RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1365
(140 letters)
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 209 bits (534), Expect = 3e-71
Identities = 74/140 (52%), Positives = 98/140 (70%), Gaps = 3/140 (2%)
Query: 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR 60
++TNIDGKR ALT I+G GRRF+ I+ K ID N RAG +E++ +KI ++ +P
Sbjct: 18 LNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIADPE 77
Query: 61 QYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVR 120
+ IP W LNR D DGK Q+ + LD+K+REDLERLKKI++HRG+RH+WGL+VR
Sbjct: 78 AHGIPTWLLNRINDFKDGKNYQMA---SNTLDTKMREDLERLKKIKSHRGLRHFWGLKVR 134
Query: 121 GQHTKTTGRRGRTVGVSKKK 140
GQHTKT+GR G GV +K
Sbjct: 135 GQHTKTSGRHGVVCGVVRKN 154
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 152
Score = 209 bits (533), Expect = 5e-71
Identities = 98/140 (70%), Positives = 125/140 (89%), Gaps = 3/140 (2%)
Query: 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR 60
++TN+DGK+K+MFALT+IKG GRRFSNIV KKADID+NKRAGE S EE+D+++ ++ NPR
Sbjct: 16 LNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVHNPR 75
Query: 61 QYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVR 120
Q+K+PDWFLNR+KD DG++SQ++ + +D KLR+DLERLKKIR HRG+RHYWG+RVR
Sbjct: 76 QFKVPDWFLNRKKDYKDGRFSQVV---SNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVR 132
Query: 121 GQHTKTTGRRGRTVGVSKKK 140
GQHTKTTGRRG+TVGVSKK+
Sbjct: 133 GQHTKTTGRRGKTVGVSKKR 152
>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A;
translation, ribosome, ribosomal, ribosomal R ribosomal
protein, eukaryotic ribosome, RNA-protein C; 3.00A
{Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L
3u5g_S 1s1h_M 3jyv_M* 2zkq_m
Length = 146
Score = 190 bits (486), Expect = 6e-64
Identities = 86/129 (66%), Positives = 105/129 (81%), Gaps = 3/129 (2%)
Query: 3 TNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQY 62
TN+DG K+++ALT IKG GRR+SN+V KKAD+DL+KRAGE ++EE+++I+ IM NP Y
Sbjct: 20 TNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHY 79
Query: 63 KIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQ 122
KIP WFLNRQ DI DGK L ++SKLR+DLERLKKIRAHRG+RH+WGLRVRGQ
Sbjct: 80 KIPAWFLNRQNDITDGKDYHTL---ANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRGQ 136
Query: 123 HTKTTGRRG 131
HTKTTGRR
Sbjct: 137 HTKTTGRRR 145
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
1xmq_M* ...
Length = 126
Score = 66.4 bits (163), Expect = 3e-15
Identities = 37/139 (26%), Positives = 63/139 (45%), Gaps = 27/139 (19%)
Query: 4 NIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYK 63
I ++V ALT I G G+ + L+K I+ R + +E EV ++
Sbjct: 8 EIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRL----------- 56
Query: 64 IPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQH 123
++ V+ + +L +++ +++RL I +RG+RH GL VRGQ
Sbjct: 57 ---------REYVENTW-----KLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQR 102
Query: 124 TKTTGR--RGRTVGVSKKK 140
T+T R +G V+ KK
Sbjct: 103 TRTNARTRKGPRKTVAGKK 121
>3r8n_M 30S ribosomal protein S13; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_M 3oaq_M 3ofa_M 3ofx_M
3ofo_M 3r8o_M 4a2i_M 3i1m_M 1vs7_M* 3e1a_F 3e1c_F 1vs5_M
3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 3iyx_M 3iyy_M 3izv_Q*
...
Length = 114
Score = 62.1 bits (152), Expect = 8e-14
Identities = 35/126 (27%), Positives = 55/126 (43%), Gaps = 26/126 (20%)
Query: 4 NIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYK 63
NI + + ALT+I G G+ S +L A I + + E SE ++D + + +
Sbjct: 7 NIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK---FV 63
Query: 64 IPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQH 123
V+G L ++ ++RL + +RG+RH GL VRGQ
Sbjct: 64 ------------VEG-----------DLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQR 100
Query: 124 TKTTGR 129
TKT R
Sbjct: 101 TKTNAR 106
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 55.0 bits (133), Expect = 8e-11
Identities = 37/126 (29%), Positives = 50/126 (39%), Gaps = 37/126 (29%)
Query: 4 NIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYK 63
I ++V ++L I G GR S +L + D NK + SEEEV +
Sbjct: 53 EIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFD-NKVTKDLSEEEVIIL----------- 100
Query: 64 IPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQH 123
+ R +ERLK+IR +RG+RH GL VRGQ
Sbjct: 101 -------------------------RKEKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQR 135
Query: 124 TKTTGR 129
TK R
Sbjct: 136 TKNNCR 141
>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 = 32.7 bits (74), Expect = 0.029
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 15/62 (24%)
Query: 42 GECSEEEVDKIITIMTNPRQYKIPDWFLNR-QKDIVDGKYSQ--ILLTSTAQLDSKLRED 98
G+ E++ K I + ++ L+ Q ++Q + L A ED
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ-------FTQPALTLMEKAAF-----ED 1746
Query: 99 LE 100
L+
Sbjct: 1747 LK 1748
>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 = 30.6 bits (68), Expect = 0.15
Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 45 SEEEVDKIITIMTNP--RQYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLRED 98
S+EE+D II + + ++ L++Q+++V ++L + L S ++ +
Sbjct: 47 SKEEIDHII-MSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE 101
Score = 29.4 bits (65), Expect = 0.46
Identities = 17/118 (14%), Positives = 38/118 (32%), Gaps = 39/118 (33%)
Query: 29 VLKKADID--LNKRAGECSEEEVDKIITIM--TNPRQYKI-------PDW-FL------- 69
+L K +ID + + + ++ + + ++ FL
Sbjct: 45 ILSKEEIDHIIMSKD---AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE 101
Query: 70 NRQKDIVDGKYSQIL--LTSTAQLDSK-----------LREDLERLKK---IRAHRGM 111
RQ ++ Y + L + Q+ +K LR+ L L+ + G+
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID-GV 158
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.9 bits (64), Expect = 0.43
Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 22/57 (38%)
Query: 21 CGRRFSNIVLKKADIDLNKRAGE--CSE-EEV--DKIITIMTNPRQYKIPDW--FLN 70
C IV G+ C+ V DK++ + R +W F N
Sbjct: 27 CKVYPPKIV-------ERFSEGDVVCALCGLVLSDKLV----DTR----SEWRTFSN 68
>3bg2_A DGTP triphosphohydrolase; structural genomics, NYSGXRC, target
10395N, triphosphohydro PSI-2, protein structure
initiative; 1.95A {Leeuwenhoekiella blandensis}
Length = 444
Score = 28.5 bits (64), Expect = 0.78
Identities = 7/55 (12%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 68 FLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQ 122
F+ +++I+ G + Q L+ S + + + + R +
