RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent
[Candidatus Liberibacter asiaticus str. psy62]
(119 letters)
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 63.7 bits (155), Expect = 9e-12
Identities = 22/66 (33%), Positives = 33/66 (50%)
Query: 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
+++ EA + L + +H YY L +P +D YDR+ L L+E+FPE D P
Sbjct: 1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSP 60
Query: 114 WNTVGY 119
VG
Sbjct: 61 TEQVGA 66
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli K12}
Length = 671
Score = 57.6 bits (138), Expect = 8e-10
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 62 EVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119
++ L HH+ Y+ +D P D YDR+ L L+ + PEL D P VG
Sbjct: 7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGA 64
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA
NMN; 1.80A {Enterococcus faecalis V583} SCOP: d.142.2.2
PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Length = 332
Score = 57.3 bits (137), Expect = 8e-10
Identities = 20/66 (30%), Positives = 30/66 (45%)
Query: 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
L+ A + L K + YY D P D +YDR+ + L ++ +FP+L D P
Sbjct: 6 LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSP 65
Query: 114 WNTVGY 119
VG
Sbjct: 66 TQRVGG 71
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA
replication, magnesium, manganese, metal-binding, NAD,
zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB:
3jsn_A*
Length = 318
Score = 53.7 bits (128), Expect = 1e-08
Identities = 18/57 (31%), Positives = 25/57 (43%)
Query: 62 EVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118
V L + + YY DNP D YD++ L ++E+ PE D P VG
Sbjct: 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVG 63
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus
stearothermophilus} SCOP: d.142.2.2
Length = 318
Score = 51.9 bits (123), Expect = 3e-08
Identities = 20/60 (33%), Positives = 31/60 (51%)
Query: 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
+ + +A L ++ + YY LD P D YDR+ + L A++EQ+PEL D P
Sbjct: 1 MDRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSP 60
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Length = 328
Score = 51.9 bits (123), Expect = 4e-08
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 48 AKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPEL 107
+ + E + + + L + HQ YY D P+ +D +D + RL+AL+EQ PEL
Sbjct: 2 SSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPEL 61
Query: 108 FDEDHPWNTVGY 119
D P VG
Sbjct: 62 RTPDSPTQLVGG 73
>1tue_B Regulatory protein E2; helicase, replication, E1E2 complex, AAA+
protein; 2.10A {Human papillomavirus type 18} SCOP:
b.91.1.1
Length = 218
Score = 27.3 bits (61), Expect = 0.76
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 91 DRVSERLDALQEQFPELFDED 111
+ +SERL ALQ++ + ++ D
Sbjct: 9 ETLSERLSALQDKIIDHYEND 29
>1r6n_A HPV11 E2 TAD, HPV11 regulatory protein E2, E2 protein; ,
transcription, replication, transcription, replication;
HET: 434; 2.40A {Human papillomavirus type 11} SCOP:
b.91.1.1 PDB: 1r6k_A
Length = 211
Score = 27.3 bits (61), Expect = 0.80
Identities = 9/21 (42%), Positives = 17/21 (80%)
Query: 91 DRVSERLDALQEQFPELFDED 111
+ +++RLDA Q+Q EL++E+
Sbjct: 8 EAIAKRLDACQDQLLELYEEN 28
>2nnu_A Regulatory protein E2; protein-peptide complex, helical peptide,
three helix bundle, amphipathic helix, transcription;
1.59A {Human papillomavirus type 16} SCOP: b.91.1.1 PDB:
1dto_A
Length = 205
