Aligments for a candidate for agx1 in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Aligments for a candidate for agx1 in Klebsiella michiganensis M5al

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__Koxy:BWI76_RS14020
          Length = 461

 Score =  196 bits (499), Expect = 1e-54
 Identities = 139/434 (32%), Positives = 212/434 (48%), Gaps = 19/434 (4%)

Query: 59  DVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDV 118
           D  L+++ EF S       + PL I   +  +L D   ++YLD  AG   +  GH HPDV
Sbjct: 21  DTFLARQAEFESNVRSYPRKLPLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDV 80

Query: 119 VEPVINQIKRLQHPTVLYLNHAIAD-FSEALASKLPGDLK---VVFFTNSGTEANELALM 174
           ++ + + I        L L   + D FSE L S LPG+ K   + F   SG +A E AL 
Sbjct: 81  LQSIQSVITSGLPLHTLDLTTPLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALK 140

Query: 175 MAKLYTGCQDIVAVRNGYHGNAAATMGATGQSMWK--FNVVQNSVHHALNPDPYRGVFGS 232
           +AK YTG   +++   GYHG     +  TG    K   N +   V     P  YR   G 
Sbjct: 141 LAKKYTGRSSVISFSGGYHGMTHGALSVTGNLSPKAAVNGMMPEVQFMPYPHQYRCPLGI 200

Query: 233 DGEKYAKDL----QDLIQYGTTG--HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAG 286
            GE   K L    ++LI    +G    A  I EA+QG GG+      +L       ++ G
Sbjct: 201 GGEAGVKALTYYFENLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHG 260

Query: 287 GLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRS 346
            L I DEVQ+GFARTG F+ FE   + PDI+ M+K +G G PL AV+   +         
Sbjct: 261 ILLIIDEVQAGFARTGKFFAFEHAGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGH 319

Query: 347 YFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGL 406
           +  TF GN ++   GL  L  ++  K+ +  A  G +LK KL ++++++ +IG VRG GL
Sbjct: 320 HTGTFRGNQLAMATGLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGL 379

Query: 407 MLGVELVSDRKLKT-----PATAETLHIMD-QMKELGVLIGKGGYFGNVFRITPPLCFTK 460
           M+G+E+V   +        PA  E   ++  +  E G+++ +GG  G V R+ P L  + 
Sbjct: 380 MIGIEIVKPNEAPDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISN 439

Query: 461 DDADFLVEAMDYSM 474
            + +   +  + ++
Sbjct: 440 AELEIFFDKFEQAL 453


Lambda     K      H
   0.320    0.136    0.403 

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: 520
Number of extensions: 33
Number of successful extensions: 4
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: 477
Length of database: 461
Length adjustment: 33
Effective length of query: 444
Effective length of database: 428
Effective search space:   190032
Effective search space used:   190032
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis