RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12
[Candidatus Liberibacter asiaticus str. psy62]
(124 letters)
>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1
PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L*
1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O*
1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ...
Length = 135
Score = 166 bits (421), Expect = 1e-42
Identities = 84/124 (67%), Positives = 103/124 (83%), Gaps = 1/124 (0%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
+PT+NQL+RK R+ R +KV AL+G P +RGVC V TVTPKKPNSALRKV K RLTS
Sbjct: 4 LPTINQLVRKGRE-KVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTS 62
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG
Sbjct: 63 GYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT 122
Query: 121 ERPK 124
++PK
Sbjct: 123 KKPK 126
>2zkq_l 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1h_L
Length = 143
Score = 95.7 bits (238), Expect = 2e-21
Identities = 32/119 (26%), Positives = 61/119 (51%), Gaps = 11/119 (9%)
Query: 9 RKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS-GVEVIAY 67
++ +K K G +G+ L V K+PNSA+RK ++ +L G ++ A+
Sbjct: 25 KQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAF 84
Query: 68 VPGEG--HNLQEHSVVMLC-----GGRVKDLPGVKYRVIRGV---LDAQGVKNRKQARS 116
VP +G + ++E+ V++ G V D+PGV+++V++ L A +++ RS
Sbjct: 85 VPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPRS 143
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 38.0 bits (88), Expect = 6e-04
Identities = 30/180 (16%), Positives = 44/180 (24%), Gaps = 97/180 (53%)
Query: 7 LIRKPRKGSFRACAKVTALRGNPQK-RGVCLRVYTVT----------P---KKPN----- 47
L+ + + V + G PQ G+ L + P +K
Sbjct: 370 LVNGAK--NL-----VVS--GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
Query: 48 ---SA------LRKV---IKARL-TSGVEVIAYVPGE-----------GHNLQEHS---- 79
++ L I L + V + G +L+ S
Sbjct: 421 LPVASPFHSHLLVPASDLINKDLVKNNVSF----NAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 80 ---VVMLC----------------------GG---------RVKDLPGVKYRVI-RGVLD 104
V + GG R KD GV RVI G LD
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV--RVIVAGTLD 534
>1yi9_A PAM, peptidyl-glycine alpha-amidating monooxygenase; bioactive
peptide activation, copper, ascorbate, oxidoreductase;
1.70A {Rattus norvegicus} SCOP: b.121.1.2 b.121.1.2
PDB: 1sdw_A* 1yip_A 1phm_A 1opm_A 3phm_A 1yjl_A 1yjk_A
Length = 309
Score = 27.0 bits (59), Expect = 1.1
Identities = 10/58 (17%), Positives = 22/58 (37%)
Query: 36 LRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPG 93
+R+ VTPK+ ++ ++ + VI + P + H ++ C
Sbjct: 20 IRMPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSY 77
>2pgd_A 6-phosphogluconate dehydrogenase; oxidoreductase
(CHOH(D)-NADP+(A)); 2.00A {Ovis aries} SCOP: a.100.1.1
c.2.1.6 PDB: 1pgo_A* 1pgp_A* 1pgq_A* 1pgn_A 2jkv_A*
Length = 482
Score = 26.2 bits (57), Expect = 2.2
Identities = 13/79 (16%), Positives = 24/79 (30%), Gaps = 7/79 (8%)
Query: 27 GNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGG 86
N G + + T K + L K G + + L++ ++L
Sbjct: 19 LNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVS---KLKKPRRIILL-- 73
Query: 87 RVKDLPGVKYRVIRGVLDA 105
VK V I ++
Sbjct: 74 -VKAGQAVD-NFIEKLVPL 90
>2p4q_A 6-phosphogluconate dehydrogenase, decarboxylating 1; rossmann fold,
oxidoreductase; HET: FLC; 2.37A {Saccharomyces
cerevisiae}
Length = 497
Score = 26.2 bits (57), Expect = 2.2
Identities = 17/79 (21%), Positives = 24/79 (30%), Gaps = 7/79 (8%)
Query: 27 GNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGG 86
N G + Y T K + L K + G I L+ VML
Sbjct: 27 LNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIGATSIEDFIS---KLKRPRKVMLL-- 81
Query: 87 RVKDLPGVKYRVIRGVLDA 105
VK V +I ++
Sbjct: 82 -VKAGAPVD-ALINQIVPL 98
>1pgj_A 6PGDH, 6-PGDH, 6-phosphogluconate dehydrogenase; oxidoreductase,
CHOH(D)-NADP+(B); 2.82A {Trypanosoma brucei} SCOP:
a.100.1.1 c.2.1.6
Length = 478
Score = 25.5 bits (55), Expect = 3.0
Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 4/82 (4%)
Query: 24 ALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVML 83
L N ++G + V+ T K ++ A ++ + +L++ ++
Sbjct: 15 NLALNIAEKGFKVAVFNRTYSKSEEFMKANASAPFAGNLKAFETMEAFAASLKKPRKALI 74
Query: 84 CGGRVKDLPGVKYRVIRGVLDA 105
V+ I +
Sbjct: 75 L---VQAGAATD-STIEQLKKV 92
>3lme_A Possible translation initiation inhibitor; structural genomics,
RPA2473, PSI-2, protein structure initiative; 2.74A
{Rhodopseudomonas palustris}
Length = 138
Score = 25.2 bits (55), Expect = 3.9
Identities = 4/11 (36%), Positives = 6/11 (54%)
Query: 62 VEVIAYVPGEG 72
++ Y P EG
Sbjct: 122 IDGTFYAPAEG 132
>3opy_A 6-phosphofructo-1-kinase alpha-subunit; ATP binding,
fructose-6-phosphate bindi magnesium binding, citrate
binding, ADP binding; HET: ATP; 3.05A {Pichia pastoris}
Length = 989
Score = 24.2 bits (52), Expect = 7.9
Identities = 8/24 (33%), Positives = 8/24 (33%)
Query: 47 NSALRKVIKARLTSGVEVIAYVPG 70
N A R L G V A G
Sbjct: 614 NPATRVATLNSLAKGHRVFAIRNG 637
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.320 0.136 0.400
Gapped
Lambda K H
0.267 0.0575 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,029,288
Number of extensions: 43974
Number of successful extensions: 117
Number of sequences better than 10.0: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 14
Length of query: 124
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 43
Effective length of database: 3,729,466
Effective search space: 160367038
Effective search space used: 160367038
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 (21.8 bits)
S2: 51 (23.8 bits)