GapMind for Amino acid biosynthesis

 

Alignments 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:

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