RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780131|ref|YP_003064544.1| DNA ligase, NAD-dependent
[Candidatus Liberibacter asiaticus str. psy62]
(119 letters)
>gnl|CDD|128805 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 55.7 bits (135), Expect = 2e-09
Identities = 24/60 (40%), Positives = 31/60 (51%)
Query: 59 AMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118
A E+ L K+ H YY LD P+ +D YDR+ L L+E+ PEL D P VG
Sbjct: 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVG 60
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 53.6 bits (130), Expect = 1e-08
Identities = 25/61 (40%), Positives = 31/61 (50%)
Query: 58 EAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTV 117
EA +E L + HH YY LD P +D YDR+ L AL+ + PEL D P V
Sbjct: 4 EAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRV 63
Query: 118 G 118
G
Sbjct: 64 G 64
>gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent. The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed.
Length = 652
Score = 50.4 bits (121), Expect = 1e-07
Identities = 23/53 (43%), Positives = 29/53 (54%)
Query: 66 LVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118
L K+ HH YY LD+P +D YDR+ L L+E+ PEL D P VG
Sbjct: 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVG 53
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 689
Score = 45.1 bits (107), Expect = 4e-06
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDE 110
V LS+ EA + E L + H YY DP+ D YD + RL AL++ F +L E
Sbjct: 24 VEELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTE 82
Query: 111 DHPWNTVG 118
+ P VG
Sbjct: 83 NSPTRRVG 90
>gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed.
Length = 562
Score = 30.7 bits (70), Expect = 0.10
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 70 ALHHQ--KW---YYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
AL Q +W Y+R D +YD++ RL Q F D P
Sbjct: 36 ALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVP 84
>gnl|CDD|163456 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves.
Length = 893
Score = 27.7 bits (62), Expect = 0.80
Identities = 9/17 (52%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 98 DALQEQFPELFDEDHPW 114
DALQ+ F EL ++ PW
Sbjct: 67 DALQDSFDEL--DEAPW 81
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 26.3 bits (58), Expect = 2.1
Identities = 17/52 (32%), Positives = 23/52 (44%)
Query: 62 EVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
E+ L K+ K YY P D YD+ RL L+ ++PE D P
Sbjct: 8 EILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSP 59
>gnl|CDD|128619 smart00324, RhoGAP, GTPase-activator protein for Rho-like GTPases.
GTPase activator proteins towards Rho/Rac/Cdc42-like
small GTPases. etter domain limits and outliers.
Length = 174
Score = 26.1 bits (58), Expect = 2.1
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 9/40 (22%)
Query: 80 LDDPLFTDGLYDR---------VSERLDALQEQFPELFDE 110
L +PL LY+ +ERL AL+E L
Sbjct: 70 LPEPLIPYELYEEFIEAAKVEDETERLRALRELISLLPPA 109
>gnl|CDD|162228 TIGR01161, purK, phosphoribosylaminoimidazole carboxylase, PurK
protein. Phosphoribosylaminoimidazole carboxylase is a
fusion protein in plants and fungi, but consists of two
non-interacting proteins in bacteria, PurK and PurE.
This model represents PurK, N5-carboxyaminoimidazole
ribonucleotide synthetase, which hydrolyzes ATP and
converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR.
In the presence of high concentrations of bicarbonate,
PurE is reported able to convert AIR to CAIR directly
and without ATP.
Length = 352
Score = 25.8 bits (57), Expect = 2.7
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 13 FENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAK 49
FE EH A +KL K P+ AL D+
Sbjct: 66 FEFEHVDVEA-LEKLEARGVKLFPSPDALAIIQDRLT 101
>gnl|CDD|172832 PRK14356, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 456
Score = 25.8 bits (57), Expect = 2.8
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 78 YRLDDPLFTDGLYDRVSERLDALQEQFPEL 107
YR PLF D ++ V R D ++ FP+
Sbjct: 40 YRALRPLFGDNVWTVVGHRADMVRAAFPDE 69
>gnl|CDD|184903 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 25.4 bits (57), Expect = 3.2
Identities = 17/75 (22%), Positives = 29/75 (38%)
Query: 32 AKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYD 91
K + RA+ +D+ ++ + EA+I L L + LD T Y
Sbjct: 581 EKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAALDADFLTSAEYR 640
Query: 92 RVSERLDALQEQFPE 106
R+ E + L+ E
Sbjct: 641 RLVELAEKLRGLIEE 655
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 25.1 bits (56), Expect = 4.3
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 7/27 (25%)
Query: 17 HN-----ITPAQWKKL--LTLEAKFLP 36
HN +TP QW +L L E +P
Sbjct: 182 HNPTGADLTPEQWDELAELLKERGLIP 208
>gnl|CDD|178811 PRK00035, hemH, ferrochelatase; Reviewed.
Length = 333
Score = 25.1 bits (56), Expect = 4.4
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 6/51 (11%)
Query: 61 IEVEYLVKIALHHQKWYYRL-----DDPLFTDGLYDRVSERLDALQEQFPE 106
I++EY +IA +R D P F + L D V E L +
Sbjct: 283 IDIEYR-EIAEEAGGEEFRRIPCLNDSPEFIEALADLVRENLQGWPPRLLG 332
>gnl|CDD|147874 pfam05957, DUF883, Bacterial protein of unknown function (DUF883).
This family consists of several hypothetical bacterial
proteins of unknown function.
Length = 94
Score = 25.2 bits (56), Expect = 4.7
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 17/45 (37%)
Query: 91 DRVSERLDALQEQFPELFDE-----------------DHPWNTVG 118
+R LD +E+ + D ++PW VG
Sbjct: 34 ERAEAALDDARERLGDAADAAAERARDAADAADDYVHENPWQAVG 78
>gnl|CDD|177793 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 25.1 bits (55), Expect = 4.8
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 91 DRVSERLDALQEQFPE 106
+R ER+ AL+E+FP+
Sbjct: 297 NRSEERVAALREEFPD 312
>gnl|CDD|185028 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 24.8 bits (55), Expect = 4.8
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 34 FLPNKRALESWLDKAK 49
F+P+ AL++WL++A
Sbjct: 251 FIPSVPALKNWLERAG 266
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 24.7 bits (53), Expect = 6.4
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 76 WYYRLDDPLFTDGLYD 91
W+ R DD ++DG+YD
Sbjct: 328 WFGRRDDNYWSDGVYD 343
>gnl|CDD|149065 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 24.5 bits (54), Expect = 6.7
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 81 DDPLFTDGLYDRVSERLDALQEQF---PELFDE 110
DD D LY ++ E + + +F P LF E
Sbjct: 417 DDDGLRDSLYAKIEEIVQRILNEFDDDPSLFAE 449
>gnl|CDD|130387 TIGR01320, mal_quin_oxido, malate:quinone-oxidoreductase. This
membrane-associated enzyme is an alternative to the
better-known NAD-dependent malate dehydrogenase as part
of the TCA cycle. The reduction of a quinone rather than
NAD+ makes the reaction essentially irreversible in the
direction of malate oxidation to oxaloacetate. Both
forms of malate dehydrogenase are active in E. coli;
disruption of this form causes less phenotypic change.
In some bacteria, this form is the only or the more
important malate dehydrogenase.
Length = 483
Score = 24.4 bits (53), Expect = 7.1
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 95 ERLDALQEQFPELFDEDHPWNTV 117
ER+ AL+E +PE D D W +
Sbjct: 364 ERVSALREFYPEAIDSD--WELI 384
>gnl|CDD|179484 PRK02854, PRK02854, primosomal protein DnaI; Provisional.
Length = 179
Score = 24.4 bits (53), Expect = 7.3
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 19 ITPAQWKKLLTLEAKF 34
+TPA+ +LL LE K
Sbjct: 45 VTPARLAELLALEEKL 60
>gnl|CDD|151766 pfam11325, DUF3127, Protein of unknown function (DUF3127). This
bacterial family of proteins has no known function.
Length = 84
Score = 24.1 bits (53), Expect = 8.6
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 24 WKK---LLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWY 77
WKK +L E ++ P K E W DK + SL+ G+ ++V + ++ + KW+
Sbjct: 21 WKKREFVLETEGQY-PQKICFEFWGDKIDLLDSLNVGD-EVKVSFDLEGREWNGKWF 75
>gnl|CDD|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 24.0 bits (52), Expect = 8.7
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 64 EYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPE 106
L I + +LD+P + + ++E LD L +++ E
Sbjct: 55 GALEPIEQKKKDLEKKLDNPDISLEEAESINEELDTLAKEYEE 97
>gnl|CDD|139424 PRK13247, PRK13247, dihydrobiliverdin:ferredoxin oxidoreductase;
Provisional.
Length = 238
Score = 24.2 bits (53), Expect = 9.2
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 83 PLFTDGLY-DRVSERLDALQEQFPEL 107
PL D Y DR E L +L+E+FP+L
Sbjct: 102 PLVQDKDYLDRYFEGLKSLKERFPDL 127
>gnl|CDD|183578 PRK12536, PRK12536, RNA polymerase sigma factor; Provisional.
Length = 181
Score = 23.9 bits (52), Expect = 9.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 62 EVEYLVK---IALHHQKWYYRLDDPL 84
EVE LV+ +A+H+ + YR D PL
Sbjct: 48 EVEDLVQEILLAVHNARHTYRADQPL 73
>gnl|CDD|183961 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 24.2 bits (53), Expect = 9.7
Identities = 7/24 (29%), Positives = 16/24 (66%)
Query: 45 LDKAKKVTSLSKGEAMIEVEYLVK 68
L+KA+ + S + +A + ++ LV+
Sbjct: 37 LEKAENLASKTGAKACLSIDELVE 60
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.136 0.420
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,022,718
Number of extensions: 115450
Number of successful extensions: 357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 357
Number of HSP's successfully gapped: 39
Length of query: 119
Length of database: 5,994,473
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,244,225
Effective search space: 161280550
Effective search space used: 161280550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.5 bits)