Sbjct: 322 FMKYEEEILAGTFDQSLID-----KSNYQAQITDIINLSIERIYNSREVIEKEIA 371
>2pgs_A Putative deoxyguanosinetriphosphate triphosphohyd;
deoxyguanosinetriphosphate triphsphohydrolase,
pseudomonas S PV. phaseolicola 1448A; 2.35A {Pseudomonas
syringae PV}
Length = 451
Score = 28.1 bits (63), Expect = 1.1
Identities = 5/47 (10%), Positives = 16/47 (34%), Gaps = 3/47 (6%)
Query: 68 FLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHY 114
F+ +Q ++ G L+ + + + K + + +
Sbjct: 314 FVEQQDALLAGTLPGDLV---EHMHGPAKRCVLNAKDMARKKIFQDK 357
>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 148
Score = 26.3 bits (57), Expect = 3.5
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 101 RLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 140
RL+K R RG G G+H K G RG G+ +
Sbjct: 4 RLRKTRKLRGHVS-HGHGRIGKHRKHPGGRGNAGGMHHHR 42
>3o58_Y 60S ribosomal protein L28; ribosomal RNA and proteins, ribosome;
4.00A {Saccharomyces cerevisiae} PDB: 3o5h_Y 3izc_O
3izs_O 3u5e_a 3u5i_a 1s1i_V 3jyw_V
Length = 149
Score = 25.8 bits (56), Expect = 3.8
Identities = 14/41 (34%), Positives = 15/41 (36%), Gaps = 4/41 (9%)
Query: 101 RLKKIRAHRGMR-HYWGLRVRGQHTKTTGRRGRTVGVSKKK 140
R K R HRG G G+H K G RG G
Sbjct: 4 RFTKTRKHRGHVSAGKGR--IGKHRKHPGGRGMA-GGEHHH 41
>3eag_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME diaminopimelate
ligase; UDP-N-acetylmuramate:L-alanyl-G
glutamyl-MESO-diaminopimelate ligase; 2.55A {Neisseria
meningitidis MC58}
Length = 326
Score = 26.5 bits (59), Expect = 3.8
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 111 MRHYWGLRVRGQHTKTT 127
+ H+W L V G H KTT
Sbjct: 105 LHHHWVLGVAGTHGKTT 121
>2hnh_A DNA polymerase III alpha subunit; DNA replication,
nucleotidyltransferase, beta, PHP, transferase; HET:
DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Length = 910
Score = 26.3 bits (59), Expect = 4.5
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 17/57 (29%)
Query: 5 IDGKRKVMFALTAIKGCGR--------------RFSNIV--LKKADI-DLNKRAGEC 44
++ ++++ + AIKG G F + + D LN+R E
Sbjct: 825 VNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEK 881
>1ta9_A Glycerol dehydrogenase; oxidoredu; 1.90A {Schizosaccharomyces
pombe}
Length = 450
Score = 25.9 bits (57), Expect = 4.7
Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 16 TAIKGCGRRFSNIVLKKADIDLNKR--AGECSEEEVDKIITIMTN 58
C + + L + + + K GE S E+DK+ +
Sbjct: 101 NVWNICANKIVDS-LSQNGMTVTKLVFGGEASLVELDKLRKQCPD 144
>3din_C Preprotein translocase subunit SECY; protein translocation,
membrane protein, ATPase, ATP-binding membrane,
nucleotide-binding, protein transport; HET: ADP; 4.50A
{Thermotoga maritima MSB8}
Length = 431
Score = 26.0 bits (58), Expect = 4.8
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 99 LERLKKIRAHRGMRHYWGLRVRGQHTKTTGRR 130
L+ ++++ H MRHY G +G K GRR
Sbjct: 403 LDIIQQMETHMVMRHYEGFIKKG---KIRGRR 431
>3hn7_A UDP-N-acetylmuramate-L-alanine ligase; ATP-binding,
nucleotide-binding, structural genomics, joint for
structural genomics, JCSG; HET: MSE; 1.65A
{Psychrobacter arcticus 273-4}
Length = 524
Score = 26.1 bits (58), Expect = 5.5
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 111 MRHYWGLRVRGQHTKTT 127
++ + V G H KTT
Sbjct: 119 LQSRHVIAVAGTHGKTT 135
>1jq5_A Glycerol dehydrogenase; oxidoreductase, NAD, glycerol metabolism;
HET: NAD; 1.70A {Geobacillus stearothermophilus} SCOP:
e.22.1.2 PDB: 1jpu_A* 1jqa_A*
Length = 370
Score = 25.4 bits (56), Expect = 7.5
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 16 TAIKGCGRRFSNIVLKKADIDLNKR--AGECSEEEVDKIITIM 56
K G N LKK +I + +GE S EV++I I
Sbjct: 41 IVWKIAGHTIVNE-LKKGNIAAEEVVFSGEASRNEVERIANIA 82
>4adm_A Fumarase C, fumarate hydratase class II; lyase, tricarboxylic acid
cycle; HET: SRT; 1.65A {Mycobacterium tuberculosis} PDB:
4adl_A* 3no9_A 4apa_A 4apb_A 3qbp_A 3rd8_A 3rrp_A
Length = 495
Score = 25.3 bits (56), Expect = 8.6
Identities = 7/37 (18%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 27 NIVLKKADIDLNKRAGECSEEEVDKII--TIMTNPRQ 61
+++ ID S E++D+ + M Q
Sbjct: 454 RKTIRQTVIDRGLIGDRLSIEDLDRRLDVLAMAKAEQ 490
>3j01_A Preprotein translocase SECY subunit; ribonucleoprotein,
nucleotide-binding, PR biosynthesis, translation,
zinc-finger, 70S ribosome, ribos translocon; 7.10A
{Escherichia coli 536} PDB: 2akh_Y 2aki_Y
Length = 435
Score = 25.2 bits (56), Expect = 8.8
Identities = 2/27 (7%), Positives = 10/27 (37%), Gaps = 4/27 (14%)
Query: 99 LERLKKIRAHRGMRHYWGL----RVRG 121
++ + +++ Y ++G
Sbjct: 407 MDFMAQVQTLMMSSQYESALKKANLKG 433
>3uhj_A Probable glycerol dehydrogenase; structural genomics, PSI-biology,
NEW YORK structural genomi research consortium, nysgrc;
2.34A {Sinorhizobium meliloti}
Length = 387
Score = 25.1 bits (55), Expect = 8.9
Identities = 7/40 (17%), Positives = 13/40 (32%)
Query: 16 TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITI 55
R DI + GEC E++++ +
Sbjct: 62 VLFDALSERIGKSCGDSLDIRFERFGGECCTSEIERVRKV 101
>1kq3_A Glycerol dehydrogenase; structural genomics, joint center FO
structural genomics, JCSG, protein structure
initiative, PS oxidoreductase; 1.50A {Thermotoga
maritima} SCOP: e.22.1.2
Length = 376
Score = 25.4 bits (56), Expect = 8.9
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 30 LKKADIDLNKRAGECSEEEVDKI 52
K ++ GECS+EE++++
Sbjct: 65 FTKVRVNKQIFGGECSDEEIERL 87
>2h1v_A Ferrochelatase; rossman fold, PI-helix, lyase; 1.20A {Bacillus
subtilis} PDB: 2hk6_A 1c1h_A* 1ld3_A 1n0i_A 1ak1_A
3goq_A 1doz_A 2q2n_A* 3m4z_A 2h1w_A 2ac2_A 2q3j_A*
2ac4_A 2q2o_A* 1c9e_A* 2c8j_A
Length = 310
Score = 25.2 bits (56), Expect = 9.9
Identities = 13/61 (21%), Positives = 19/61 (31%), Gaps = 12/61 (19%)
Query: 63 KIPDWFLNRQKDIVDGKYSQI-----LLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGL 117
K L + +Y I L T Q L + L +I+ + Y GL
Sbjct: 34 KPEPEMLQD----LKDRYEAIGGISPLAQITEQQAHNLEQ---HLNEIQDEITFKAYIGL 86
Query: 118 R 118
Sbjct: 87 A 87
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
0.320 0.136 0.396
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,203,986
Number of extensions: 126658
Number of successful extensions: 441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 34
Length of query: 140
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 56
Effective length of database: 4,356,429
Effective search space: 243960024
Effective search space used: 243960024
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: 52 (23.7 bits)