RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12583
(96 letters)
>1usg_A Leucine-specific binding protein; leucine-binding protein, X-RAY
crystallography, protein structure, ABC transport
systems, transport protein; 1.53A {Escherichia coli}
SCOP: c.93.1.1 PDB: 1usi_A* 1usk_A 2lbp_A 1z15_A 1z16_A
1z17_A 1z18_A 2liv_A
Length = 346
Score = 32.2 bits (74), Expect = 0.012
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 7 DSEGYPRQDVDVYQGLVKDDIILEFGPINSSNFKSLQDIASTVRAGV 53
D P+Q V V +V D I G + SS+ + DI G+
Sbjct: 50 DDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYE--DEGI 94
>3ipc_A ABC transporter, substrate binding protein (amino; venus flytrap
domain, transport protein; 1.30A {Agrobacterium
tumefaciens} PDB: 3ip5_A 3ip6_A 3ip7_A 3ip9_A 3ipa_A
Length = 356
Score = 32.3 bits (74), Expect = 0.012
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 6 VDSEGYPRQDVDVYQGLVKDDIILEFGPINSSNFKSLQDIASTVRAGV 53
D P+Q + V V D + G NS ++ + G+
Sbjct: 49 GDDVSDPKQGISVANKFVADGVKFVVGHANSGVSIPASEVYA--ENGI 94
>3lkb_A Probable branched-chain amino acid ABC transporter, amino acid
binding protein; branched amino acid, PSI-II, NYSGXRC,
structural genomics; 2.40A {Thermus thermophilus}
Length = 392
Score = 30.5 bits (69), Expect = 0.062
Identities = 5/47 (10%), Positives = 12/47 (25%), Gaps = 2/47 (4%)
Query: 7 DSEGYPRQDVDVYQGLVKDDIILEFGPINSSNFKSLQDIASTVRAGV 53
D + ++ V I F + L+ + +
Sbjct: 55 DDQYNNANTQRFFEEAVDRFKIPVFLSYATGANLQLKPLIQ--ELRI 99
>3pv2_A DEGQ; trypsin fold, PDZ domain, chaperone protease, hydrolase;
2.15A {Legionella fallonii} PDB: 3pv3_A 3pv5_A 3pv4_A
Length = 451
Score = 29.6 bits (67), Expect = 0.10
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVL 73
G+ DII+ N ++ + + + + + VLR G+ LV+
Sbjct: 403 GIRPGDIIIS---ANKKPVTDVKSLQTIAQEKKKE-LLVQVLRGPGSMYLLVI 451
Score = 25.0 bits (55), Expect = 4.5
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
GL DII + + ++ S +R G + + I V R+
Sbjct: 299 GLKAGDIITQINDTKITQATQVKTTISLLRVG--STVKIIVERD 340
>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 = 29.6 bits (66), Expect = 0.15
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 19/53 (35%)
Query: 28 ILEFGPINSSNFKSLQD-----------IASTVRAGVNTDIPITVLRNEGTRQ 69
IL+FGP +S L +A T+ + D G +Q
Sbjct: 501 ILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDY--------GFKQ 545
Score = 28.1 bits (62), Expect = 0.40
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 14/78 (17%)
Query: 22 LVKDDI---ILEFGPINSSNFKSLQDIAST-VRAGVNTDIPIT------VLRNEGTRQ-R 70
L +DI + N + +++ + A + P + R G +
Sbjct: 96 LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQ 155
Query: 71 LVLRPQPFEGQGLVGCYF 88
LV F GQG YF
Sbjct: 156 LVAI---FGGQGNTDDYF 170
>3hut_A Putative branched-chain amino acid ABC transporter; extracellular
ligand-binding receptor,transport protein; 1.93A
{Rhodospirillum rubrum atcc 11170}
Length = 358
Score = 29.2 bits (66), Expect = 0.17
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 6 VDSEGYPRQDVDVYQGLVKDD-IILEFGPINSSNFKSLQDIASTVRAGV 53
DS Q + + V D ++ G +S+ + I + G+
Sbjct: 51 ADSRDDADQARTIARAFVDDPRVVGVLGDFSSTVSMAAGSIYG--KEGM 97
>4a8c_A Periplasmic PH-dependent serine endoprotease DEGQ; chaperone,
hydrolase; 7.50A {Escherichia coli} PDB: 4a8a_A 4a8b_A
4a9g_A
Length = 436
Score = 29.2 bits (66), Expect = 0.18
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLR 74
GL KDD+I+ +N S+ ++ + A I + ++R + L++R
Sbjct: 380 GLQKDDVIIG---VNRDRVNSIAEMRKVLAAKPAI-IALQIVRGNESI-YLLMR 428
Score = 25.3 bits (56), Expect = 3.7
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
G+ DII ++F L+ +T G T + + +LRN
Sbjct: 280 GVKAGDIITSLNGKPLNSFAELRSRIATTEPG--TKVKLGLLRN 321
>2hga_A Conserved protein MTH1368; GFT structural genomics, PSI, protein
structure initiative; NMR
{Methanothermobacterthermautotrophicus} SCOP: b.36.1.6
Length = 125
Score = 28.7 bits (64), Expect = 0.18
