIGYTP----SDSDNISGKPFSGKTGNMLDKMLQSI 143 (261)
Q Consensus 109 ~imiVgeaP----g~~Ed~~G~pF~G~aG~lL~~mL~ai 143 (261)
-|..|||.| .-.|...+..--+.+-+-||++|+++
T Consensus 85 a~iqVG~~~nlkE~nL~~~~~~k~~~~~~~Rld~~fA~~ 123 (123)
T TIGR02375 85 ALIQVGDPPNLKEANLEAAKSAKHPKKAKERLDKLFAQV 123 (123)
T ss_pred EEEEECCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 899746976664024487751787303589988886319
Done!