Score = 27.3 bits (61), Expect = 0.88
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 88 GLYDRVSERLDALQEQFPELFDED 111
G + + +RL+ Q++ ++ D
Sbjct: 3 GSMETLCQRLNVCQDKILTHYEND 26
>2nyx_A Probable transcriptional regulatory protein, RV1404; alpha/beta,
structural genomics, PSI-2, protein structure
initiative; 2.30A {Mycobacterium tuberculosis H37RV}
Length = 168
Score = 27.0 bits (59), Expect = 0.93
Identities = 17/111 (15%), Positives = 30/111 (27%), Gaps = 7/111 (6%)
Query: 4 FDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEV 63
+ S + + NIT Q++ L+ L N L + L T + +
Sbjct: 28 LVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATG----RMVDRL 83
Query: 64 EYLVKIALHHQKWYYRLDNPLFTD---GLYDRVSERLDALQEQFPELFDED 111
I R T + +V+E + E
Sbjct: 84 VGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPA 134
>2jex_A Regulatory protein E2; nuclear protein, DNA replication,
phosphorylation, transcription regulation, viral
transcription factor; 2.35A {Bovine papillomavirus type
1} PDB: 2jeu_A
Length = 209
Score = 27.0 bits (60), Expect = 1.2
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 91 DRVSERLDALQEQFPELFDED 111
+ ERL QE +L ++
Sbjct: 2 ETACERLHVAQETQMQLIEKS 22
>3k07_A Cation efflux system protein CUSA; transmembrane helix, cell inner
membrane, cell membrane, COP transport, ION transport,
membrane; 3.52A {Escherichia coli k-12} PDB: 3kso_A
3kss_A
Length = 1055
Score = 25.9 bits (56), Expect = 2.4
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 17/69 (24%)
Query: 39 RALESWLDKAKKVTSLSK-GEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERL 97
+ S + AK V S+ G++ + V + +P RV E L
Sbjct: 79 TTMLS-VPGAKTVRGFSQFGDSYVYVIFEDGT------------DP---YWARSRVLEYL 122
Query: 98 DALQEQFPE 106
+ +Q + P
Sbjct: 123 NQVQGKLPA 131
>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR
{Lactococcus lactis subsp}
Length = 99
Score = 25.6 bits (56), Expect = 2.6
Identities = 5/26 (19%), Positives = 13/26 (50%)
Query: 5 DRVFRSSKFENEHNITPAQWKKLLTL 30
+ F+ + E E N++ A+ + +
Sbjct: 19 NLYFQGAMNEVEFNVSNAELIVMRVI 44
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.7 bits (55), Expect = 2.8
Identities = 12/68 (17%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 40 ALESWLDKAKK-VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLD 98
++ W ++ +K + L ++E E+ K ++W R + + + +R++++
Sbjct: 86 SIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK-- 143
Query: 99 ALQEQFPE 106
A +Q P+
Sbjct: 144 AFYQQ-PD 150
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 25.2 bits (54), Expect = 3.5
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 13/57 (22%)
Query: 28 LTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKW---YYRLD 81
L LEA+ +P++ E L++ +++ + E E ++ A Q+W +Y+ D
Sbjct: 1271 LKLEAEEIPSEDQNEFLLERTREIHN--------EAESQLRAA--QQQWGNDFYKRD 1317
>1evs_A Oncostatin M; 4-helix bundle, GP130 binding cytokine; 2.20A {Homo
sapiens} SCOP: a.26.1.1
Length = 187
Score = 25.0 bits (54), Expect = 4.0
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 3/34 (8%)
Query: 79 RLDNPLFTDGLY---DRVSERLDALQEQFPELFD 109
L F L V RL L+++ P+ D
Sbjct: 64 GLGRRGFLQTLNATLGCVLHRLADLEQRLPKAQD 97
>2j8s_A ACRB, acriflavine resistance protein B; membrane protein/complex,
designed ankyrin repeat protein, multidrug resistance
protein; HET: LMT LMU; 2.54A {Escherichia coli} PDB:
2dhh_A 1iwg_A 2dr6_A* 2drd_A* 2hqf_A 2hqg_A 2hqd_A
2hqc_A 2i6w_A 1oy6_A* 1oy9_A* 1oyd_A* 1oy8_A* 1oye_A
2rdd_A* 2w1b_A* 3d9b_A 1t9x_A* 1t9t_A* 1t9v_A* ...
