RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3
[Candidatus Liberibacter asiaticus str. psy62]
(221 letters)
>gnl|CDD|30436 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 243 bits (621), Expect = 4e-65
Identities = 111/214 (51%), Positives = 138/214 (64%), Gaps = 3/214 (1%)
Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNV 61
G + K+GMT V++ G +PVTV+ + VV +T + +GY AVQVGAG+ K K V
Sbjct: 1 MLGFLGYKVGMTHVFDERGISVPVTVIEVPPNVVVQVKTYETDGYRAVQVGAGDRKAKRV 60
Query: 62 SKPMRGFFSSVNVSPKKKLFEFRVQKDD--DLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119
+KP+ G F+ V PK+ L EFRV D + VG + F G+LVDVTG+T GKG
Sbjct: 61 NKPLVGHFAKAGVKPKRHLAEFRVGGGDVAEKFEVGQEITVDVFKEGELVDVTGVTKGKG 120
Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179
F G MKR F G A+HG S+SHR GS G RQ PGRVFK KKMAG MG RVTV+NLEV
Sbjct: 121 FQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEV 180
Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213
V VD + LILVKG VPGAKK ++VR + K+
Sbjct: 181 VKVDVENNLILVKGAVPGAKK-RLVVVRPAVKAK 213
>gnl|CDD|38351 KOG3141, KOG3141, KOG3141, Mitochondrial/chloroplast ribosomal
protein L3 [Translation, ribosomal structure and
biogenesis].
Length = 310
Score = 229 bits (584), Expect = 6e-61
Identities = 101/215 (46%), Positives = 132/215 (61%), Gaps = 3/215 (1%)
Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRT-LDKNGYMAVQVGAGEAKVKN 60
R GV+ARKLGM +++ +G RIPVT+L +D+ V+ + T K GY AVQVG G K K
Sbjct: 62 RVGVIARKLGMMPLWDKDGERIPVTILQVDDNHVIKYITPEAKGGYFAVQVGYGTVKPKK 121
Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
++K G F S V PK+ L EFRV ++ LLP G+ +F GQ VDVTG TIGKGF
Sbjct: 122 LTKAELGHFRSAGVPPKRHLREFRV-TEEALLPPGTPLFARHFKPGQYVDVTGKTIGKGF 180
Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
G MKRH F G A+HG S SHR GS G PGRV+ +KM G MG T+K L+V
Sbjct: 181 QGVMKRHGFKGGPASHGTSKSHRRPGSIGQGTTPGRVWPGRKMPGHMGNEWRTIKGLKVW 240
Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVN 215
+D + +I VKG VPG K + + ++D+ V+
Sbjct: 241 KIDTELNVIWVKGSVPG-PKGNLVKIKDAILPTVD 274
>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated.
Length = 207
Score = 190 bits (484), Expect = 3e-49
Identities = 88/201 (43%), Positives = 126/201 (62%), Gaps = 2/201 (0%)
Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60
M G++ K+GMT +++ G IPVT+L + C + +TL +GY A+Q+G + K
Sbjct: 1 MSIGLLGTKIGMTQIFDETGNAIPVTILKVGPCVITQIKTLTTDGYNAIQIGYKQVSTKK 60
Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
++KP G NV P K L EFRV+ ++ VG + F+VGQLV+V+G +IGKGF
Sbjct: 61 LTKPQLGHLQKSNVPPLKYLKEFRVKSSEEF-EVGQPLTVDAFSVGQLVNVSGKSIGKGF 119
Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
+G KRHNF THG S +HR+ GS G PGRV+ KKMAGR+G +VT+KNL+++
Sbjct: 120 AGLQKRHNFSRGPMTHG-SKNHRAPGSIGAGTTPGRVYPGKKMAGRLGNKKVTIKNLKIL 178
Query: 181 SVDDKRGLILVKGCVPGAKKN 201
VD + L+++KG VPG N
Sbjct: 179 KVDSENNLLVLKGSVPGKPGN 199
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3.
