RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5
[Candidatus Liberibacter asiaticus str. psy62]
(199 letters)
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E
3i1q_E 3i1s_E 3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E
2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E
2qbf_E 2qbh_E* ... (E:)
Length = 167
Score = 137 bits (347), Expect = 8e-34
Identities = 76/159 (47%), Positives = 109/159 (68%), Gaps = 1/159 (0%)
Query: 14 NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRK 73
+ E++ + ++++A+NRVS + GGR F+F+ L VVGD +VGF + AREVP A++K
Sbjct: 3 HIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQK 62
Query: 74 ATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133
A E A+RNMI+V L+ TL H G H +V M+ A GTG+IAGGA+RAV EV G+H
Sbjct: 63 AMEKARRNMINV-ALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVH 121
Query: 134 DVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
+V+AK+ GS+NP NV+RAT + L + + P VA +RG
Sbjct: 122 NVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS 160
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} (E:1-143)
Length = 143
Score = 125 bits (314), Expect = 6e-30
Identities = 59/142 (41%), Positives = 83/142 (58%), Gaps = 1/142 (0%)
Query: 18 RDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEA 77
+ ++++ I R + GGRRF F LVVVGD + +VG A EVP AV+KA
Sbjct: 2 PETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYY 61
Query: 78 AKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVA 137
A+RNM+ V L T+ H+ GA K++++ A GTGVIAG RA+ E+ G+ D++
Sbjct: 62 ARRNMVEVPL-QNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT 120
Query: 138 KSIGSSNPHNVIRATFEVLRSQ 159
K +GS NP N+ AT E LR
Sbjct: 121 KELGSRNPINIAYATMEALRQL 142
>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} (e:82-179)
Length = 98
Score = 90.6 bits (225), Expect = 1e-19
Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 90 GRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP-HNV 148
T+ GR G+ V + A GTG+++ + + + G+ D + G + N
Sbjct: 4 PHTVPCKVTGRSGSVPVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNF 63
Query: 149 IRATFEVLR---SQSHPRDVANRRGIK 172
+ATF+ + S P K
Sbjct: 64 AKATFDAISKTYSYLTPDLWKETVFTK 90
>3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1
protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG
PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus}
PDB: 1s1h_E (E:75-162)
Length = 88
Score = 86.8 bits (215), Expect = 2e-18
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 90 GRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP-HNV 148
+L G+ G+ V + A G+G++A A++ + ++ G+ DV +S G + N
Sbjct: 3 PHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENT 62
Query: 149 IRATFEVL---RSQSHPRDVANRR 169
++A F + P A +
Sbjct: 63 LKAAFVAIGNTYGFLTPNLWAEQP 86
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(E:221-289)
Length = 69
Score = 86.7 bits (215), Expect = 2e-18
Identities = 28/67 (41%), Positives = 42/67 (62%)
Query: 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRA 151
T H +GA +V++R A GTGVIAGGA+R V E+ G+ + + K +GS+N N RA
Sbjct: 2 TFPHRNEADYGAARVMLRPAAPGTGVIAGGAVRTVLEMAGVENALGKQLGSNNALNNARA 61
Query: 152 TFEVLRS 158
T +++
Sbjct: 62 TIVAVQT 68
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus}
(A:79-150)
Length = 72
Score = 86.3 bits (214), Expect = 2e-18
Identities = 34/68 (50%), Positives = 51/68 (75%)
Query: 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRA 151
T+ H+ +G GAG++I++ A GTGVIAGG RAV E+ G+ D+++KSIGS+ P N++RA
Sbjct: 2 TIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRA 61
Query: 152 TFEVLRSQ 159
TF+ L+
Sbjct: 62 TFDGLKQL 69
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus
stearothermophilus} (A:1-78)
Length = 78
Score = 78.6 bits (194), Expect = 6e-16
Identities = 36/76 (47%), Positives = 49/76 (64%)
Query: 13 QNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVR 72
+ + +R+VA+NRV+ + GGRR FS LVVVGD VGF A+EVPEA+R
Sbjct: 2 RRINPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIR 61
Query: 73 KATEAAKRNMISVSLL 88
KA E AK+N+I V ++
Sbjct: 62 KAIEDAKKNLIEVPIV 77
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(E:1-220)
Length = 220
Score = 71.7 bits (175), Expect = 7e-14
Identities = 28/87 (32%), Positives = 48/87 (55%)
Query: 1 MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFA 60
K+ + + +E+ + + +V + RV+ + GG+ F +VVVGD K +VG
Sbjct: 131 SKIKKATGFGSKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVG 190
Query: 61 HSTAREVPEAVRKATEAAKRNMISVSL 87
A+EV AV+KA A+RN+I+V +
