GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Amycolatopsis halophila YIM 93223

Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

Query= BRENDA::Q9SR86
         (481 letters)



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  197 bits (502), Expect = 4e-55
 Identities = 138/400 (34%), Positives = 199/400 (49%), Gaps = 37/400 (9%)

Query: 75  ALFHFYNTP-LNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLIN 133
           A+   Y TP L +V      VFD +G  YLD  GGIA  + GH HP VV +V +Q+  + 
Sbjct: 10  AMMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLG 69

Query: 134 HSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLYTGCNDIVSLRN 193
           H++ LY+N      AE L+  + G    V F NSG EA E A+ + RL TG + +V+   
Sbjct: 70  HTSNLYINPVALSLAETLLD-IAGLSGKVLFCNSGAEAVEAAIKITRL-TGKSKLVACDG 127

Query: 194 SYHGNAAATMGATAQSNWK--FNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFG 251
            +HG     +  T Q + +  F  +  GV H     P+       G+  A      ++  
Sbjct: 128 GFHGRTMGALSVTGQPSKREPFEPLLPGVTHV----PF-------GDTAA------LESA 170

Query: 252 TSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGF 311
             G  A    E + G GG+V    G+L AA +I   AG + + DEVQ+G  R G+ F  F
Sbjct: 171 VDGDTAAVFVEPVLGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWF-AF 229

Query: 312 QSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRV 371
           Q  GV PD++T+AKG+G G+PLGAV+   +   +L    +  TFGGNP+  AAGHAV+R 
Sbjct: 230 QQAGVTPDVITLAKGLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRT 289

Query: 372 LHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETL 431
           + E+ L ++   +G  L   +   K  + L+ +VRG GL+ G+   K      P  A   
Sbjct: 290 IREQGLLDHVETLGKDLAAGVR--KLDHPLVSEVRGAGLLQGIGLTKP---VAPTVATA- 343

Query: 432 HLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSD-ADFL 470
                 +  G L+       +V R+ PPL  T    ADFL
Sbjct: 344 -----AQRAGYLINP--VQPDVIRLAPPLIITERQVADFL 376


Lambda     K      H
   0.320    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 513
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 481
Length of database: 393
Length adjustment: 32
Effective length of query: 449
Effective length of database: 361
Effective search space:   162089
Effective search space used:   162089
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: 51 (24.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory