RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3842
(139 letters)
>3i9v_3 NADH-quinone oxidoreductase subunit 3; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_3* 2fug_3* 3iam_3* 3ias_3*
3m9s_3*
Length = 783
Score = 127 bits (320), Expect = 3e-35
Identities = 26/72 (36%), Positives = 40/72 (55%)
Query: 1 MKGWRVKTNSEMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRFTDI 60
G V T S++ R A+ G++EF L+NHPLDCP CD+GG C+LQD+++ +G +
Sbjct: 88 ADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCPTCDKGGACELQDRTVEYGLYEKYYQKG 147
Query: 61 DFSGKRWGYLRE 72
+
Sbjct: 148 PLELPVYTRFEF 159
Score = 106 bits (266), Expect = 6e-28
Identities = 21/44 (47%), Positives = 32/44 (72%)
Query: 90 AREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRFTD 133
A+ G++EF L+NHPLDCP CD+GG C+LQD+++ +G +
Sbjct: 103 AQAGMVEFTLLNHPLDCPTCDKGGACELQDRTVEYGLYEKYYQK 146
>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur
binding, oxidoreductase; HET: HCN; 1.39A {Clostridium
pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB:
1c4c_A* 1c4a_A* 1feh_A*
Length = 574
Score = 61.7 bits (150), Expect = 3e-12
Identities = 11/55 (20%), Positives = 22/55 (40%)
Query: 3 GWRVKTNSEMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRF 57
G + TNS+ + + LL H C C++ C+ + + + S+
Sbjct: 69 GMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKP 123
Score = 48.2 bits (115), Expect = 1e-07
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 90 AREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRF 131
+ + LL H C C++ C+ + + + S+
Sbjct: 82 KIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKP 123
>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 = 27.3 bits (60), Expect = 2.2
Identities = 23/120 (19%), Positives = 34/120 (28%), Gaps = 28/120 (23%)
Query: 11 EMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRFTDIDFSGKRWG-- 68
+ R + FL V P + L S D + ++ F+ K
Sbjct: 408 PFSERKLKFSNRFLPVASPFHSHL--------LVPASDLINKDLVK-NNVSFNAKDIQIP 458
Query: 69 -Y-------LREKLFLSELSGK--RESTCAPAR-EGVMEFLLVNHPLDCPICDQGGECDL 117
Y LR +S + P + E +F H LD GG L
Sbjct: 459 VYDTFDGSDLRV--LSGSISERIVDCIIRLPVKWETTTQF-KATHILD---FGPGGASGL 512
>3s5j_B Ribose-phosphate pyrophosphokinase 1; nucleotide synthesis,
transferase; 2.02A {Homo sapiens} PDB: 2hcr_A* 3efh_A
2h06_A 2h07_A 2h08_A
Length = 326
Score = 26.4 bits (59), Expect = 3.7
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 85 STCAPAREGVMEFLL 99
S C + +ME L+
Sbjct: 58 SGCGEINDNLMELLI 72
>3dah_A Ribose-phosphate pyrophosphokinase; pyrophosphoki seattle
structural genomics center for infectious disease,
magnesium, metal binding; HET: AMP; 2.30A {Burkholderia
pseudomallei}
Length = 319
Score = 26.0 bits (58), Expect = 4.1
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 85 STCAPAREGVMEFLL 99
STCAP + +ME ++
Sbjct: 62 STCAPTNDNLMELMI 76
>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA
replication, MCM complex, AAA+ Pro ATP-binding,
DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}
Length = 595
Score = 26.1 bits (58), Expect = 4.7
Identities = 8/53 (15%), Positives = 17/53 (32%), Gaps = 7/53 (13%)
Query: 7 KTNSEMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRFTD 59
+ E ++ P CP C + G+ L ++++ D
Sbjct: 140 HPDCMQEFEWPEDEEMPEVLEMPTICPKCGKPGQFRLI-------PEKTKLID 185
>1dku_A Protein (phosphoribosyl pyrophosphate synthetase); open
alpha-beta structure, domain duplication,
phosphoribosyltransferase type I fold; HET: AP2 ABM;
2.20A {Bacillus subtilis} SCOP: c.61.1.2 c.61.1.2 PDB:
1dkr_A* 1ibs_A*
Length = 317
Score = 25.6 bits (57), Expect = 5.6
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 85 STCAPAREGVMEFLL 99
ST P E +ME L+
Sbjct: 64 STSDPVNEHIMELLI 78
>2vl6_A SSO MCM N-TER, minichromosome maintenance protein MCM; helicase,
hydrolase, zinc-finger, ATP-binding, DNA-BIND ssDNA
binding; 2.8A {Sulfolobus solfataricus}
Length = 268
Score = 25.4 bits (56), Expect = 7.2
Identities = 7/54 (12%), Positives = 16/54 (29%), Gaps = 7/54 (12%)
Query: 6 VKTNSEMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFGSDRSRFTD 59
+ + E ++ P CP C + G ++++ D
Sbjct: 145 IHPDCMQEFEWPEDEEMPEVLEMPTICPKCGKPG-------QFRLIPEKTKLID 191
>2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2;
phosphorylation, nucleotide biosynthesis, transferase;
2.55A {Homo sapiens} PDB: 2c4k_A*
Length = 379
Score = 25.4 bits (56), Expect = 8.1
Identities = 3/15 (20%), Positives = 6/15 (40%)
Query: 85 STCAPAREGVMEFLL 99
+ +ME L+
Sbjct: 87 TVSKDVNTTIMELLI 101
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
0.322 0.139 0.440
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,093,671
Number of extensions: 108714
Number of successful extensions: 190
Number of sequences better than 10.0: 1
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 15
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
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 (21.9 bits)
S2: 52 (23.7 bits)