RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 042342
(87 letters)
>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 = 80.5 bits (198), Expect = 3e-21
Identities = 53/77 (68%), Positives = 61/77 (79%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
PF G SHAKG+V EKIGIE+KQPN A+RKC RV L KN KKI FVP DGCLN++ END+
Sbjct: 41 PFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDE 100
Query: 61 VLIAGFGRKGHAVATSP 77
VL+AG GR+GHAV P
Sbjct: 101 VLVAGLGRQGHAVGDIP 117
>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 = 73.2 bits (179), Expect = 2e-18
Identities = 57/77 (74%), Positives = 66/77 (85%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
PF G SHAKGIVLEK+GIE+KQPN AIRKC RVQLIKNGKK+ FVP+DGCLN+++END+
Sbjct: 42 PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE 101
Query: 61 VLIAGFGRKGHAVATSP 77
VL+AGFGRKG A P
Sbjct: 102 VLLAGFGRKGKAKGDIP 118
>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 = 36.9 bits (85), Expect = 1e-04
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
G +G+ + K+PN A+RK ++V+L +G ++ ++P +G + ++E+
Sbjct: 26 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEG--HNLQEHSV 82
Query: 61 VLIAGFGRKGH 71
VLI G GR
Sbjct: 83 VLIRG-GRVKD 92
>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 = 36.2 bits (83), Expect = 4e-04
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 12/72 (16%)
Query: 14 EKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGF-GRKGHA 72
+ P +I ++ Q+ K + +P +V I+ G K +
Sbjct: 328 LENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP---------AGKQVEISLVNGAK-NL 377
Query: 73 VATSPPIISLKG 84
V + PP SL G
Sbjct: 378 VVSGPP-QSLYG 388
>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 = 32.4 bits (74), Expect = 0.009
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 56 EENDKVLIAGFGRKGHAVA 74
+V+IAGFGR G
Sbjct: 2 SHGMRVIIAGFGRFGQITG 20
>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 = 29.8 bits (68), Expect = 0.059
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 53 NYIEENDKVLIAGFGRKGHAVA 74
N ++ + L+ G+GR G +
Sbjct: 2 NAVDICNHALLVGYGRVGSLLG 23
>3c85_A Putative glutathione-regulated potassium-efflux S protein KEFB;
TRKA domain; HET: AMP; 1.90A {Vibrio parahaemolyticus
rimd 2210633}
Length = 183
Score = 27.8 bits (62), Expect = 0.38
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 56 EENDKVLIAGFGRKGHAVA 74
+ +VLI G GR G
Sbjct: 37 PGHAQVLILGMGRIGTGAY 55
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT;
1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A*
3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A*
3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A*
3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ...
Length = 903
Score = 27.6 bits (60), Expect = 0.51
Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 9/38 (23%)
Query: 5 PSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKI 42
P H +G N AI+ + G+K+
Sbjct: 802 PFHIRG---------ILTYNRAIKGNIDAPQVVEGEKV 830
>1yrl_A Ketol-acid reductoisomerase; branched-chain amino acid
biosynthesis, knotted protein, oxidoreductase; 2.60A
{Escherichia coli}
Length = 491
Score = 27.3 bits (61), Expect = 0.63
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 24 NFAIRKCSRVQLIKNGKKIVTFVPSDG-CLNYIEENDKVLIAGFGRKGHA 72
N+ R QL + GK +Y++ KV+I G G +G
Sbjct: 3 NYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQ-GKKVVIVGCGAQGLN 51
>3h4u_A Amidohydrolase; signature of Zn ligands, structural genomics,
NYSGXRC, target 9236E, PSI-2, protein structure
initiative; 2.20A {Unidentified} PDB: 3hpa_A
Length = 479
Score = 26.8 bits (60), Expect = 0.88
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 35 LIKNGKKIVTFVPSDGCLN----YIEENDKVLIAGFGRKGHAVATSPPIISLKGC 85
L+K+ +VT + L YIE+N I G T+ ++ L+G
Sbjct: 32 LVKHADVLVTMDDTRRELRDAGLYIEDN---RIVAVGPSAELPETADEVLDLRGH 83
>2x5h_A ORF 131; viral protein; 1.80A {Sulfolobus islandicus rudivirus 1}
PDB: 2x5g_A* 2x5t_A
Length = 97
Score = 25.1 bits (54), Expect = 2.1
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 12 VLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIV---TFVPSDGCLNY 54
+++++G +AK+ N + SR+ IK K+IV VP DG + Y
Sbjct: 8 IIDELGKQAKEQN---KIASRIMKIKGIKRIVVQLNAVPQDGKIRY 50
>1e8c_A UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate
ligase; peptidoglycan biosynthesis; HET: KCX UAG API;
2.00A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1
c.72.2.1
Length = 498
Score = 25.6 bits (57), Expect = 2.6
Identities = 10/16 (62%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 56 EENDKVLIAGFGRKGH 71
+END VL+AG KGH
Sbjct: 455 KENDVVLVAG---KGH 467
>3llv_A Exopolyphosphatase-related protein; NAD(P)-binding, rossmann,
PSI, M structural genomics; 1.70A {Archaeoglobus
fulgidus}
Length = 141
Score = 24.9 bits (55), Expect = 3.2
Identities = 2/17 (11%), Positives = 6/17 (35%)
Query: 58 NDKVLIAGFGRKGHAVA 74
+ ++ G G +
Sbjct: 6 RYEYIVIGSEAAGVGLV 22
>2hmt_A YUAA protein; RCK, KTN, KTR, KTRA, ktrab, membrane protein, ION
transporter, symporter, transport protein; HET: NAI;
2.20A {Bacillus subtilis} SCOP: c.2.1.9 PDB: 2hms_A*
2hmu_A* 2hmv_A* 2hmw_A* 1lsu_A*
Length = 144
Score = 25.0 bits (55), Expect = 3.3
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 57 ENDKVLIAGFGRKGHAVAT 75
+N + + G GR G ++
Sbjct: 5 KNKQFAVIGLGRFGGSIVK 23
>1id1_A Putative potassium channel protein; RCK domain, E.coli potassium
channel, BK channel, rossmann fold, membrane protein;
2.40A {Escherichia coli} SCOP: c.2.1.9
Length = 153
Score = 24.7 bits (54), Expect = 3.8
Identities = 2/16 (12%), Positives = 4/16 (25%)
Query: 59 DKVLIAGFGRKGHAVA 74
D ++ G
Sbjct: 4 DHFIVCGHSILAINTI 19
>2z9v_A Aspartate aminotransferase; pyridoxamine, pyruvate; HET: PXM;
1.70A {Mesorhizobium loti} PDB: 2z9u_A* 2z9w_A* 2z9x_A*
Length = 392
Score = 24.9 bits (55), Expect = 3.9
Identities = 6/36 (16%), Positives = 10/36 (27%), Gaps = 7/36 (19%)
Query: 43 VTFVPSDG-------CLNYIEENDKVLIAGFGRKGH 71
+ + + I +D VL G G
Sbjct: 61 PVILHGEPVLGLEAAAASLISPDDVVLNLASGVYGK 96
>3zrp_A Serine-pyruvate aminotransferase (AGXT); HET: PLP; 1.75A
{Sulfolobus solfataricus} PDB: 3zrq_A* 3zrr_A*
Length = 384
Score = 24.9 bits (55), Expect = 4.4
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 51 CLNYIEENDKVLIAGFGRKGH 71
+ ++ NDK+L+ G G
Sbjct: 70 VTSLLKPNDKILVVSNGVFGD 90
>3qfa_A Thioredoxin reductase 1, cytoplasmic; protein-protein complex,
rossmann fold, HO pyridine nucleotide disulfide
oxidoreductase, electron TRAN oxidoreductase; HET: FAD;
2.20A {Homo sapiens} PDB: 3qfb_A* 2j3n_A* 2zzc_A*
2zzb_A* 2zz0_A* 2cfy_A* 1h6v_A* 3ean_A* 3eao_A*
Length = 519
Score = 24.5 bits (54), Expect = 5.4
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 13 LEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRK 69
+E+ GI+ F K +++ G+ V ++ E + V++A GR
Sbjct: 260 MEEHGIKF-IRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLA-IGRD 314
>2d1c_A Isocitrate dehydrogenase; structural genomics, NPPSFA, national
project protein structural and functional analyses;
HET: NAP CIT; 1.80A {Thermus thermophilus}
Length = 496
Score = 24.6 bits (54), Expect = 5.7
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 23 PNFAIRKCSRVQLIKNGKKIVTFVPSDG 50
P ++ ++++G+K++T +P DG
Sbjct: 2 PLITTETGKKMHVLEDGRKLITVIPGDG 29
>3nnk_A Ureidoglycine-glyoxylate aminotransferase; PLP-dependent; HET: LLP;
2.58A {Klebsiella pneumoniae}
Length = 411
Score = 24.5 bits (54), Expect = 5.9
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 51 CLNYIEENDKVLIAGFGRKGH 71
++ I DKVL+ FGR GH
Sbjct: 81 LVSAIRPGDKVLVPVFGRFGH 101
>2ch1_A 3-hydroxykynurenine transaminase; PLP-enzyme, kynurenine pathway,
transferase; HET: LLP; 2.4A {Anopheles gambiae} SCOP:
c.67.1.3 PDB: 2ch2_A*
Length = 396
Score = 24.5 bits (54), Expect = 6.0
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 50 GCLNYIEENDKVLIAGFGRKGH 71
N +EE D+VLIA G
Sbjct: 85 MLSNLLEEGDRVLIAVNGIWAE 106
>3isl_A Purine catabolism protein PUCG; pyridoxalphosphate, PLP dependent
enzymes, purine metabolism transaminases,
aminotransferases; HET: PLP; 2.06A {Bacillus subtilis}
