RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780146|ref|YP_003064559.1| 50S ribosomal protein L1
[Candidatus Liberibacter asiaticus str. psy62]
(232 letters)
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 379 bits (975), Expect = e-106
Identities = 142/229 (62%), Positives = 185/229 (80%)
Query: 3 SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62
+K+SKR + ++ +DR+ LY L +A+ ++KE ATA+FDETV++A+NLG+DPR A+Q VRG
Sbjct: 1 AKLSKRYRAAAEKVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRG 60
Query: 63 VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122
V +P+GTG VRVAVFA KA+EA+ AGADIVGGEDL E +KGG +DFD IATPDMM
Sbjct: 61 AVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGGEDLIEKIKGGWLDFDVVIATPDMM 120
Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
VG+LGRILGPRG+MPN + GTVT DVA AV+E+K+G V+FR +KAGIIHA IGKVSF+
Sbjct: 121 GKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDKAGIIHAPIGKVSFD 180
Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
+K++EN+ A + A+ KAKP+ AKG Y+K V+LSSTMG G+KVD SS +
Sbjct: 181 AEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVKVDPSSLA 229
>gnl|CDD|162232 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.
This model describes bacterial (and chloroplast)
ribosomal protein L1. The apparent mitochondrial L1 is
sufficiently diverged to be the subject of a separate
model.
Length = 227
Score = 335 bits (860), Expect = 8e-93
Identities = 139/227 (61%), Positives = 178/227 (78%)
Query: 4 KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63
K+SKR + + +DR+ LY L +A+ +LKE ATA+FDETVE+A+ LGIDPR ++Q VRG
Sbjct: 1 KLSKRYRAAREKVDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGT 60
Query: 64 VTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMP 123
V +P+GTG VRVAVFA KA+EA+ AGAD VG +DL E +K G +DFD IATPDMM
Sbjct: 61 VVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGSDDLIEKIKKGWLDFDVVIATPDMMR 120
Query: 124 LVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFEN 183
+VG+LGRILGPRG+MPN + GTVT DVA AV+ +K G V+FR++KAG IHA IGKVSF++
Sbjct: 121 VVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADKAGNIHASIGKVSFDS 180
Query: 184 KKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSF 230
+K++EN+ A + A+ KAKPS AKG Y+K + LSSTMG GIKVDLSS
Sbjct: 181 EKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPGIKVDLSSL 227
>gnl|CDD|179783 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
Length = 215
Score = 109 bits (274), Expect = 8e-25
Identities = 66/214 (30%), Positives = 104/214 (48%), Gaps = 19/214 (8%)
Query: 24 LSDAVVMLKERATAR-FDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
+ +AV E A R F ++V++ +NL ID + + V +P+G G V++AV A
Sbjct: 7 IEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAK 66
Query: 82 SSKADEAREAGADIV-GGEDLFEIVK--------GGQIDFDRCIATPDMMPLVGR-LGRI 131
A +A+EAGAD V E+L E+ + DF IA D+MPL+GR LG +
Sbjct: 67 GELALQAKEAGADYVITREELEELGGDKRAAKKLANEYDF--FIAEADLMPLIGRYLGPV 124
Query: 132 LGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191
LGPRG MP D+ V K+ V R++ H +G +++ EN+
Sbjct: 125 LGPRGKMP--TPLPPNADIKPLVERLKN-TVRIRTKDQPTFHVRVGTEDMSPEELAENID 181
Query: 192 AFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKV 225
A ++ + + +K V + +TMG +KV
Sbjct: 182 AVLNRIESKLEKGRQ--NIKSVYVKTTMGPAVKV 213
>gnl|CDD|162233 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial. This
model represents the mitochondrial homolog of bacterial
ribosomal protein L1. Unlike chloroplast L1, this form
was not sufficiently similar to bacterial forms to
include in a single bacterial/organellar L1.
Length = 141
Score = 91.0 bits (226), Expect = 2e-19
Identities = 49/141 (34%), Positives = 87/141 (61%), Gaps = 2/141 (1%)
Query: 22 YGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
Y + A V LK ++ + + + +++G+ + V+G+ + P+ G ++AVF
Sbjct: 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKESVQGMFSFPHPFGKEPKIAVFTK 60
Query: 82 -SSKADEAREAGADIVGGEDLFEIVKGGQID-FDRCIATPDMMPLVGRLGRILGPRGIMP 139
+S+ +EAREAGAD VGG+DL + ++ G+I FD IA PD++P + +L R+LGP+G+MP
Sbjct: 61 GASEVEEAREAGADYVGGDDLIKKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMP 120
Query: 140 NLRVGTVTTDVATAVRESKSG 160
+ + GTV ++ + + K G
Sbjct: 121 SPKRGTVGDNLLSMIETFKKG 141
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 53.6 bits (129), Expect = 4e-08
Identities = 56/227 (24%), Positives = 107/227 (47%), Gaps = 22/227 (9%)
Query: 9 MQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMP 67
M ++S R A+ ++ E +F ETVE+ + L D + ++ G V +P
Sbjct: 1 MSKLSSEALRKAI----AEILEGSEEKKRKFVETVELQIGLKDYDTQK-DKRFSGSVKLP 55
Query: 68 NGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDM 121
N N++V V + DEA++ G D + E L + K ++ +D +A+ +
Sbjct: 56 NVPKPNLKVCVLGDAVHCDEAKKLGLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSL 115
Query: 122 MPLVGR-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180
+P + R LG L G P L T D+ + E KS +V F+ +K + +G V
Sbjct: 116 LPQIPRLLGPGLNKAGKFPTLI--THNDDIEDKINELKS-SVKFQLKKVLCLGVAVGNVE 172
Query: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDY--VKRVTLSSTMGCGIKV 225
+++ +N++ ++ +V S+ K ++ +K + + STMG ++
Sbjct: 173 MTEEQLRQNIVLSINFLV----SLLKKNWQNIKTLHIKSTMGKPQRI 215
>gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional.
