RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3777
(99 letters)
>gnl|CDD|235418 PRK05338, rplS, 50S ribosomal protein L19; Provisional.
Length = 116
Score = 138 bits (351), Expect = 3e-44
Identities = 53/93 (56%), Positives = 72/93 (77%), Gaps = 3/93 (3%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
MNLI++IE E++ +K+IP+F GDT+ V++ V+EG ++RIQA+EG+VI+RR +GLN
Sbjct: 1 MNLIKEIEAEQL---RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNET 57
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
F VRKISY G+ERTF L+SP I SI V RRG
Sbjct: 58 FTVRKISYGVGVERTFPLHSPRIDSIEVVRRGK 90
>gnl|CDD|201683 pfam01245, Ribosomal_L19, Ribosomal protein L19.
Length = 113
Score = 120 bits (304), Expect = 3e-37
Identities = 48/93 (51%), Positives = 68/93 (73%), Gaps = 3/93 (3%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
MNLI++IE E++ KK++P+F GDT+ V++ + EG ++RIQ +EG+VI++R +GLNS
Sbjct: 1 MNLIKEIEAEQL---KKDLPEFRVGDTVKVHVKIKEGNKERIQVFEGVVIAKRGRGLNST 57
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
F VRKIS G+ER F L+SP I I V RRG
Sbjct: 58 FTVRKISQGVGVERVFPLHSPRIDKIEVVRRGK 90
>gnl|CDD|223412 COG0335, RplS, Ribosomal protein L19 [Translation, ribosomal
structure and biogenesis].
Length = 115
Score = 116 bits (292), Expect = 3e-35
Identities = 50/99 (50%), Positives = 75/99 (75%), Gaps = 4/99 (4%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
+ +IQ++EQE+I KK+IP F GDT+ V++ ++EG+++R+QA+EG+VI+RR +G++
Sbjct: 3 IPIIQQLEQEQI---KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISET 59
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD-RNAYI 98
F VRKISY G+ER F L+SP+I SI V RRG R A +
Sbjct: 60 FTVRKISYGVGVERVFPLHSPLIESIEVVRRGKVRRAKL 98
>gnl|CDD|130096 TIGR01024, rplS_bact, ribosomal protein L19, bacterial type.
This model describes bacterial ribosomoal protein L19
and its chloroplast equivalent. Putative mitochondrial
L19 are found in several species (but not Saccharomyces
cerevisiae) and score between trusted and noise cutoffs
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 110 bits (278), Expect = 3e-33
Identities = 52/99 (52%), Positives = 71/99 (71%), Gaps = 4/99 (4%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
NLI++IEQE +LKK++PDF GDT+ V++ ++EG ++RIQ +EG+VI+RR G+
Sbjct: 1 QNLIKQIEQE---QLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGET 57
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD-RNAYI 98
F VRKISY G+ER F L+SP I SI V RRG R A +
Sbjct: 58 FTVRKISYGVGVERIFPLHSPNIDSIEVVRRGKVRRAKL 96
>gnl|CDD|177023 CHL00084, rpl19, ribosomal protein L19.
Length = 117
Score = 83.4 bits (207), Expect = 2e-22
Identities = 40/90 (44%), Positives = 60/90 (66%), Gaps = 3/90 (3%)
Query: 2 NLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNF 61
L+++IE E + KKN+P GDT+ V + + EG ++R+Q YEG VI+++N GLN+
Sbjct: 6 QLVKEIESEFL---KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTI 62
Query: 62 IVRKISYNEGIERTFQLYSPIISSIIVKRR 91
VRK+ G+ER F L+SP ++SI V RR
Sbjct: 63 TVRKVFQGIGVERVFLLHSPKLASIEVLRR 92
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 28.6 bits (65), Expect = 0.44
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 2 NLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVI--SRRNKGLNS 59
LI ++ EI LK PDF TG II + G R+ + G + ++
Sbjct: 163 ALIALLDGPEITLLKIPGPDFPTGGGIIGS----GGIREAYKTGRGKITVRAKIEIEERK 218
Query: 60 NFIVRKISYN 69
++ ++ Y
Sbjct: 219 TIVITELPYG 228
>gnl|CDD|233615 TIGR01880, Ac-peptdase-euk, N-acyl-L-amino-acid amidohydrolase.
This model represents a family of eukaryotic
N-acyl-L-amino-acid amidohydrolases active on fatty acid
and acetyl amides of L-amino acids.
