RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14581
(124 letters)
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell
divisi damage; HET: DNA AMP; 3.00A {Homo sapiens}
Length = 579
Score = 84.0 bits (208), Expect = 2e-20
Identities = 45/80 (56%), Positives = 57/80 (71%), Gaps = 3/80 (3%)
Query: 21 HKKGNEFKYFSRSLKP---VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDD 77
K + ++ P V + K VWEI+GAEFS++E HTADGISIRFPR T+IRDD
Sbjct: 500 PSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDD 559
Query: 78 KDWKTATNLPELKVLFKKSK 97
KDWK+ATNLP+LK L++ SK
Sbjct: 560 KDWKSATNLPQLKELYQLSK 579
Score = 58.6 bits (142), Expect = 2e-11
Identities = 28/38 (73%), Positives = 30/38 (78%)
Query: 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHK 41
+SEIKYDGERVQVHK G+ F YFSRSLKPVL HK
Sbjct: 246 PNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHK 283
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A
{Sulfolobus solfataricus} PDB: 2hix_A*
Length = 621
Score = 77.5 bits (191), Expect = 4e-18
Identities = 24/97 (24%), Positives = 47/97 (48%), Gaps = 8/97 (8%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTAD------- 62
++ +++ K+ + + ++P + + V EI G+E + + +HT
Sbjct: 513 QLDELQKKLMEIKRDVKHPRVNSKMEPDIWVEPVYVAEIIGSEITISPLHTCCQDVVEKD 572
Query: 63 -GISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKE 98
G+SIRFPR + RDDK + AT E+ ++ K +
Sbjct: 573 AGLSIRFPRFIRWRDDKSPEDATTTDEILEMYNKQPK 609
Score = 56.7 bits (137), Expect = 1e-10
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 5 ERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37
+ KYDGER Q+HKK ++ FSR L+ +
Sbjct: 273 GNAIVDYKYDGERAQIHKKEDKIFIFSRRLENI 305
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle,
cell division, DNA damage, DNA recombination, DNA
repair, DNA replication; HET: AMP; 1.8A {Pyrococcus
furiosus} PDB: 3rr5_A*
Length = 561
Score = 77.4 bits (191), Expect = 5e-18
Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 26 EFKYFSRSLKPVLEHKAQP--------VWEISGAEFSQAEIHTADGISIRFPRVTKIRDD 77
+ F++ LKP++ + V E++ E ++ + + G ++RFPR +RDD
Sbjct: 475 DLVEFTKMLKPLIIKEEGKRVWLQPKVVIEVTYQEIQKSPKYRS-GFALRFPRFVALRDD 533
Query: 78 KDWKTATNLPELKVLFKKSKETS 100
K + A + + L++ ++
Sbjct: 534 KGPEDADTIERIAQLYELQEKMK 556
Score = 57.8 bits (140), Expect = 4e-11
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37
EIKYDG RVQVHK G++ +SR L+ V
Sbjct: 241 GGEAEFEIKYDGARVQVHKDGSKIIVYSRRLENV 274
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain,
ATP-binding, cell cycle, cell division, DNA damage, DNA
recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus}
Length = 558
Score = 77.0 bits (190), Expect = 8e-18
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94
+E + V+E++ E ++ + + G ++RFPR ++RDDKD A + ++ L+K
Sbjct: 492 GKKVEFIPKYVFEVAYQEIQKSPKYES-GYALRFPRFVRLRDDKDVDEADTIERVENLYK 550
Query: 95 KSKETS 100
E
Sbjct: 551 LQFEVK 556
Score = 59.3 bits (144), Expect = 1e-11
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 1 MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37
+ + E K+DG RVQVH G+ +SR L+ V
Sbjct: 241 VREMRTAAVEWKFDGSRVQVHWDGSRVTIYSRRLENV 277
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L
complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP:
a.235.1.1 b.40.4.6 d.142.2.1
Length = 688
Score = 72.7 bits (178), Expect = 2e-16
Identities = 23/110 (20%), Positives = 45/110 (40%), Gaps = 9/110 (8%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA------ 61
E + + + + ++ P VWE+ A+ S + I+ A
Sbjct: 574 LEEHHQSLKALVLPSPRPYVRIDG-AVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVD 632
Query: 62 --DGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYD 109
GIS+RFPR ++R+DK + AT ++ L++K + + +
Sbjct: 633 SDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGS 682
