Query gi|254780131|ref|YP_003064544.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs 121 out of 1551
Neff 3.6
Searched_HMMs 39220
Date Sun May 29 14:35:19 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780131.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 1.2E-21 3E-26 153.6 4.7 53 66-118 1-53 (706)
2 PRK08097 ligB NAD-dependent DN 99.8 3.9E-20 1E-24 144.4 8.6 68 51-118 23-90 (563)
3 COG0272 Lig NAD-dependent DNA 99.8 1.4E-19 3.5E-24 141.0 8.1 65 54-118 2-66 (667)
4 PRK07956 ligA NAD-dependent DN 99.8 9.7E-19 2.5E-23 135.8 8.4 64 56-119 2-65 (668)
5 smart00532 LIGANc Ligase N fam 99.7 3.5E-18 8.8E-23 132.5 7.3 61 59-119 1-61 (441)
6 pfam01653 DNA_ligase_aden NAD- 99.7 3.9E-18 9.9E-23 132.1 7.5 63 57-119 1-63 (315)
7 cd00114 LIGANc NAD+ dependent 99.7 3.1E-16 7.9E-21 120.5 7.4 59 61-119 1-59 (307)
8 TIGR00631 uvrb excinuclease AB 52.3 18 0.00046 18.1 3.4 64 11-75 577-649 (667)
9 pfam03976 PPK2 Polyphosphate k 47.1 27 0.00068 17.1 4.2 31 54-84 2-32 (229)
10 COG0556 UvrB Helicase subunit 43.7 30 0.00077 16.8 3.7 83 11-104 576-659 (663)
11 TIGR01149 mtrG tetrahydrometha 33.4 37 0.00094 16.3 2.5 23 83-105 9-31 (72)
12 pfam08819 DUF1802 Domain of un 29.9 31 0.00078 16.7 1.6 19 79-97 159-177 (177)
13 KOG1405 consensus 29.6 51 0.0013 15.4 4.6 65 30-110 351-417 (484)
14 TIGR01203 HGPRTase hypoxanthin 27.8 55 0.0014 15.2 3.2 26 54-83 3-28 (183)
15 COG1962 MtrH Tetrahydromethano 27.6 55 0.0014 15.2 4.2 46 51-96 103-148 (313)
16 COG0634 Hpt Hypoxanthine-guani 26.5 58 0.0015 15.1 3.0 30 52-85 10-39 (178)
17 pfam04485 NblA Phycobilisome d 24.3 64 0.0016 14.8 3.3 44 26-77 2-45 (53)
18 pfam11272 DUF3072 Protein of u 24.0 58 0.0015 15.1 2.1 20 51-70 36-55 (57)
19 TIGR02434 CobF precorrin-6A sy 23.9 27 0.00068 17.1 0.4 31 42-72 21-51 (259)
20 KOG0257 consensus 21.5 51 0.0013 15.4 1.5 29 59-94 190-218 (420)
21 pfam04201 TPD52 Tumour protein 20.9 74 0.0019 14.4 3.3 23 81-103 22-44 (162)
22 TIGR01674 phage_lambda_G phage 20.4 48 0.0012 15.6 1.1 33 33-70 1-33 (138)
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=99.84 E-value=1.2e-21 Score=153.63 Aligned_cols=53 Identities=42% Similarity=0.711 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 99999999997544589856989999999999999997874268989735388
Q gi|254780131|r 66 LVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 66 L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.82 E-value=3.9e-20 Score=144.36 Aligned_cols=68 Identities=22% Similarity=0.284 Sum_probs=66.7
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 77789999999999999999999997544589856989999999999999997874268989735388
Q gi|254780131|r 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 51 v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.80 E-value=1.4e-19 Score=141.01 Aligned_cols=65 Identities=38% Similarity=0.579 Sum_probs=63.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 89999999999999999999997544589856989999999999999997874268989735388
Q gi|254780131|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.77 E-value=9.7e-19 Score=135.84 Aligned_cols=64 Identities=39% Similarity=0.520 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 9999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 56 KGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 56 k~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.74 E-value=3.5e-18 Score=132.47 Aligned_cols=61 Identities=39% Similarity=0.593 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 9999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 59 AMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 59 A~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.74 E-value=3.9e-18 Score=132.15 Aligned_cols=63 Identities=41% Similarity=0.630 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 57 GEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 57 ~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=99.65 E-value=3.1e-16 Score=120.55 Aligned_cols=59 Identities=37% Similarity=0.563 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 61 IEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 61 ~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~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=52.34 E-value=18 Score=18.15 Aligned_cols=64 Identities=20% Similarity=0.173 Sum_probs=41.0
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHC-CCCCHHHH--------HHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2013200758999899864416524-55221689--------86214777778999999999999999999999
Q gi|254780131|r 11 SKFENEHNITPAQWKKLLTLEAKFL-PNKRALES--------WLDKAKKVTSLSKGEAMIEVEYLVKIALHHQK 75 (119)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--------~m~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
>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=47.11 E-value=27 Score=17.11 Aligned_cols=31 Identities=32% Similarity=0.365 Sum_probs=12.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 8999999999999999999999754458985
Q gi|254780131|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDDPL 84 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ 84 (119)
|+|.+.+.++..|...|..-+...+....|+
T Consensus 2 l~K~eyk~~~~~L~~~L~~lQ~~l~~~~~~v 32 (229)
T pfam03976 2 LSKDEYEAELAKLQIELVKLQEWVYAEGKKL 32 (229)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 8989999999999999999999999759948
No 10
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=43.65 E-value=30 Score=16.78 Aligned_cols=83 Identities=22% Similarity=0.157 Sum_probs=48.3
Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCC-CHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
Q ss_conf 201320075899989986441652455221689862147-7777899999999999999999999975445898569899
Q gi|254780131|r 11 SKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAK-KVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGL 89 (119)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~kak-~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~E 89 (119)
-.|..+|+|||-+-+|...-......+...+ -.+.+ ....|++.+....++.|-++...+-..--=. .
T Consensus 576 ~~yN~~hgItP~ti~K~i~d~l~~~~~~~~~---~~~~~~~~~~~~~~e~~~~I~~Le~~M~~aA~~l~FE--------~ 644 (663)
T COG0556 576 MAYNEEHGITPQTIKKKIRDILDGEYEEDEY---KAKIEKKASKMSKKELEKLIKKLEKEMKEAAKNLEFE--------E 644 (663)
T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH---HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHH--------H
T ss_conf 9999966999712201156664201101233---3201222234898999999999999999999847888--------8
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999999978
Q gi|254780131|r 90 YDRVSERLDALQEQF 104 (119)
Q Consensus 90 YD~L~~eL~~LE~~~ 104 (119)
=-.++.++..|.++.
T Consensus 645 Aa~lRD~i~~L~~~~ 659 (663)
T COG0556 645 AARLRDEIKELKEEL 659 (663)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999876
No 11
>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=33.40 E-value=37 Score=16.26 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 85698999999999999999787
Q gi|254780131|r 83 PLFTDGLYDRVSERLDALQEQFP 105 (119)
Q Consensus 83 P~ISD~EYD~L~~eL~~LE~~~P 105 (119)
-.++.++|.++..||.+||++--
T Consensus 9 ~~~~~~ef~~~~~rLDeie~kve 31 (72)
T TIGR01149 9 VLVEPDEFNEVKKRLDEIEEKVE 31 (72)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 10597669999987417867887
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=29.95 E-value=31 Score=16.75 Aligned_cols=19 Identities=11% Similarity=0.357 Sum_probs=15.0
Q ss_pred HCCCCCCCHHHHHHHHHHH
Q ss_conf 4589856989999999999
Q gi|254780131|r 79 RLDDPLFTDGLYDRVSERL 97 (119)
Q Consensus 79 ~~D~P~ISD~EYD~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
>KOG1405 consensus
Probab=29.60 E-value=51 Score=15.40 Aligned_cols=65 Identities=18% Similarity=0.308 Sum_probs=40.9
Q ss_pred HHHHHCCCC--CHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 416524552--216898621477777899999999999999999999975445898569899999999999999978742
Q gi|254780131|r 30 LEAKFLPNK--RALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPEL 107 (119)
Q Consensus 30 ~~~~~~~~~--~~~~~~m~kak~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL 107 (119)
....||||| |-+..||-.+-..-- +++.+++|..-+-+= -.+..=|.|...|..|+++||+.