Length = 199
Score = 175 bits (445), Expect = 9e-45
Identities = 79/195 (40%), Positives = 105/195 (53%), Gaps = 5/195 (2%)
Query: 9 KLGMTCVY-NIEGRRIPVTVLHLDNCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPM 65
K GMT ++ +G PVTV+ + VV +T ++ +GY A+QVG K V K +
Sbjct: 1 KAGMTHIFTEKKGVLEPVTVIEVPPMVVVQVKTYEETNDGYKAIQVGLESIKKYRVVKRV 60
Query: 66 RGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMK 125
G PK + EFRV ++ P ++ F G+ VDVTG+T GKGF G MK
Sbjct: 61 LGHTQKRGTPPKAHVMEFRVNGGEEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVMK 120
Query: 126 RHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDK 185
R F L HG HR GS G PGRVF KMAG+MG + T +NL++ +D +
Sbjct: 121 RWGFKRLPRKHGRGY-HRKPGSIG-AWHPGRVFPGVKMAGQMGNHHRTEQNLKIYRIDQE 178
Query: 186 RGLILVKGCVPGAKK 200
L+LVKG VPG KK
Sbjct: 179 NNLLLVKGSVPGPKK 193
>gnl|CDD|40019 KOG4822, KOG4822, KOG4822, Predicted nuclear membrane protein
involved in mRNA transport and sex determination via
splicing modulation [RNA processing and modification,
Signal transduction mechanisms].
Length = 1906
Score = 28.2 bits (62), Expect = 2.1
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 54 GEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTG 113
GE+K K + P ++ P E + L+ GS S S G +V G
Sbjct: 24 GESKFKRLCNPF--LYTPSAPYP----LEVEAVVTNHLVVRGSYRSLSLIVYGNIVKDLG 77
Query: 114 M 114
Sbjct: 78 Q 78
>gnl|CDD|110448 pfam01446, Rep_1, Replication protein. Replication proteins (rep)
are involved in plasmid replication. The Rep protein
binds to the plasmid DNA and nicks it at the double
strand origin (dso) of replication. The 3'-hydroxyl end
created is extended by the host DNA replicase, and the
5' end is displaced during synthesis. At the end of one
replication round, Rep introduces a second single
stranded break at the dso and ligates the ssDNA
extremities generating one double-stranded plasmid and
one circular ssDNA form. Complementary strand synthesis
of the circular ssDNA is usually initiated at the
single-stranded origin by the host RNA polymerase.
Length = 232
Score = 26.9 bits (60), Expect = 4.9
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 19/55 (34%)
Query: 57 KVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDD-------LLPVGSVFSPSYFT 104
+ K V K + G+ S V+ K D LL V PSYFT
Sbjct: 54 QYKKVKKNLLGYIRSTEVTVNK--------DDGSYHPHFHVLLMV----KPSYFT 96
>gnl|CDD|38005 KOG2794, KOG2794, KOG2794, Delta-aminolevulinic acid dehydratase
[Coenzyme transport and metabolism].
Length = 340
Score = 26.1 bits (57), Expect = 9.2
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 65 MRGFFSSVNVSPKKKLFE-FRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFS 121
+R + N+SP ++ F + +DD P+ S+ V +L + + KG
Sbjct: 27 LRAWQQETNISPANLIYPLFIHEGEDDFTPIDSMPGIYRLGVNRLKEELAPLVAKGLR 84
>gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA
helicase [RNA processing and modification].
Length = 1042
Score = 25.8 bits (56), Expect = 9.2
Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 16 YNIEGRRIPVTVLHL-DNCQVVVHRTLDKNGYMAVQVGAGE 55
+ I GR PV +++ + V + + + + G+
Sbjct: 525 FTIPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGD 565
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,581,360
Number of extensions: 129431
Number of successful extensions: 267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 256
Number of HSP's successfully gapped: 12
Length of query: 221
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,318,927
Effective search space: 565779437
Effective search space used: 565779437
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: 55 (25.0 bits)