RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein
[Candidatus Liberibacter asiaticus str. psy62]
(190 letters)
>gnl|CDD|178881 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 172
Score = 127 bits (322), Expect = 2e-30
Identities = 47/170 (27%), Positives = 83/170 (48%), Gaps = 6/170 (3%)
Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRK 56
M K + L+++ I + HG+ GEV + S+ + P + + + +E+ I
Sbjct: 1 MSKPEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFH 60
Query: 57 NKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYW 116
I F G+D+ ++A L+ +L+ R ELEEDE++ DL +E D G+
Sbjct: 61 KGFLIVKFEGVDDRNAAEALKGCELFVPRSQL--PELEEDEYYWHDLIGLEVVDEDGEEL 118
Query: 117 GQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIA 166
G+V + GA +L + ++ LIPF + V EV+L+ +I +D
Sbjct: 119 GKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLEAKRITVDWPE 168
>gnl|CDD|162792 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM. This family
consists of the bacterial protein RimM (YfjA, 21K), a
30S ribosomal subunit-binding protein implicated in 16S
ribsomal RNA processing. It has been partially
characterized in Escherichia coli, is found with other
translation-associated genes such as trmD. It is broadly
distributed among bacteria, including some minimal
genomes such the aphid endosymbiont Buchnera aphidicola.
The protein contains a PRC-barrel domain that it shares
with other protein families (pfam05239) and a unique
domain (pfam01782). This model describes the full-length
protein. A member from Arabidopsis (plant) has
additional N-terminal sequence likely to represent a
chloroplast transit peptide.
Length = 165
Score = 122 bits (309), Expect = 5e-29
Identities = 52/166 (31%), Positives = 90/166 (54%), Gaps = 8/166 (4%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKMYRK---NKRFI 61
L+++ IG HG+ GEV + S+ + P L Y L +++ + +K+ R N + I
Sbjct: 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSKQWQTVKVARVRKQNNKLI 60
Query: 62 ATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCG 121
F GID+ +A L+ L+L+ R+ ELEEDE++ TDL +E +G+ G+V
Sbjct: 61 VKFEGIDDREAAEALKGLELFVPREAL--PELEEDEYYWTDLIGLEVVTEEGEELGKVVE 118
Query: 122 VYNFGAGSILEIKN-TMEKTFLIPFTKFAVLEVNLQENKILIDPIA 166
+ GA +L +++ +K LIPF + V E++L++ I +D
Sbjct: 119 ILETGANDVLVVRSKKGKKEVLIPFVEEIVKEIDLEKKIITVDWPE 164
>gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 161
Score = 102 bits (256), Expect = 6e-23
Identities = 51/148 (34%), Positives = 75/148 (50%), Gaps = 7/148 (4%)
Query: 21 GEVYIDSYANNPIDLNRY-VLYSND-NRELRILKMYRKNK-RFIATFSGIDNIHSASELR 77
GEV + S+ +P+ + Y L + D R + R K +A G+ +A LR
Sbjct: 3 GEVRLKSFTEDPLAIADYGPLTTEDGARSFTVALA-RPAKDGLVARLKGVATREAAEALR 61
Query: 78 DLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTM 137
L+LY R EL++DEF++ DL + D G G+V V+NFGAG ILEI
Sbjct: 62 GLELYVPRDRLP--ELDDDEFYHADLIGLAAVDTGGALLGRVKAVHNFGAGDILEIAPPG 119
Query: 138 EK-TFLIPFTKFAVLEVNLQENKILIDP 164
T L+PFT+ V V+L +++ DP
Sbjct: 120 GGPTLLLPFTRAVVPTVDLAAGRVVADP 147
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 165
Score = 80.5 bits (199), Expect = 2e-16
Identities = 50/161 (31%), Positives = 88/161 (54%), Gaps = 6/161 (3%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKMYRKNKRFIATF 64
L+ + I + HG+ G V I ++ +P +++ Y + ++ ++ ++ + N IA
Sbjct: 2 LICLGVITSPHGIKGHVKIKTFTEDPENISAYGKLTDGSNTYKISVVSVIGANL-VIAKI 60
Query: 65 SGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYN 124
SGI++ A LR+ KLY +R K L EDEF+ +DL ME +G + +YN
Sbjct: 61 SGINSRTEAELLRNKKLYVERS--KLPNLNEDEFYQSDLIGMEVKLEDNTIYGYIKKIYN 118
Query: 125 FGAGSILEIKNT-MEKTFLIPFTKFAVLEVNLQENKILIDP 164
FG+ I+EI T +K+ ++PFTK +N++E I++ P
Sbjct: 119 FGSCDIIEISLTSTKKSTMLPFTKEIFPHINVKERYIILVP 159
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 171
Score = 44.5 bits (105), Expect = 2e-05
Identities = 32/121 (26%), Positives = 56/121 (46%), Gaps = 5/121 (4%)
Query: 47 ELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEM 106
E+ +L++ +F+ F G D A + R L+ ++ E + EF++ DL +
Sbjct: 47 EIALLEIRPHGGKFLVRFEGYDTPEEAVKWRGGSLFLPQELLPKIE-TKGEFYSEDLIGL 105
