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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR322 IGR320 IGR318 IGR321 IGR315 IGR316 IGR319 IGR323 IGR324 IGR317 HD0451 orn, - HD0452 amiB, - HD0450 opsX, - HD0445 kdtA,waaA, - HD0454 prtC,yegQ, - HD0455 pykA, - HD0446 fis, - HD0449 sixA, - HD0447 HD0448 HD0451 orn, - HD0452 amiB, - HD0450 opsX, - HD0445 kdtA,waaA, - HD0454 prtC,yegQ, - HD0455 pykA, - HD0446 fis, - HD0449 sixA, - HD0447 HD0448 HD0451 orn, - HD0452 amiB, - HD0450 opsX, - HD0445 kdtA,waaA, - HD0454 prtC,yegQ, - HD0455 pykA, - HD0446 kdtB,coaD, - HD0453 kdtB,coaD, - HD0453 fis, - HD0449 sixA, - HD0447 HD0448
* Calculated from Protein Sequence

Gene ID: HD0450

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
amiB  

Definition:
N-acetylmuramoyl-L-alanine amidase II

Gene Start:
356714

Gene Stop:
355683

Gene Length:
1032

Molecular Weight*:
38074

pI*:
10.60

Net Charge*:
22.12

EC:
3.5.1.28  

Functional Class:
Cell envelope; Murein sacculus and peptidoglycan  

Pathway: pathway table
Peptideglycan biosynthesis

Secondary Evidence:
Wilson SA, Williams RJ, Pearl LH, Drew RE.
Identification of two new genes in the Pseudomonas aeruginosa amidase operon, encoding an ATPase (AmiB) and a putative integral membrane protein (AmiS).
J Biol Chem. 1995 Aug 11;270(32):18818-24.
PMID: 7642533

Alloing G, Trombe MC, Claverys JP.
The ami locus of the gram-positive bacterium Streptococcus pneumoniae is similar to binding protein-dependent transport operons of gram-negative bacteria.
Mol Microbiol. 1990 Apr;4(4):633-44.
PMID: 2352474

Comment:
This sequence is not similar to HD0112 and HD0501 which, paralogous to one another, appear to be members of the amidase amiB family.

Blast Summary:  PSI-Blast Search
Residues 12 to 342 are 45% ( EScore : 5e-72 ) identical to sp|P44493|AMIB_HAEIN PROBABLE N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMIB PRECURSOR >1075049|pir||D64046 N-acetylmuramoyl-L-alanine amidase homolog between residues 6 and 335 in [Haemophilus influenzae Rd]
Residues 24 to 254 are 49% ( EScore : 2e-59 ) identical to sp|P26365|AMIB_ECOLI N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMIB PRECURSOR >628763|pir||S41741 N-acetylmuramoyl-L-alanine amidase between residues 191 and 420 in [Escherichia coli]
Residues 19 to 342 are 37% ( EScore : 3e-49 ) identical to gb|AAF93517.1| (AE004123) N-acetylmuramoyl-L-alanine amidase between residues 169 and 459 in [Vibrio cholerae]
Residues 20 to 254 are 36% ( EScore : 5e-34 ) identical to gb|AAF83569.1|AE003917_3 N-acetylmuramoyl-L-alanine amidase precursor between residues 284 and 513 in [Xylella fastidiosa]
Residues 25 to 251 are 33% ( EScore : 4e-32 ) identical to pir||B65064 hypothetical protein b2817 between residues 218 and 438 in [Escherichia coli]
Residues 25 to 251 are 33% ( EScore : 4e-32 ) identical to sp|Q46929|AMIC_ECOLI between residues 188 and 408
Residues 23 to 255 are 35% ( EScore : 2e-30 ) identical to sp|P33772|AMIA_SALTY PROBABLE N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMIA PRECURSOR >1073679|pir||A53302 hemF 5-prime-region hypothetical protein - Salmonella typhimurium >310641|gb|AAA27138.1| between residues 55 and 281 in [Salmonella typhimurium]
Residues 24 to 255 are 35% ( EScore : 8e-30 ) identical to sp|P36548|AMIA_ECOLI PROBABLE N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMIA PRECURSOR >1073563|pir||A36964 N-acetylmuramoyl-L-alanine amidase between residues 56 and 281 in [Escherichia coli]
Residues 26 to 249 are 36% ( EScore : 1e-28 ) identical to gb|AAF06680.1|AF163663_5 putative N-acetylmuramoyl-L-alanine amidase-precursor AmiC between residues 233 and 449 in [Neisseria meningitidis]
Residues 26 to 249 are 36% ( EScore : 1e-28 ) identical to emb|CAB85247.1| (AL162757) N-acetylmuramoyl-L-alanine amidase between residues 191 and 407 in [Neisseria meningitidis]

