RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 036919
(132 letters)
>3v2d_O 50S ribosomal protein L14; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_O 2jl6_O 2jl8_O 2v47_O 2v49_O 2wdi_O 2wdj_O 2wdl_O
2wdn_O 2wh2_O 2wh4_O 2wrj_O 2wrl_O 2wro_O 2wrr_O 2x9s_O
2x9u_O 2xg0_O 2xg2_O 2xqe_O ...
Length = 122
Score = 94.3 bits (234), Expect = 3e-26
Identities = 49/88 (55%), Positives = 64/88 (72%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ +T L+VADN+G + +MCI+ LKG K A +GD IV SVKE +P VK+G+VVKAV
Sbjct: 2 IQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR + R DGS ++FDDNA V+I+N
Sbjct: 62 VVRTKKEIKRPDGSAIRFDDNAAVIINN 89
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 90.5 bits (224), Expect = 9e-25
Identities = 39/88 (44%), Positives = 60/88 (68%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ +T L VADNSG + +MCI+ + ++ AR+GD IV +KE +PN +++ EV++AV
Sbjct: 2 IQPQTHLNVADNSGARELMCIRIIGASNRRYARIGDVIVAVIKEAIPNTPLERSEVIRAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR + R +G +++DDNA V+ID
Sbjct: 62 VVRTCKELKRDNGMIIRYDDNAAVIIDQ 89
>3r8s_K 50S ribosomal protein L14; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3oat_K* 3oas_K* 3ofd_K 3ofc_K 3ofr_K* 3ofz_K* 3og0_K
3ofq_K 3r8t_K 3i1n_K 1p85_I 1p86_I 1vs8_K 1vs6_K 2aw4_K
2awb_K 1vt2_K 2i2v_K 2i2t_K* 2qao_K* ...
Length = 122
Score = 90.5 bits (224), Expect = 1e-24
Identities = 46/88 (52%), Positives = 63/88 (71%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ +T+L VADNSG + VMCI+ L G ++ A +GD I +++KE +P KVKKG+V+KAV
Sbjct: 2 IQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR R DGS ++FD NA VL++N
Sbjct: 62 VVRTKKGVRRPDGSVIRFDGNACVLLNN 89
>1whi_A Ribosomal protein L14; rRNA-binding; 1.50A {Geobacillus
stearothermophilus} SCOP: b.39.1.1 PDB: 1giy_N 1ml5_n*
1c04_D 1yl3_N 2b66_O 2b9n_O 2b9p_O 487d_M
Length = 122
Score = 90.1 bits (223), Expect = 1e-24
Identities = 43/88 (48%), Positives = 60/88 (68%), Gaps = 2/88 (2%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAV 93
IQ + LKVADNSG + V+ I+ L G ++ A +GD +V +VK+ P VKKG+VVKAV
Sbjct: 2 IQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAV 61
Query: 94 VVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
VVR R DGS+++FD+NA V+I +
Sbjct: 62 VVRTKRGVRRPDGSYIRFDENACVIIRD 89
>3u5e_V L17A, YL32, 60S ribosomal protein L23-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_M
1s1i_R 3izs_M* 3j16_I 3o5h_U 3o58_U 3u5i_V 2x7n_C 3jyw_R
2zkr_k 3iz5_M 3izr_M 4a17_J 4a1a_J 4a1c_J 4a1e_J
Length = 137
Score = 79.8 bits (196), Expect = 2e-20
Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 9/92 (9%)
Query: 36 IQMRTVLKVADNSGVKTVMCIQPLKGK------KVARLGDTIVVSVKEVMPNAKVKKGEV 89
+ + ++ ADNSG + + I A LGD ++ +VK+ P + +V
Sbjct: 17 LPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVKKGKPE---LRKKV 73
Query: 90 VKAVVVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
+ A+VVR A R DG F+ F+DNA V+ +
Sbjct: 74 MPAIVVRQAKSWRRRDGVFLYFEDNAGVIANP 105
>1vq8_K 50S ribosomal protein L14P; 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.39.1.1 PDB: 1vq4_K*
1vq5_K* 1vq6_K* 1vq7_K* 1s72_K* 1vq9_K* 1vqk_K* 1vql_K*
1vqm_K* 1vqn_K* 1vqo_K* 1vqp_K* 1yhq_K* 1yi2_K* 1yij_K*
1yit_K* 1yj9_K* 1yjn_K* 1yjw_K* 2otj_K* ...
