RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4529
(123 letters)
>3mlp_A Transcription factor COE1; transcription factor, pseudo-IG-fold,
TIG-domain, IPT-domain loop-helix; HET: DNA CIT; 2.80A
{Mus musculus} PDB: 3n50_A
Length = 402
Score = 83.4 bits (205), Expect = 3e-20
Identities = 59/66 (89%), Positives = 62/66 (93%)
Query: 53 TLITSHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVSLNEPTIDYGFQRLQKL 112
LIT HAIRVQTPPRHIPGVVEVTLSYKSKQFCKG PGRF+Y +LNEPTIDYGFQRLQK+
Sbjct: 273 ELITPHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGTPGRFIYTALNEPTIDYGFQRLQKV 332
Query: 113 IPRHPG 118
IPRHPG
Sbjct: 333 IPRHPG 338
>3muj_A Transcription factor COE3; immunoglobulin like fold,
helix-loop-helix, structural genom consortium, SGC, DNA
binding protein; 1.92A {Homo sapiens} PDB: 3mqi_A
Length = 138
Score = 76.2 bits (187), Expect = 4e-19
Identities = 61/67 (91%), Positives = 63/67 (94%)
Query: 52 CTLITSHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVSLNEPTIDYGFQRLQK 111
LIT HAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVY +LNEPTIDYGFQRLQK
Sbjct: 46 SELITPHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVYTALNEPTIDYGFQRLQK 105
Query: 112 LIPRHPG 118
+IPRHPG
Sbjct: 106 VIPRHPG 112
>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 = 0.007
Identities = 18/123 (14%), Positives = 33/123 (26%), Gaps = 40/123 (32%)
Query: 1 LPTGSSYSYDH---HTLSSDPDEKSAFIPVTRASSPTSTPNSHFINANTSGWNHCTLITS 57
P Y Y H H + + E+ + + F+
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL-------DFRFLEQ------------- 505
Query: 58 HAIRVQTPPRHIPGVVEVTLS----YKSKQFCKGAPGRFVYVSLNEPTIDYGFQRLQKLI 113
IR + + G + TL YK Y+ N+P + + +
Sbjct: 506 -KIRHDSTAWNASGSILNTLQQLKFYKP------------YICDNDPKYERLVNAILDFL 552
Query: 114 PRH 116
P+
Sbjct: 553 PKI 555
>1at0_A 17-hedgehog; developmental signaling molecule, cholesterol
transfer, signaling protein; 1.90A {Drosophila
melanogaster} SCOP: b.86.1.1
Length = 145
Score = 26.6 bits (58), Expect = 2.0
Identities = 18/110 (16%), Positives = 33/110 (30%), Gaps = 9/110 (8%)
Query: 14 LSSDPDEKSAFIPVTRASSPTSTPNSHFINANTSGWNHCTLITSHAIRVQTPPRHIPGVV 73
LS + ++ + V +F+ +T G T+ +H + V P V
Sbjct: 28 LSMTANGQAVYSEVILFMDRNLEQMQNFVQLHTDGGAVLTVTPAHLVSVWQPESQKLTFV 87
Query: 74 EVTLSYKSKQFCKGAPGRFVYVSLNEPTIDYGFQRLQKLIPRHPGLYVPL 123
+ V V E + ++ R G+ PL
Sbjct: 88 FAD---------RIEEKNQVLVRDVETGELRPQRVVKVGSVRSKGVVAPL 128
>2oa2_A BH2720 protein; 10175341, structural genomics, joint center for
STRU genomics, JCSG, protein structure initiative,
PSI-2, unknow function; HET: MSE; 1.41A {Bacillus
halodurans}
Length = 148
Score = 26.3 bits (58), Expect = 2.6
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 60 IRVQTPPRHIPGVVEVT 76
+ PP+H G V T
Sbjct: 119 YSIYAPPQHPHGTVHET 135
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 26.4 bits (59), Expect = 3.3
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV + P I D +RL+ L +HP L P
Sbjct: 32 YV-RDAPIISDAEFDELLRRLEALEEQHPELRTP 64
>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 = 25.9 bits (58), Expect = 3.9
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV L +P I D + L++L R P P
Sbjct: 25 YV-LADPEISDAEYDRLLRELKELEERFPEFKSP 57
>3mfd_A D-alanyl-D-alanine carboxypeptidase DACB; penicillin-binding
protein 5*, beta-lactamase, structural GE PSI-2, protein
structure initiative; HET: CIT; 1.75A {Bacillus
subtilis}
Length = 334
