Query gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs 120 out of 1548
Neff 3.5
Searched_HMMs 39220
Date Mon May 30 05:58:59 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781196.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00575 dnlj DNA ligase, NAD 99.8 1.3E-20 3.3E-25 151.8 4.7 53 66-118 1-53 (706)
2 PRK08097 ligB NAD-dependent DN 99.8 2.2E-19 5.6E-24 144.0 8.6 68 51-118 23-90 (563)
3 COG0272 Lig NAD-dependent DNA 99.8 1.2E-18 3.1E-23 139.3 8.1 65 54-118 2-66 (667)
4 PRK07956 ligA NAD-dependent DN 99.7 4.8E-18 1.2E-22 135.5 8.4 64 56-119 2-65 (668)
5 smart00532 LIGANc Ligase N fam 99.7 1.6E-17 4.1E-22 132.3 7.3 61 59-119 1-61 (441)
6 pfam01653 DNA_ligase_aden NAD- 99.7 1.8E-17 4.5E-22 132.0 7.5 63 57-119 1-63 (315)
7 cd00114 LIGANc NAD+ dependent 99.6 9.8E-16 2.5E-20 121.0 7.4 59 61-119 1-59 (307)
8 TIGR00631 uvrb excinuclease AB 52.5 22 0.00057 17.7 4.3 64 11-75 577-649 (667)
9 cd00280 TRFH Telomeric Repeat 47.9 17 0.00044 18.4 2.7 42 29-70 71-116 (200)
10 COG0556 UvrB Helicase subunit 38.7 36 0.00092 16.3 3.8 82 11-104 576-659 (663)
11 pfam03976 PPK2 Polyphosphate k 38.6 36 0.00093 16.3 4.2 13 54-66 144-156 (229)
12 pfam08819 DUF1802 Domain of un 32.3 26 0.00067 17.2 1.6 19 79-97 159-177 (177)
13 TIGR01149 mtrG tetrahydrometha 30.7 43 0.0011 15.8 2.5 22 83-104 9-30 (72)
14 pfam05793 TFIIF_alpha Transcri 29.8 26 0.00067 17.2 1.3 61 15-75 118-180 (528)
15 KOG1086 consensus 29.6 51 0.0013 15.4 2.9 84 9-104 165-263 (594)
16 PRK01356 hscB co-chaperone Hsc 28.7 49 0.0013 15.5 2.5 14 70-83 50-63 (166)
17 COG0634 Hpt Hypoxanthine-guani 28.4 53 0.0014 15.3 3.0 29 53-85 11-39 (178)
18 pfam04201 TPD52 Tumour protein 27.1 56 0.0014 15.1 3.3 24 81-104 22-45 (162)
19 COG1962 MtrH Tetrahydromethano 26.6 57 0.0015 15.1 4.2 45 51-95 103-147 (313)
20 pfam10534 CRIC_ras_sig Connect 26.5 58 0.0015 15.1 2.8 46 27-72 41-86 (95)
21 TIGR01203 HGPRTase hypoxanthin 24.8 62 0.0016 14.9 3.5 26 54-83 3-28 (183)
22 TIGR02434 CobF precorrin-6A sy 23.9 22 0.00057 17.7 0.0 30 43-72 22-51 (259)
23 PRK09162 hypoxanthine-guanine 22.0 70 0.0018 14.5 3.4 29 53-85 16-44 (181)
24 TIGR01616 nitro_assoc nitrogen 21.4 34 0.00086 16.5 0.5 44 16-62 30-81 (131)
No 1
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=99.81 E-value=1.3e-20 Score=151.76 Aligned_cols=53 Identities=42% Similarity=0.700 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 99999999997554589856989999999999999997864268989735388
Q gi|254781196|r 66 LVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 66 L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VG 118 (119)
|+++|++|++.||++|+|+|||++||+|+++|++||++||+|+.+||||||||
T Consensus 1 L~~~i~~h~y~YYVld~P~i~D~~YD~L~~~L~~LE~~~PeL~~pDSPTqrVG 53 (706)
T TIGR00575 1 LRKLIRKHDYRYYVLDEPSISDAEYDRLMRELQELEEKHPELITPDSPTQRVG 53 (706)
T ss_pred CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 94677767551346577988828888999999998654888536898642137
No 2
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=99.80 E-value=2.2e-19 Score=144.01 Aligned_cols=68 Identities=22% Similarity=0.285 Sum_probs=66.6
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 88789999999999999999999997554589856989999999999999997864268989735388
Q gi|254781196|r 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 51 v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VG 118 (119)
.-+|+.++|+.||++|+++|++||++||++|+|+|||++||+|+++|.+||++||++.+++|||++||
T Consensus 23 ~~~~~p~~ak~~I~~Lr~~i~~hn~~YY~~d~P~IsD~eYD~L~~eL~~LE~~~p~~~~~~SPt~~vg 90 (563)
T PRK08097 23 CPDWSPARAQEEISALQQQLAQWDDAYWRQGKSPVDDEVYDQLRARLTQWQRCFGLPVPRDPPLPPAN 90 (563)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 96989899999999999999999998752899978889999999999999986867679999978999
No 3
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=99.77 E-value=1.2e-18 Score=139.33 Aligned_cols=65 Identities=38% Similarity=0.579 Sum_probs=63.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 89999999999999999999997554589856989999999999999997864268989735388
Q gi|254781196|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VG 118 (119)
++..+++.++++|+++|++|++.||++|+|+|||++||+|+++|.+||.+||+|+.+||||++||
T Consensus 2 ~~~~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~lE~~~Pel~~~dSPtqrVG 66 (667)
T COG0272 2 WSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDSPTQRVG 66 (667)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 53678999999999999997788722699979858999999999999986877678999965557
No 4
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=99.75 E-value=4.8e-18 Score=135.52 Aligned_cols=64 Identities=41% Similarity=0.528 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 9999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r 56 KGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 56 k~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
-.+++.|+++|+++|.+||++||++|+|+|||++||+|+++|..||++||+++.++|||++||.
T Consensus 2 m~~~~~~i~~L~~~i~~~n~~YY~~~~p~isD~eYD~L~~eL~~lE~~~P~~~~~~SPt~~VG~ 65 (668)
T PRK07956 2 MEEAKKRIEELREELNHHAYAYYVLDNPEISDAEYDRLYRELLALEAEHPELITPDSPTQRVGG 65 (668)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 7799999999999999999986438998788899999999999999869055589998443366
No 5
>smart00532 LIGANc Ligase N family.
Probab=99.72 E-value=1.6e-17 Score=132.27 Aligned_cols=61 Identities=39% Similarity=0.593 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 9999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r 59 AMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 59 A~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
|+.||++|+++|.+||++||+.|+|+|||++||+|+++|..||++||+|+.++|||++||.
T Consensus 1 ak~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~Le~~~P~l~~~~SPt~~VG~ 61 (441)
T smart00532 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGG 61 (441)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 9789999999999999987618998799899999999999999869144689998545576
No 6
>pfam01653 DNA_ligase_aden NAD-dependent DNA ligase adenylation domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism.
Probab=99.72 E-value=1.8e-17 Score=131.96 Aligned_cols=63 Identities=43% Similarity=0.638 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r 57 GEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 57 ~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
++|+.||++|+++|.+||++||+.++|+|||++||+|+++|..||.+||+|+.++|||++||.
T Consensus 1 e~~k~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~le~~~P~l~~~~spt~~VG~ 63 (315)
T pfam01653 1 EEAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELITPDSPTQRVGA 63 (315)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCC
T ss_conf 958999999999999999998648999799999999999999999869100489995223587
No 7
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=99.62 E-value=9.8e-16 Score=120.96 Aligned_cols=59 Identities=37% Similarity=0.553 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r 61 IEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 61 ~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
.||++|.++|.+||++||+.++|+|||++||+|+++|..||.+||+|+.++|||++||.
T Consensus 1 ~ri~~L~~~I~~~n~~Yy~~~~p~ISD~eYD~L~~eL~~le~~~p~l~~~~spt~~VG~ 59 (307)
T cd00114 1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGG 59 (307)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 97999999999999998648999798899999999999999868233689998655587
No 8
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=52.51 E-value=22 Score=17.68 Aligned_cols=64 Identities=20% Similarity=0.183 Sum_probs=42.2
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHH--CCCCCHHHH-------HHHHCCCHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 201320075887724662020565--566006999-------99721378878999999999999999999999
Q gi|254781196|r 11 SKFENEHNITPAQWKKLLTLEAKF--LPNKRALES-------WLDKAKKVTSLSKGEAMIEVEYLVKIALHHQK 75 (119)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-------~~~kak~v~~Lsk~EA~~eie~L~k~I~~Hn~ 75 (119)
-+|--+|+|||-+=+|-..-...- .-.+.+... .+- +....+|++.+....|++|.+...++-.
T Consensus 577 ~~YNe~HgItP~ti~K~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~I~~Le~~M~~aA~ 649 (667)
T TIGR00631 577 IAYNEEHGITPQTIRKKIKDILDIELKEKEDAAKKKKKGKVAEEP-AEDASDLSEKELKKLIKQLEKEMKQAAR 649 (667)
T ss_pred HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH-HCCHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 999975389788540568887777764445555532023112221-0313208987999999999999999997
No 9
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=47.88 E-value=17 Score=18.38 Aligned_cols=42 Identities=26% Similarity=0.290 Sum_probs=24.3
Q ss_pred HHHHHHCCCC--CHHHHHHHHCCCH-HHCCHHH-HHHHHHHHHHHH
Q ss_conf 0205655660--0699999721378-8789999-999999999999
Q gi|254781196|r 29 TLEAKFLPNK--RALESWLDKAKKV-TSLSKGE-AMIEVEYLVKIA 70 (119)
Q Consensus 29 ~~~~~~~~~~--~~~~~~~~kak~v-~~Lsk~E-A~~eie~L~k~I 70 (119)
.|..-|-.|+ |||||+|.==..| ..++..+ --.+|+.|.++-
T Consensus 71 ~LD~~Fd~~~~lTPLESAl~v~~~I~kE~~~~e~l~e~I~~lik~q 116 (200)
T cd00280 71 NLDCQFENDEELTPLESALMVLESIEKEFSLPETLHEEIRKLIKEQ 116 (200)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 8787168877768089999999999985177076899999999999
No 10
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=38.70 E-value=36 Score=16.33 Aligned_cols=82 Identities=22% Similarity=0.246 Sum_probs=48.6
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCC-HHHCCHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCHH
Q ss_conf 2013200758877246620205655660069999972137-887899999999999999999999975-54589856989
Q gi|254781196|r 11 SKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKK-VTSLSKGEAMIEVEYLVKIALHHQKWY-YRLDNPLFTDG 88 (119)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~-v~~Lsk~EA~~eie~L~k~I~~Hn~~Y-Y~~D~P~ISDa 88 (119)
-.|..+|+|||-+-++-..-......+. ...-.+.++ ...|++.+....|+.|.+....+-..- |.
T Consensus 576 ~~yN~~hgItP~ti~K~i~d~l~~~~~~---~~~~~~~~~~~~~~~~~e~~~~I~~Le~~M~~aA~~l~FE--------- 643 (663)
T COG0556 576 MAYNEEHGITPQTIKKKIRDILDGEYEE---DEYKAKIEKKASKMSKKELEKLIKKLEKEMKEAAKNLEFE--------- 643 (663)
T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHH---HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHH---------
T ss_conf 9999966999712201156664201101---2333201222234898999999999999999999847888---------
Q ss_pred HHHHHHHHHHHHHHHC
Q ss_conf 9999999999999978
Q gi|254781196|r 89 LYDRVSERLDALQEQF 104 (119)
Q Consensus 89 EYD~L~~eL~~LE~~~ 104 (119)
.=-.++.++..|+++.
T Consensus 644 ~Aa~lRD~i~~L~~~~ 659 (663)
T COG0556 644 EAARLRDEIKELKEEL 659 (663)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 8999999999999876
No 11
>pfam03976 PPK2 Polyphosphate kinase 2 (PPK2). Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases.
Probab=38.63 E-value=36 Score=16.32 Aligned_cols=13 Identities=15% Similarity=0.130 Sum_probs=5.1
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 8999999999999
Q gi|254781196|r 54 LSKGEAMIEVEYL 66 (119)
Q Consensus 54 Lsk~EA~~eie~L 66 (119)
+|+.|-+.+++++
T Consensus 144 Isk~eQ~~Rl~~r 156 (229)
T pfam03976 144 ISDEEQLERFKER 156 (229)
T ss_pred CCHHHHHHHHHHH
T ss_conf 4989999999987
No 12
>pfam08819 DUF1802 Domain of unknown function (DUF1802). The function of this family is unknown. This region is found associated with a pfam04471 suggesting they could be part of a restriction modification system..
Probab=32.33 E-value=26 Score=17.20 Aligned_cols=19 Identities=11% Similarity=0.363 Sum_probs=15.0
Q ss_pred HCCCCCCCHHHHHHHHHHH
Q ss_conf 4589856989999999999
Q gi|254781196|r 79 RLDNPLFTDGLYDRVSERL 97 (119)
Q Consensus 79 ~~D~P~ISDaEYD~L~~eL 97 (119)
..+.|++||.+|+++.+++
T Consensus 159 ~~~~PVlsD~~f~~~~~~i 177 (177)
T pfam08819 159 AGSKPVLSDEEFAQRAQEI 177 (177)
T ss_pred CCCCCCCCHHHHHHHHHHC
T ss_conf 7786557889999998619
No 13
>TIGR01149 mtrG tetrahydromethanopterin S-methyltransferase, subunit G; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane.
Probab=30.72 E-value=43 Score=15.84 Aligned_cols=22 Identities=27% Similarity=0.521 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 8569899999999999999978
Q gi|254781196|r 83 PLFTDGLYDRVSERLDALQEQF 104 (119)
Q Consensus 83 P~ISDaEYD~L~~eL~~LE~~~ 104 (119)
-.++.+||.++..+|.++|++-
T Consensus 9 ~~~~~~ef~~~~~rLDeie~kv 30 (72)
T TIGR01149 9 VLVEPDEFNEVKKRLDEIEEKV 30 (72)
T ss_pred HCCCHHHHHHHHHHHHHHHHHH
T ss_conf 1059766999998741786788
No 14
>pfam05793 TFIIF_alpha Transcription initiation factor IIF, alpha subunit (TFIIF-alpha). Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.
Probab=29.80 E-value=26 Score=17.20 Aligned_cols=61 Identities=16% Similarity=0.071 Sum_probs=47.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHC--CCHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2007588772466202056556600699999721--378878999999999999999999999
Q gi|254781196|r 15 NEHNITPAQWKKLLTLEAKFLPNKRALESWLDKA--KKVTSLSKGEAMIEVEYLVKIALHHQK 75 (119)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ka--k~v~~Lsk~EA~~eie~L~k~I~~Hn~ 75 (119)
-|..|+-|+=-++||-+|---=.--|+.+|-+=. .....|+-.||..+..+-.+.+++.+.
T Consensus 118 rEGgv~enasYYvft~~~dg~feA~Pv~~WYNF~pi~~yktLt~EEAEee~~rR~K~~n~F~~ 180 (528)
T pfam05793 118 REGGVSENATYYVFTKCPDGAFEAYPVGEWYNFNPVAQYKTLTAEEAEEEMKRRKKTANGFQL 180 (528)
T ss_pred ECCCCCCCCEEEEEEECCCCCEEEEECCHHHCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 316767774058998258984477653021225604431116689999998755547778799
No 15
>KOG1086 consensus
Probab=29.59 E-value=51 Score=15.40 Aligned_cols=84 Identities=27% Similarity=0.300 Sum_probs=41.9
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCC-HHHCCHHHH------------HHHHHHHHHHHHHHHH
Q ss_conf 432013200758877246620205655660069999972137-887899999------------9999999999999999
Q gi|254781196|r 9 RSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKK-VTSLSKGEA------------MIEVEYLVKIALHHQK 75 (119)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~-v~~Lsk~EA------------~~eie~L~k~I~~Hn~ 75 (119)
+||-|++|..- -|-+..++-.+|- -|..|.+ |.+|.++|- ..|+--+++++.+---
T Consensus 165 kssvFddEEks---------klL~rLLkSn~Pe--DLqaANkLIK~lVkeee~k~eKiskR~~aleev~n~vk~l~em~l 233 (594)
T KOG1086 165 KSSVFDDEEKS---------KLLARLLKSNHPE--DLQAANKLIKTLVKEEEHKLEKISKRVKALEEVNNNVKLLEEMLL 233 (594)
T ss_pred CCCCCCCHHHH---------HHHHHHHHCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 76665747899---------9999997428858--899999999999888899999999999899999989999999998
Q ss_pred HHHHCCCCCCCHHH--HHHHHHHHHHHHHHC
Q ss_conf 75545898569899--999999999999978
Q gi|254781196|r 76 WYYRLDNPLFTDGL--YDRVSERLDALQEQF 104 (119)
Q Consensus 76 ~YY~~D~P~ISDaE--YD~L~~eL~~LE~~~ 104 (119)
-|-+.++. -.|.| --.++++++.+..-+