Length = 132
Score = 74.8 bits (183), Expect = 2e-18
Identities = 32/100 (32%), Positives = 49/100 (49%), Gaps = 9/100 (9%)
Query: 28 LSQLQRTFIQMRTVLKVADNSGVKTVMCIQPLKGKK------VARLGDTIVVSVKEVMPN 81
L ++ +++ ADN+G + + I A LGD I VSV + P
Sbjct: 4 LGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTPE 63
Query: 82 AKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDDNAVVLIDN 121
+ +V++AVVVR R DG+ VKF+DNA V++D
Sbjct: 64 ---MRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDE 100
>3qsl_A Putative exported protein; unknown, structural genomics,
PSI-biology, midwest center FO structural genomics,
MCSG, unknown function; HET: MSE CIT; 2.00A {Bordetella
bronchiseptica}
Length = 346
Score = 31.0 bits (70), Expect = 0.075
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 40 TVLKVADNSGVKTVMCIQPLKGKKVA--RLGDTIVVSVKEVMPNAKVKKGEVVKAVVV-- 95
+ + G K LKG+K+ G + + V + +K +V V
Sbjct: 120 VGVSKKNLPGYKGP---ADLKGRKIGVTAPGSSTNMVVNFFLAKHGLKASDVSFIGVGAG 176
Query: 96 ---RAAMDHGRCDGSFV 109
A+ G+ D
Sbjct: 177 AGAVTALRSGQIDAISN 193
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 30.7 bits (70), Expect = 0.11
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 9/75 (12%)
Query: 45 ADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGR 103
A+N+ +K+ I L GK +A + G + +K + ++++ A++ GR
Sbjct: 117 ANNTTIKS---IDDLNGKVIAAKTGTATIDWIKAHLKPKEIRQFP--NIDQAYLALEAGR 171
Query: 104 CDGSFVKFDDNAVVL 118
D + D VL
Sbjct: 172 VDAA---MHDTPNVL 183
>2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB;
SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A
{Bacillus subtilis}
Length = 271
Score = 29.6 bits (67), Expect = 0.28
Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 16/92 (17%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAM 99
+++ D SG+KT ++ LKGKK A + ++ + +
Sbjct: 115 IVRKDDLSGIKT---LKDLKGKKAAGAATTVYMEVARKYGAKEVIYDNA--TNEQYLKDV 169
Query: 100 DHGRCDGSFVKFDDNAVVLIDNLCVLAFAEHT 131
+GR D +L D
Sbjct: 170 ANGRTDV----------ILNDYYLQTLALAAF 191
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, arginine protein binding, transport protein;
1.92A {Chlamydia trachomatis}
Length = 242
Score = 28.8 bits (65), Expect = 0.40
Identities = 7/78 (8%), Positives = 26/78 (33%), Gaps = 8/78 (10%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMD 100
++ V + + + VA T + + + ++ + + V +
Sbjct: 101 LVLVFKGENKHP---LPLTQYRSVAVQTGTYQEAYLQSLSEVHIRSFD--STLEVLMEVM 155
Query: 101 HGRCDGSFVKFDDNAVVL 118
HG+ + + + ++
Sbjct: 156 HGKSPVAVL---EPSIAQ 170
>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide,
complex (binding protein/peptide); 1.94A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1ggg_A
Length = 226
Score = 28.7 bits (65), Expect = 0.41
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 9/75 (12%)
Query: 45 ADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGR 103
A+N+ VK+ ++ L GK VA + G V K + +++ + R
Sbjct: 96 ANNNDVKS---VKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFP--NIDNAYMELGTNR 150
Query: 104 CDGSFVKFDDNAVVL 118
D D +L
Sbjct: 151 ADAVLH---DTPNIL 162
>2o1m_A Probable amino-acid ABC transporter extracellular-binding protein
YTMK; NESG X-RAY O34852 YTMK_bacsu, structural genomics,
PSI-2; 2.00A {Bacillus subtilis}
Length = 258
Score = 27.7 bits (62), Expect = 1.0
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 7/70 (10%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAM 99
+ + +N ++ I+ LKGK+V + +K+ + +
Sbjct: 108 ITVLQNNDTIRG---IEDLKGKRVITSATSNGALVLKKWNEDNGRPFEIAYEGQGANETA 164
Query: 100 DH---GRCDG 106
+ GR D
Sbjct: 165 NQLKSGRADA 174
>3uif_A Sulfonate ABC transporter, periplasmic sulfonate- protein SSUA;
structural genomics; 2.60A {Methylobacillus flagellatus}
Length = 348
Score = 28.0 bits (62), Expect = 1.1
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 40 TVLKVADNSGVKTVMCIQPLKGKKVA 65
+ L V NS K++ + LKGKK+A
