RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13666
(278 letters)
>gnl|CDD|225567 COG3023, ampD, N-acetyl-anhydromuramyl-L-alanine amidase [Cell
envelope biogenesis, outer membrane].
Length = 257
Score = 151 bits (383), Expect = 1e-44
Identities = 92/278 (33%), Positives = 126/278 (45%), Gaps = 42/278 (15%)
Query: 6 HGMPGYVIDPFPEWEKNRNHYDSR-DGMSVKYLILHYTV-YNFAHIITAFTSNRAHNLHS 63
P I P N G +++LHYT + F S
Sbjct: 13 APSPHIDIRPSLLVSHN---ISLPPGGFGPDFIVLHYTGALDPKAHP--FFLTIPELRVS 67
Query: 64 SHYVISEKEGKYLPGGKVIQIVPDNMRAWHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEK 123
+HY+I G+++Q+VP+ RAWHAG+ W+ N SIGI LVN G
Sbjct: 68 AHYLIDRD-------GRIVQLVPEERRAWHAGVSSWQGRERCNDFSIGIELVNRG----- 115
Query: 124 FRSTNYYPFDENQIHTLGLLGKDIVSQF-KIKPQYVLGHTDIAPGSKMDPGPLFPWGKLY 182
+ P+ E QI L L KDI++++ I P+ ++GH+DIAPG K DPGPLFPW +L
Sbjct: 116 -TDASGPPYTEAQIQALIALLKDIIARYPNITPERIVGHSDIAPGRKTDPGPLFPWKRLA 174
Query: 183 LDYGIGAWLSPDEMTVEAIVRKFKPARPYPRKLDRGIFLELLKAYGYNVTI----TNKRS 238
GIGAWL A V+K+ + D E+L YGY V I +
Sbjct: 175 EALGIGAWLDT------AQVQKYLALL---KGEDVAALQEMLARYGYGVEIGVFDQETQQ 225
Query: 239 VIRAFKTHFSANQNPERI--YADITTEDMFWAWALVAK 274
V+RAF+ HF P AD+ T + AL+ K
Sbjct: 226 VVRAFQMHF----RPGLYDGEADVETIAI--LQALLEK 257
>gnl|CDD|236984 PRK11789, PRK11789, N-acetyl-anhydromuranmyl-L-alanine amidase;
Provisional.
Length = 185
Score = 86.4 bits (215), Expect = 1e-20
Identities = 53/175 (30%), Positives = 82/175 (46%), Gaps = 36/175 (20%)
Query: 25 HYDSR-DGMSVKYLILHYT-----VYNFAHIITAFTSNR----AH----NLH----SSHY 66
++D+R DG + L++H + +I FT NR AH + S+H+
Sbjct: 20 NFDARPDGEDISLLVIHNISLPPGEFGGPYIDALFT-NRLDPDAHPYFAEIAGLRVSAHF 78
Query: 67 VISEKEGKYLPGGKVIQIVPDNMRAWHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRS 126
+I G+++Q V + RAWHAG+ ++ N SIGI L G
Sbjct: 79 LIRR-------DGEIVQFVSFDDRAWHAGVSSFQGRERCNDFSIGIEL-EG--------- 121
Query: 127 TNYYPFDENQIHTLGLLGKDIVSQFKIKPQYVLGHTDIAPGSKMDPGPLFPWGKL 181
T+ PF + Q L L + + + + I + + GH+DIAPG K DPGP F W +
Sbjct: 122 TDTLPFTDAQYQALAALTRALRAAYPIIAERITGHSDIAPGRKTDPGPAFDWQRF 176
>gnl|CDD|133475 cd06583, PGRP, Peptidoglycan recognition proteins (PGRPs) are
pattern recognition receptors that bind, and in certain
cases, hydrolyze peptidoglycans (PGNs) of bacterial cell
walls. PGRPs have been divided into three classes: short
PGRPs (PGRP-S), that are small (20 kDa) extracellular
proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa
and are predicted to be transmembrane proteins; and long
PGRPs (PGRP-L), up to 90 kDa, which may be either
intracellular or transmembrane. Several structures of
PGRPs are known in insects and mammals, some bound with
substrates like Muramyl Tripeptide (MTP) or Tracheal
Cytotoxin (TCT). The substrate binding site is conserved
in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This
family includes Zn-dependent N-Acetylmuramoyl-L-alanine
Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond
between N-acetylmuramoyl and L-amino acids,
preferentially D-lactyl-L-Ala, in bacterial cell walls.
