RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11
[Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 192 bits (490), Expect = 3e-50
Identities = 70/127 (55%), Positives = 94/127 (74%)
Query: 3 KSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFA 62
K ++ + +KNI SG AH+ +TFNNT +TITD GN I+W+S +GF GSRK++P+A
Sbjct: 2 KKKKTVKKKVKKNIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYA 61
Query: 63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCR 122
AQVA +D + KA+ HGM ++EV V G G+GR+SA+RAL+A G + SI DVT I HNGCR
Sbjct: 62 AQVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCR 121
Query: 123 PRKRRRI 129
P KRRR+
Sbjct: 122 PPKRRRV 128
>gnl|CDD|163365 TIGR03632, bact_S11, 30S ribosomal protein S11. This model
describes the bacterial 30S ribosomal protein S11.
Cutoffs are set such that the model excludes archaeal
and eukaryotic ribosomal proteins, but many chloroplast
and mitochondrial equivalents of S11 are detected.
Length = 108
Score = 163 bits (414), Expect = 2e-41
Identities = 61/108 (56%), Positives = 82/108 (75%)
Query: 19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHG 78
G AH+ +TFNNT +TITDP GN ++W+S VGF GS+K++P+AAQ+A +D + KA+ G
Sbjct: 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFG 60
Query: 79 MSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
M +++V V G GAGR+SA+RAL+A G + SI DVT I HNGCRP KR
Sbjct: 61 MKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108
>gnl|CDD|181987 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
Length = 132
Score = 72.7 bits (179), Expect = 2e-14
Identities = 47/126 (37%), Positives = 66/126 (52%), Gaps = 9/126 (7%)
Query: 12 ERKNIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDC 70
+ G AH+ ++FNNT ITITD G TIA SS +V + ++SP+AA A +
Sbjct: 3 SMRKEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKA 62
Query: 71 SAKAQNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCR 122
+ A+ G++ + +KV G G +A+RAL G I I DVT I H+G R
Sbjct: 63 AEDAKEKGITGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTR 122
Query: 123 PRKRRR 128
P RR
Sbjct: 123 PPGGRR 128
>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This model
describes exclusively the archaeal ribosomal protein
S11P. It excludes homologous ribosomal proteins S14 from
eukaryotes and S11 from bacteria.
Length = 114
Score = 67.5 bits (165), Expect = 8e-13
Identities = 46/112 (41%), Positives = 61/112 (54%), Gaps = 9/112 (8%)
Query: 19 GRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77
G AH+ S+FNNT ITITD G TIA SS +V + ++SP+AA A + KA+
Sbjct: 3 GIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKER 62
Query: 78 GMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGC 121
G++ L +KV G G +A+RAL G I I DVT I H+G
Sbjct: 63 GITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114
>gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional.
Length = 149
Score = 52.6 bits (126), Expect = 3e-08
Identities = 39/122 (31%), Positives = 64/122 (52%), Gaps = 9/122 (7%)
Query: 16 IVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA 74
+V G AH+ ++FN+T I +TD G T+ + + + ++SP+AA +A D +A+
Sbjct: 26 LVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARC 85
Query: 75 QNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
+ G+++L +K+ G G +ALRAL G I I DVT I + R +
Sbjct: 86 KELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGG 145
Query: 127 RR 128
RR
Sbjct: 146 RR 147
>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
Length = 409
Score = 28.2 bits (63), Expect = 0.59
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 88 GLGAGRDS---ALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
GL AG D A+ L +GF V I VT + G P+ R
Sbjct: 88 GLAAGFDKNAEAVEGLLGLGFGFVEIGSVTPLPQPG-NPKPR 128
>gnl|CDD|173384 PTZ00090, PTZ00090, 40S ribosomal protein S11; Provisional.
Length = 233
Score = 28.0 bits (62), Expect = 0.66
Identities = 28/121 (23%), Positives = 50/121 (41%), Gaps = 18/121 (14%)
Query: 20 RAHVVSTFNNTRITITDPHGN--TIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77
+ ++ NN + + N T+ S VGF + S A ++ + K +
Sbjct: 120 MLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKLQQSERCAYRIGENIAKKCRRL 179
Query: 78 GMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAH---------NGCRPRKRRR 128
G+ ++++K + ++ L+A A G VT I H N +PRKRRR
Sbjct: 180 GIFAVDIKFRRI-MRVETVLQAFYANGL------QVTQIIHEPRLPKCGLNAVKPRKRRR 232
Query: 129 I 129
+
Sbjct: 233 V 233
>gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 27.8 bits (63), Expect = 0.84
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 86 VSGL-GAGRDSALRALRAIGFTIV 108
V+GL GAG+ ALRAL +G+ V
Sbjct: 11 VTGLSGAGKSVALRALEDLGYYCV 34
>gnl|CDD|162334 TIGR01391, dnaG, DNA primase, catalytic core. This protein
contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim
domain (Pfam:PF01751).
Length = 415
Score = 26.0 bits (58), Expect = 2.6
Identities = 17/49 (34%), Positives = 17/49 (34%), Gaps = 21/49 (42%)
Query: 23 VVSTFNNTRIT--ITDPHGNTIAWSSPKVVGFSGSRK---------NSP 60
F N RI I DP G VVGF G R NSP
Sbjct: 195 YYDRFRN-RIMFPIHDPKGR--------VVGFGG-RALGDEKPKYLNSP 233
>gnl|CDD|164924 PHA02523, 43B, DNA polymerase subunit B; Provisional.