Score = 50.0 bits (119), Expect = 2e-08
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 4 NERCYSEIKYDGERVQVHK-KGNEFKYFSRSLKPVLEHK 41
E KYDG+R Q+H +G E K FSR+ +
Sbjct: 329 EAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKY 367
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET:
DNA; 2.90A {Homo sapiens}
Length = 139
Score = 59.3 bits (144), Expect = 1e-12
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEH 40
Y E K DGER+Q+HK G+ +KYFSR+ +
Sbjct: 2 YIETKLDGERMQMHKDGDVYKYFSRNGYNYTDQ 34
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria
phage T7} SCOP: b.40.4.6 d.142.2.1
Length = 348
Score = 46.6 bits (110), Expect = 3e-07
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 1 MAKNERCYSEIKYDGERVQVHKKGNE-FKYFSRSLKPVLE 39
+ +EIKYDG R + + SR K +
Sbjct: 22 LDNAGYLIAEIKYDGVRGNICVDNTANSYWLSRVSKTIPA 61
Score = 28.5 bits (63), Expect = 0.51
Identities = 10/31 (32%), Positives = 12/31 (38%), Gaps = 7/31 (22%)
Query: 45 VWEISGAEFSQAEIHTADGISIRFPRVTKIR 75
+IS E T DG S+R P R
Sbjct: 325 ACQISYMEE------TPDG-SLRHPSFVMFR 348
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 45.4 bits (107), Expect = 9e-07
Identities = 22/112 (19%), Positives = 38/112 (33%), Gaps = 30/112 (26%)
Query: 9 SEIKYDGERVQVHKKGNEF-----KYFSRSLKPVLEHKAQPVWEISGAEFSQAEI----- 58
S I + +++ N F + S L P + + + + + F+ +I
Sbjct: 405 SRIPFSERKLKFS---NRFLPVASPFHSHLLVPASDLINKDLVK-NNVSFNAKDIQIPVY 460
Query: 59 HTADGISIR------FPRVTK--IRDDKDWKTATNLPELKVLFKKSKETSDF 102
T DG +R R+ IR W+T T +L DF
Sbjct: 461 DTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHIL--------DF 504
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold,
nucleotidyl transferase, structural genomic protein
structure initiative; HET: APK MSE; 2.40A
{Mycobacterium tuberculosis}
Length = 310
Score = 42.2 bits (100), Expect = 8e-06
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
E +DG R+ V + SRS + V
Sbjct: 30 EGXWDGYRLLVEADHGAVRLRSRSGRDV 57
Score = 33.4 bits (77), Expect = 0.012
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTAT 84
+KP L V E+ +E+ T +G +R +R DK
Sbjct: 271 VKPAL------VAEVRYSEW------TPEGR-LRQSSWRGLRPDKKPSEVV 308
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP;
2.9A {Pyrococcus abyssi GE5}
Length = 389
Score = 35.7 bits (82), Expect = 0.002
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLK 35
K Y E K DG V+V + +R
Sbjct: 93 KRGEFYVEEKVDGYNVRVVMYKGKMLGITRGGF 125
>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET:
AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1
PDB: 2q2t_A* 2q2u_A* 1p8l_A*
Length = 297
Score = 33.1 bits (75), Expect = 0.012
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 5/34 (14%)
Query: 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37
C + K G R + SR+ KP+
Sbjct: 18 QFPCLATPKIAGIRSVKQT-----QMLSRTFKPI 46
Score = 30.0 bits (67), Expect = 0.17
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 51 AEFSQAEIHTADGISIRFPRVTKIRDDKD 79
+F E+ + RFP IR ++D
Sbjct: 270 VKFKYFEM-GSKD-CPRFPVFIGIRHEED 296
>3qwu_A DNA ligase; structural genomics, PSI-2, midwest center for
structural GE MCSG; HET: DNA ADN; 2.35A {Aquifex
aeolicus}
Length = 370
Score = 27.5 bits (61), Expect = 1.2
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRS 33
E K DG ++ K G+ + SR
Sbjct: 78 EEKVDGYNTRIFKYGDNYYALSRG 101
>2imz_A Endonuclease PI-MTUI; N-terminal cysteine sulfinic acid
C-terminal aminosuccinimide, hydrolase; 1.70A
{Mycobacterium tuberculosis}
Length = 168
Score = 27.1 bits (59), Expect = 1.5
Identities = 9/77 (11%), Positives = 23/77 (29%), Gaps = 10/77 (12%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69
++ + + V + +R + + + V + A G +
Sbjct: 21 DVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGL----------RIAGGAILWAT 70