Sbjct: 191 VGKAKEVVSAVQKAAVDARRNIITVPM 217
>3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1
protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG
PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus}
PDB: 1s1h_E (E:1-74)
Length = 74
Score = 66.3 bits (162), Expect = 2e-12
Identities = 23/72 (31%), Positives = 34/72 (47%)
Query: 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKR 80
+ D ++ I V G+R F +VVVGD+ VG TA+EV A+R AK
Sbjct: 1 GLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKL 60
Query: 81 NMISVSLLDGRT 92
++I + T
Sbjct: 61 SVIPIRRGYWGT 72
>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} (e:1-81)
Length = 81
Score = 62.9 bits (153), Expect = 3e-11
Identities = 20/65 (30%), Positives = 31/65 (47%)
Query: 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKR 80
S+ D ++ I V G+R F V +GD VG ++EV A+R A AK
Sbjct: 9 SLKDEVLKIVPVQKQTRAGQRTRFKAFVAIGDHNGHVGLGVKCSKEVATAIRGAIILAKL 68
Query: 81 NMISV 85
+++ V
Sbjct: 69 SIVPV 73
>2of5_H Leucine-rich repeat and death domain-containing protein;
death domain complex, apoptosis; 3.20A {Homo sapiens}
(H:)
Length = 118
Score = 29.2 bits (65), Expect = 0.36
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 2/59 (3%)
Query: 124 RAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRS--QSHPRDVANRRGIKHSLLQARR 180
AV LG+ + I ++ +L S + + +L Q+ R
Sbjct: 28 PAVALHLGVSYREVQRIRHEFRDDLDEQIRHMLFSWAERQAGQPGAVGLLVQALEQSDR 86
>3go2_A Putative L-alanine-DL-glutamate epimerase; structural
genomics, isomerase, PSI-2, protein structure
initiative; 1.70A {Burkholderia xenovorans LB400} PDB:
2oo6_A (A:1-110,A:381-409)
Length = 139
Score = 28.0 bits (62), Expect = 1.0
Identities = 19/147 (12%), Positives = 46/147 (31%), Gaps = 26/147 (17%)
Query: 25 RIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMIS 84
++V+++ + V + + VG++ V E + ++
Sbjct: 4 KVVSVDTLCCDAGWRNY----HFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVG 59
Query: 85 VSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIG--- 141
S+++ + TG + I A+ + D AK++
Sbjct: 60 ASVMEHERFFAE----------AYCLTRPATGGVVSEGIGAI--ENALLDAKAKTLNVPC 107
Query: 142 -------SSNPHNVIRATFEVLRSQSH 161
++P V+ + RS+ H
Sbjct: 108 YELEEAILAHPPKVMGGLLQYKRSEGH 134
>2fxu_A Alpha-actin-1, actin, alpha skeletal muscle; actin complexed
to bistramide A, structural protein; HET: HIC ATP BID;
1.35A {Oryctolagus cuniculus} (A:138-182,A:263-352)
Length = 135
Score = 26.0 bits (57), Expect = 3.1
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 16/72 (22%)
Query: 76 EAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDV 135
++ +V + +G L H IMR +AG G E G+H+
Sbjct: 17 DSGDGVTHNVPIYEGYALPHA----------IMRLDLAGQPSFIG------MESAGIHET 60
Query: 136 VAKSIGSSNPHN 147
SI +
Sbjct: 61 TYNSIMKCDIDI 72
>2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON
willebrand factor A domain, beta- sheet, RNA binding
protein; 1.89A {Deinococcus radiodurans} (A:289-358)
Length = 70
Score = 26.3 bits (58), Expect = 3.2
Identities = 12/60 (20%), Positives = 16/60 (26%)
Query: 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAA 78
D++ V ++ AL GR L G V A E A
Sbjct: 3 DSATVQAVIERLTDPAALKRGRIHPLDALKARLVYAQGQGVRGKGTWLPVPRVVDALEEA 62
>1fad_A Protein (FADD protein); apoptosis, death domain; NMR {Mus
musculus} (A:)
Length = 99
Score = 25.2 bits (55), Expect = 5.6
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 124 RAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRS--QSHPRDVANRRGIKHSLLQARR 180
+ + L + + I P ++ E L+ + ++ A+ G+ +L R
Sbjct: 29 KRLARELKVSEAKMDGIEEKYPRSLSERVRESLKVWKNAEKKN-ASVAGLVKALRTCRL 86
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like
nucleotidyltransferase fold; HET: DNA; 3.00A {Thermus
aquaticus} PDB: 2hpm_A* 3e0d_A* (A:451-623)
Length = 173
Score = 25.2 bits (55), Expect = 6.1
Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPH 146
G ++ ++A A++ V V G+ A+ + P
Sbjct: 35 GEDKVAQIGTFGSLASKA-----ALKDVARVYGIPHKKAEELAKLIPV 77
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.316 0.129 0.359
Gapped
Lambda K H
0.267 0.0653 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,426,987
Number of extensions: 60684
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 210
Number of HSP's successfully gapped: 35
Length of query: 199
Length of database: 4,956,049
Length adjustment: 84
Effective length of query: 115
Effective length of database: 2,116,429
Effective search space: 243389335
Effective search space used: 243389335
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 (21.7 bits)
S2: 52 (24.0 bits)