RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7476
(143 letters)
>3u5c_X RP37, S28, YS14, 40S ribosomal protein S23-A; translation,
ribosome, ribosomal, ribosomal R ribosomal protein,
eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_L 3o30_P 3o2z_P 3u5g_X 3jyv_L*
1s1h_L* 2zkq_l 3iz6_L
Length = 145
Score = 148 bits (374), Expect = 4e-47
Identities = 108/142 (76%), Positives = 128/142 (90%)
Query: 2 GKPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQ 61
GKPRG+ +ARK +RR RWA+ +YKK LGT +K++PFGG+SHAKGIVLEK+G+E+KQ
Sbjct: 4 GKPRGLNSARKLRVHRRNNRWAENNYKKRLLGTAFKSSPFGGSSHAKGIVLEKLGIESKQ 63
Query: 62 PNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFK 121
PNSAIRKCVRVQLIKNGKK+TAFVP DGCLN+++ENDEVL+AGFGRKG A GDIPGVRFK
Sbjct: 64 PNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFK 123
Query: 122 VVKVANVSLLALYKEKKERPRS 143
VVKV+ VSLLAL+KEKKE+PRS
Sbjct: 124 VVKVSGVSLLALWKEKKEKPRS 145
>2xzm_L 40S ribosomal protein S12; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_L 3j0o_L 3j0l_L
3j0p_L 3j0q_L 3iz6_L 3jyv_L* 1s1h_L*
Length = 142
Score = 144 bits (364), Expect = 1e-45
Identities = 99/140 (70%), Positives = 116/140 (82%), Gaps = 1/140 (0%)
Query: 1 MGKPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAK 60
+GKPRGIR RK +R+ QRWAD D+ K LG+RW+ NPF GASHAKG+V EK+G+E+K
Sbjct: 3 VGKPRGIRAGRKLARHRKDQRWADNDFNKRLLGSRWR-NPFMGASHAKGLVTEKIGIESK 61
Query: 61 QPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRF 120
QPNSA+RKCVRV L KN KKI AFVP DGCLN++ ENDEVLVAG GR+GHAVGDIPGVRF
Sbjct: 62 QPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGVRF 121
Query: 121 KVVKVANVSLLALYKEKKER 140
KVV V +SLLAL+K KKE+
Sbjct: 122 KVVCVKGISLLALFKGKKEK 141
>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 = 50.0 bits (119), Expect = 6e-09
Identities = 33/107 (30%), Positives = 59/107 (55%), Gaps = 11/107 (10%)
Query: 37 KANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEE 96
K GA +G+ V K+PNSA+RK +V+L +G ++TA++P +G + ++E
Sbjct: 23 KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEG--HNLQE 79
Query: 97 NDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPRS 143
+ VL+ +G V D+PGVR+ +V+ A + +++ RS
Sbjct: 80 HSVVLI-----RGGRVKDLPGVRYHIVRGV---YDAAGVKDRKKSRS 118
>1k4m_A NAMN adenylyltransferase; nucleotidyltransferase; HET: NAD CIT;
1.90A {Escherichia coli} SCOP: c.26.1.3 PDB: 1k4k_A*
Length = 213
Score = 30.7 bits (70), Expect = 0.13
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
+ IR + ++NG+ +P + L YI +
Sbjct: 182 TIIR-----ERLQNGESCEDLLP-EPVLTYINQQ 209
>1yum_A 'probable nicotinate-nucleotide adenylyltransferase; alpha/beta
domain; HET: CIT NCN; 1.70A {Pseudomonas aeruginosa}
PDB: 1yul_A* 1yun_A*
Length = 242
Score = 30.4 bits (69), Expect = 0.15
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
+ IR L+ G+ + VP D LNYIE +
Sbjct: 200 TQIR-----ALLGAGRSVRFLVP-DAVLNYIEAH 227
>2qtr_A Nicotinate (nicotinamide) nucleotide adenylyltran; NAD,
nucleotidyltransferase, pyridine nucleotide biosynthesi
transferase; HET: NXX; 1.70A {Bacillus anthracis} PDB:
3dv2_A 3mla_A* 3hfj_A* 3mlb_A* 3mmx_A* 3e27_A* 2qtn_A*
2qtm_A*
Length = 189
Score = 30.2 bits (69), Expect = 0.15
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
S +R + K K +P + YIE N
Sbjct: 157 SLLR-----ERYKEKKTCKYLLP-EKVQVYIERN 184
>1kam_A Deamido-NAD(+), nicotinate-nucleotide adenylyltransferase; rossman
fold; 2.10A {Bacillus subtilis} SCOP: c.26.1.3 PDB:
1kaq_A*
Length = 194
Score = 30.2 bits (69), Expect = 0.16
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
+ IR + K+ K +P D Y+EEN
Sbjct: 162 TMIR-----ERFKSKKPTDYLIP-DKVKKYVEEN 189
>2h29_A Probable nicotinate-nucleotide adenylyltransferase; NADD, namnat,
nmnat; HET: DND; 2.00A {Staphylococcus aureus} PDB:
2h2a_A*
Length = 189
Score = 30.2 bits (69), Expect = 0.18
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
+ IR Q + GK I VP NYI+
Sbjct: 157 TMIR-----QRVSEGKSIQVLVP-KSVENYIKGE 184
>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 = 30.0 bits (67), Expect = 0.25