T Consensus 351 h~~~frpn~pYrifNTWmGdP~k~ll---------l~~vv~~I~~~~Ll~-------n~~~vG~~l~~gL~~Lq~~~p~~ 414 (484)
T KOG1405 351 HDEEFRPNEPYRIFNTWMGDPSKNLL---------LEEVVQEIKREDLLN-------NVAHVGKALLKGLLELQAKYPGK 414 (484)
T ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHH---------HHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHCCHH
T ss_conf 47334878447876543078588899---------999999985888998-------89999999998899998868425
Q ss_pred CCC
Q ss_conf 689
Q gi|254780131|r 108 FDE 110 (119)
Q Consensus 108 ~~~ 110 (119)
+..
T Consensus 415 ~~~ 417 (484)
T KOG1405 415 INN 417 (484)
T ss_pred HHC
T ss_conf 542
No 14
>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=27.78 E-value=55 Score=15.21 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 899999999999999999999975445898
Q gi|254780131|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDDP 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 15
>COG1962 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme metabolism]
Probab=27.63 E-value=55 Score=15.19 Aligned_cols=46 Identities=11% Similarity=0.086 Sum_probs=39.9
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 7778999999999999999999999754458985698999999999
Q gi|254780131|r 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSER 96 (119)
Q Consensus 51 v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~e 96 (119)
+-+-+.+|++.--.+-+.++-..+++-|+-=++.|.|+|+++|...
T Consensus 103 liDSt~gevr~aaak~a~EvGladR~iyNSIn~si~~~EieaL~eS 148 (313)
T COG1962 103 LIDSTEGEVRAAAAKYASEVGLADRAIYNSINASIEDAEIEALAES 148 (313)
T ss_pred EECCCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCHHHHHHHHHC
T ss_conf 6416506789988745655243566665236755348999998845
No 16
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=26.53 E-value=58 Score=15.07 Aligned_cols=30 Identities=20% Similarity=0.231 Sum_probs=23.2
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 7789999999999999999999997544589856
Q gi|254780131|r 52 TSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLF 85 (119)
Q Consensus 52 ~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~I 85 (119)
--.|+++...++++|+++|.. .|..++|.+
T Consensus 10 vLisee~I~~ri~ela~~I~~----~y~g~~~~v 39 (178)
T COG0634 10 VLISEEQIKARIKELAAQITE----DYGGKDPLV 39 (178)
T ss_pred EEECHHHHHHHHHHHHHHHHH----HHCCCCEEE
T ss_conf 742899999999999999977----627996199
No 17
>pfam04485 NblA Phycobilisome degradation protein nblA. In the cyanobacterium Synechococcus PCC 7942, nblA triggers degradation of light-harvesting phycobiliproteins in response to deprivation nutrients including nitrogen, phosphorus and sulphur. The mechanism of nblA function is not known, but it has been hypothesized that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae.
Probab=24.27 E-value=64 Score=14.81 Aligned_cols=44 Identities=27% Similarity=0.277 Sum_probs=32.8
Q ss_pred HHHHHHHHHCCCCCHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9864416524552216898621477777899999999999999999999975
Q gi|254780131|r 26 KLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWY 77 (119)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~m~kak~v~~Lsk~EA~~eie~L~k~I~~Hn~~Y 77 (119)
+-||++-.| .=|.+ ...|..||..+|+.-+-.+.+.+--++..|
T Consensus 2 ~~LSLEQqF--~l~~~------~~~v~~ls~eqa~~~Lv~~~kqmmikeN~~ 45 (53)
T pfam04485 2 FSLSLEQEF--QLRLY------KQKVDTLSREQAKELLVELLKQMMIKDNII 45 (53)
T ss_pred CCCCHHHHH--HHHHH------HHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 652399999--89999------999814489999999999999999899999
No 18
>pfam11272 DUF3072 Protein of unknown function (DUF3072). This bacterial family of proteins has no known function.