Length = 416
Score = 24.2 bits (53), Expect = 7.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 51 CLNYIEENDKVLIAGFGRKGH 71
+ IE D VLI +GR G+
Sbjct: 79 LASVIEPEDDVLIPIYGRFGY 99
>1o58_A O-acetylserine sulfhydrylase; TM0665, structural genomics, J
protein structure initiative, joint center for
structural G transferase; 1.80A {Thermotoga maritima}
SCOP: c.79.1.1 PDB: 3fca_A*
Length = 303
Score = 24.0 bits (53), Expect = 7.3
Identities = 3/13 (23%), Positives = 5/13 (38%)
Query: 38 NGKKIVTFVPSDG 50
++VT P
Sbjct: 284 PDARVVTVAPDHA 296
>3d4o_A Dipicolinate synthase subunit A; NP_243269.1, structural GEN joint
center for structural genomics, JCSG, protein structu
initiative, PSI-2; HET: MSE TAR; 2.10A {Bacillus
halodurans}
Length = 293
Score = 24.1 bits (52), Expect = 8.0
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 60 KVLIAGFGRKGHAVA 74
V + G GR G +VA
Sbjct: 157 NVAVLGLGRVGMSVA 171
>3kgw_A Alanine-glyoxylate aminotransferase; AAH25799.1, putative
aminotransferase, structural genomics, center for
structural genomics, JCSG; HET: PLP; 1.65A {Mus
musculus} PDB: 3kgx_A 3imz_A* 3r9a_A* 1h0c_A* 1j04_A*
Length = 393
Score = 23.7 bits (52), Expect = 8.8
Identities = 6/22 (27%), Positives = 7/22 (31%)
Query: 50 GCLNYIEENDKVLIAGFGRKGH 71
N +E D L G G
Sbjct: 90 ALFNLLEPGDSFLTGTNGIWGM 111
>3ls9_A Triazine hydrolase; atrazine chlorohydrolase TRZN; 1.40A
{Arthrobacter aurescens} PDB: 3lsc_A* 3lsb_A*
Length = 456
Score = 23.7 bits (52), Expect = 8.9
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 8/55 (14%)
Query: 35 LIKNGKKIVTFVPSDGCLN----YIEENDKVLIAGFGRKGHAVATSPPIISLKGC 85
LI+ +++TF + L I+ I G K + + I +G
Sbjct: 3 LIRGLTRVITFDDQERELEDADILIDGP---KIVAVG-KDLSDRSVSRTIDGRGM 53
>1vjo_A Alanine--glyoxylate aminotransferase; 17130350, ALR1004, STR
genomics, JCSG, PSI, protein structure initiative, joint
CE structural genomics; HET: PLP; 1.70A {Nostoc SP}
SCOP: c.67.1.3
Length = 393
Score = 23.8 bits (52), Expect = 9.2
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 50 GCLNYIEENDKVLIAGFGRKGH 71
N +E D VLI G G+
Sbjct: 101 TIANAVEPGDVVLIGVAGYFGN 122
>2huf_A Alanine glyoxylate aminotransferase; alpha and beta protein,
PLP-dependent transferase; HET: LLP; 1.75A {Aedes
aegypti} PDB: 2hui_A* 2huu_A*
Length = 393
Score = 23.8 bits (52), Expect = 9.3
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 53 NYIEENDKVLIAGFGRKGH 71
N +E+ D +LI G G
Sbjct: 89 NLLEDGDVILIGHTGHWGD 107
>1m3s_A Hypothetical protein YCKF; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.95A {Bacillus subtilis} SCOP:
c.80.1.3 PDB: 1viv_A
Length = 186
Score = 23.8 bits (52), Expect = 9.4
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 49 DGCLNYIEENDKVLIAGFGRKGHA 72
D ++I + ++ AG GR G
Sbjct: 28 DQLADHILSSHQIFTAGAGRSGLM 51
>2aef_A Calcium-gated potassium channel MTHK; rossmann fold,
helix-turn-helix, Ca2+ binding, flexible interface;
1.70A {Methanothermobacterthermautotrophicus} PDB:
2aej_A 2aem_A 3rbx_A 2ogu_A 2fy8_A 3kxd_A
Length = 234
Score = 23.9 bits (52), Expect = 9.5
Identities = 3/17 (17%), Positives = 6/17 (35%)
Query: 58 NDKVLIAGFGRKGHAVA 74
+ V+I G+
Sbjct: 9 SRHVVICGWSESTLECL 25
>1vim_A Hypothetical protein AF1796; structural genomics, unknown
function; 1.36A {Archaeoglobus fulgidus} SCOP: c.80.1.3
Length = 200
Score = 23.8 bits (52), Expect = 9.9
Identities = 5/24 (20%), Positives = 10/24 (41%)
Query: 49 DGCLNYIEENDKVLIAGFGRKGHA 72
+ I+ + + G GR G+
Sbjct: 38 GEMIKLIDSARSIFVIGAGRSGYI 61
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
0.321 0.140 0.421
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: 1,342,417
Number of extensions: 70955
Number of successful extensions: 353
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 39
Length of query: 87
Length of database: 6,701,793
Length adjustment: 55
Effective length of query: 32
Effective length of database: 5,166,138
Effective search space: 165316416
Effective search space used: 165316416
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 (23.3 bits)