Identities = 11/67 (16%), Positives = 21/67 (31%), Gaps = 4/67 (5%)
Query: 19 YQGLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLRPQPF 78
+ L +I + +SN + T+ G I IT + + P
Sbjct: 39 SKVLTPGLVIESINGMPTSNLTTYSAALKTISVG--EVINITTDQG-TFHLKTGRNPNN- 94
Query: 79 EGQGLVG 85
+ +G
Sbjct: 95 SSRAYMG 101
>1ky9_A Protease DO, DEGP, HTRA; protein quality control, serine protease,
trypsin, chaperone, PDZ, ATP-independent,
temperature-regulated, periplasm; 2.80A {Escherichia
coli} SCOP: b.36.1.4 b.47.1.1 PDB: 3ou0_A 4a8d_A 3otp_A
3mh7_A 3mh4_A 3mh5_A* 3mh6_A* 3cs0_A 2zle_A
Length = 448
Score = 28.8 bits (65), Expect = 0.25
Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLR 74
GL K D+I+ N K++ ++ + + + + + + R + T L+++
Sbjct: 400 GLKKGDVIIG---ANQQAVKNIAELRKVLDSKPSV-LALNIQRGDSTI-YLLMQ 448
Score = 25.0 bits (55), Expect = 5.4
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
G+ D+I S+F +L+ T+ G + + + +LR+
Sbjct: 303 GIKAGDVITSLNGKPISSFAALRAQVGTMPVG--SKLTLGLLRD 344
>3td9_A Branched chain amino acid ABC transporter, peripl amino
acid-binding protein; leucine binding, structural
genomics; HET: MSE PHE; 1.90A {Thermotoga maritima}
Length = 366
Score = 28.4 bits (64), Expect = 0.29
Identities = 6/49 (12%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 6 VDSEGYPRQDVDVYQGLVKDD-IILEFGPINSSNFKSLQDIASTVRAGV 53
+D+ + + + + ++ G + S++ ++ IA V
Sbjct: 60 LDTRSEKTEAANAAARAIDKEKVLAIIGEVASAHSLAIAPIAE--ENKV 106
>1te0_A Protease DEGS; two domains, serine protease, PDZ, alpha-beta
protein, hydro; 2.20A {Escherichia coli} SCOP: b.36.1.4
b.47.1.1 PDB: 3gdv_A* 3gcn_A* 3gds_A* 3gdu_A* 3gco_A*
1sot_A 1soz_A 1vcw_A 2r3y_A
Length = 318
Score = 28.3 bits (64), Expect = 0.29
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
G+ +D+I+ + + D + +R G + IP+ V+R+
Sbjct: 261 GIQVNDLIISVDNKPAISALETMDQVAEIRPG--SVIPVVVMRD 302
>3num_A Serine protease HTRA1; DEGP, hydrolase; 2.75A {Homo sapiens} PDB:
3nzi_A 3nwu_A 2ytw_A 2joa_A
Length = 332
Score = 27.2 bits (61), Expect = 0.73
Identities = 9/63 (14%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 21 GLVKDDIILEFG--PINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLRPQPF 78
GL ++D+I+ + S+ D++ ++ + + + V R + + P+
Sbjct: 271 GLKENDVIISINGQSVVSA-----NDVSDVIKRE--STLNMVVRRG-NEDIMITVIPEEI 322
Query: 79 EGQ 81
+
Sbjct: 323 DPL 325
>2l97_A HTRA, putative serine protease; HTRA-PDZ, protein binding; NMR
{Streptococcus pneumoniae}
Length = 134
Score = 26.4 bits (59), Expect = 1.3
Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
L K D+I + ++ LQ G I IT RN
Sbjct: 73 HLEKYDVITKVDDKEIASSTDLQSALYNHSIG--DTIKITYYRN 114
>3stj_A Protease DEGQ; serine protease, PDZ domain, protease, chaperone,
DEGP, DEGQ hydrolase; 2.60A {Escherichia coli}
Length = 345
Score = 26.1 bits (58), Expect = 2.1
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRN 64
G+ DII ++F L+ +T G T + + +LRN
Sbjct: 280 GVKAGDIITSLNGKPLNSFAELRSRIATTEPG--TKVKLGLLRN 321
>3k3w_B Penicillin G acylase; hydrolase; 3.31A {Alcaligenes faecalis} PDB:
3ml0_B
Length = 551
Score = 24.6 bits (53), Expect = 7.6
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 61 VLRNEGTRQRLVLRPQP 77
+ RN + L+++PQP
Sbjct: 535 IRRNAQSSTMLLIQPQP 551
>2bh9_A G6PD, glucose-6-phosphate 1-dehydrogenase; oxidoreductase,
oxidoreductase (CHOH(D)-NADP), carbohydrate metabolism,
glucose metabolism; HET: NAP; 2.5A {Homo sapiens} PDB:
2bhl_A* 1qki_A*
Length = 489
Score = 24.4 bits (54), Expect = 8.5
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 56 DIPITVLRNEGTRQRLVLRPQPFEG 80
D+ + + R LV+R QP E
Sbjct: 349 DVAGDIFHQQCKRNELVIRVQPNEA 373
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
0.318 0.140 0.403
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,398,702
Number of extensions: 70819
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 28
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
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 (23.4 bits)