COGS Summary:  COGS Search
BeTs to 8 clades of COG0860
COG name: N-acetylmuramoyl-L-alanine amidase
Functional Class:  M
The phylogenetic pattern of COG0860 is -----q-CEBRhuj--olin-
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB002508 (Cell wall hydrolase/autolysin) with a combined E-value of 5.3e-41.
    IPB002508A    29-41
    IPB002508B    45-68
    IPB002508C    96-105
    IPB002508D    200-239


ProDom Summary:  Protein Domain Search
Residues 118-192 are 60% similar to a (AMIDASE N-ACETYLMURAMOYL-L-ALANINE) protein domain (PD344236) which is seen in Q9CMC8_PASMU.

Residues 200-246 are 72% similar to a (N-ACETYLMURAMOYL-L-ALANINE AMIDASE COMPLETE PROTEOME) protein domain (PD002984) which is seen in AMIB_HAEIN.



Paralogs:  Local Blast Search


HD0450 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 88 to 251 (E-value = 1.5e-60) place HD0450 in the Amidase_3 family which is described as N-acetylmuramoyl-L-alanine amidase (PF01520)
Residues 301 to 343 (E-value = 4.7e-14) place HD0450 in the LysM family which is described as LysM domain (PF01476)

PDB Hit:
No significant hits to the NCBI PDB database.

Gene Protein Sequence:
MKTLAQYIITSLFTLCFSLTGYAKMVVVIDAGHGGKDPGAIGQNLRIQEK
NVTLAISKELKALLDADPHFKAVMTRNDDSFIQLSQRTEIARKNKANLFV
SIHADSSPSSNSAKGASVWVLSNRRASNEMGKWLEDHEKQSELLGGAGSL
LSNKNERYLNQTVLDLQFSHSQRSGYELGKAVLSYLEKVTPLAKKTPQHA
SLSVLRSPDITSILVETGFLSNAIEEKQLASSIYRRKIAQAIYKGLNTYW
AYHPNINKVKENNKKEVKPSPKKDSAQKSTSTTQSTATANKENGKLNNGY
HIVQKNETLYSIARLYNTTPDKLSKLNKIQNNHIVVGKKLKIQ$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAGACATTAGCACAATATATTATAACGAGTTTATTTACTTTATGTTT
TAGTCTGACCGGTTATGCAAAAATGGTGGTCGTCATTGATGCAGGACACG
GCGGTAAAGATCCAGGCGCTATCGGTCAAAATCTTCGTATTCAAGAAAAG
AATGTTACCTTAGCTATTTCCAAAGAATTAAAAGCATTATTGGACGCCGA
TCCTCACTTTAAGGCAGTAATGACACGTAATGATGATTCCTTTATTCAAC
TATCACAACGGACTGAAATAGCACGAAAAAATAAAGCCAATTTATTTGTC
TCTATTCACGCAGACTCCTCACCTAGCTCAAATAGTGCAAAAGGTGCTTC
AGTATGGGTATTATCAAATAGACGCGCTAGCAATGAAATGGGTAAATGGT
TAGAAGATCACGAAAAGCAATCAGAATTACTCGGCGGTGCAGGCTCATTA
TTATCTAATAAAAATGAACGTTATCTTAATCAAACCGTATTGGATTTACA
GTTTTCTCATTCACAACGTTCGGGTTATGAATTAGGTAAAGCCGTATTAT
CTTACCTTGAAAAAGTTACTCCACTTGCTAAAAAAACGCCTCAACACGCA
AGTTTAAGCGTCTTACGTTCGCCAGATATCACCTCAATTTTAGTCGAAAC
GGGGTTTTTATCTAATGCAATTGAAGAAAAACAACTCGCCAGCTCTATTT
ATCGACGCAAAATCGCACAAGCTATTTATAAAGGCTTAAATACTTATTGG
GCATATCACCCTAATATAAACAAGGTGAAAGAAAATAACAAAAAAGAAGT
TAAACCGTCGCCTAAAAAAGATAGCGCCCAAAAATCAACTTCAACAACCC
AATCAACAGCAACGGCCAACAAAGAAAATGGTAAATTGAACAATGGCTAT
CACATTGTGCAAAAAAATGAAACGCTTTATTCGATTGCCCGTTTATATAA
CACCACACCAGATAAATTGAGTAAATTAAATAAAATCCAAAACAATCATA
TTGTTGTCGGCAAAAAATTAAAAATTCAATAA


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