RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2274
(244 letters)
>gnl|CDD|185648 PTZ00469, PTZ00469, 60S ribosomal subunit protein L18; Provisional.
Length = 187
Score = 80.1 bits (197), Expect = 2e-18
Identities = 47/94 (50%), Positives = 60/94 (63%), Gaps = 2/94 (2%)
Query: 54 SKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRFMKKPTREGRV 113
SK+ YL LLVKLYRFL RRTN+ FNKII KRL M K RPP+++SK+ R M + V
Sbjct: 21 SKNPYLRLLVKLYRFLARRTNANFNKIIAKRLIMPKRFRPPLSLSKLHRHMA--SYPDDV 78
Query: 114 AVIVGTIVDDPRMWTIPKLTIVRFMKKPTREGRV 147
AV+VG+I DD R++ KL + T R+
Sbjct: 79 AVVVGSITDDKRLYDCKKLKVCALRFTETARKRI 112
Score = 39.3 bits (91), Expect = 7e-04
Identities = 19/25 (76%), Positives = 20/25 (80%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSK 192
LYRFL RRTN+ FNKII KRL M K
Sbjct: 32 LYRFLARRTNANFNKIIAKRLIMPK 56
>gnl|CDD|216140 pfam00828, Ribosomal_L18e, Ribosomal protein L18e/L15. This family
includes eukaryotic L18 as well as prokaryotic L15.
Length = 122
Score = 78.0 bits (193), Expect = 2e-18
Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 11/101 (10%)
Query: 37 VDICHKYDRRVRRTKPKSKDV-YLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPM 95
+ R+ R + + + V LYR L +R ++LF S+ NRPP+
Sbjct: 3 IGKTRGRGRKGGRGRAGGQKHHFEGGQVPLYRRLGKRGF--------RKLFKSRKNRPPV 54
Query: 96 AISKIVRFMKK--PTREGRVAVIVGTIVDDPRMWTIPKLTI 134
+SK+ R M K +G V+VGT+ DD ++ +LT
Sbjct: 55 NLSKLDRKMLKDGEEVDGETLVVVGTVTDDVKVLGNGELTK 95
>gnl|CDD|140222 PTZ00195, PTZ00195, 60S ribosomal protein L18; Provisional.
Length = 198
Score = 79.7 bits (196), Expect = 2e-18
Identities = 41/103 (39%), Positives = 66/103 (64%), Gaps = 8/103 (7%)
Query: 45 RRVRRTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRFM 104
RV R S + Y++LL+KLY+FL +RT+S FNK++ +RL S+ NR P+++S+I M
Sbjct: 12 SRVVRHHTYSTNPYIKLLIKLYKFLAKRTSSGFNKVVYQRLIKSRSNRAPISLSRIAVVM 71
Query: 105 KKPT------REGRVAVIVGTIVDDPRMWTIPKLTI--VRFMK 139
K+ ++ +AV+VG ++DD RM IP + + +RF K
Sbjct: 72 KRKAVFTAKGKKAPIAVVVGDVLDDVRMARIPAMRVCALRFSK 114
Score = 36.2 bits (83), Expect = 0.008
Identities = 14/29 (48%), Positives = 22/29 (75%)
Query: 166 LTLYRFLTRRTNSKFNKIILKRLFMSKIN 194
+ LY+FL +RT+S FNK++ +RL S+ N
Sbjct: 30 IKLYKFLAKRTSSGFNKVVYQRLIKSRSN 58
>gnl|CDD|224641 COG1727, RPL18A, Ribosomal protein L18E [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 73.9 bits (182), Expect = 6e-17
Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 8/94 (8%)
Query: 49 RTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRFMKKPT 108
K S +VYL L++ R RR+++ K + +RL + NR + +SKI R+
Sbjct: 3 MKKTGSTNVYLRKLIRFLRKAARRSSAPIWKDVAERLEKPRRNRAEVNVSKINRY----A 58
Query: 109 REGRVAVIVGTIVDDPRMWTIPKLTI--VRFMKK 140
+EG V+ G ++ D + K+T+ +RF K
Sbjct: 59 KEGDTVVVPGKVLGDGK--LDKKVTVAALRFSKT 90
Score = 31.9 bits (73), Expect = 0.10
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
R RR+++ K + +RL + N
Sbjct: 19 FLRKAARRSSAPIWKDVAERLEKPRRN 45
>gnl|CDD|130916 TIGR01857, FGAM-synthase, phosphoribosylformylglycinamidine
synthase, clade II. This model represents a
single-molecule form of
phosphoribosylformylglycinamidine synthase, also called
FGAM synthase, an enzyme of purine de novo biosynthesis.