The structure for the bacteriophage T7 lysozyme shows
that two of the conserved histidines and a cysteine are
zinc binding residues. Site-directed mutagenesis of T7
lysozyme indicates that two conserved residues, a Tyr
and a Lys, are important for amidase activity.
Length = 126
Score = 75.8 bits (187), Expect = 3e-17
Identities = 39/150 (26%), Positives = 60/150 (40%), Gaps = 31/150 (20%)
Query: 33 SVKYLILHYTV----YNFAHIITAFTSNRAHNLH--SSHYVISEKEGKYLPGGKVIQIVP 86
VKY+++H+T Y A + + S H+++ G++ Q
Sbjct: 1 PVKYVVIHHTANPNCYTAAAAVRYLQNYHMRGWSDISYHFLVGG-------DGRIYQGRG 53
Query: 87 DNMRAWHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTNYYPFDENQIHTLGLLGKD 146
N WHAG N NS SIGI L+ + P Q+ L L
Sbjct: 54 WNYVGWHAGG-------NYNSYSIGIELIGNF---------DGGPPTAAQLEALAELLAY 97
Query: 147 IVSQFKIKPQY-VLGHTDIAPGSKMDPGPL 175
+V ++ I P Y ++GH D++PG PG
Sbjct: 98 LVKRYGIPPDYRIVGHRDVSPG-TECPGDA 126
>gnl|CDD|216541 pfam01510, Amidase_2, N-acetylmuramoyl-L-alanine amidase. This
family includes zinc amidases that have
N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28.
This enzyme domain cleaves the amide bond between
N-acetylmuramoyl and L-amino acids in bacterial cell
walls (preferentially: D-lactyl-L-Ala). The structure is
known for the bacteriophage T7 structure and shows that
two of the conserved histidines are zinc binding.
Length = 114
Score = 75.1 bits (185), Expect = 4e-17
Identities = 35/137 (25%), Positives = 54/137 (39%), Gaps = 24/137 (17%)
Query: 32 MSVKYLILHYTVYNFAHIITAFTSNRAHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMRA 91
+ K +++H+T A HY++ G + Q VP + RA
Sbjct: 1 LPPKGIVIHHTAGPNCATAAACAMRLRGRDAGYHYLVG-------RDGTIYQGVPLSYRA 53
Query: 92 WHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTNYYPFDENQIHTLGLLGKDIVSQF 151
WHAG NS SIGI L G + P + Q+ L L + ++
Sbjct: 54 WHAG--------GGNSASIGIELCGSGDKDD--------PPTDAQLEALAALLAWLCRRY 97
Query: 152 KIKPQY-VLGHTDIAPG 167
I P Y ++GH D++P
Sbjct: 98 GIPPDYTIVGHRDVSPT 114
>gnl|CDD|214760 smart00644, Ami_2, Ami_2 domain.
Length = 126
Score = 53.5 bits (129), Expect = 3e-09
Identities = 32/141 (22%), Positives = 55/141 (39%), Gaps = 23/141 (16%)
Query: 34 VKYLILHYTVYNFA---HIITAFTSNRAHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMR 90
+ +++H+T + A + +N +++ H+++ G+V Q V N
Sbjct: 3 PRGIVIHHTANSNASCANEARYMQNNHMNDI-GYHFLVGG-------DGRVYQGVGWNYV 54
Query: 91 AWHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTNYYPFDENQIHTLGLLGKDIVSQ 150
AWHAG N +SIGI + ++ PF E L LL K +
Sbjct: 55 AWHAGGAHT---PGYNDISIGIEFIG-------SFDSDDEPFAEALYAALDLLAKLLKGA 104
Query: 151 F--KIKPQYVLGHTDIAPGSK 169
++GH D+AP
Sbjct: 105 GLPPDGRYRIVGHRDVAPTED 125
>gnl|CDD|227919 COG5632, COG5632, N-acetylmuramoyl-L-alanine amidase [Cell envelope
biogenesis, outer membrane].
Length = 302
Score = 30.6 bits (69), Expect = 0.76
Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 16/100 (16%)
Query: 20 EKNRNHYDSRDGMSVKYLILHYTVYN--FAHIITAFTSNRAHNLHSSHYVISEKEGKYLP 77
KN+ + + M + +++H T + A ++ N +N S H + + E
Sbjct: 10 PKNKYSRNGPNAMKPEKIVIHNTANDGSTADNEISYMKN-NYNNASVHIFVDDAE----- 63
Query: 78 GGKVIQIVPDNMRAWHAG-----IGKWRRDRNLNSMSIGI 112
+IQI+P N AWHAG + N SIG+
Sbjct: 64 ---IIQIIPLNENAWHAGDGTNARFTVALNGTGNRNSIGV 100
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 29.8 bits (67), Expect = 1.7
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 5/57 (8%)
Query: 221 LELLKAYGYNV--TITNKRSVIRAFKTHFSANQNPERIYADITTEDMFWAWALVAKY 275
L A GY+V I + SV+ F N +R ++ + A + Y
Sbjct: 510 APALIAAGYHVEPDIYDPTSVLVEFPVKAG---NADRTANTVSIVEQLSLLAFLQTY 563
>gnl|CDD|173796 cd04857, Peptidases_S8_Tripeptidyl_Aminopeptidase_II, Peptidase S8
family domain in Tripeptidyl aminopeptidases_II.
Tripeptidyl aminopeptidases II are member of the
peptidase S8 or Subtilase family. Subtilases, or
subtilisin-like serine proteases, have an Asp/His/Ser
catalytic triad similar to that found in trypsin-like
proteases, but do not share their three-dimensional
structure (an example of convergent evolution).
Tripeptidyl aminopeptidase II removes tripeptides from
the free N terminus of oligopeptides as well as having
endoproteolytic activity. Some tripeptidyl
aminopeptidases have been shown to cleave tripeptides
and small peptides, e.g. angiotensin II and glucagon,
while others are believed to be involved in MHC I
processing.
Length = 412
Score = 28.4 bits (64), Expect = 4.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 186 GIGAWLSPDEMTVEAIVRKFKPARPYP 212
G+GA++SP+ M E +R+ P Y
Sbjct: 305 GVGAYVSPEMMAAEYSLREKLPGNQYT 331
>gnl|CDD|177282 PHA00447, PHA00447, lysozyme.
Length = 142
Score = 27.4 bits (61), Expect = 4.7
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 103 RNLNSMSIGIHLVNGGVVGEKFRSTNYYPFDENQIHTLGLLGKDIVSQFKIKPQYVL-GH 161
+ NS S+G+ LV GG+ + N+ P Q+ +L L + +++ P + H
Sbjct: 69 KGYNSNSVGVCLV-GGIDDKGKFDANFTP---AQMQSLKSLLVTLKAKY---PGAEIKAH 121
Query: 162 TDIAP 166
D+AP
Sbjct: 122 HDVAP 126
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
0.321 0.139 0.442
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,868,384
Number of extensions: 1421181
Number of successful extensions: 1115
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1103
Number of HSP's successfully gapped: 14
Length of query: 278
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 182
Effective length of database: 6,679,618
Effective search space: 1215690476
Effective search space used: 1215690476
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: 58 (26.2 bits)