Probab=23.96 E-value=58 Score=15.06 Aligned_cols=20 Identities=25% Similarity=0.214 Sum_probs=17.2
Q ss_pred HHHCCHHHHHHHHHHHHHHH
Q ss_conf 77789999999999999999
Q gi|254780131|r 51 VTSLSKGEAMIEVEYLVKIA 70 (119)
Q Consensus 51 v~~Lsk~EA~~eie~L~k~I 70 (119)
-..|+|.+|..+|+.|.+..
T Consensus 36 ~~~ltKAeAS~~Id~L~~~t 55 (57)
T pfam11272 36 PEDLTKAEASELIDELQQQT 55 (57)
T ss_pred CCCHHHHHHHHHHHHHHHHH
T ss_conf 85101989999999999985
No 19
>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=27 Score=17.12 Aligned_cols=31 Identities=23% Similarity=0.153 Sum_probs=27.5
Q ss_pred HHHHHCCCCHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 8986214777778999999999999999999
Q gi|254780131|r 42 ESWLDKAKKVTSLSKGEAMIEVEYLVKIALH 72 (119)
Q Consensus 42 ~~~m~kak~v~~Lsk~EA~~eie~L~k~I~~ 72 (119)
.++|+.|.=+=.|.|+++|.+|-.|++.|-.
T Consensus 21 v~AL~~adV~f~~dKG~~KsdL~~lRr~I~~ 51 (259)
T TIGR02434 21 VEALNHADVFFVLDKGEDKSDLVELRREICE 51 (259)
T ss_pred HHHHHCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 9887148389997587323799999999998
No 20
>KOG0257 consensus
Probab=21.46 E-value=51 Score=15.38 Aligned_cols=29 Identities=17% Similarity=0.326 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 999999999999999997544589856989999999
Q gi|254780131|r 59 AMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVS 94 (119)
Q Consensus 59 A~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~ 94 (119)
-+.|+++|+++..+|+ -=+|||..|+.++
T Consensus 190 sReeLe~ia~l~~k~~-------~lvisDevYe~~v 218 (420)
T KOG0257 190 SREELERIAELCKKHG-------LLVISDEVYEWLV 218 (420)
T ss_pred CHHHHHHHHHHHHHCC-------EEEEEHHHHHHHH
T ss_conf 7999999999998789-------7999825747882
No 21
>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=20.95 E-value=74 Score=14.40 Aligned_cols=23 Identities=13% Similarity=0.303 Sum_probs=13.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 89856989999999999999997
Q gi|254780131|r 81 DDPLFTDGLYDRVSERLDALQEQ 103 (119)
Q Consensus 81 D~P~ISD~EYD~L~~eL~~LE~~ 103 (119)
..|.+|+++...|+.+|..+|.+
T Consensus 22 ~~~~lseee~eel~~EL~kvEeE 44 (162)
T pfam04201 22 TKIVLSEAEKEELRTELAKLEEE 44 (162)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 53327899999999999999999
No 22
>TIGR01674 phage_lambda_G phage minor tail protein G; InterPro: IPR010027 This entry identifies a family of bacteriophage proteins including G of phage lambda. This protein has been described as undergoing a translational frameshift at a Gly-Lys dipeptide near the C terminus of protein G from phage lambda, with about 4 0.000000e+00fficiency, to produce tail assembly protein G-T..
Probab=20.38 E-value=48 Score=15.55 Aligned_cols=33 Identities=21% Similarity=0.355 Sum_probs=24.3
Q ss_pred HHCCCCCHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf 52455221689862147777789999999999999999
Q gi|254780131|r 33 KFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIA 70 (119)
Q Consensus 33 ~~~~~~~~~~~~m~kak~v~~Lsk~EA~~eie~L~k~I 70 (119)
||||.|+ ++.-+..-+|++-.|..|||+|.=+=
T Consensus 1 MFLK~E~-----f~~~~~sV~L~eLSaLQRIEyL~f~k 33 (138)
T TIGR01674 1 MFLKKET-----FERNGSSVTLFELSALQRIEYLEFLK 33 (138)
T ss_pred CCCCCCC-----CCCCCCEEEHHHHHHHHHHHHHHHHH
T ss_conf 9765421-----00178223144420657999999999
Done!