RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3
[Candidatus Liberibacter asiaticus str. psy62]
(221 letters)
>gnl|CDD|178784 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 303 bits (778), Expect = 3e-83
Identities = 106/213 (49%), Positives = 138/213 (64%), Gaps = 4/213 (1%)
Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60
M G++ +K+GMT ++ +G IPVTV+ V +T++K+GY AVQ+G G+ K K
Sbjct: 1 MMKGILGKKVGMTQIFTEDGESIPVTVIEAGPNVVTQVKTVEKDGYNAVQLGFGDKKEKR 60
Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
V+KP G F+ V PK+ L EFRV + VG + F GQ VDVTG + GKGF
Sbjct: 61 VNKPEAGHFAKAGVEPKRHLREFRV---VEEYEVGQEITVDIFEAGQKVDVTGTSKGKGF 117
Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
+G +KRHNF G A+HG S SHR GS G RQ PGRVFK KKMAG MG RVTV+NLEVV
Sbjct: 118 AGVIKRHNFSGGPASHGNSRSHRRPGSIGARQTPGRVFKGKKMAGHMGNERVTVQNLEVV 177
Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213
VD +R L+LVKG VPGA K ++++ + K+
Sbjct: 178 KVDAERNLLLVKGAVPGA-KGGLVIIKPAVKAK 209
>gnl|CDD|163362 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 291 bits (748), Expect = 9e-80
Identities = 108/204 (52%), Positives = 139/204 (68%), Gaps = 2/204 (0%)
Query: 4 GVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSK 63
G++ +K+GMT ++ +G+ +PVTV+ + V +T++K+GY AVQ+G GE K K V+K
Sbjct: 1 GLLGKKVGMTQIFTEDGKAVPVTVIEVGPNVVTQVKTVEKDGYSAVQLGFGEKKEKRVNK 60
Query: 64 PMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGA 123
P G F+ V PK+ L EFRV D + VG + F GQ VDVTG + GKGF+G
Sbjct: 61 PEAGHFAKAGVEPKRHLREFRV-DDLEGYEVGDEITVDIFEAGQKVDVTGTSKGKGFAGV 119
Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183
MKRHNF G A+HG S SHR+ GS G RQ PGRVFK KKMAG MG RVTV+NLEVV VD
Sbjct: 120 MKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEVVKVD 179
Query: 184 DKRGLILVKGCVPGAKKNSWILVR 207
+R L+LVKG VPGA K S +L++
Sbjct: 180 AERNLLLVKGAVPGA-KGSLVLIK 202
>gnl|CDD|163363 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam family
pfam00297. Eukaryotic proteins are excluded from this
model.
Length = 330
Score = 63.9 bits (156), Expect = 3e-11
Identities = 48/154 (31%), Positives = 63/154 (40%), Gaps = 32/154 (20%)
Query: 76 PKKK--LFEFRVQKDD---------DLLPVGSVFSPS-YFTVGQLVDVTGMTIGKGFSGA 123
PKKK + E R+ +L G S S F GQLVDV +T GKGF G
Sbjct: 151 PKKKPEIMEIRIGGGSVEERFEYALSIL--GKEISVSDVFKEGQLVDVIAVTKGKGFQGV 208
Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183
+KR L H R G+ G P RV AG+MG ++ T N ++ +
Sbjct: 209 VKRWGVKLLPRKHKRRKGGRHIGTLGPWT-PSRVRWTVPQAGQMGYHQRTEYNKRILKIG 267
Query: 184 D------------KRGL-----ILVKGCVPGAKK 200
+ GL +L+KG VPG K
Sbjct: 268 EDGDEITPKGGFVNYGLVRNDYVLIKGSVPGPSK 301
>gnl|CDD|179795 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
Length = 337
Score = 53.7 bits (130), Expect = 4e-08
Identities = 48/154 (31%), Positives = 63/154 (40%), Gaps = 32/154 (20%)
Query: 76 PKKK--LFEFRVQKDD---------DLLPVGSVFSPS-YFTVGQLVDVTGMTIGKGFSGA 123
PKKK + E R+ +LL G S S F GQLVDV +T GKGF G