Score = 25.7 bits (57), Expect = 4.1
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 12/34 (35%)
Query: 38 NSHFINANTSGW----NHCT------LITSHAIR 61
N+ F N + G NH + ++T +A++
Sbjct: 125 NTRFQNPH--GLDDHENHYSTAYDMAILTKYAMK 156
>2bcf_A Probable D-alanyl-D-alanine carboxypeptidase DACB2;
penicillin-binding protein, DD-2 carboxypeptidase,
directed evolution; 2.30A {Mycobacterium tuberculosis}
Length = 276
Score = 25.6 bits (57), Expect = 5.0
Identities = 6/50 (12%), Positives = 14/50 (28%), Gaps = 16/50 (32%)
Query: 38 NSHFINAN---TSGWNHCT------LITSHAIR-------VQTPPRHIPG 71
++H + G + + +I A+ + P P
Sbjct: 134 STHATTPSGLDGPGGSGASTAHDLVVIFRAAMANPVFAQIIAEPSAMFPS 183
>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 = 25.5 bits (57), Expect = 5.0
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV + P++ D L K+ HP
Sbjct: 23 YV-EDNPSVPDSEYDKLLHELIKIEEEHPEYKTV 55
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Length = 328
Score = 25.6 bits (57), Expect = 5.3
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV + P I D +RL+ L +HP L P
Sbjct: 32 YV-RDAPIISDAEFDELLRRLEALEEQHPELRTP 64
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus
stearothermophilus} SCOP: d.142.2.2
Length = 318
Score = 25.5 bits (57), Expect = 5.7
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV L+ P++ D Q L + ++P L
Sbjct: 25 YV-LDRPSVPDAEYDRLMQELIAIEEQYPELKTS 57
>1es5_A DD-transpeptidase; penicillin-binding, serine peptidase, BET
lactamase, hydrolase carboxypeptidase, hydrolase; 1.40A
{Streptomyces SP} SCOP: e.3.1.1 PDB: 1skf_A 1es2_A
1j9m_A 1esi_A 1es3_A 1es4_A
Length = 262
Score = 25.2 bits (56), Expect = 5.8
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 11/33 (33%)
Query: 38 NSHFINANTSGW---NHCT------LITSHAIR 61
N+HF + + G + + I S A++
Sbjct: 136 NTHFDSFD--GIGNGANYSTPRDLTKIASSAMK 166
>1uwv_A 23S rRNA (uracil-5-)-methyltransferase RUMA; RNA modification,
iron-sulfur cluster, RNA processing; 1.95A {Escherichia
coli} SCOP: b.40.4.12 c.66.1.40 PDB: 2bh2_A*
Length = 433
Score = 25.6 bits (57), Expect = 6.1
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 7/32 (21%)
Query: 65 PPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVS 96
P R G V +Q K P R VYVS
Sbjct: 364 PAR--AGAAGV-----MQQIIKLEPIRIVYVS 388
>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 = 7.4
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
+V ++ P I D + L++L +HP L P
Sbjct: 23 HV-MDAPEIPDAEYDRLMRELRELETKHPELITP 55
>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S
rRNA-protein complex, cadmium IONS, ribosome; 2.30A
{Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T
2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z
2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z
2wrl_Z 2wro_Z ...
Length = 206
Score = 24.6 bits (54), Expect = 9.9
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 55 ITSHAIRVQTPPRHIPGVVEVTLS 78
I V+ PR+IP +EV +S
Sbjct: 119 EIHRDILVKVSPRNIPEFIEVDVS 142
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 0.133 0.417
Gapped
Lambda K H
0.267 0.0847 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,908,057
Number of extensions: 95548
Number of successful extensions: 257
Number of sequences better than 10.0: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 22
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
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 (21.7 bits)
S2: 51 (23.2 bits)