RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 041704
(86 letters)
>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB:
1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T*
1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T*
1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...
Length = 120
Score = 37.9 bits (88), Expect = 5e-05
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29
++ V D V+V+ G + G EG+ + +
Sbjct: 40 NVRVNAGDTVEVLRGDFAGEEGEVINVD 67
>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L
2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 1s1i_U 3izc_Y 3izs_Y
3jyw_U
Length = 127
Score = 37.7 bits (87), Expect = 7e-05
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 2 SMSVRKDDEVQVVGGTYKGREGKFVQI 28
++ +R+DDEV VV G+ KG+EGK +
Sbjct: 47 ALPIRRDDEVLVVRGSKKGQEGKISSV 73
>4a17_S RPL26, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_S 4a1c_S 4a1e_S
Length = 135
Score = 37.3 bits (86), Expect = 8e-05
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 2 SMSVRKDDEVQVVGGTYKGREGKFVQI 28
SM VRKDDEV +V G +KG +GK Q+
Sbjct: 46 SMPVRKDDEVLIVRGKFKGNKGKVTQV 72
>3iz5_Y 60S ribosomal protein L26 (L24P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_Y
Length = 150
Score = 36.3 bits (83), Expect = 2e-04
Identities = 20/28 (71%), Positives = 25/28 (89%)
Query: 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29
S+ +RKDDEVQVV G+YKGREGK VQ++
Sbjct: 46 SIPIRKDDEVQVVRGSYKGREGKVVQVY 73
>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y
2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y
2wh4_Y 2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ...
Length = 110
Score = 35.3 bits (82), Expect = 4e-04
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIF 29
+ M V+K D V V G YKGR GK ++
Sbjct: 3 VKMHVKKGDTVLVASGKYKGRVGKVKEVL 31
>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S*
1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R*
3dll_R* 3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V
1vow_V 1voy_V 1vp0_V
Length = 115
Score = 34.5 bits (80), Expect = 8e-04
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 3 MSVRKDDEVQVVGGTYKGREGKFVQIF 29
+ +K D V V+ G +KG+ GK +
Sbjct: 14 LHFKKGDTVIVLSGKHKGQTGKVLLAL 40
>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 145
Score = 34.2 bits (78), Expect = 0.001
Identities = 19/29 (65%), Positives = 23/29 (79%), Gaps = 1/29 (3%)
Query: 1 MSMSVRKDDEVQVVGGTYKGRE-GKFVQI 28
SM +RKDDEVQVV G YKG++ GK VQ+
Sbjct: 45 RSMPIRKDDEVQVVRGHYKGQQIGKVVQV 73
>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
2j28_U* 3fik_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U
3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U
1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U 3i20_U ...
Length = 102
Score = 33.7 bits (78), Expect = 0.001
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF----AIFSGV 35
+ +R+DDEV V+ G KG+ GK + I G+
Sbjct: 1 AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGI 38
>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 = 34.6 bits (79), Expect = 0.002
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 14/70 (20%)
Query: 21 REGKFVQIFAIFSG-------VK--RDLVVSYEPIFDPRIPLEPVGHSSVMSSVGRMSPE 71
EG Q+ AIF G + RDL +Y + I + +S + R + +
Sbjct: 150 GEGN-AQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKF----SAETLSELIRTTLD 204
Query: 72 VSTSFSKSND 81
F++ +
Sbjct: 205 AEKVFTQGLN 214
Score = 27.3 bits (60), Expect = 0.56
Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 18/82 (21%)
Query: 2 SMSVRKDDE-VQVVGGTYKGREGKFVQI---------FAIFSGVKRDL-----VVSYEPI 46
++ E +Q V R G V+I + +G R L V+++ +
Sbjct: 1816 RVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA-AGDLRALDTVTNVLNFIKL 1874