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 72 VQLIKN-GKKITAFVPRD--GCLNY--IEENDEVLVAGFGRKG--HAVGDIPGVRFKVVK 124
V+++ G + VPRD G NY I N + A F ++ + V + +V+
Sbjct: 1783 VEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVE 1842
Query: 125 VAN 127
+ N
Sbjct: 1843 IVN 1845
>3h05_A Uncharacterized protein VPA0413; nucleotidylyl, transferase, MCSG,
midwest center for structu genomics, PSI; 1.65A {Vibrio
parahaemolyticus}
Length = 177
Score = 29.5 bits (67), Expect = 0.29
Identities = 5/34 (14%), Positives = 10/34 (29%), Gaps = 6/34 (17%)
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEEN 97
+ IR + GK I+ + +
Sbjct: 140 TDIR-----NALIEGKDISTYTT-PTVSELLLNE 167
>3l9w_A Glutathione-regulated potassium-efflux system Pro linker, ancillary
protein KEFF; potassium channel regulation, domains,
antiport; HET: FMN AMP GSH; 1.75A {Escherichia coli}
PDB: 3eyw_A* 3l9x_A*
Length = 413
Score = 29.4 bits (66), Expect = 0.35
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 95 EENDEVLVAGFGRKGHAVGDI 115
V++AGFGR G G +
Sbjct: 2 SHGMRVIIAGFGRFGQITGRL 22
>3fwz_A Inner membrane protein YBAL; TRKA-N domain, E.coli, structural
genomics, PSI-2, Pro structure initiative; HET: MSE AMP;
1.79A {Escherichia coli k-12}
Length = 140
Score = 27.1 bits (61), Expect = 1.4
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 92 NYIEENDEVLVAGFGRKGHAVGDI 115
N ++ + L+ G+GR G +G+
Sbjct: 2 NAVDICNHALLVGYGRVGSLLGEK 25
>1r9d_A Glycerol dehydratase; radical SAM, lyase; 1.80A {Clostridium
butyricum} SCOP: c.7.1.1 PDB: 1r8w_A 1r9e_A
Length = 787
Score = 27.2 bits (60), Expect = 2.4
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 57 VEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGD 114
V+ QP+ ++R + + A + R+G NDEV++ +G + D
Sbjct: 369 VKLPQPSLSVR--IWNKTPDEFLLRAAELTREGLGLPAYYNDEVIIPALVSRGLTLED 424
>1wty_A Hypothetical protein TTHA0048; structural genomics, riken
structural genomics/proteomics in RSGI, unknown
function; 2.20A {Thermus thermophilus} SCOP: a.24.16.2
PDB: 2ywa_A
Length = 119
Score = 26.1 bits (57), Expect = 3.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 51 VLEKVGVEAKQPNSAIRKCVRVQLIKNG 78
LE G+EA+ P +AIR +V L+
Sbjct: 45 FLELQGLEARSPRAAIRGAFQVGLLPED 72
>3c85_A Putative glutathione-regulated potassium-efflux S protein KEFB;
TRKA domain; HET: AMP; 1.90A {Vibrio parahaemolyticus
rimd 2210633}
Length = 183
Score = 26.3 bits (58), Expect = 3.3
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 95 EENDEVLVAGFGRKGHAVGD 114
+ +VL+ G GR G D
Sbjct: 37 PGHAQVLILGMGRIGTGAYD 56
>2lpd_A Uncharacterized protein; infectious disease, melioidosis, seattle
structural genomics for infectious disease, ssgcid,
drug target; NMR {Burkholderia pseudomallei}
Length = 95
Score = 24.8 bits (54), Expect = 6.3
Identities = 4/12 (33%), Positives = 6/12 (50%)
Query: 86 PRDGCLNYIEEN 97
+ CL IE+
Sbjct: 58 TKQQCLQRIEQL 69
>2pst_X Hypothetical protein PA2412; pyoverdine synthesis, non-ribosomal
peptide synthesis cluste like family, COG3251, unknown
function; 1.80A {Pseudomonas aeruginosa PAO1} SCOP:
d.100.2.1 PDB: 2gpf_A
Length = 74
Score = 24.3 bits (53), Expect = 6.4
Identities = 6/12 (50%), Positives = 7/12 (58%)
Query: 86 PRDGCLNYIEEN 97
+ CL YIEE
Sbjct: 45 LKKDCLAYIEEV 56
>2jx3_A Protein DEK; alpha helix, SAF/SAP motif, DNA binding, chromosomal
rearrangement, DNA-binding, nucleus, phosphorylation,
proto oncogene; NMR {Homo sapiens}
Length = 131
Score = 24.9 bits (54), Expect = 7.7
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 108 KGHAVGDIPGVRFKVVKVANVSLLALYK 135
KG + +I + F + K L L+K
Sbjct: 7 KGQKLCEIERIHFFLSKKKTDELRNLHK 34
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
0.319 0.137 0.409
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,255,069
Number of extensions: 128541
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 27
Length of query: 143
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 59
Effective length of database: 4,356,429
Effective search space: 257029311
Effective search space used: 257029311
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 (21.7 bits)
S2: 52 (23.7 bits)