Length = 1055
Score = 25.1 bits (54), Expect = 4.2
Identities = 9/70 (12%), Positives = 20/70 (28%), Gaps = 18/70 (25%)
Query: 39 RALESWLDKAKKVTSLSK--GEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSER 96
+ + +D ++S S G I + + + D +V +
Sbjct: 67 QNMNG-IDNLMYMSSNSDSTGTVQITLTF---------ESGTDADIAQ------VQVQNK 110
Query: 97 LDALQEQFPE 106
L P+
Sbjct: 111 LQLAMPLLPQ 120
>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural
genomics, PSI, protein structure initiative; 2.10A
{Pseudomonas aeruginosa} SCOP: a.4.5.28
Length = 142
Score = 25.0 bits (54), Expect = 4.9
Identities = 13/98 (13%), Positives = 33/98 (33%), Gaps = 5/98 (5%)
Query: 16 EHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTS--LSKGEAMIEVEYLVKIALHH 73
+H +T QW+ + L + L + + + L++ E V
Sbjct: 31 QHGLTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQR 90
Query: 74 QKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDED 111
+ + + + +S ++ ++ E F E+
Sbjct: 91 RVYVNLTEK---GQQCFVSMSGDMEKNYQRIQERFGEE 125
>2h1v_A Ferrochelatase; rossman fold, PI-helix, lyase; 1.20A {Bacillus
subtilis} PDB: 2hk6_A 1c1h_A* 1ld3_A 1n0i_A 1ak1_A
1doz_A 2q2n_A* 2h1w_A 2ac2_A 2q3j_A* 2ac4_A 2q2o_A*
1c9e_A* 2c8j_A
Length = 310
Score = 24.7 bits (53), Expect = 5.5
Identities = 10/42 (23%), Positives = 14/42 (33%), Gaps = 5/42 (11%)
Query: 61 IEVEYLVKIALHHQKWYYRL----DNPLFTDGLYDRVSERLD 98
+ E + YYR P F D L V ++L
Sbjct: 269 NDYEC-KVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLG 309
>3dh4_A Sodium/glucose cotransporter; membrane protein, symporter, sugar
transport, SGLT, ION transport, membrane, sodium
transport, symport; HET: GAL; 2.70A {Vibrio
parahaemolyticus}
Length = 530
Score = 24.6 bits (53), Expect = 6.0
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 86 TDGLYDRVSERLDALQEQFPELFDEDHP 113
TDG + VS+ +DA F + D+ +P
Sbjct: 185 TDGWFAGVSKMVDAAPGHFEMILDQSNP 212
>2ikb_A Hypothetical protein NMB1012; structural genomics, PSI-2, MCSG,
protein structure initiative, midwest center for
structural genomics; 1.70A {Neisseria meningitidis MC58}
SCOP: d.2.1.9 PDB: 2is5_A*
Length = 167
Score = 24.1 bits (52), Expect = 7.2
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 39 RALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRL-DNPLFTDGLYDRVSERL 97
RA D SL ++ E + L++ +Y +L F G RV++ L
Sbjct: 99 RAAGVPDDGVIGAVSLKAINSLPENDLLLRFNAERLVFYTKLGTFTSFGKGWVRRVAQNL 158
>2prs_A High-affinity zinc uptake system protein ZNUA; protein consists
of two (beta/ALFA)4 domains, metal transport; 1.70A
{Escherichia coli} PDB: 2osv_A 2ps0_A 2ps3_A 2ps9_A
2ogw_A
Length = 284
Score = 24.1 bits (51), Expect = 8.4
Identities = 7/59 (11%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 20 TPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYY 78
P+ K+L + + +E+++ K +K + ++E + + +
Sbjct: 39 RPSDVKRLQNADL-VVWVGPEMEAFMQKPVSKLPGAKQVTIAQLEDVKPLLMKSIHGDD 96
>1w25_A Stalked-cell differentiation controlling protein; two-component
system, response regulator, diguanylate cyclase, ggdef
domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP:
c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A*
Length = 459
Score = 24.0 bits (51), Expect = 9.2
Identities = 10/63 (15%), Positives = 19/63 (30%), Gaps = 5/63 (7%)
Query: 35 LPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVS 94
L N+R + LD + + + + I + K D + +
Sbjct: 296 LHNRRYMTGQLDSL-----VKRATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFA 350
Query: 95 ERL 97
RL
Sbjct: 351 LRL 353
>1dvo_A FINO, fertility inhibition protein O; repressor, bacterial
conjugation, X-RAY crystallography; 2.00A {Escherichia
coli} SCOP: a.136.1.1
Length = 152
Score = 24.0 bits (52), Expect = 9.4
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 91 DRVSERLDALQEQFPELFDEDHP 113
+ E ++ L+ +P LFD D P
Sbjct: 39 PTLDEAVNTLKPWWPGLFDGDTP 61
>1vbg_A Pyruvate,orthophosphate dikinase; transferase, maize, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.30A {Zea mays} SCOP: c.1.12.2
c.8.1.1 d.142.1.5 PDB: 1vbh_A*
Length = 876
Score = 23.7 bits (50), Expect = 9.6
Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 1/40 (2%)
Query: 76 WYYRLDNPLFTDGLYDRVSERLDALQEQFPELF-DEDHPW 114
Y+ GL+ + + L ++E D P
Sbjct: 53 QQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPL 92
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.135 0.419
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,106,260
Number of extensions: 46895
Number of successful extensions: 246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 62
Length of query: 119
Length of database: 5,693,230
Length adjustment: 80
Effective length of query: 39
Effective length of database: 3,753,710
Effective search space: 146394690
Effective search space used: 146394690
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: 50 (23.2 bits)