This model represents a second clade of these enzymes
found in Clostridia, Bifidobacteria and Streptococcus
species. This enzyme performs the fourth step in IMP
biosynthesis (the precursor of all purines) from PRPP
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 1239
Score = 30.2 bits (68), Expect = 1.1
Identities = 25/108 (23%), Positives = 37/108 (34%), Gaps = 26/108 (24%)
Query: 136 RFMKKPTREGRVAVIVGTIVDDPRMWTIPKLTLYRFLTRRTNSKFNKII-LKRLFMSKIN 194
F+ E A +V T+ + PR+ N I+ L R F+ N
Sbjct: 559 AFLAYCNEENLEATVVATVTEKPRL--------------VMNWNGKTIVDLSRRFLDT-N 603
Query: 195 SISERELDVKPTNTLALLPVFPTVTR---------KLTSDLKAASLNG 233
+ + +D K + LP T K+ SDL AS G
Sbjct: 604 GVRQ-VIDAKVVDKDVKLPEERQKTSAETLEEDWLKVLSDLNVASQKG 650
Score = 27.5 bits (61), Expect = 8.8
Identities = 25/103 (24%), Positives = 40/103 (38%), Gaps = 13/103 (12%)
Query: 102 RFMKKPTREGRVAVIVGTIVDDPRM---WTIPKLTIVRFMKKPTREGRVAVIVGTIVDDP 158
F+ E A +V T+ + PR+ W TIV ++ V ++ V D
Sbjct: 559 AFLAYCNEENLEATVVATVTEKPRLVMNWN--GKTIVDLSRRFLDTNGVRQVIDAKVVDK 616
Query: 159 RMWTIPKLTLYRFLTRRTNSKFNKIILKRLFMSKINSISEREL 201
+ KL R T + + LK L S +N S++ L
Sbjct: 617 DV----KLPEERQKT--SAETLEEDWLKVL--SDLNVASQKGL 651
>gnl|CDD|237723 PRK14479, PRK14479, dihydroxyacetone kinase; Provisional.
Length = 568
Score = 28.6 bits (65), Expect = 3.0
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 124 PRMWTIPKLTIVRFMKKPTREGRVAVIVG 152
P + + +VR + PT EG+VAV+ G
Sbjct: 24 PDLVRLVPGGVVR--RTPTPEGKVAVVSG 50
>gnl|CDD|224283 COG1364, ArgJ, N-acetylglutamate synthase (N-acetylornithine
aminotransferase) [Amino acid transport and metabolism].
Length = 404
Score = 28.4 bits (64), Expect = 3.8
Identities = 31/116 (26%), Positives = 40/116 (34%), Gaps = 24/116 (20%)
Query: 80 IILKRLFMSKINRPPMAISKIVRFMKKPTREGRVA-VIVGTIVDDPRMWTIPKLTIVRFM 138
+I +RL M KI I K+V + A I+ T D T+PK V
Sbjct: 119 VIGERLPMDKILA---GIEKLVSDLGSEDGWLEAAEAIMTT---D----TVPKQAAVEAE 168
Query: 139 -KKPTREGRVAVIVGTIVDDPRMWT----------IPKLTLYRFLTRRTNSKFNKI 183
G +A G I P M T I L + L R + FN I
Sbjct: 169 IGGTVTIGGIAKGSGMI--HPNMATMLAFITTDAAIEPAALQKALRRAVDKTFNMI 222
>gnl|CDD|179544 PRK03140, PRK03140, phosphatidylserine decarboxylase;
Provisional.