T Consensus 234 ~~s~eg~a-~pd~E~~lq~v~~~ce~lr~tl 263 (594)
T KOG1086 234 DYSQEGNA-SPDNELLLQEVYNRCEQLRPTL 263 (594)
T ss_pred HHCCCCCC-CCCHHHHHHHHHHHHHHHHHHH
T ss_conf 64147889-9737899999999999987999
No 16
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=28.70 E-value=49 Score=15.48 Aligned_cols=14 Identities=29% Similarity=0.282 Sum_probs=8.9
Q ss_pred HHHHHHHHHHCCCC
Q ss_conf 99999975545898
Q gi|254781196|r 70 ALHHQKWYYRLDNP 83 (119)
Q Consensus 70 I~~Hn~~YY~~D~P 83 (119)
-..-|.+|-++-+|
T Consensus 50 Ss~IN~AY~tLk~P 63 (166)
T PRK01356 50 ASELNKAYSTLKDA 63 (166)
T ss_pred HHHHHHHHHHHCCH
T ss_conf 99999999997898
No 17
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=28.40 E-value=53 Score=15.27 Aligned_cols=29 Identities=17% Similarity=0.210 Sum_probs=23.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 789999999999999999999997554589856
Q gi|254781196|r 53 SLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLF 85 (119)
Q Consensus 53 ~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~I 85 (119)
-.|+++...++++|.++|++ .|..+.|++
T Consensus 11 Lisee~I~~ri~ela~~I~~----~y~g~~~~v 39 (178)
T COG0634 11 LISEEQIKARIKELAAQITE----DYGGKDPLV 39 (178)
T ss_pred EECHHHHHHHHHHHHHHHHH----HHCCCCEEE
T ss_conf 42899999999999999977----627996199
No 18
>pfam04201 TPD52 Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
Probab=27.06 E-value=56 Score=15.12 Aligned_cols=24 Identities=13% Similarity=0.309 Sum_probs=14.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 898569899999999999999978
Q gi|254781196|r 81 DNPLFTDGLYDRVSERLDALQEQF 104 (119)
Q Consensus 81 D~P~ISDaEYD~L~~eL~~LE~~~ 104 (119)
..|.+|+.|...|+.+|..+|.+-
T Consensus 22 ~~~~lseee~eel~~EL~kvEeEI 45 (162)
T pfam04201 22 TKIVLSEAEKEELRTELAKLEEEI 45 (162)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 533278999999999999999999
No 19
>COG1962 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme metabolism]
Probab=26.56 E-value=57 Score=15.06 Aligned_cols=45 Identities=13% Similarity=0.101 Sum_probs=38.6
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 887899999999999999999999975545898569899999999
Q gi|254781196|r 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSE 95 (119)
Q Consensus 51 v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~L~~ 95 (119)
+-+-+.+|++.--.+-+.++-..+++-|+-=++.|.|+|+++|..
T Consensus 103 liDSt~gevr~aaak~a~EvGladR~iyNSIn~si~~~EieaL~e 147 (313)
T COG1962 103 LIDSTEGEVRAAAAKYASEVGLADRAIYNSINASIEDAEIEALAE 147 (313)
T ss_pred EECCCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 641650678998874565524356666523675534899999884
No 20
>pfam10534 CRIC_ras_sig Connector enhancer of kinase suppressor of ras. The CRIC - Connector enhancer of kinase suppressor of ras - domain functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis.
Probab=26.47 E-value=58 Score=15.05 Aligned_cols=46 Identities=13% Similarity=0.125 Sum_probs=29.7
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 6202056556600699999721378878999999999999999999
Q gi|254781196|r 27 LLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALH 72 (119)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~kak~v~~Lsk~EA~~eie~L~k~I~~ 72 (119)
.++...-..---.+|-+||+|..=.....-..-+.+|-.|..++..
