RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780275|ref|YP_003064688.1| SsrA-binding protein
[Candidatus Liberibacter asiaticus str. psy62]
(159 letters)
>1j1h_A Small protein B; SMPB, SSRA associated protein, OB fold, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Thermus thermophilus} SCOP:
b.111.1.1
Length = 144
Score = 189 bits (481), Expect = 3e-49
Identities = 71/143 (49%), Positives = 96/143 (67%)
Query: 12 KVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIP 71
V +NR+AR++Y I+ ++EAGI L GTEVKSLR KV+ + S+A FE+ E++L N YI
Sbjct: 2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIA 61
Query: 72 EYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQ 131
Y + + N PRR RKLLL K E+ RL V + G+TLVP+KIYFN +G AK+ L LA+
Sbjct: 62 PYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLAR 121
Query: 132 GKKNYDKRETEKKRDWDRQKHRI 154
GKK Y+KR +KK R +
Sbjct: 122 GKKAYEKRREDKKEAVRRALEEL 144
>1p6v_A SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA
complex, RNA binding protein/RNA complex; 3.20A {Aquifex
aeolicus} SCOP: b.111.1.1 PDB: 2ob7_B 1k8h_A 1zc8_K
Length = 156
Score = 173 bits (439), Expect = 2e-44
Identities = 65/148 (43%), Positives = 91/148 (61%), Gaps = 2/148 (1%)
Query: 11 KKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLR-VSKVNISDSYATFENDEIWLTNSY 69
+++N++A+ Y I+ ++EAGIVL G+EVKSLR V+ DS+ EN E WL N Y
Sbjct: 6 IIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLY 65
Query: 70 IPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLAL 129
I Y A NH P R RKLLL KREI RLY V+ G T++P+K+Y+ K+ +AL
Sbjct: 66 IAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWK-NNKVKVLIAL 124
Query: 130 AQGKKNYDKRETEKKRDWDRQKHRILRE 157
A+GKK YD+R K++ R+ R +
Sbjct: 125 AKGKKLYDRRRELKEKAMKRELEREFKG 152
>1wjx_A Small protein B, SSRA-binding protein; RNA binding protein,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 1.70A {Thermus
thermophilus} SCOP: b.111.1.1 PDB: 2czj_A*
Length = 122
Score = 152 bits (386), Expect = 3e-38
Identities = 64/120 (53%), Positives = 86/120 (71%)
Query: 14 VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEY 73
V +NR+AR++Y I+ ++EAGI L GTEVKSLR KV+ + S+A FE+ E++L N YI Y
Sbjct: 3 VLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPY 62
Query: 74 LQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK 133
+ + N PRR RKLLL K E+ RL V + G+TLVP+KIYFN +G AK+ L LA+GK
Sbjct: 63 EKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 122
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 32.2 bits (73), Expect = 0.056
Identities = 23/134 (17%), Positives = 41/134 (30%), Gaps = 49/134 (36%)
Query: 3 LKSRGNPPKKVVSDNRK-------ARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSY 55
K P + +D+ ++ ++ E V +V L +
Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQV--LNLC-------L 88
Query: 56 ATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVP--- 112
FEN YL+ N +IH L A + ++ T +
Sbjct: 89 TEFENC-----------YLEGN-----------------DIHALAAKLLQENDTTLVKTK 120
Query: 113 --MKIYFNAKGLAK 124
+K Y A+ +AK
Sbjct: 121 ELIKNYITARIMAK 134
Score = 31.5 bits (71), Expect = 0.087
Identities = 20/139 (14%), Positives = 43/139 (30%), Gaps = 47/139 (33%)
Query: 26 IVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSY---------IPEYLQA 76
+ FE L G ++ +L + +D T + + N + +
Sbjct: 87 CLTEFENCY-LEGNDIHALAAKLLQEND--TTLVKTKELIKNYITARIMAKRPFDKKSNS 143
Query: 77 NRFNHYPRRNRKLL---------------LSKREIHRLYAAVRRD-----GMTLVPM--- 113
F N +L+ L R++++ Y + D TL +
Sbjct: 144 ALFRAVGEGNAQLVAIFGGQGNTDDYFEEL--RDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 114 -----KIYFNAKGLAKIDL 127
K++ +GL ++
Sbjct: 202 TLDAEKVF--TQGL---NI 215
Score = 29.1 bits (65), Expect = 0.45
Identities = 39/201 (19%), Positives = 54/201 (26%), Gaps = 100/201 (49%)
Query: 9 PPKKVVSDNRKARYNYHIVRSFEAGIVLTGT-----EVKSLRVSKVNISDSYATFENDEI 63
PP ++ D S E G + +L +V Y +
Sbjct: 320 PPS-ILED------------SLENN---EGVPSPMLSISNLTQEQV---QDY-------V 353
Query: 64 WLTNSYIPEYLQ-----AN---------------RFNHYPRRN---------------RK 88