Length = 259
Score = 27.6 bits (62), Expect = 4.9
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 64 KLYRFLTRRTNSKFNKIILKRLFMSKINRP 93
LYR L TN +F +L++ S+++
Sbjct: 4 TLYRLLIELTNGRFTSYLLRKFAQSRLSSI 33
>gnl|CDD|169548 PRK08666, PRK08666, 5'-methylthioadenosine phosphorylase;
Validated.
Length = 261
Score = 27.4 bits (61), Expect = 6.2
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 112 RVAVIVGTIVDDPRMWTIPKLTIVRFMKKPTREGRVAVIVGT 153
R+A+I G+ V DP++ L +R T G V V +GT
Sbjct: 3 RIAIIGGSGVYDPKI-----LENIREETVETPYGEVKVKIGT 39
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 27.9 bits (62), Expect = 6.6
Identities = 24/132 (18%), Positives = 52/132 (39%), Gaps = 28/132 (21%)
Query: 47 VRRTKPKSKDVYLELL---VKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRF 103
+R T+P D ++L+ + LTR + + +I +R S++ + K +
Sbjct: 1426 IRPTRPIDTDRLIQLIREGIIQVPGLTRN-HLRLYDLIFRRFMASQMKPAKVLYEKAL-- 1482
Query: 104 MKKPTREGRVAVIVGTIVD------DPRMWTIPKLTIVRFMKKPTREGRVAVIVGTIVDD 157
++ ++ V V D + +PKL +G++ V+ +
Sbjct: 1483 IRYDGKDVEVEGYVEIEGDGWSRLYSLPLRVLPKL----------EKGKLKVL------E 1526
Query: 158 PRMWTIPKLTLY 169
++ PK+ LY
Sbjct: 1527 AKIRKAPKVPLY 1538
>gnl|CDD|133032 cd04189, G1P_TT_long, G1P_TT_long represents the long form of
glucose-1-phosphate thymidylyltransferase. This family
is the long form of Glucose-1-phosphate
thymidylyltransferase. Glucose-1-phosphate
thymidylyltransferase catalyses the formation of
dTDP-glucose, from dTTP and glucose 1-phosphate. It is
the first enzyme in the biosynthesis of dTDP-L-rhamnose,
a cell wall constituent and a feedback inhibitor of the
enzyme.There are two forms of Glucose-1-phosphate
thymidylyltransferase in bacteria and archeae; short
form and long form. The long form, which has an extra
50 amino acids c-terminal, is found in many species for
which it serves as a sugar-activating enzyme for
antibiotic biosynthesis and or other, unknown pathways,
and in which dTDP-L-rhamnose is not necessarily
produced.The long from enzymes also have a left-handed
parallel helix domain at the c-terminus, whereas, th
eshort form enzymes do not have this domain. The
homotetrameric, feedback inhibited short form is found
in numerous bacterial species that produce
dTDP-L-rhamnose.
Length = 236
Score = 27.1 bits (61), Expect = 7.1
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 99 KIVRFMKKPTREGRVAVIVGTIVDDPRMWTIPKL---TIVRFMKKP 141
I ++ E A I+ V+DPR + + + IVR ++KP
Sbjct: 113 GISPLVRDFLEEDADASILLAEVEDPRRFGVAVVDDGRIVRLVEKP 158
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
0.323 0.136 0.398
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,361,574
Number of extensions: 1183139
Number of successful extensions: 958
Number of sequences better than 10.0: 1
Number of HSP's gapped: 952
Number of HSP's successfully gapped: 26
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)