Length = 214
Score = 37.7 bits (87), Expect = 0.003
Identities = 49/212 (23%), Positives = 97/212 (45%), Gaps = 27/212 (12%)
Query: 24 LSDAV-VMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
LS+A+ +LK +F E++++ +NL DP+ ++ G + +PN + V +
Sbjct: 9 LSEAIQAVLKVDKERKFKESIDLQVNLKNYDPQK-DKRFSGSLKLPNVCRPRMTVCLLCD 67
Query: 82 SSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDMMPLVGRLGRILGPR 135
D A++ G + E+L ++ K ++ +D + + ++ V RL +GP
Sbjct: 68 LVHEDIAKKEGVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRL---VGPH 124
Query: 136 ----GIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENV- 190
G P V + + + V E +S V F+ +K + +G V +++ +NV
Sbjct: 125 MHRMGKFPT--VCSPSESLPDKVVELRS-TVKFQLKKVLCLGTCVGHVEMTEEQLRQNVV 181
Query: 191 --LAFVSAVVKAKPSVAKGDYVKRVTLSSTMG 220
+ F+ +++K K Y+K STMG
Sbjct: 182 MAINFLVSLLKKNWQNLKSAYIK-----STMG 208
>gnl|CDD|161874 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both.
Length = 322
Score = 30.1 bits (68), Expect = 0.52
Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 3/68 (4%)
Query: 56 ANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRC 115
A+ MVRG+ + G VAV EA G ++ +D+ KG D R
Sbjct: 254 ADLMVRGIARLEKGIEKGDTVAVITLKG---EAVAVGIALMSTKDIANADKGVVADVKRV 310
Query: 116 IATPDMMP 123
I P
Sbjct: 311 IMERGTYP 318
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 29.4 bits (66), Expect = 0.73
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 14/77 (18%)
Query: 44 EIAMNLGIDPRHANQMVRGVVTM-PNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLF 102
E+A + ++ VRGV + PN VR ++ + E G +I +++
Sbjct: 101 ELAREYNLIDENSGATVRGVFIIDPNQI---VRWMIYYPA-------ETGRNI---DEII 147
Query: 103 EIVKGGQIDFDRCIATP 119
I K Q+++ R +ATP
Sbjct: 148 RITKALQVNWKRKVATP 164
>gnl|CDD|183509 PRK12409, PRK12409, D-amino acid dehydrogenase small subunit;
Provisional.
Length = 410
Score = 27.7 bits (62), Expect = 2.8
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 138 MPNLRVGTV-TTDVATAVRE-----SKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191
+PN R T+ T +A A R+ ++ +DF E+ GI+H K F++ K +L
Sbjct: 97 IPNYRANTIETVRLAIAARKHLFDIAEREGIDFDLERRGILHIYHDKAGFDHAKRVNALL 156
Query: 192 A 192
A
Sbjct: 157 A 157
>gnl|CDD|180244 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 27.0 bits (61), Expect = 4.6
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 77 AVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD 120
A A ++KA E + G D++ G+ DFD TP+
Sbjct: 15 ATLAVTAKAKELKAQGRDVIS----LGA---GEPDFD----TPE 47
>gnl|CDD|178209 PLN02599, PLN02599, dihydroorotase.
Length = 364
Score = 26.6 bits (59), Expect = 5.6
Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 116 IATPDMMPLVGRLG-----------RILGPRGIMPNLRVGTVTTDVATAVRESKSGAV 162
I PD L R G R G +MPNL+ TT A A RE A+
Sbjct: 25 ITRPDDWHLHLRDGAKLAAVVPHSARHFGRAIVMPNLKPPVTTTARALAYRERIMKAL 82
>gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional.
Length = 202
Score = 26.1 bits (58), Expect = 7.5
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 115 CIAT----PDM--MPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDF 164
C+ T P + + L+ RL RG + V T DV AV K GAVDF
Sbjct: 50 CVVTDVRMPGIDGIELLRRLKA----RGSPLPVIVMTGHGDVPLAVEAMKLGAVDF 101
>gnl|CDD|180850 PRK07116, PRK07116, flavodoxin; Provisional.
Length = 160
Score = 26.2 bits (58), Expect = 8.2
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 76 VAVFATSSKADEAREAGADIVGGEDLFEIV 105
VA F+ + + E A++ G DLFEI
Sbjct: 7 VAYFSATGTTKKVAEKLAEVTGA-DLFEIK 35
>gnl|CDD|132281 TIGR03237, dnd_assoc_2, dnd system-associated protein 2. cereus
E33L, Hahella chejuensis KCTC 2396, and
Pseudoalteromonas haloplanktis TAC12.
Length = 1256
Score = 26.0 bits (57), Expect = 8.9
Identities = 10/62 (16%), Positives = 24/62 (38%)
Query: 53 PRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDF 112
P H N +V+ + + + ++ ++ E G E+L+ + G ++F
Sbjct: 125 PWHPNSIVKLLRQEIDSSMLDKTASICLLDMIKQEQAHDQVTFFGFEELYSTIADGDLEF 184
Query: 113 DR 114
Sbjct: 185 QE 186
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 0.134 0.367
Gapped
Lambda K H
0.267 0.0822 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,686,153
Number of extensions: 240626
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 553
Number of HSP's successfully gapped: 40
Length of query: 232
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 142
Effective length of database: 4,049,753
Effective search space: 575064926
Effective search space used: 575064926
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: 55 (24.8 bits)