RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5978
(159 letters)
>2xzm_7 Plectin/S10 domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_7
Length = 162
Score = 177 bits (449), Expect = 5e-58
Identities = 47/164 (28%), Positives = 74/164 (45%), Gaps = 9/164 (5%)
Query: 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFA 60
+ + K + IY+ L ++GV V KKDF H E VPNL ++SLK +G++ E F
Sbjct: 2 VHVLKATKIRIYKQLLQDGVFVLKKDFE-GHHEETGVPNLHCYILVRSLKDRGFLEEIFN 60
Query: 61 WRHYYWYITNDGIEKLRGVLNIPDE-IVPSTLKRQARTTDASKVP---RQMTQRPDGGRG 116
W Y+Y+ +G E L+ L I + ++P T K + + R Q GGR
Sbjct: 61 WGFTYYYLNKEGCEYLKTKLGISADNVIPKTFKASNVNFISKEEDEEERPRRQFNKGGRT 120
Query: 117 AD-DRMSYRKGPQGVDKKADVGAGSTEVEFKGYGGFGRGKAPPQ 159
+ D + R +G ++ + A E G + P Q
Sbjct: 121 GERDGRNKRGVGRGTRREGEEAAKE---EGAAETAQGNQETPAQ 161
>3u5c_K 40S ribosomal protein S10-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3u5g_K
Length = 105
Score = 170 bits (433), Expect = 3e-56
Identities = 54/99 (54%), Positives = 74/99 (74%)
Query: 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFA 60
MLMPK++R I++YLF+EGV+VAKKDF+ KH E+D NL VIK LQSL SKG+V QF+
Sbjct: 1 MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS 60
Query: 61 WRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTTD 99
W++YY+ +T +G+E LR LN+P+ IVP T ++ T
Sbjct: 61 WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPTQ 99
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription
initiation, preinitiation complex, RNA polymerase II,
transcription bubble; 2.90A {Sulfolobus solfataricus}
SCOP: a.4.5.41
Length = 110
Score = 28.0 bits (62), Expect = 0.76
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 34 ELDVPNLQVIKTLQSLKSKGWV------NEQFAWRHYYWYITNDGIEKL 76
+L++ V K L L+ +G+V ++ W YYW D I ++
Sbjct: 42 QLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYWKPNIDQINEI 90
>2yx1_A Hypothetical protein MJ0883; methyl transferase, tRNA modification
enzyme, transferase; HET: SFG; 2.20A {Methanocaldococcus
jannaschii} PDB: 2zzn_A* 3ay0_A* 2zzm_A*
Length = 336
Score = 27.5 bits (61), Expect = 1.8
Identities = 11/76 (14%), Positives = 31/76 (40%), Gaps = 7/76 (9%)
Query: 37 VPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQAR 96
+ +T + L +N+ + IT++G + ++ ++I+ S L +
Sbjct: 7 INKKHGEQTRRILIENNLLNKDYK-------ITSEGNYLYLPIKDVDEDILKSILNIEFE 59
Query: 97 TTDASKVPRQMTQRPD 112
D +++ ++P
Sbjct: 60 LVDKELEEKKIIKKPS 75
>3ly1_A Putative histidinol-phosphate aminotransferase; structural G joint
center for structural genomics, JCSG; HET: MSE PLP CIT;
1.80A {Erwinia carotovora atroseptica}
Length = 354
Score = 27.5 bits (62), Expect = 2.0
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 10/52 (19%)
Query: 11 IYEYLFKEGVLVAKKDFHAPKH-------PELDVPNLQVIKTLQSLKSKGWV 55
++ GVL+ + A P+ V T++ + K W+
Sbjct: 306 YQTHMADAGVLIGRAFPPADNWCRISLGTPQ---EMQWVADTMREFRKKSWI 354
>3qph_A TRMB, A global transcription regulator; transcriptional
regulator; HET: SUC; 2.99A {Pyrococcus furiosus}
Length = 342
Score = 27.0 bits (59), Expect = 2.6
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 11 IYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYW 66
Y L G AK+ + +P +V T+ SLK +G+V E Y
Sbjct: 23 TYWTLLVYGPSTAKE-----ISTKSGIPYNRVYDTISSLKLRGFVTEIEGTPKVYA 73
>1xpj_A Hypothetical protein; structural genomics, MCSG, protein STR
initiative, PSI, midwest center for structural
genomics, UN function; HET: TLA; 2.30A {Vibrio
cholerae} SCOP: c.108.1.18
Length = 126
Score = 26.0 bits (57), Expect = 4.5
Identities = 10/46 (21%), Positives = 15/46 (32%)
Query: 27 FHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDG 72
+P L VI+ L+ G+ R+ Y N G
Sbjct: 14 QANTSDYRNVLPRLDVIEQLREYHQLGFEIVISTARNMRTYEGNVG 59
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.7 bits (58), Expect = 4.6
Identities = 9/49 (18%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 8 RYIIY-EYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWV 55
YI + L+ + + AK ++ + L++ + L L+ V
Sbjct: 111 MYIEQRDRLYNDNQVFAK--YNVSRLQPY----LKLRQALLELRPAKNV 153
>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 = 26.6 bits (58), Expect = 5.3
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 9/53 (16%)
Query: 104 PRQMTQRPDGGRGADDR-----MSYRKGPQGVDKK----ADVGAGSTEVEFKG 147
P +T G +G R M + G K ++ ST F+
Sbjct: 1669 PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS 1721
>1foe_A T-lymphoma invasion and metastasis inducing protein 1; DBL homology
domain, pleckstrin homology domain, GTPase, guanine
nucleotide exchange factor; 2.80A {Mus musculus} SCOP:
a.87.1.1 b.55.1.1
Length = 377
Score = 26.1 bits (57), Expect = 6.9
Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 3/49 (6%)
Query: 5 KKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKG 53
+ ++FK V++ KD K + L + + + +
Sbjct: 259 EPELAA---FVFKTAVVLVYKDGSKQKKKLVGSHRLSIYEEWDPFRFRH 304
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 25.3 bits (54), Expect = 8.5
Identities = 7/11 (63%), Positives = 8/11 (72%), Gaps = 1/11 (9%)
Query: 41 QVIKTLQ-SLK 50
Q +K LQ SLK
Sbjct: 20 QALKKLQASLK 30
>3m5k_A Putative NADH dehydrogenase/NAD(P)H nitroreductas; structural
genomics, joint center for structural genomics; HET: MSE
FMN; 1.86A {Parabacteroides distasonis}
Length = 172
Score = 25.2 bits (56), Expect = 9.6
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 66 WYITNDGIEKLRGVLNIPDEIVP 88
Y D IE +R L +PD I+P
Sbjct: 121 VYPYPDRIEIVRKELRLPDHIMP 143
>3kwk_A Putative NADH dehydrogenase/NAD(P)H nitroreductas; structur
genomics, joint center for structural genomics, JCSG;
HET: MSE FMN; 1.54A {Bacteroides thetaiotaomicron
vpi-5482}
Length = 175
Score = 25.2 bits (56), Expect = 9.7
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 66 WYITNDGIEKLRGVLNIPDEIVP 88
Y D +E +R ++P+ I+P
Sbjct: 124 AYPYEDRMEVVRKYTHLPENILP 146
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 0.137 0.419
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,523,988
Number of extensions: 140399
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 21
Length of query: 159
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,300,587
Effective search space: 313942851
Effective search space used: 313942851
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: 53 (24.2 bits)