RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13610
(123 letters)
>gnl|CDD|188357 TIGR03632, bact_S11, 30S ribosomal protein S11. This model
describes the bacterial 30S ribosomal protein S11.
Cutoffs are set such that the model excludes archaeal
and eukaryotic ribosomal proteins, but many chloroplast
and mitochondrial equivalents of S11 are detected
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 108
Score = 70.3 bits (173), Expect = 6e-17
Identities = 31/74 (41%), Positives = 44/74 (59%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGV 86
+ +I T NNTI++++D +G V S G GFK ++K T AAQ A KKA E G+
Sbjct: 2 VAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGM 61
Query: 87 SSVRINVRGLGPGR 100
+V + V+G G GR
Sbjct: 62 KTVDVYVKGPGAGR 75
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 70.6 bits (174), Expect = 6e-17
Identities = 35/80 (43%), Positives = 48/80 (60%), Gaps = 2/80 (2%)
Query: 23 KNLP--IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKK 80
KN+P + +I T NNTI++++D +G V S G GFK +RK T AAQ A KK
Sbjct: 13 KNIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKK 72
Query: 81 ALEIGVSSVRINVRGLGPGR 100
A E G+ +V + V+G G GR
Sbjct: 73 AKEHGMKTVEVFVKGPGSGR 92
>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 66.5 bits (163), Expect = 2e-15
Identities = 38/92 (41%), Positives = 53/92 (57%), Gaps = 4/92 (4%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGV 86
+ +I + NNTI++++D G V + S G GFK +RK T AAQ A KKA E G+
Sbjct: 20 VAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGI 79
Query: 87 SSVRINVRGLGPGR---LKALE-IGVSSVRIN 114
SV + V+G GPGR ++AL G+ RI
Sbjct: 80 KSVEVKVKGPGPGREAAIRALAAAGLKITRIE 111
>gnl|CDD|189537 pfam00411, Ribosomal_S11, Ribosomal protein S11.
Length = 109
Score = 65.8 bits (161), Expect = 3e-15
Identities = 33/79 (41%), Positives = 47/79 (59%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGV 86
I +I+ + NNTI++++D G V L S G GFK +RK T AAQ A K A E G+
Sbjct: 2 IAHIQASFNNTIITITDVIGRVVLWSSAGGCGFKGSRKSTPYAAQTAAENAAKIAKEQGI 61
Query: 87 SSVRINVRGLGPGRLKALE 105
++ + ++G GPGR AL
Sbjct: 62 KALEVKIKGPGPGRESALR 80
>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11.
Length = 116
Score = 65.7 bits (161), Expect = 4e-15
Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 6/89 (6%)
Query: 30 IRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSV 89
I+ + NNTI++++D +G V S G GFK ARKGT AAQ A + ++ G+
Sbjct: 18 IQASFNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMKRA 77
Query: 90 RINVRGLGPGR---LKALE---IGVSSVR 112
+ ++G G GR L+A+ + +SS+R
Sbjct: 78 EVMIKGPGLGRDTALRAIRRSGLKLSSIR 106
>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This
model describes exclusively the archaeal ribosomal
protein S11P. It excludes homologous ribosomal proteins
S14 from eukaryotes and S11 from bacteria [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 114
Score = 37.5 bits (87), Expect = 2e-04
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIG 85
I +I + NNTI++++D G + RS G K R + + AA A +KA E G
Sbjct: 4 IAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERG 63
Query: 86 VSSVRINVRGLG 97
++ + I VR G
Sbjct: 64 ITGLHIKVRAPG 75
>gnl|CDD|236588 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
Length = 132
Score = 34.6 bits (80), Expect = 0.004
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIG 85
I +I + NNTI++++D G + +S G K R + + AA A + A E G
Sbjct: 11 IAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKG 70
Query: 86 VSSVRINVRGLGPGRLK 102
++ V I VR G K
Sbjct: 71 ITGVHIKVRAPGGNGQK 87
>gnl|CDD|239052 cd02137, Nitroreductase_1, Nitroreductase-like family 1. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 148
Score = 31.0 bits (71), Expect = 0.085
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 53 SCGMEGF--KNARKGTNIAAQAA---GITIGKKALEIGVSSVRINV 93
+C M GF + + N+ A+ I IGK A E G S R+ V
Sbjct: 100 TCPMGGFDAEKVAELLNLPARYVPVMLIAIGKAAEEEGPPSYRLPV 145
>gnl|CDD|226733 COG4283, COG4283, Uncharacterized conserved protein [Function
unknown].
Length = 170
Score = 27.9 bits (62), Expect = 1.2
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 18 DGLKFKNLPIMNIRVTKNNTILSLSDAK 45
G K+ NL +N K LSL + K
Sbjct: 78 PGYKWNNLGELNQWFWKKYQHLSLKELK 105
>gnl|CDD|240235 PTZ00032, PTZ00032, 60S ribosomal protein L18; Provisional.
Length = 211
Score = 27.1 bits (60), Expect = 2.3
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 65 GTNIAAQAAGITIGKKALEIGVSSVRINVRGLGP--GRLKALEIGVSSVRIN 114
GT AA G IG+KAL G+S VR + R G+++AL G +V +
Sbjct: 160 GTIKAAYELGKLIGRKALSKGISKVRFD-RAHYKYAGKVEALAEGARAVGLQ 210
>gnl|CDD|130890 TIGR01831, fabG_rel, 3-oxoacyl-(acyl-carrier-protein) reductase,
putative. This model represents a small, very well
conserved family of proteins closely related to the FabG
family, TIGR01830, and possibly equal in function. In
all completed genomes with a member of this family, a
FabG in TIGR01830 is also found [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 239
Score = 26.8 bits (59), Expect = 2.8
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 12/70 (17%)
Query: 30 IRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGVSSV 89
IR + I++L+ GV+ R N +A AG+ KAL + ++
Sbjct: 123 IRARQGGRIITLASVSGVM------------GNRGQVNYSAAKAGLIGATKALAVELAKR 170
Query: 90 RINVRGLGPG 99
+I V + PG
Sbjct: 171 KITVNCIAPG 180
>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
Length = 117
Score = 25.9 bits (58), Expect = 4.5
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 59 FKNARKGTNI-AAQAAGITIGKKALEIGVSSV 89
+ KG N AA+ G I ++A G+ V
Sbjct: 59 VRAGLKGGNKEAAKKVGKLIAERAKAKGIKQV 90
>gnl|CDD|168128 PRK05613, PRK05613, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 437
Score = 26.4 bits (58), Expect = 5.4
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 4 KDIFPDENTPDLIFDGLKFKNL 25
K +FP TPD + GLK+ +L
Sbjct: 244 KPVFPYFVTPDPAYHGLKYADL 265
>gnl|CDD|226329 COG3807, COG3807, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 171
Score = 25.9 bits (57), Expect = 5.4
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 65 GTNIAAQAAGITIGKKALEI----GVSSVRINVRGLGPGRLKALE 105
T AA A G TIG L + + S +N R +GPG A+E
Sbjct: 14 ITAGAAAAQGTTIGASGLPLPRFVSLKSAEVNAR-VGPGTDYAVE 57
>gnl|CDD|225892 COG3356, COG3356, Predicted membrane protein [Function unknown].
Length = 578
Score = 26.3 bits (58), Expect = 5.8
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 82 LEIGVSSVRINVRGLGPGRLKALEIGVSSVR 112
+E+GV +V++ V LG + L V S
Sbjct: 523 VEVGVRTVKVKVEVLGENNFQTLVSTVESTV 553
>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a
ribosomal protein found in the central protuberance (CP)
of the large subunit. L18 binds 5S rRNA and induces a
conformational change that stimulates the binding of L5
to 5S rRNA. Association of 5S rRNA with 23S rRNA depends
on the binding of L18 and L5 to 5S rRNA. L18/L5e is
generally described as L18 in prokaryotes and archaea,
and as L5e (or L5) in eukaryotes. In bacteria, the CP
proteins L5, L18, and L25 are required for the ribosome
to incorporate 5S rRNA into the large subunit, one of
the last steps in ribosome assembly. In archaea, both
L18 and L5 bind 5S rRNA; in eukaryotes, only the L18
homolog (L5e) binds 5S rRNA but a homolog to L5 is also
identified.
Length = 103
Score = 25.2 bits (56), Expect = 6.9
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 59 FKNARKGTNI-AAQAAGITIGKKALEIGVSSVRINVRG-LGPGRLKALEIGVS 109
G N+ AA G + K+ALE G+ V + G GR+KAL G
Sbjct: 47 KGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRYHGRVKALAKGAR 99
>gnl|CDD|233961 TIGR02644, Y_phosphoryl, pyrimidine-nucleoside phosphorylase. In
general, members of this protein family are designated
pyrimidine-nucleoside phosphorylase, enzyme family EC
2.4.2.2, as in Bacillus subtilis, and more narrowly as
the enzyme family EC 2.4.2.4, thymidine phosphorylase
(alternate name: pyrimidine phosphorylase), as in
Escherichia coli. The set of proteins encompassed by
this model is designated subfamily rather than equivalog
for this reason; the protein name from this model should
be used when TIGR02643 does not score above trusted
cutoff [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 405
Score = 25.7 bits (57), Expect = 8.3
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 57 EGFKNARKGTNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGRLK 102
+ A+ + A+ +G A E+G+++V LG GR +
Sbjct: 325 DKLPKAKYKEEVKAEKSGYISEIDAEELGLAAVD-----LGAGRAR 365
>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 25.3 bits (56), Expect = 8.4
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 65 GTNI-AAQAAGITIGKKALEIGVSSVRINVRGLGP----GRLKAL 104
G N AA G I ++AL G+ V V G GR+ AL
Sbjct: 73 GGNTEAAYLVGKLIAERALAKGIEEV---VFDRGGYKYHGRVAAL 114
>gnl|CDD|235441 PRK05388, argJ, bifunctional ornithine
acetyltransferase/N-acetylglutamate synthase protein;
Validated.
Length = 395
Score = 25.4 bits (57), Expect = 9.7
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 55 GMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88
G +G ++AR A+ GI A E+ V+S
Sbjct: 77 GEQGLQDARATAEAVAELLGI----PAEEVLVAS 106
>gnl|CDD|216811 pfam01960, ArgJ, ArgJ family. Members of the ArgJ family
catalyze the first EC:2.3.1.1 and fifth steps
EC:2.3.1.35 in arginine biosynthesis.
Length = 380
Score = 25.5 bits (57), Expect = 9.7
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 55 GMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88
G +G ++AR+ + A+ GI E+ V+S
Sbjct: 70 GEQGLEDAREMAELVAELLGI----PPEEVLVAS 99
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
0.319 0.140 0.391
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,209,128
Number of extensions: 543205
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 583
Number of HSP's successfully gapped: 32
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (21.7 bits)
S2: 53 (24.1 bits)