T Consensus 41 ~LtavVelI~aak~Ll~WLdR~pFs~~~d~s~~k~~I~~LclEL~t 86 (95)
T pfam10534 41 VLTAVVELIIAAKSLLAWLNRYPFTGLTDFSATKNKIIQLCLELTT 86 (95)
T ss_pred HHHHHHHHHHHHCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999841306664558666630589999999999999998
No 21
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase; InterPro: IPR005904 Phosphoribosyltransferases (PRT) are enzymes that catalyze the synthesis of beta-n-5'-monophosphates from phosphoribosylpyrophosphate (PRPP) and an enzyme specific amine. A number of PRT's are involved in the biosynthesis of purine, pyrimidine, and pyridine nucleotides, or in the salvage of purines and pyrimidines. Purine nucleotides are synthesized both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. This entry presents hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC), which belongs to phosphoribosyltransferase family and is involved in purine salvage.; GO: 0004422 hypoxanthine phosphoribosyltransferase activity, 0006166 purine ribonucleoside salvage, 0005737 cytoplasm.
Probab=24.75 E-value=62 Score=14.85 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 899999999999999999999975545898
Q gi|254781196|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNP 83 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P 83 (119)
+++++.+.++++|+++|+. .|...+|
T Consensus 3 i~~~~i~~r~~eLa~~I~~----~Y~~~~~ 28 (183)
T TIGR01203 3 ISEEQIKARIAELAKQITE----DYQGKKP 28 (183)
T ss_pred CCHHHHHHHHHHHHHHHHH----HHCCCCC
T ss_conf 6789999999999999998----7356789
No 22
>TIGR02434 CobF precorrin-6A synthase (deacetylating); InterPro: IPR012797 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobF precorrin-6A synthase (2.1.1.152 from EC), a pathway-specific enzyme in the aerobic pathway. After precorrin-4 is methylated at C-11 by CobM to produce precorrin-5, the extruded acyl group is then removed in the subsequent step, which also sees a methyl group added at C-1 in a reaction catalysed by CobF. The product of this reaction is precorrin-6A, which is subsequently reduced by an NADH-dependent reductase to precorrin-6B . This entry identifies CobF in high GC Gram-positive, alphaproteobacteria and pseudomonas-related species..
Probab=23.90 E-value=22 Score=17.66 Aligned_cols=30 Identities=23% Similarity=0.179 Sum_probs=27.0
Q ss_pred HHHHHCCCHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 999721378878999999999999999999
Q gi|254781196|r 43 SWLDKAKKVTSLSKGEAMIEVEYLVKIALH 72 (119)
Q Consensus 43 ~~~~kak~v~~Lsk~EA~~eie~L~k~I~~ 72 (119)
++||.|.=+=-|.||+++.++-.|++.|-.
T Consensus 22 ~AL~~adV~f~~dKG~~KsdL~~lRr~I~~ 51 (259)
T TIGR02434 22 EALNHADVFFVLDKGEDKSDLVELRREICE 51 (259)
T ss_pred HHHHCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 887148389997587323799999999998
No 23
>PRK09162 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=21.99 E-value=70 Score=14.52 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=23.7
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 789999999999999999999997554589856
Q gi|254781196|r 53 SLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLF 85 (119)
Q Consensus 53 ~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~I 85 (119)
-.|+++...++++|+++|.. +|....|++
T Consensus 16 lis~eeI~~rI~~lA~~I~~----~y~~~~~vi 44 (181)
T PRK09162 16 LVSAAEVEAAIDRMADEITA----DLADENPLV 44 (181)
T ss_pred CCCHHHHHHHHHHHHHHHHH----HHCCCCCEE
T ss_conf 26799999999999999999----828998489
No 24
>TIGR01616 nitro_assoc nitrogenase-associated protein; InterPro: IPR006503 This set of sequences describe a small family of uncharacterised proteins only found so far in alpha and gamma proteobacteria and in the Cyanobacterium Nostoc sp. PCC 7120. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. .
Probab=21.40 E-value=34 Score=16.54 Aligned_cols=44 Identities=23% Similarity=0.442 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCC--------HHHCCHHHHHHH
Q ss_conf 00758877246620205655660069999972137--------887899999999
Q gi|254781196|r 16 EHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKK--------VTSLSKGEAMIE 62 (119)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~--------v~~Lsk~EA~~e 62 (119)
-|||--..|.- =||-|-|+. .|..+|.|+|-| .+++++.+|..-
T Consensus 30 v~dil~epW~A-~~LRpyFg~--kPV~~WfNraAPrvKsGEV~p~s~de~sALal 81 (131)
T TIGR01616 30 VRDILKEPWQA-DTLRPYFGD--KPVKEWFNRAAPRVKSGEVRPDSLDEASALAL 81 (131)
T ss_pred EEECCCCCCCH-HHCCHHHCC--CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 41000478661-221522315--88201146567851224566100385889998
Done!