RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12
[Candidatus Liberibacter asiaticus str. psy62]
(124 letters)
>gnl|CDD|179949 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 210 bits (536), Expect = 9e-56
Identities = 87/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
MPT+NQL+RK RK S +K AL PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1 MPTINQLVRKGRK-SKVKKSKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD GVK+RKQ RS+YGA
Sbjct: 60 GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQGRSKYGA 119
Query: 121 ERPK 124
+RPK
Sbjct: 120 KRPK 123
>gnl|CDD|130054 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/organelle.
This model recognizes ribosomal protein S12 of Bacteria,
mitochondria, and chloroplasts. The homologous ribosomal
proteins of Archaea and Eukarya, termed S23 in Eukarya
and S12 or S23 in Archaea, score below the trusted
cutoff.
Length = 124
Score = 182 bits (464), Expect = 2e-47
Identities = 88/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
MPT+NQLIRK RK + +K AL PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1 MPTINQLIRKGRKKKKKK-SKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD GVKNRKQ RS+YGA
Sbjct: 60 GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQGRSKYGA 119
Query: 121 ERPK 124
+RPK
Sbjct: 120 KRPK 123
>gnl|CDD|185456 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 124 bits (313), Expect = 6e-30
Identities = 53/95 (55%), Positives = 70/95 (73%)
Query: 25 LRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLC 84
L G PQK+G+C++V TP+KPNS LRKV + RL++G V Y+PG GHNL HSVV++
Sbjct: 120 LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGHNLNTHSVVLVR 179
Query: 85 GGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYG 119
GGR KD+PG Y+ +RGV D VKNR ++RS+YG
Sbjct: 180 GGRCKDVPGCNYKAVRGVYDLLPVKNRARSRSKYG 214
>gnl|CDD|179789 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
Length = 145
Score = 54.6 bits (132), Expect = 7e-09
Identities = 41/108 (37%), Positives = 62/108 (57%), Gaps = 11/108 (10%)
Query: 21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPGEG--HNLQE 77
K L G P RG+ L V K+PNSA+RK ++ +L +G +V A+ PG+G + + E
Sbjct: 38 KADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDE 97
Query: 78 HSVVMLCG-----GRVK-DLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
H V++ G GR D+PGV+Y+VI+ GV + VK +K+ R
Sbjct: 98 HDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145
>gnl|CDD|130055 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12). This model
represents the eukaryotic and archaeal homologs of
bacterial ribosomal protein S12. This protein is known
typically as S23 in eukaryotes and as either S12 or S23
in the Archaea.
Length = 139
Score = 54.1 bits (130), Expect = 1e-08
Identities = 38/120 (31%), Positives = 64/120 (53%), Gaps = 11/120 (9%)
Query: 9 RKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAY 67
R+ ++ R K L G P RG+ L V ++PNSA+RK ++ +L +G V A+
Sbjct: 20 RRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAF 79
Query: 68 VPGEG--HNLQEHSVVML------CGGRVKDLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
PG+G + + EH V++ G + D+PGV+Y+V++ V + VK +K+ R
Sbjct: 80 CPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 43.6 bits (103), Expect = 2e-05
Identities = 28/97 (28%), Positives = 54/97 (55%), Gaps = 8/97 (8%)
Query: 12 RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPG 70
+K K G +G+ + + K+PNSA+RK ++ +L +G ++ A+VP
Sbjct: 28 KKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPN 87
Query: 71 EG--HNLQEHSVVMLCG-GR----VKDLPGVKYRVIR 100
+G + + E+ V++ G GR V D+PGV+++V++
Sbjct: 88 DGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVK 124
>gnl|CDD|179368 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 28.6 bits (65), Expect = 0.48
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 61 GVEVIAYVPGEGHNLQEH 78
G+ V+ +PG G NLQ+H
Sbjct: 282 GIPVVHDLPGVGENLQDH 299
>gnl|CDD|185641 PTZ00462, PTZ00462, Serine-repeat antigen protein; Provisional.
Length = 1004
Score = 28.1 bits (62), Expect = 0.68
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 49 ALRKVIKARLTSGVEVIAYVPGE---GHNLQEHSVVMLCGGRVKD 90
A K+IK + + VIAY+ E G+ V LCG D
Sbjct: 678 AFIKIIKDEIMNKGSVIAYIKAENVLGYEFNGKKVQNLCGDDTAD 722
>gnl|CDD|163029 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 25.7 bits (56), Expect = 3.1
Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 5/56 (8%)
Query: 39 YTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGV 94
Y + P A + + + VE IA NL HS V L K LP V
Sbjct: 1690 YMQSKVSPTDATDPKVATTVPAAVEAIARTVETAVNLPPHSEVEL-----KKLPAV 1740
>gnl|CDD|181677 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 25.4 bits (56), Expect = 3.9
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNP 29
+P R+ R G F A A + L NP
Sbjct: 1814 VPYTKSTARELRDGRFDAEAALARLEDNP 1842
>gnl|CDD|183935 PRK13271, treA, trehalase; Provisional.
Length = 569
Score = 25.3 bits (55), Expect = 5.0
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 50 LRKVIKARLTSGVEVIAYVPGEGHNLQEH 78
LR + T E YVP EG +L+EH
Sbjct: 94 LRHFVNVNFTLPKEGEKYVPPEGQSLREH 122
>gnl|CDD|179894 PRK04926, dgt, deoxyguanosinetriphosphate triphosphohydrolase;
Provisional.
Length = 503
Score = 24.9 bits (55), Expect = 5.1
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 96 YRVIRGVLD 104
YRVI G+LD
Sbjct: 403 YRVISGLLD 411
>gnl|CDD|162541 TIGR01810, betA, choline dehydrogenase. This enzyme is a member of
the GMC oxidoreductase family (pfam00732 and pfam05199),
sharing a common evoluntionary origin and enzymatic
reaction with alcohol dehydrogenase. Outgrouping from
this model, Caulobacter crescentus shares sequence
homology with choline dehydrogenase, yet other genes
participating in this enzymatic reaction have not
currently been identified.
Length = 532
Score = 24.8 bits (54), Expect = 6.4
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 61 GVEVIAYVPGEGHNLQEH 78
G+E ++PG G NLQ+H
Sbjct: 275 GIEPRIHLPGVGENLQDH 292
>gnl|CDD|117685 pfam09129, Chol_subst-bind, Cholesterol oxidase,
substrate-binding. The substrate-binding domain found
in Cholesterol oxidase is composed of an eight-stranded
mixed beta-pleated sheet and six alpha-helices. This
domain is positioned over the isoalloxazine ring system
of the FAD cofactor bound by FAD_binding_4 (PF:PF01565)
and forms the roof of the active site cavity, allowing
for catalysis of oxidation and isomerisation of
cholesterol to cholest-4-en-3-one.
Length = 321
Score = 24.9 bits (54), Expect = 6.5
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 36 LRVYTVTPKKPNSA 49
L+V+TV+P KP+ A
Sbjct: 49 LKVWTVSPTKPDGA 62
>gnl|CDD|182549 PRK10560, hofQ, outer membrane porin HofQ; Provisional.
Length = 386
Score = 24.4 bits (53), Expect = 8.4
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 7 LIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL 58
L P K + + K L ++ G L V++ + N A ++ +AR
Sbjct: 36 LTDVPWKQALQTVVKSAGLI--LRQEGNILSVHSQAWQNENIARQEAEQARA 85
>gnl|CDD|148074 pfam06246, Isy1, Isy1-like splicing family. Isy1 protein is
important in the optimisation of splicing.
Length = 253
Score = 24.2 bits (53), Expect = 8.7
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 86 GRVKDLPGVK 95
GR K+LPGVK
Sbjct: 128 GRAKELPGVK 137
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
0.320 0.136 0.400
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,989,323
Number of extensions: 114572
Number of successful extensions: 197
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 23
Length of query: 124
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,222,617
Effective search space: 177349914
Effective search space used: 177349914
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 (23.4 bits)