Query: 70 RVTKIRDDKDWKTATNL 86
K+ + W+ A L
Sbjct: 71 PDHKVLTEYGWRAAGEL 87
>2vqr_A Putative sulfatase; phosphonate monoester hydrolase, hydrolase,
plasmid, formylglycine, phosphodiesterase; 1.42A
{Rhizobium leguminosarum BV} PDB: 2w8s_A
Length = 543
Score = 27.0 bits (60), Expect = 1.7
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 7/56 (12%)
Query: 32 RSLKPVLEHKAQPVW------EISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWK 81
SL P L W E + +E + G+ + + I+D+ +K
Sbjct: 421 LSLLPFLSEGRPQDWRTELHYEYDFRDVYYSEPQSFLGLGMNDCSLCVIQDE-RYK 475
>3uws_B Hypothetical protein; clostripain family protein, peptidase_C11,
structural genomi center for structural genomics, JCSG;
HET: MSE; 1.70A {Parabacteroides merdae}
Length = 228
Score = 27.0 bits (59), Expect = 1.7
Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 1/74 (1%)
Query: 13 YD-GERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRV 71
YD + ++ ++ F L + +KA A + I + G++I P+
Sbjct: 148 YDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQE 207
Query: 72 TKIRDDKDWKTATN 85
+ + + +K
Sbjct: 208 SLPKMLEWYKQRVG 221
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.8 bits (58), Expect = 1.8
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 16 ERVQVHKKGNEFKYFSRSLKPVLEHKAQ 43
E+ + K K ++ P L KA
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKAT 45
>2jhp_A VP4 core protein; viral protein, viral capping enzyme, virion PR
viral protein; HET: SAH GUN; 2.5A {Bluetongue virus 10}
PDB: 2jh8_A* 2jha_A* 2jhc_A* 2jh9_A*
Length = 644
Score = 25.8 bits (56), Expect = 5.0
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 29 YFSRSLKPVLEHKAQPVWEISGAE 52
Y + L +++ P+W+++G E
Sbjct: 9 YVTNELSHIVKDGFLPIWKLTGDE 32
>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA
synthetase, ATP-binding, ligas binding,
nucleotide-binding, protein biosynthesis; HET: CIT;
1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A
3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A*
1pg2_A* 1qqt_A 1mea_A 1med_A
Length = 560
Score = 25.7 bits (57), Expect = 5.1
Identities = 13/75 (17%), Positives = 22/75 (29%), Gaps = 7/75 (9%)
Query: 11 IKYDGERVQVHKK----GNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTAD-GIS 65
K +G + N F+ LKPVL + E + I G
Sbjct: 477 AKQEGRDADLQAICSMGINLFRVLMTYLKPVLPKLTERAEAFLNTELTWDGIQQPLLGHK 536
Query: 66 IRFPRV--TKIRDDK 78
+ + +I +
Sbjct: 537 VNPFKALYNRIDMRQ 551
>1a3q_A Protein (nuclear factor kappa-B P52); transcription factor, immune
response, DNA-protein complex, transcription/DNA
complex; HET: DNA; 2.10A {Homo sapiens} SCOP: b.1.18.1
b.2.5.3 PDB: 3do7_B 3jv6_B 3jv5_A
Length = 285
Score = 25.5 bits (55), Expect = 5.4
Identities = 9/43 (20%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 28 KYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPR 70
K ++ + W+ G +FS ++H I R P
Sbjct: 210 KVQKDDIEVRFYEDDENGWQAFG-DFSPTDVHKQYAIVFRTPP 251
>2apl_A Hypothetical protein PG0816; structural genomics, PSI, protein
initiative, midwest center for structural genomics,
MCSG, U function; 2.01A {Porphyromonas gingivalis} SCOP:
a.258.1.1
Length = 157
Score = 24.6 bits (53), Expect = 8.6
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 87 PELKVLFKKSKETSDFTLKPKYDRIK 112
++ +F K T DF P+Y+ +
Sbjct: 106 KAIQSVFAKYDLTDDFEASPEYEHLY 131
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.132 0.389
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,803,091
Number of extensions: 92853
Number of successful extensions: 184
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 38
Length of query: 124
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,412,271
Effective search space: 185315382
Effective search space used: 185315382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.5 bits)