TNS++P Q N N R+ RK
Sbjct: 354 NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK 413
Query: 89 LLLSKR--EI------HRLYAA---VRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYD 137
L S R + H L A + +D LV + FNAK D+ + YD
Sbjct: 414 LKFSNRFLPVASPFHSHLLVPASDLINKD---LVKNNVSFNAK-----DIQIPV----YD 461
Query: 138 KRETEKKRDWDRQKHRILREH 158
T D LR
Sbjct: 462 ---TFDGSD--------LRVL 471
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.0 bits (61), Expect = 1.1
Identities = 22/88 (25%), Positives = 32/88 (36%), Gaps = 32/88 (36%)
Query: 75 QANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKK 134
QA+R P RK RE R K L ++D A ++
Sbjct: 76 QADRLTQEPESIRKW----REEQR---------------------KRLQELDAASKVMEQ 110
Query: 135 NYDKRETEKK--RDWD-RQKHRILREHN 159
+ RE KK +W+ RQ ++ E N
Sbjct: 111 EW--REKAKKDLEEWNQRQSEQV--EKN 134
>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 = 27.3 bits (59), Expect = 1.9
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 12/33 (36%)
Query: 93 KREIHRLYAAVRRDGMTLVPMKIYFN--AKGLA 123
K+ + +L A+ +K+Y + A LA
Sbjct: 19 KQALKKLQAS----------LKLYADDSAPALA 41
>2ghj_A 50S ribosomal protein L20; folding intermediate, ribosomal protein
extension, structural protein; 2.90A {Aquifex aeolicus}
PDB: 1gyz_A
Length = 118
Score = 26.2 bits (58), Expect = 3.9
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 84 RRNRKLLLSKREIHRLYAAVRRDGMT-------LVPMKIYFNAKGLAKI 125
R+ RK + I R+ AAVR G+ L I + K LA +
Sbjct: 48 RKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADM 96
>2fzv_A Putative arsenical resistance protein; flavin binding protein,
structural genomics, PSI, protein structure initiative;
1.70A {Shigella flexneri 2a str} SCOP: c.23.5.4
Length = 279
Score = 25.8 bits (56), Expect = 5.2
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 3/59 (5%)
Query: 9 PPKKV---VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIW 64
PP ++ R ++ V + G E + S + + D + ++ +
Sbjct: 57 PPVRILLLYGSLRARSFSRLAVEEAARLLQFFGAETRIFDPSDLPLPDQVQSDDHPAVK 115
>1mve_A Truncated 1,3-1,4-beta-D-glucanase; circular-permutated jellyroll
protein, hydrolase; 1.70A {Fibrobacter succinogenes}
SCOP: b.29.1.2 PDB: 1zm1_A* 2r4a_A 3hr9_A 2r49_A
Length = 243
Score = 25.5 bits (55), Expect = 6.1
Identities = 6/48 (12%), Positives = 14/48 (29%)
Query: 40 EVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNR 87
+ ++V K + W N + + + + NR
Sbjct: 162 FINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNR 209
>1vf1_A Glutathione S-transferase 3; detoxification; HET: GSH; 1.77A
{Gallus gallus} PDB: 1vf2_A* 1vf3_A* 1vf4_A
Length = 229
Score = 25.2 bits (54), Expect = 7.6
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 108 MTLVPMKIYFNAKGLA-KIDLALAQGKKNYDKRETEKKRDWDRQKH 152
M P+ YFN +G I LA +++ E + +++
Sbjct: 1 MAAKPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQ 46
>3i1n_Q 50S ribosomal protein L20; ribosome structure, protein-RNA complex,
acetylation, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1vs8_Q 3e1b_J 3e1d_J 1vs6_Q
3i1p_Q 3i1r_Q 3i1t_Q 3i20_Q 3i22_Q 2qam_Q* 1p85_O 1p86_O
2awb_Q 2aw4_Q 2i2v_Q 2j28_Q 2i2t_Q* 2qao_Q* 2qba_Q*
2qbc_Q* ...
Length = 118
Score = 25.1 bits (55), Expect = 7.6
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 84 RRNRKLLLSKREIHRLYAAVRRDGMTLVPM-------KIYFNAKGLAKI 125
RR RK + I R+ AA R++G++ + + K LA I
Sbjct: 50 RRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADI 98
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.134 0.387
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,367,728
Number of extensions: 59367
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 157
Number of HSP's successfully gapped: 25
Length of query: 159
Length of database: 5,693,230
Length adjustment: 85
Effective length of query: 74
Effective length of database: 3,632,490
Effective search space: 268804260
Effective search space used: 268804260
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 (21.7 bits)
S2: 53 (24.2 bits)