Sbjct: 101 SYLVVPKNSTAKSI---KDLKGKKIA 123
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 27.2 bits (61), Expect = 1.3
Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 11/76 (14%)
Query: 45 ADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVMPNAKVKK-GEVVKAVVVRAAMDHG 102
D+ ++ L+G+KVA + + E + A+ + G
Sbjct: 104 RDSPPAAG---LEDLRGRKVALHRDGIMHEYLAERGYGKDLVLTPTPADAL---RLLAAG 157
Query: 103 RCDGSFVKFDDNAVVL 118
CD + V +
Sbjct: 158 GCDYAVV---AMVPGM 170
>2x26_A Periplasmic aliphatic sulphonates-binding protein; transport
protein; 1.75A {Escherichia coli}
Length = 308
Score = 27.4 bits (61), Expect = 1.4
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 44 VADNSGVKTVMCIQPLKGKKVA 65
VA+NS +KTV LKG KVA
Sbjct: 91 VAENSPIKTV---ADLKGHKVA 109
>3ksx_A Nitrate transport protein; SSUA, alkanesulfonate-binding protein,
periplasmic-binding P transport protein; HET: MPO; 1.70A
{Xanthomonas axonopodis PV} PDB: 3e4r_A* 3ksj_A*
Length = 324
Score = 27.1 bits (60), Expect = 2.0
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 44 VADNSGVKTVMCIQPLKGKKVA 65
V S ++TV LKGK++A
Sbjct: 117 VPSKSALRTV---ADLKGKRIA 135
>1yw6_A Succinylglutamate desuccinylase; alpha-beta protein., structural
genomics, PSI, protein structure initiative; 3.10A
{Escherichia coli} SCOP: c.56.5.7
Length = 335
Score = 26.5 bits (58), Expect = 2.9
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 60 KGKKVARLGDTIVVSVKE----VMPNAKVKKGEVVKAVVVRAAMDH 101
KG +A+ G+ + + PN V G ++ + +++H
Sbjct: 285 KGTLLAQDGEERFTVTHDVEYVLFPNPLVALGLRAGLMLEKISLEH 330
>2k0m_A Uncharacterized protein; structural genomics, unknown function,
PSI-2, protein structure initiative; NMR {Rhodospirillum
rubrum atcc 11170}
Length = 104
Score = 25.6 bits (56), Expect = 3.2
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 80 PNAKVKKGEVVKAVVVRAAMDHGRC------DGSFVKF 111
P+A K G V+ VR+A +C DGS +F
Sbjct: 53 PDATSKIGPGVRNFEVRSADYGTQCFWILRTDGSEERF 90
>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 = 3.4
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 7/38 (18%)
Query: 2 RSFFGGLGSLLSGLL--TTSHEMASCNFLSQLQRTFIQ 37
R GSL LL T S +AS QLQ F +
Sbjct: 7 RPLTLSHGSLEHVLLVPTASFFIAS-----QLQEQFNK 39
>3r44_A Fatty acyl COA synthetase FADD13 (fatty-acyl-COA synthetase);
ligase; HET: HIS; 1.80A {Mycobacterium tuberculosis}
PDB: 3t5c_A 3t5b_A
Length = 517
Score = 26.4 bits (59), Expect = 3.7
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 85 KKGEVVKAVVVR 96
K GE+ A+VV
Sbjct: 450 KWGEIAAAIVVA 461
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta
protein, cytoplasm, structural genomics, NPPSFA; 3.20A
{Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1
Length = 235
Score = 26.2 bits (57), Expect = 3.9
Identities = 9/42 (21%), Positives = 16/42 (38%)
Query: 40 TVLKVADNSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPN 81
TV+ + G LK V + GD ++ ++ V
Sbjct: 39 TVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQSVGIM 80
>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein
synthetase, PSI-2, protein structure initiative; 2.30A
{Staphylococcus aureus subsp}
Length = 501
Score = 26.0 bits (58), Expect = 4.3
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 85 KKGEVVKAVVVRAA 98
G+V K V +
Sbjct: 435 TWGQVPKLYFVSES 448
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 26.0 bits (58), Expect = 4.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 60 KGKKVARLGDTIVVSVKEV 78
KG+ V ++ D I V++ EV
Sbjct: 613 KGETVYKVTDVIDVTIAEV 631
>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-BIND protein; HET: CYS GOL;
1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A
Length = 283
Score = 25.8 bits (57), Expect = 4.7
Identities = 18/95 (18%), Positives = 32/95 (33%), Gaps = 22/95 (23%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKVKKGEVVK---AVVVRA 97
VL ++S +K++ +KG K A+ + AK ++V
Sbjct: 147 VLVAHNDSNIKSI---ADIKGVKTAQSLTSNYGEK------AKAAGAQLVPVDGLAQSLT 197
Query: 98 AMDHGRCDGSFVKFDDNAVVLIDNLCVLAFAEHTA 132
++ R D L D L VL + +
Sbjct: 198 LIEQKRADA----------TLNDELAVLDYLKKNP 222
>3g7s_A Long-chain-fatty-acid--COA ligase (FADD-1); protein structure
initiative, PSI-II, NYSGXRC, 11193J, structural
genomics; 2.15A {Archaeoglobus fulgidus dsm 4304}
Length = 549
Score = 26.0 bits (58), Expect = 4.9
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 74 SVKEV----MPNAKVKKGEVVKAVVVR 96
+V +V P+ + GEV KA +V
Sbjct: 463 AVMDVAVIGKPDEE--AGEVPKAFIVL 487
>3ivr_A Putative long-chain-fatty-acid COA ligase; structural genomics,
PSI-2, protein S initiative, fatty acid synthesis; HET:
GOL; 2.00A {Rhodopseudomonas palustris}
Length = 509
Score = 26.0 bits (58), Expect = 5.0
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 85 KKGEVVKAVVVRAA 98
+ E +KAV V
Sbjct: 437 QWSEAIKAVCVCKP 450
>3hn0_A Nitrate transport protein; ABC transporter, structural genomics,
joint center for struc genomics, JCSG, protein structure
initiative; 1.75A {Parabacteroides distasonis}
Length = 283
Score = 25.6 bits (56), Expect = 6.0
Identities = 7/68 (10%), Positives = 21/68 (30%), Gaps = 5/68 (7%)
Query: 47 NSGVKTVMCIQPLKGKKVA--RLGDTIVVSVKEVMPNAKVKKGEVVKAVV---VRAAMDH 101
G ++ PLK + G T + + + ++ + +
Sbjct: 82 IWGTLYLVEKTPLKEPALYVFGNGTTPDILTRYYLGRQRLDYPLNYAFNTAGEITQGILA 141
Query: 102 GRCDGSFV 109
G+ + + +
Sbjct: 142 GKVNRAVL 149
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 25.3 bits (56), Expect = 6.2
Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 18/92 (19%)
Query: 45 ADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVK----EVMPNAKVKKGEVVKAVVVRAAM 99
D+S +K+ + + GK T ++ E N + + +
Sbjct: 102 KDDSSIKS---LDDIGGKSTEVVQATTSAKQLEAYNAEHTDNPTILNYTKADFQQIMVRL 158
Query: 100 DHGRCDGSFVKFDDNAVVLIDNLCVLAFAEHT 131
G+ D + D + V ++
Sbjct: 159 SDGQFDY----------KIFDKIGVETVIKNQ 180
>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9
Length = 415
Score = 25.6 bits (55), Expect = 6.5
Identities = 3/22 (13%), Positives = 8/22 (36%)
Query: 17 TTSHEMASCNFLSQLQRTFIQM 38
E + +++R F +
Sbjct: 66 GAQDEEIHKQIVIEMKRCFENL 87
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 25.4 bits (56), Expect = 6.7
Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 41 VLKVADNSGVKTVMCIQPLKGKKVA-RLGDTIVVSVKEVM-PNAKVKKGEVVKAVVVRAA 98
V+ V S VK LKGK + + T + +++ +KK E VV
Sbjct: 130 VILVKQGSPVKN---ALDLKGKTIGVQNATTGQEAAEKLFGKGPHIKKFE--TTVVAIME 184
Query: 99 MDHGRCDGSFVKFDDNAVVL 118
+ +G D DNAV
Sbjct: 185 LLNGGVDAVIT---DNAVAN 201
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 24.4 bits (53), Expect = 7.9
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 76 KEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDD 113
+EV + K GEV + V DH + +VKF
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV-YVKFRR 77
>3nrf_A APAG protein; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-2, unknown
function; 1.50A {Pseudomonas aeruginosa} PDB: 3sb3_A
Length = 106
Score = 24.4 bits (52), Expect = 9.3
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 74 SVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDDN 114
+V E + +K G V+ + A+ D S V+ D
Sbjct: 64 TVDEELTADTLKPGASVEGDAIFASEDDAVYGASLVRLSDR 104
>4fuq_A Malonyl COA synthetase; ANL superfamily, methylma malonate, ligase;
HET: MSE; 1.70A {Rhodopseudomonas palustris} PDB:
4fut_A*
Length = 503
Score = 24.8 bits (55), Expect = 9.8
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 85 KKGEVVKAVVVRAA 98
GE V AVVVR
Sbjct: 436 DFGEGVTAVVVRDK 449
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
0.323 0.136 0.387
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,913,515
Number of extensions: 108635
Number of successful extensions: 358
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 41
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (23.7 bits)