RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2702
(87 letters)
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.1 bits (77), Expect = 0.003
Identities = 13/50 (26%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 38 KDAKYDLMKNELLDLMQKEKPDLVQEEMSDLMKHKMSVLMKDEKSVRPET 87
D KY+ + N +LD + K + +L+ + +DL++ LM +++++ E
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKYTDLLR---IALMAEDEAIFEEA 583
Score = 31.0 bits (69), Expect = 0.032
Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 3/77 (3%)
Query: 1 MPDLMREEKPDLMQEGKPDLMKDELPALMKEEKPDLMKDAKYDLMKNELLDLMQKEKPDL 60
+ + + D+ K L KEE ++ L + ++ ++
Sbjct: 22 LSVFEDAFVDNFDCKDVQDMPK---SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 61 VQEEMSDLMKHKMSVLM 77
VQ+ + ++++ LM
Sbjct: 79 VQKFVEEVLRINYKFLM 95
>3otg_A CALG1; calicheamicin, TDP, structural genomics, PSI-2, protein STRU
initiative, center for eukaryotic structural genomics,
CESG fold; HET: TYD; 2.08A {Micromonospora echinospora}
PDB: 3oth_A*
Length = 412
Score = 27.0 bits (60), Expect = 0.85
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 2 PDLMREEKPDLMQEGKPDLMKDELPALMKEEKPDL 36
P+ + E + P + DEL +++ +PDL
Sbjct: 99 PEQLSELPQIVFGRVIPQRVFDELQPVIERLRPDL 133
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 26.4 bits (59), Expect = 1.3
Identities = 8/74 (10%), Positives = 23/74 (31%), Gaps = 8/74 (10%)
Query: 18 PDLMKDELPALMKEE---KPDLMKDAKYDLMKNELLDLMQKEKPDLVQEEMSDLMKHKMS 74
PDL +++ E + + + + L ++ + +L E+ +
Sbjct: 15 PDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQ 74
Query: 75 VLM-----KDEKSV 83
L+ +
Sbjct: 75 ELLFLLSPEASDKA 88
>1iru_N 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
PDB: 3unb_M* 3une_M 3unf_M* 3unh_M
Length = 219
Score = 25.3 bits (56), Expect = 2.5
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 49 LLDLMQKEKPDLVQEEMSDLMKHKMSVLMK 78
LL + +++P L Q E DL++ M VL
Sbjct: 149 LLREVLEKQPVLSQTEARDLVERCMRVLYY 178
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 25.6 bits (56), Expect = 2.8
Identities = 6/41 (14%), Positives = 14/41 (34%)
Query: 15 EGKPDLMKDELPALMKEEKPDLMKDAKYDLMKNELLDLMQK 55
G ++ L + K+ + L D++Q+
Sbjct: 525 PGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQR 565
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 25.2 bits (56), Expect = 3.3
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLVQE 63
DA+YD + EL +L + + P+L+
Sbjct: 32 DAEYDRLMRELREL-ETKHPELITP 55
>2fgc_A Acetolactate synthase, small subunit; regulatory subunit,
structural genomi protein structure initiative; 2.30A
{Thermotoga maritima} SCOP: d.58.18.6 d.58.18.6
Length = 193
Score = 24.9 bits (55), Expect = 3.7
Identities = 4/27 (14%), Positives = 12/27 (44%)
Query: 54 QKEKPDLVQEEMSDLMKHKMSVLMKDE 80
+E + +H +S+L+ ++
Sbjct: 13 GRENLYFQGHMTDQIREHLVSMLVHNK 39
>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold,
adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus
influenzae} PDB: 3pn1_A* 3bac_A*
Length = 322
Score = 24.7 bits (55), Expect = 4.5
Identities = 7/23 (30%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
D++YD + ++L L + E P+ +
Sbjct: 30 DSEYDRLFHQLKAL-ELEHPEFL 51
>3szy_A Phosphonoacetate hydrolase; alkaline phosphatase superfamily; 1.35A
{Sinorhizobium meliloti} PDB: 3szz_A 3t00_A 3t01_A
3t02_A
Length = 427
Score = 24.8 bits (53), Expect = 4.5
Identities = 10/56 (17%), Positives = 27/56 (48%)
Query: 17 KPDLMKDELPALMKEEKPDLMKDAKYDLMKNELLDLMQKEKPDLVQEEMSDLMKHK 72
+ + D A + P++ A + + + L+++ +PD++ +D ++HK
Sbjct: 164 RAEHGIDNASAWLGRPVPEVYSAALSEFVFAAGVKLLREFRPDIMYLTTTDYVQHK 219
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA
NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB:
3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Length = 332
Score = 24.4 bits (54), Expect = 5.7
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
D YD + EL+D+ + E PDL+
Sbjct: 39 DYVYDRLYKELVDI-ETEFPDLI 60
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 24.5 bits (53), Expect = 6.0
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 12 LMQEGKPDLMKDELPALMKEEKPDLMKDAKYDLMKNEL-LDLMQKEKPDLVQEEMSDL 68
+ E K D+ + L + + A Y L L L LM+K + EM+ +
Sbjct: 420 FLGEQKEDVHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARV 477
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus
stearothermophilus} SCOP: d.142.2.2
Length = 318
Score = 24.4 bits (54), Expect = 6.3
Identities = 8/23 (34%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
DA+YD + EL+ + +++ P+L
Sbjct: 34 DAEYDRLMQELIAI-EEQYPELK 55
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 24.4 bits (54), Expect = 6.6
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
DA++D + L L +++ P+L
Sbjct: 41 DAEFDELLRRLEAL-EEQHPELR 62
>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 = 24.4 bits (54), Expect = 6.8
Identities = 7/23 (30%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
D++YD + +EL+ + ++E P+
Sbjct: 32 DSEYDKLLHELIKI-EEEHPEYK 53
>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 = 24.4 bits (54), Expect = 6.8
Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
DA+YD + EL +L ++ P+
Sbjct: 34 DAEYDRLLRELKEL-EERFPEFK 55
>3aek_B Light-independent protochlorophyllide reductase S; iron/sulfur
cluster, oxidoreductase, bacteriochlorophyll
biosynthesis; HET: PMR; 2.30A {Rhodobacter capsulatus}
PDB: 3aeq_B* 3aer_B 3aes_B* 3aeu_B 3aet_B
Length = 525
Score = 24.0 bits (52), Expect = 7.6
Identities = 6/37 (16%), Positives = 13/37 (35%)
Query: 1 MPDLMREEKPDLMQEGKPDLMKDELPALMKEEKPDLM 37
M +R + E E+ ++ P+L+
Sbjct: 317 MARPLRTAAAEYGLEALITDDYLEVEKAIEAAAPELI 353
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Length = 328
Score = 24.0 bits (53), Expect = 7.6
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 39 DAKYDLMKNELLDLMQKEKPDLV 61
DA++D + L L +++ P+L
Sbjct: 41 DAEFDELLRRLEAL-EEQHPELR 62
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
0.310 0.130 0.347
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,296,536
Number of extensions: 68546
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 90
Length of query: 87
Length of database: 6,701,793
Length adjustment: 55
Effective length of query: 32
Effective length of database: 5,166,138
Effective search space: 165316416
Effective search space used: 165316416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.6 bits)