Query: 47 FDPRIPLEPVGHSSVMSSVGRM 68
+I + + S + V
Sbjct: 1875 --QKIDIIELQKSLSLEEVEGH 1894
Score = 26.6 bits (58), Expect = 1.3
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 11/36 (30%)
Query: 32 FSGVKRDLVVSYE--PIFDPRIPLEPVGHSSVMSSV 65
FS +R L S P+ P HS ++
Sbjct: 409 FS--ERKLKFSNRFLPVA------SPF-HSHLLVPA 435
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
Length = 191
Score = 34.1 bits (78), Expect = 0.002
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 3 MSVRKDDEVQVVGGTYKGREGKFVQIF 29
V+ D V+V+ G KG+ G+ +I
Sbjct: 67 RHVKVGDTVKVISGGEKGKIGEISKIH 93
>3qan_A 1-pyrroline-5-carboxylate dehydrogenase 1; proline oxidation, redox
control, apoptosis, NAD binding, oxidoreductase,
PSI-biology; 1.95A {Bacillus halodurans} PDB: 3rjl_A
Length = 538
Score = 29.1 bits (66), Expect = 0.11
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
+ GG G F+Q I + + + V+ E IF P
Sbjct: 386 MTGGEGDSSTGFFIQP-TIIADLDPEAVIMQEEIFGP 421
>1bxs_A Aldehyde dehydrogenase; retinal, class 1, tetramer, NAD, cytosolic,
oxidoreductase; HET: NAD; 2.35A {Ovis aries} SCOP:
c.82.1.1 PDB: 1o9j_A* 1bi9_A*
Length = 501
Score = 29.1 bits (66), Expect = 0.14
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
GG G +G F+Q +FS V D+ ++ E IF P
Sbjct: 369 ECGGGPWGNKGYFIQP-TVFSDVTDDMRIAKEEIFGP 404
>1o04_A Aldehyde dehydrogenase, mitochondrial precursor; ALDH, NAD, NADH,
isomerization, oxidoreductase; HET: NAD; 1.42A {Homo
sapiens} SCOP: c.82.1.1 PDB: 1nzw_A* 3inl_A* 3n80_A*
1nzz_A* 1o00_A* 1nzx_A* 1o01_A* 1o05_A 1of7_A* 1o02_A*
3inj_A* 3sz9_A* 1zum_A 2onm_A* 2onp_A* 2onn_A 2ono_A*
3n81_A 3n82_A* 3n83_A* ...
Length = 500
Score = 28.7 bits (65), Expect = 0.16
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
+ GG G F+Q +F V+ + ++ E IF P
Sbjct: 368 LCGGGIAADRGYFIQP-TVFGDVQDGMTIAKEEIFGP 403
>2o2p_A Formyltetrahydrofolate dehydrogenase; aldehyde dehydrogenase, FDH,
oxidoreductase; 1.70A {Rattus norvegicus} PDB: 2o2q_A*
2o2r_A* 3rho_A* 3rhm_A* 3rhj_A* 3rhq_A* 3rhp_A* 3rhr_A*
3rhl_A*
Length = 517
Score = 28.7 bits (65), Expect = 0.16
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
V GG R G F Q +F+ V+ + ++ E F P
Sbjct: 388 VCGGNQVPRPGFFFQP-TVFTDVEDHMYIAKEESFGP 423
>4f3x_A Putative aldehyde dehydrogenase; structural genomics, protein
structure initiative, nysgrc, P biology; HET: MSE NAD;
2.01A {Sinorhizobium meliloti} PDB: 4dal_A*
Length = 498
Score = 27.9 bits (63), Expect = 0.36
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
GG EG F Q + +G ++ + +F P
Sbjct: 370 TTGGRTGSDEGFFFQP-TVVAGATQEDEIVRREVFGP 405
>1wnd_A Putative betaine aldehyde dehydrogenase; NADH, fluorescence,
kinetics, oxidor; 2.10A {Escherichia coli} SCOP:
c.82.1.1 PDB: 1wnb_A
Length = 495
Score = 27.5 bits (62), Expect = 0.42
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49
+ GG + G + + +G +D + + +F P
Sbjct: 368 ITGGEKRKGNGYYYAP-TLLAGALQDDAIVQKEVFGP 403
>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus} PDB: 3iy9_N
Length = 96
Score = 26.8 bits (60), Expect = 0.47
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 9 DEVQVVGGTYKGREGKFVQIF 29
D V+++ G G++GK VQ+
Sbjct: 2 DTVEILEGKDAGKQGKVVQVI 22
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear
protein; 1.45A {Homo sapiens}
Length = 127
Score = 26.8 bits (59), Expect = 0.74
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 6 RKDDEVQVVGGTYKGREGKFVQI 28
+ V+ G Y+G EG I
Sbjct: 72 APGKRILVLNGGYRGNEGTLESI 94
>3r64_A NAD dependent benzaldehyde dehydrogenase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.57A {Corynebacterium glutamicum}
Length = 508
Score = 26.8 bits (60), Expect = 0.91
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPV 56
V G EG+ V +FS V D+ ++ E IF P I +
Sbjct: 360 QVEG---PIEGRLVHP-HVFSDVTSDMEIAREEIFGPLISVLKA 399
>3u4j_A NAD-dependent aldehyde dehydrogenase; PSI-biology, nysgrc,
structural genomics, NEW YORK structura genomics
research consortium, tetramer; 2.00A {Sinorhizobium
meliloti}
Length = 528
Score = 26.4 bits (59), Expect = 1.0
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 13 VVGGTYKGRE-GKFVQIFAIFSGVKRDLVVSYEPIFDP 49
++GG GRE G + +F+GV D+ ++ E IF P
Sbjct: 370 LLGGERIGREAGLYYAP-TVFAGVTPDMSIAREEIFGP 406
>3r31_A BADH, betaine aldehyde dehydrogenase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.15A {Agrobacterium tumefaciens}
Length = 517
Score = 25.6 bits (57), Expect = 2.2
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 13 VVGGTYKGREGK---FVQIFAIFSGVKRDLVVSYEPIFDP 49
+ GG +VQ +F+ V D+ ++ E IF P
Sbjct: 358 ITGGGIPNNVAGEGAYVQP-TVFADVTDDMTIAREEIFGP 396
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 25.1 bits (54), Expect = 3.0
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 16/65 (24%)
Query: 2 SMSVRKD-DEVQVVGGTYKGREGKFVQIFAIFSGV---------KRDLVVSYEP---I-F 47
M+++ + + K + I SG+ K+ LV++YEP I
Sbjct: 117 GMAIQVNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKFLVIAYEPFENIAI 176
Query: 48 DPRIP 52
+P
Sbjct: 177 --ELP 179
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 25.2 bits (56), Expect = 3.0
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 24 KFVQIFAIFSGVK 36
+I A+ SGVK
Sbjct: 77 DVERISAVTSGVK 89
>3s6d_A Putative triosephosphate isomerase; seattle structural genomics
center for infectious disease, S pathogenic fungus,
eukaryote; 2.20A {Coccidioides immitis RS}
Length = 310
Score = 24.6 bits (54), Expect = 4.3
Identities = 7/22 (31%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 27 QIFAIFSGVKRD--LVVSYEPI 46
QI + + RD ++ +YEP+
Sbjct: 204 QIRPVLEALPRDAPVIFAYEPV 225
>2imp_A Lactaldehyde dehydrogenase; protein-lactate-NADH ternary complex,
oxidoreductase; HET: NAI; 2.10A {Escherichia coli} PDB:
2ilu_A* 2hg2_A* 2opx_A*
Length = 479
Score = 24.8 bits (55), Expect = 4.8
Identities = 8/41 (19%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPL 53
GG +G + + V++++ + +E F P +P+
Sbjct: 352 AFGGKAVEGKGYYYPP-TLLLDVRQEMSIMHEETFGPVLPV 391
>3iwj_A Putative aminoaldehyde dehydrogenase; rossmann fold, dimer, betaine
aldehyde dehydrogenase, NAD, oxidoreductase; HET: NAD;
2.15A {Pisum sativum} PDB: 3iwk_A* 4a0m_A*
Length = 503
Score = 24.4 bits (54), Expect = 6.0
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 13 VVGGTYKGREGK--FVQIFAIFSGVKRDLVVSYEPIFDP 49
+ GG+ K F++ I + V ++ + E +F P
Sbjct: 360 LTGGSRPEHLKKGFFIEP-TIITDVTTNMQIWREEVFGP 397
>4dng_A Uncharacterized aldehyde dehydrogenase ALDY; structural genomics,
protein structure initiative, nysgrc, P biology; 2.50A
{Bacillus subtilis}
Length = 485
Score = 24.5 bits (54), Expect = 6.2
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 13 VVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPV 56
V G R G + +F G + ++ +F P +
Sbjct: 353 AVEGK---RVGNVLTP-YVFVGADNNSKIAQTELFAPIATIIKA 392
>2jgq_A Triosephosphate isomerase; glycolysis, pentose shunt,
gluconeogenesis, lipid synthesis, fatty acid
biosynthesis; HET: QGA; 2.3A {Helicobacter pylori}
Length = 233
Score = 24.0 bits (53), Expect = 8.1
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 14 VGGTYKGRE-GKFV---QIFAIFSGVKRD---LVVSYEPI 46
+G RE G + + + LVV+YEPI
Sbjct: 121 IGEELTTREKGFKAVKEFLSEQLENIDLNYPNLVVAYEPI 160
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
0.313 0.130 0.355
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,216,293
Number of extensions: 61312
Number of successful extensions: 108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 35
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.3 bits)