Sbjct: 156 PKKKPEIMEIRIGGGSVEERLEYAKELL--GKEISISDVFKEGQLVDVIAVTKGKGFQGV 213
Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183
+KR L H R G+ G P RV AG+MG ++ T N ++ +
Sbjct: 214 VKRWGVKLLPRKHKRRGGSRHIGTLGPWN-PSRVMWTVPQAGQMGFHQRTEYNKRILKIG 272
Query: 184 D-----------------KRGLILVKGCVPGAKK 200
D + +L+KG VPG K
Sbjct: 273 DDGDEITPKGGFLHYGLVRNDYVLIKGSVPGPAK 306
>gnl|CDD|185447 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
Length = 390
Score = 33.9 bits (78), Expect = 0.030
Identities = 47/190 (24%), Positives = 64/190 (33%), Gaps = 63/190 (33%)
Query: 43 KNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSY 102
K M +QV G K V K L E V PV SVF
Sbjct: 174 KAHVMEIQVNGGSVAEK--------------VDFAKSLLEKEV-------PVDSVFQQ-- 210
Query: 103 FTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGC--RQDPGRVFKN 160
+++DV G+T G GF G +KR +G T +HR C P RV
Sbjct: 211 ---NEMIDVIGVTKGHGFEGVVKR--WG---VTRLPRKTHRGLRKVACIGAWHPARVQYT 262
Query: 161 KKMAGRMGGNRVTVKNLEVVSV---DDKRG---------------------------LIL 190
AG+ G + T N ++ + +D ++
Sbjct: 263 VPRAGQHGYHHRTELNKKIYRIGVAEDPNNATTEADLTEKTITPMGGFPHYGTVRNDFLM 322
Query: 191 VKGCVPGAKK 200
+KGCV G KK
Sbjct: 323 LKGCVVGPKK 332
>gnl|CDD|162117 TIGR00932, 2a37, transporter, monovalent cation:proton antiporter-2
(CPA2) family.
Length = 273
Score = 28.4 bits (64), Expect = 1.4
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 81 FEFRVQKDDDLLPVGSVFSPSYF-TVGQLVD 110
E+R + + DL P+G V P +F +VG VD
Sbjct: 243 SEYRHKLESDLEPIGGVLLPLFFISVGMSVD 273
>gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I,
proteobacterial subset. This enzyme resembles some
other chorismate-binding enzymes, including
para-aminobenzoate synthase (pabB) and isochorismate
synthase. There is a fairly deep split between two sets,
seen in the pattern of gaps as well as in amino acid
sequence differences. This group includes proteobacteria
such as E. coli and Helicobacter pylori but also the
gram-positive organism Corynebacterium glutamicum. The
second group includes eukaryotes, archaea, and most
other bacterial lineages; sequences from the second
group may resemble pabB more closely than other trpE
from this group.
Length = 498
Score = 27.9 bits (62), Expect = 2.0
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 10/53 (18%)
Query: 12 MTCVYNIEGRRI-----PVTVL----HLDNCQVVVHRTLDKNGYMAVQVGAGE 55
M +Y EG+R V L LD C +V+ +NG VQ GAG
Sbjct: 418 MQLIYQAEGQRRGSYGGAVGYLTSHGDLDTC-IVIRSAFVENGIATVQAGAGI 469
>gnl|CDD|163551 TIGR03839, termin_org_P1, adhesin P1. Members of this protein family
are the major adhesin of the Mycoplasma terminal
organelle. The protein is called adhesin P1, cytadhesin
P1, P140, attachment protein, and MgPa, with locus names
MG191 in Mycoplasma genitalium and MPN141 in M.
pneumoniae. A conserved C-terminal region is shared by
additional paralogs in M. pneumoniae and M.
gallisepticum, as well as by the member of this family.