Length = 391
Score = 25.8 bits (56), Expect = 3.0
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 32 ITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLE 83
+ + D G A K++G R ++P A Q + + + G SSL+
Sbjct: 197 LNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEGESSLQ 248
>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family
of proteins found in this equivalog include the
characterized LysX from Thermus thermophilus which is
part of a well-organized lysine biosynthesis gene
cluster. LysX is believed to carry out an ATP-dependent
acylation of the amino group of alpha-aminoadipate in
the prokaryotic version of the fungal AAA lysine
biosynthesis pathway. No species having a sequence in
this equivalog contains the elements of the more common
diaminopimelate lysine biosythesis pathway, and none has
been shown to be a lysine auxotroph. These sequences
have mainly recieved the name of the related enzyme,
"ribosomal protein S6 modification protein RimK". RimK
has been characterized in E. coli, and acts by
ATP-dependent condensation of S6 with glutamate
residues.
Length = 280
Score = 25.8 bits (57), Expect = 3.3
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 87 SGLGAGRDSALRALRAIGFTIVS 109
+ L R++AL+ A+G+ +V
Sbjct: 105 TYLAFDREAALKLAEALGYPVVL 127
>gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 25.6 bits (57), Expect = 3.5
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKN 58
+ R+ +TD G + S + VG SR N
Sbjct: 91 VDYRVYVTDAQGIVLFDSEGRAVGQDYSRWN 121
>gnl|CDD|140255 PTZ00228, PTZ00228, variable surface protein Vir21; Provisional.
Length = 350
Score = 25.5 bits (56), Expect = 3.9
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 6 SRIRNRERKNIVS--GRAH 22
S +R + KNIV+ AH
Sbjct: 313 SSLRKGKGKNIVNIDEEAH 331
>gnl|CDD|181813 PRK09382, ispDF, bifunctional 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase/2-C-methyl-D-erythritol
2,4-cyclodiphosphate synthase protein; Provisional.
Length = 378
Score = 25.6 bits (57), Expect = 4.2
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 96 ALRALRAIGFTIVSICDVTMIA 117
A +R G I++ DVT+IA
Sbjct: 297 AADFVREAGGEIIN-ADVTIIA 317
>gnl|CDD|178328 PLN02727, PLN02727, NAD kinase.
Length = 986
Score = 25.2 bits (55), Expect = 4.7
Identities = 7/19 (36%), Positives = 15/19 (78%)
Query: 10 NRERKNIVSGRAHVVSTFN 28
N+ R+ ++SGR+ ++S+F
Sbjct: 147 NKGREEVLSGRSSIMSSFR 165
>gnl|CDD|182226 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
Length = 186
Score = 24.7 bits (54), Expect = 6.6
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 90 GAGRDSALRALRA 102
G+G+DS L ALR
Sbjct: 12 GSGKDSLLAALRQ 24
>gnl|CDD|180189 PRK05667, dnaG, DNA primase; Validated.
Length = 580
Score = 24.8 bits (55), Expect = 7.4
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 88 GLG---AGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK----RRRI 129
G+G G D+ L+ L GF+ + + ++ N R RI
Sbjct: 151 GIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRI 199
>gnl|CDD|183478 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 24.5 bits (53), Expect = 7.5
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 12/61 (19%)
Query: 39 GNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR 98
G+ IA + VV G+ N F + C+ + L+VKVSG GA R +A +
Sbjct: 163 GHKIALPTYTVVATHGAAHNQQFEVE-----CT-------VPKLDVKVSGSGASRRAAEQ 210
Query: 99 A 99
A
Sbjct: 211 A 211
>gnl|CDD|178970 PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed.
Length = 505
Score = 24.5 bits (54), Expect = 7.6
Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 1/16 (6%)
Query: 29 NTRIT-ITDPHGNTIA 43
NT IT + DP G IA
Sbjct: 438 NTGITAVIDPLGRIIA 453
>gnl|CDD|185007 PRK15047, PRK15047, N-hydroxyarylamine O-acetyltransferase;
Provisional.
Length = 281
Score = 24.4 bits (53), Expect = 8.8
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 98 RALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
R LR +GF + S+ ++++ P + R+
Sbjct: 78 RVLRELGFNVRSLLGRVVLSNPPALPPRTHRL 109
>gnl|CDD|179576 PRK03381, PRK03381, PII uridylyl-transferase; Provisional.
Length = 774
Score = 24.2 bits (53), Expect = 9.3
Identities = 13/42 (30%), Positives = 14/42 (33%), Gaps = 1/42 (2%)
Query: 89 LGAG-RDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
LG G R RAL TI DV PR+
Sbjct: 256 LGLGDRFDLARALSDAARTISYAVDVGWRTAANALPRRGLSA 297
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.130 0.385
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,065,544
Number of extensions: 113915
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 257
Number of HSP's successfully gapped: 34
Length of query: 129
Length of database: 5,994,473
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,201,009
Effective search space: 193246414
Effective search space used: 193246414
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: 51 (23.3 bits)