RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent
[Candidatus Liberibacter asiaticus str. psy62]
(119 letters)
>gnl|CDD|128805 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 56.1 bits (136), Expect = 2e-09
Identities = 24/60 (40%), Positives = 31/60 (51%)
Query: 59 AMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 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 = 55.1 bits (134), Expect = 4e-09
Identities = 25/61 (40%), Positives = 31/61 (50%)
Query: 58 EAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTV 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 = 50.7 bits (122), Expect = 9e-08
Identities = 23/53 (43%), Positives = 28/53 (52%)
Query: 66 LVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 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 = 42.8 bits (101), Expect = 2e-05
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDE 110
V LS+ EA + E L + H YY +P+ 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---YYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 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 = 0.76
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 = 1.7
Identities = 17/52 (32%), Positives = 24/52 (46%)
Query: 62 EVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
E+ L K+ K YY +P D YD+ RL L+ ++PE D P
Sbjct: 8 EILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSP 59
>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 = 2.6
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|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 25.9 bits (57), Expect = 2.8
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 64 EYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPE 106
L I + +LDNP + + ++E LD L +++ E
Sbjct: 55 GALEPIEQKKKDLEKKLDNPDISLEEAESINEELDTLAKEYEE 97
>gnl|CDD|118860 pfam10339, Vel1p, Velum formation protein. This is a small family
of putative velum formation proteins found in fungi.
They are of unknown function but are highly induced in
zinc-depleted conditions and have increased expression
in NAP1 deletion mutants.
Length = 201
Score = 25.7 bits (56), Expect = 3.0
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 14/82 (17%)
Query: 24 WKKLLTLEAKFLPNKRALESWLDKAKKVTSL------------SKGEAMIEVEYLVKIAL 71
+ ++L E +F+P + + + L S +AMI V +
Sbjct: 66 FARMLEQEPRFIPKLFTIAE--NDTANFSPLIFTTNIKTCNPQSIEDAMIPFANTVTGEI 123
Query: 72 HHQKWYYRLDNPLFTDGLYDRV 93
W DN F GL +++
Sbjct: 124 EFDAWADTADNASFITGLANQL 145
>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
Length = 815
Score = 25.6 bits (56), Expect = 3.4
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 80 LDNPLFTDGLYDRVSERLDALQEQFPELFDED 111
L N L + G+YD V L+A+ EL DE+
Sbjct: 85 LSNALLSLGIYDDVQGALEAMGLDLEELIDEE 116
>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 = 3.8
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|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 = 25.3 bits (56), Expect = 3.8
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 9/40 (22%)
Query: 80 LDNPLFTDGLYDR---------VSERLDALQEQFPELFDE 110
L PL LY+ +ERL AL+E L
Sbjct: 70 LPEPLIPYELYEEFIEAAKVEDETERLRALRELISLLPPA 109
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 25.1 bits (56), Expect = 4.2
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|185028 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 25.2 bits (56), Expect = 4.7
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 34 FLPNKRALESWLDKAK 49
F+P+ AL++WL++A
Sbjct: 251 FIPSVPALKNWLERAG 266
>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|183163 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional.
Length = 852
Score = 25.0 bits (55), Expect = 5.2
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 78 YRLDNPLFTDGL 89
+RLDNPL GL
Sbjct: 492 FRLDNPLTGKGL 503
>gnl|CDD|163239 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export.
Length = 694
Score = 24.8 bits (55), Expect = 5.6
Identities = 11/37 (29%), Positives = 13/37 (35%), Gaps = 13/37 (35%)
Query: 70 ALHHQKWYYR-------------LDNPLFTDGLYDRV 93
L YR L +PLF +YDRV
Sbjct: 141 TLKESWPLYRDVLIASLLINLLALASPLFVMNVYDRV 177
>gnl|CDD|178811 PRK00035, hemH, ferrochelatase; Reviewed.
Length = 333
Score = 24.4 bits (54), Expect = 7.0
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 61 IEVEYLVKIALHHQKWYYRL-----DNPLFTDGLYDRVSERLDALQEQFPE 106
I++EY +IA +R D+P F + L D V E L +
Sbjct: 283 IDIEYR-EIAEEAGGEEFRRIPCLNDSPEFIEALADLVRENLQGWPPRLLG 332
>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 = 7.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 19 ITPAQWKKLLTLEAKF 34
+TPA+ +LL LE K
Sbjct: 45 VTPARLAELLALEEKL 60
>gnl|CDD|162549 TIGR01828, pyru_phos_dikin, pyruvate, phosphate dikinase. This
model represents pyruvate,phosphate dikinase, also
called pyruvate,orthophosphate dikinase. It is similar
in sequence to other PEP-utilizing enzymes.
Length = 856
Score = 24.2 bits (53), Expect = 7.7
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 77 YYRLDNPLFTDGLYDRVSERLDALQEQFPELF-DEDHP 113
Y + F GL + + E L L+E+ + F D ++P
Sbjct: 48 EYYANGKQFPKGLQEEIKEALTLLEEKTGKKFGDTENP 85
>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 = 8.7
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|139424 PRK13247, PRK13247, dihydrobiliverdin:ferredoxin oxidoreductase;
Provisional.
Length = 238
Score = 24.2 bits (53), Expect = 8.8
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|183961 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 23.8 bits (52), 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 0.135 0.419
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: 2,014,369
Number of extensions: 114313
Number of successful extensions: 348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 41
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)