Length = 1425
Score = 27.8 bits (61), Expect = 2.0
Identities = 19/73 (26%), Positives = 23/73 (31%)
Query: 45 GYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFT 104
+ V A RG F S S F+ D D V S + +
Sbjct: 949 TWGEVNGLYNTALNITYYNLTRGDFGSNTPSTPGIGFKPEQNNDSDATLVSSGLNWTPQD 1008
Query: 105 VGQLVDVTGMTIG 117
VG LV TG G
Sbjct: 1009 VGNLVVSTGTQQG 1021
>gnl|CDD|183059 PRK11253, ldcA, L,D-carboxypeptidase A; Provisional.
Length = 305
Score = 27.6 bits (62), Expect = 2.4
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 84 RVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFG 130
Q+DD LL VG S FT QL + FSG M +FG
Sbjct: 93 ARQQDDPLLIVGH----SDFTAIQLA-LLAQANVITFSGPMLAADFG 134
>gnl|CDD|130373 TIGR01306, GMP_reduct_2, guanosine monophosphate reductase,
bacterial. A deep split separates two families of GMP
reductase. The other (TIGR01305) is found in eukaryotic
and some proteobacterial lineages, including E. coli,
while this family is found in a variety of bacterial
lineages.
Length = 321
Score = 27.6 bits (61), Expect = 2.5
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 12/80 (15%)
Query: 32 NCQVVVHRT----LDKNGYMAVQVGAGEAKVKNVSKPM--RGFFSSVNVSPKKKLFEFRV 85
N Q ++ L +NGY + E K M RG F+S++V K +EF
Sbjct: 41 NMQTIIDEKLAEQLAENGYFYIMHRFDEESRIPFIKDMQERGLFASISVGVKACEYEFVT 100
Query: 86 QKDDDLLPVGSVFSPSYFTV 105
Q ++ L +P Y T+
Sbjct: 101 QLAEEAL------TPEYITI 114
>gnl|CDD|163300 TIGR03508, decahem_SO, decaheme c-type cytochrome, DmsE family.
Members of this family are small, decaheme c-type
cytochromes, related DmsE of Shewanella oneidensis
MR-1, which has been shown to be part of an anaerobic
dimethyl sulfoxide reductase.
Length = 258
Score = 27.8 bits (62), Expect = 2.6
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 52 GAGEAKVKNVSKPMRGFFSSVNVSPKK 78
G G VK +PM F S N+ +K
Sbjct: 42 GPGGKHVKGGGEPMITFGSFSNLPAEK 68
>gnl|CDD|179377 PRK02135, PRK02135, hypothetical protein; Provisional.
Length = 201
Score = 27.5 bits (62), Expect = 2.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 28 LHLDNCQVVVHRTLDKNGY 46
LH D+C ++H LD+ GY
Sbjct: 181 LHADHCITLIHNELDRRGY 199
>gnl|CDD|178849 PRK00082, hrcA, heat-inducible transcription repressor;
Provisional.
Length = 339
Score = 26.7 bits (60), Expect = 4.7
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 170 NRVTVKNLEVVSVDDKRGL-ILV 191
+ +K++E+V + R L +LV
Sbjct: 132 SDSRLKHIELVPLSPHRALAVLV 154
>gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This is
a bacterial family of proteins with unknown function.
Length = 452
Score = 26.9 bits (59), Expect = 4.7
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 54 GEAKVKNVSKPMRGFFSSVNVSPKKKLFEF 83
GE +++ KP FFS + + KKL+ F
Sbjct: 412 GENYMRDFKKPKSNFFSKILIFRIKKLWPF 441
>gnl|CDD|179633 PRK03699, PRK03699, putative transporter; Provisional.
Length = 394
Score = 26.8 bits (60), Expect = 5.0
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 101 SYFTVGQLVDVTGMTIG 117
SY G LV VTGM +G
Sbjct: 15 SYALTGALVIVTGMVMG 31
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
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,530,432
Number of extensions: 217591
Number of successful extensions: 362
Number of sequences better than 10.0: 1
Number of HSP's gapped: 356
Number of HSP's successfully gapped: 18
Length of query: 221
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,049,753
Effective search space: 530517643
Effective search space used: 530517643
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 (25.5 bits)