RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17954
(143 letters)
>3u5c_G RP9, S10, YS4, 40S ribosomal protein S6-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3j16_C 3u5g_G
Length = 236
Score = 137 bits (347), Expect = 9e-42
Identities = 90/193 (46%), Positives = 109/193 (56%), Gaps = 61/193 (31%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MKLNISYP G QK EI DEH++RVF+DKR+G EV +++GDE+KGY+ +ISGGNDKQG
Sbjct: 1 MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG 60
Query: 61 FPMKQG-----------------------------------------------------E 67
FPMKQG E
Sbjct: 61 FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE 120
Query: 68 IPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLYKA 127
+ GLTDTT+P+RLGPKRA+ IRK F LSKEDDVR +VI+R +G+K KA
Sbjct: 121 LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRR-----EVTKGEKTY---TKA 172
Query: 128 PKIQRLITPVTLQ 140
PKIQRL+TP LQ
Sbjct: 173 PKIQRLVTPQRLQ 185
>2xzm_Y RPS6E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_Y
Length = 293
Score = 133 bits (334), Expect = 3e-39
Identities = 80/196 (40%), Positives = 100/196 (51%), Gaps = 63/196 (32%)
Query: 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQG 60
MK NISYP TG QK +EI D+ K +F DK+MG EV D++GDE+KGY+ +I+GGNDK G
Sbjct: 1 MKFNISYPLTGAQKCIEIDDDKKCNIFMDKKMGQEVEGDTLGDEFKGYVFKIAGGNDKDG 60
Query: 61 FPMKQG-----------------------------------------------------E 67
FPMKQG E
Sbjct: 61 FPMKQGVMVRGRVRLLLSEGHSCFTSRRSGFRKRKSVRGCIVGPDMRVLALQIVKKGVAE 120
Query: 68 IPGLTDTTIPRRLGPKRASKIRKLFNLSKEDD---VRQYVIKRTLPPKPAKEGKKKVRKL 124
I GLT T+PR+LGPKRA+ I+KLF L KEDD +++ VI+RT K+
Sbjct: 121 IDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKKSVIRRTFKTAKGKDR------- 173
Query: 125 YKAPKIQRLITPVTLQ 140
K PKIQRLITP +
Sbjct: 174 TKCPKIQRLITPERIL 189
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 31.4 bits (71), Expect = 0.091
Identities = 17/110 (15%), Positives = 32/110 (29%), Gaps = 30/110 (27%)
Query: 13 QKLVEIADEHKLRVFYDKRM---------GMEVPADSIGDEWKGYIVRISGGN----DKQ 59
+ + E+ E L F + G +V I + + + + G
Sbjct: 921 EMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIPETGEYSVKLLKGATLYIPKAL 980
Query: 60 GFPMK-QGEIP-GL--TDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVI 105
F G+IP G I S++ D + +V+
Sbjct: 981 RFDRLVAGQIPTGWNAKTYGISD----DIISQV---------DPITLFVL 1017
>2po3_A 4-dehydrase; external aldimine, PLP, aminotransferase, TDP-sugar;
HET: T4K; 2.10A {Streptomyces venezuelae}
Length = 424
Score = 30.6 bits (70), Expect = 0.16
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
+L ++ADEH LR+++D A ++G G
Sbjct: 156 QLRKVADEHGLRLYFDA-------AHALGCAVDG 182
>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170,
putative RNA methylase, PSI,MCSG, structu genomics;
1.50A {Listeria monocytogenes str}
Length = 393
Score = 30.3 bits (69), Expect = 0.19
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 73 DTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKE 116
G K+A+K RKL+N D+ QY R P+P KE
Sbjct: 352 YELFEEVYG-KKATKKRKLYNGYLRTDLYQYWGPR--KPRPKKE 392
>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 = 0.40
Identities = 22/123 (17%), Positives = 41/123 (33%), Gaps = 32/123 (26%)
Query: 32 MGMEV----P--------ADSIGDEWKGY-IVRISGGNDKQGFPMKQGEIPGLTDTTIPR 78
MGM++ AD+ + G+ I+ I N P + TI
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINN-----P---------VNLTI-- 1674
Query: 79 RLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAKEGKKKVRKLYKAPKIQRLITPVT 138
G ++ +IR+ ++ + + +K K E +++ K T T
Sbjct: 1675 HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSY--TFRSEKGLLSATQFT 1732
Query: 139 LQV 141
Q
Sbjct: 1733 -QP 1734
>3df8_A Possible HXLR family transcriptional factor; APC89000, structural
genomics, midwest center for structural genomics, MCSG;
1.65A {Thermoplasma volcanium}
Length = 111
Score = 28.4 bits (64), Expect = 0.43
Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 17/75 (22%)
Query: 39 DSIGDEWKGYIVR-ISGGNDKQGFPMKQGEIPGLTDTTIPRRLGPKRASKIRKLFNLSKE 97
+G ++ I+ + G+ +Q F + IPG++ T + RR+ + L
Sbjct: 22 HLLGKKYTMLIISVLGNGSTRQNFNDIRSSIPGISSTILSRRI--------KDL-----I 68
Query: 98 DDVRQYVIKRTLPPK 112
D +++R
Sbjct: 69 DS---GLVERRSGQI 80
>3bb8_A CDP-4-keto-6-deoxy-D-glucose-3-dehydrase; aspartate
aminotransferase fold, oxidoreductase; HET: PLP; 2.35A
{Yersinia pseudotuberculosis} PDB: 3bcx_A
Length = 437
Score = 28.0 bits (63), Expect = 0.98
Identities = 7/34 (20%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ +AD++ L + D D++G + G
Sbjct: 176 EVRRVADKYNLWLIEDC-------CDALGSTYDG 202
>3b8x_A WBDK, pyridoxamine 5-phosphate-dependent dehydrase; aspartate
aminotransferase, colitose, perosamine, O-antigen,
pyridoxal phosphate,; HET: G4M; 1.70A {Escherichia coli}
PDB: 2gms_A* 2gmu_A* 2r0t_A* 3gr9_A*
Length = 390
Score = 27.6 bits (62), Expect = 1.4
Identities = 4/34 (11%), Positives = 12/34 (35%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ +I + + D +S+G +
Sbjct: 146 EINKIIGGRDIILLEDN-------CESMGATFNN 172
>3ldu_A Putative methylase; structural genomics, PSI-2, protein structure
initiative, midwest center for structural genomics,
MCSG; HET: MSE GTP; 1.70A {Clostridium difficile}
Length = 385
Score = 27.3 bits (61), Expect = 1.8
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 73 DTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTLPPKPAK 115
G ++A K RKL+N + + QY + PP+ K
Sbjct: 346 YEDFEYEFG-QKADKKRKLYNGMLKTNFFQYPGPK--PPRNNK 385
>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif,
XRE-family, structural genomics, PSI-2, protein
structure initiative; 2.00A {Agrobacterium tumefaciens
str} SCOP: a.35.1.3
Length = 99
Score = 26.1 bits (57), Expect = 2.3
Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 57 DKQGFPMKQGEIPGLTDTTIPRRLGPKRASKIRKLFNLSKED----------DVRQYVIK 106
D + + + P L+ + R IR+ L++E+ +R +
Sbjct: 7 DSEANALADPDNPPLSAEQLASAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQG 66
Query: 107 RTLPPKPAKEGKKKVRKLYKAPKI 130
R+ P +PA + ++ + P+
Sbjct: 67 RSEPDQPA---RAYLKIIAVDPEG 87
>1mvh_A Cryptic LOCI regulator 4; lysine methyltransferase, CLR4,
SET-domain; 2.30A {Schizosaccharomyces pombe} SCOP:
b.85.7.1 PDB: 1mvx_A
Length = 299
Score = 25.9 bits (57), Expect = 5.2
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 66 GEIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVI 105
GE+ +T +R I LF+L DD +Y +
Sbjct: 168 GEV--ITSAEAAKRDKNYDDDGITYLFDLDMFDDASEYTV 205
>3p2h_A AHL synthase; acyl-ACP binding, SAM binding, signaling protein-I
MTA complex, signaling protein-inhibitor complex; HET:
MTA NOO; 2.00A {Burkholderia glumae} PDB: 3p2f_A*
Length = 201
Score = 25.7 bits (56), Expect = 5.3
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 17 EIADEHKLR--VFYDKRMGMEVPADSIGDEWKGY 48
A+ R VF + ++G ++P++ E Y
Sbjct: 15 IAAELGSYRYRVFVE-QLGWQLPSEDEKMERDQY 47
>1ycy_A Conserved hypothetical protein; structural genomics, southeast
collaboratory for structural genomics, secsg, protein
structure initiative; 2.80A {Pyrococcus furiosus} SCOP:
b.38.1.4
Length = 71
Score = 24.6 bits (53), Expect = 6.1
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 32 MGMEVPADSIGDEWKGYIVRISGGND 57
MGME + + EWKG+ V +S G D
Sbjct: 1 MGMESLLEKVLKEWKGHKVAVSVGGD 26
>2rk0_A Glyoxalase/bleomycin resistance protein/dioxygena; 11002Z,
glyoxylase, dioxygenas PSI-II; 2.04A {Frankia SP}
Length = 136
Score = 25.0 bits (55), Expect = 7.4
Identities = 5/29 (17%), Positives = 10/29 (34%)
Query: 27 FYDKRMGMEVPADSIGDEWKGYIVRISGG 55
+Y + + + GD + GG
Sbjct: 22 WYTEILDWKELVRGRGDTTSFAHGVLPGG 50
>2c81_A Glutamine-2-deoxy-scyllo-inosose aminotransferase; SMAT, butirosin,
aminoglycoside antibiotics; HET: PMP; 1.7A {Bacillus
circulans} PDB: 2c7t_A*
Length = 418
Score = 25.4 bits (56), Expect = 8.5
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ EIA EH L V D A S G W
Sbjct: 148 EINEIAQEHNLFVIEDC-------AQSHGSVWNN 174
>3dr4_A Putative perosamine synthetase; deoxysugar, pyridoxal phosphate,
aspartate aminotransferase, O-antigen; HET: G4M; 1.60A
{Caulobacter crescentus} PDB: 3dr7_A* 3bn1_A*
Length = 391
Score = 25.2 bits (56), Expect = 8.6
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++E+A H L V D A+++G ++G
Sbjct: 162 PILEVARRHNLLVIEDA-------AEAVGATYRG 188
>3nyt_A Aminotransferase WBPE; PLP binding, nucleotide-sugar binding; HET:
ULP; 1.30A {Pseudomonas aeruginosa} PDB: 3nys_A* 3nyu_A*
3nu8_A* 3nu7_A* 3nub_A*
Length = 367
Score = 25.2 bits (56), Expect = 8.8
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
+ IA ++ + V D A S G +KG
Sbjct: 141 AINAIASKYGIPVIEDA-------AQSFGASYKG 167
>3frk_A QDTB; aminotransferase, sugar-modification, natural porduct; HET:
TQP; 2.15A {Thermoanaerobacteriumthermosaccharolyticum}
Length = 373
Score = 25.2 bits (56), Expect = 9.4
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 14 KLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKG 47
++ IA ++ L++ D A + G +KG
Sbjct: 142 EIKRIAKKYNLKLIEDA-------AQAHGSLYKG 168
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
0.317 0.138 0.402
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,200,745
Number of extensions: 126690
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 307
Number of HSP's successfully gapped: 31
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (23.6 bits)