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_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__Koxy:BWI76_RS26375
          Length = 421

 Score =  205 bits (522), Expect = 2e-57
 Identities = 139/389 (35%), Positives = 204/389 (52%), Gaps = 17/389 (4%)

Query: 91  LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH----AIADFSE 146
           L+D  G   +D  AGIAV+N GH HP ++  V  Q++   H     + +     +A+   
Sbjct: 34  LWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQIVPYESYVTLAERIN 93

Query: 147 ALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ- 205
           ALA  + G  K  FFT +G EA E A+ +A+ YTG   ++    G+HG    TM  TG+ 
Sbjct: 94  ALAP-IDGPAKTAFFT-TGAEAVENAVKIARAYTGRPGLITFGGGFHGRTFMTMALTGKV 151

Query: 206 SMWK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTG-HIAGFICEAIQ 262
           + +K  F     SV+HA+ P+   G+  +D     K L  + +       +A  + E IQ
Sbjct: 152 APYKIGFGPFPGSVYHAVYPNAAHGITTADA---MKSLDRIFKADIAADQVAAIVLEPIQ 208

Query: 263 GVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKG 322
           G GG     P ++ A        G L IADEVQ+GFARTG  +  + ++V PD++TMAK 
Sbjct: 209 GEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPDLMTMAKS 268

Query: 323 IGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGS 382
           +  GFPL  VV   E+           T+ GN ++  A  AVL+VIE+E+L + A  +GS
Sbjct: 269 LAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQRAERLGS 328

Query: 383 YLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGK 442
           +LKE L Q ++    I DVRG+G M+ VE  +D +   P+   T  I  + +E G+L+  
Sbjct: 329 HLKEVLNQARQSCPAIADVRGQGSMVAVEF-NDPQTGEPSAEITRQIQQKAQENGLLLLS 387

Query: 443 GGYFGNVFRITPPLCFTKDDADFLVEAMD 471
            G +GNV R   PL  T  DA F  +A+D
Sbjct: 388 CGVYGNVIRFLYPL--TIPDAQF-TKALD 413


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: 505
Number of extensions: 27
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: 421
Length adjustment: 33
Effective length of query: 444
Effective length of database: 388
Effective search space:   172272
Effective search space used:   172272
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.

Links

Downloads

Related tools

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