Query: 107 ETFDRQGKY--WGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKI-LID 163
+ D GK W ++ V + A IL + LIPF V +++L++ I LI
Sbjct: 106 QAIDETGKPLNW-KLTDVQDNPAHPILVFIKGEGEEILIPFLNVFVGDLDLEKQTIVLIQ 164
Query: 164 P 164
P
Sbjct: 165 P 165
>gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 162
Score = 42.8 bits (101), Expect = 5e-05
Identities = 37/164 (22%), Positives = 66/164 (40%), Gaps = 19/164 (11%)
Query: 13 IGTTHGLNGEVYIDSYANNP--IDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNI 70
G +G+ G + + P +DL R +Y I + R + +G+ +
Sbjct: 9 FGGPYGVQGGL---KFRGEPVVLDLPR--VYVEGLGWRAIERAERVGPELVLHLAGVTSR 63
Query: 71 HSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSI 130
A L L++YA D LEE ++ +L + + G+ G+V V + GA +
Sbjct: 64 EGAEALVGLRVYADDADLPP--LEEGSYYYHELRGLPVYV-DGEPLGEVVDVEDAGAQDL 120
Query: 131 LEIKN-----TMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGL 169
L I++ T+ +P V ++ + I D I GL
Sbjct: 121 LVIRHVGGSLRARATYFVPLQAPYVR---VELDGITADAI-PGL 160
>gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 169
Score = 38.1 bits (88), Expect = 0.002
Identities = 38/163 (23%), Positives = 74/163 (45%), Gaps = 9/163 (5%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY------VLYSNDNRELRILKMYRKNKRF 60
V +A IG T+ LNGE+ + AN+ L Y + +N ++L+ + ++ +
Sbjct: 5 FVEIAKIGATYKLNGELNLYPLANSIETLLSYGDWYIQLPATNVWQQLKGESVLKRADKV 64
Query: 61 IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
+ I+N +A + + + ++ +L EDE + DL + +G V
Sbjct: 65 YIKLANINNADTAKKYVNALIGVPKRALP--QLAEDEVYFKDLIGCSVKNINNDSFGVVV 122
Query: 121 GVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILID 163
+ GA +L K + +LIP+ K ++ +L KI++D
Sbjct: 123 DIIETGANEVLVCKEDNSE-YLIPYVKQYIVSEDLNSKKIVVD 164
>gnl|CDD|173057 PRK14593, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 184
Score = 34.2 bits (78), Expect = 0.020
Identities = 48/185 (25%), Positives = 76/185 (41%), Gaps = 23/185 (12%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYS----NDNRELRILKMY-------R 55
++L+ IG + GLNG + + ++ P L + V S N K Y
Sbjct: 4 MLLVGRIGKSVGLNGGLKLHLESDFPECLKKGVKVSVAPLNAFSCASSFKDYVIHSYEHA 63
Query: 56 KNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDE-ELEEDEFFNTDLEEMETFDRQGK 114
KN F+ T I A EL +L L+ + K L+E EFF DL + + + +
Sbjct: 64 KNLLFLET---IHTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVE-ENE 119
Query: 115 YWGQVCGVYNFGAGSILEIKNT-------MEKTFLIPFTKFAVLEVNLQENKILIDPIAA 167
G+V + ++ T + K FLIP+ F + E+ LQ+ KI
Sbjct: 120 ILGKVIEIQRISQTDYFMVETTLSLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKT 179
Query: 168 GLNNT 172
L N+
Sbjct: 180 LLENS 184
>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
Length = 815
Score = 27.1 bits (60), Expect = 3.3
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 78 DLKLYAKRQDFKDEELEED 96
+LKLY KR +KD +L+E+
Sbjct: 306 ELKLYGKRGVYKDSKLQEE 324
>gnl|CDD|182821 PRK10899, PRK10899, hypothetical protein; Provisional.
Length = 1022
Score = 26.4 bits (59), Expect = 4.3
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 152 EVNLQENKILIDPIAAGLNNTTMKN 176
EV L+ N + I P+ ++T+KN
Sbjct: 436 EVTLRNNSLFIKPL-----DSTLKN 455
>gnl|CDD|179087 PRK00685, PRK00685, metal-dependent hydrolase; Provisional.
Length = 228
Score = 25.5 bits (57), Expect = 7.5
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 7/39 (17%)
Query: 149 AVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAG 187
+ + KILIDP G NP D +
Sbjct: 9 SAFLIETGGKKILIDPFITG-------NPLADLKPEDVK 40
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
0.318 0.137 0.392
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,126,740
Number of extensions: 196188
Number of successful extensions: 358
Number of sequences better than 10.0: 1
Number of HSP's gapped: 344
Number of HSP's successfully gapped: 25
Length of query: 190
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,092,969
Effective search space: 417482838
Effective search space used: 417482838
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: 54 (24.7 bits)