Length = 400
Score = 28.6 bits (64), Expect = 0.46
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEG 37
+ I++ + + L+ N PD GD VNL ++G
Sbjct: 222 VESIRRFRESQFQLLQSN-PDLAIGDVTSVNLTKLKG 257
>gnl|CDD|235413 PRK05330, PRK05330, coproporphyrinogen III oxidase; Provisional.
Length = 300
Score = 28.2 bits (64), Expect = 0.67
Identities = 17/51 (33%), Positives = 18/51 (35%), Gaps = 22/51 (43%)
Query: 42 IQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRG 92
+ AY IV R K Y E ER FQLY RRG
Sbjct: 211 LDAYLPIV--ERRKDT---------PYGER-EREFQLY----------RRG 239
>gnl|CDD|193524 cd05646, M20_AcylaseI_like, M20 Aminoacylase-I like subfamily.
Peptidase M20 family, Aminoacylase-I like (AcyI-like;
Acylase I; N-acyl-L-amino-acid amidohydrolase; EC
3.5.1.14) subfamily. Acylase I is involved in the
hydrolysis of N-acylated or N-acetylated amino acids
(except L-aspartate) and is considered as a potential
target of antimicrobial agents. Porcine AcyI is also
shown to deacetylate certain quorum-sensing
N-acylhomoserine lactones, while the rat enzyme has been
implicated in degradation of chemotactic peptides of
commensal bacteria. Prokaryotic arginine synthesis
usually involves the transfer of an acetyl group to
glutamate by ornithine acetyltransferase in order to
form ornithine. However, Escherichia coli
acetylornithine deacetylase (acetylornithinase, ArgE)
(EC 3.5.1.16) catalyzes the deacylation of
N2-acetyl-L-ornithine to yield ornithine and acetate.
Phylogenetic evidence suggests that the clustering of
the arg genes in one continuous sequence pattern arose
in an ancestor common to Enterobacteriaceae and
Vibrionaceae, where ornithine acetyltransferase was lost
and replaced by a deacylase.
Length = 391
Score = 27.2 bits (61), Expect = 1.4
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 1 MNLIQKI---EQEEIIRLKKNIPDFVTGDTIIVNLNVIEG 37
M +I+K +E+ RLK N GD VNL +++G
Sbjct: 212 MKVIEKFMEFREEQFQRLKSN-GKLTIGDVTSVNLTMLKG 250
>gnl|CDD|218854 pfam06012, DUF908, Domain of Unknown Function (DUF908).
Length = 309
Score = 26.2 bits (58), Expect = 2.9
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 49 VISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGDRNAYI 98
VISRR+ + + + YN +E+ +L S SS I + D + +
Sbjct: 58 VISRRSSYFS--PRLLRKKYNILLEKLLKLASSWPSSPIPGGKSDGLSLV 105
>gnl|CDD|233776 TIGR02198, rfaE_dom_I, rfaE bifunctional protein, domain I. RfaE
is a protein involved in the biosynthesis of
ADP-L-glycero-D-manno-heptose, a precursor for LPS inner
core biosynthesis. RfaE is a bifunctional protein in E.
coli, and separate proteins in some other genome. The
longer, N-terminal domain I (this family) is suggested
to act in D-glycero-D-manno-heptose 1-phosphate
biosynthesis, while domain II (TIGR02199) adds ADP to
yield ADP-D-glycero-D-manno-heptose [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 315
Score = 26.0 bits (58), Expect = 3.4
Identities = 8/59 (13%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 8 EQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKI 66
++++R+ D + + + ++ R+++ + + +V+S KG+ + +V+++
Sbjct: 110 RNQQLLRVDFEERDPINAE---LEARLLAAIREQLASADAVVLSDYAKGVLTPRVVQEV 165
>gnl|CDD|179568 PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiporter;
Provisional.
Length = 504
Score = 25.5 bits (56), Expect = 6.8
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 56 GLNSNFIVRKISYNEGIERTFQLYSPIISSIIV 88
GL + + + + GI T QL + II+ I+
Sbjct: 209 GLATPLVTECMQWLFGIPHTLQLDAIIITCWII 241
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.142 0.381
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,235,851
Number of extensions: 466203
Number of successful extensions: 443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 438
Number of HSP's successfully gapped: 31
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
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 (21.9 bits)
S2: 53 (24.2 bits)