Alignments for a candidate for agx1 in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Herbaspirillum seropedicae SmR1

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__HerbieS:HSERO_RS19685
          Length = 456

 Score =  191 bits (485), Expect = 4e-53
 Identities = 136/422 (32%), Positives = 203/422 (48%), Gaps = 22/422 (5%)

Query: 51  PPYTGP--SADVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAV 108
           P Y GP  +A + LS R E ++       R P+ +         D  G  ++D  AG+ V
Sbjct: 20  PTYPGPKTAAALELSARTESMARGGG---RMPIAMDQAFGVTFKDPDGNTFIDLSAGVGV 76

Query: 109 VNCGHCHPDVVEPVINQIKRLQHPTVLYLN---HAIADFSEALASKLPGDLKVVFFTNSG 165
            + G C+P VVE +  Q + L H   +  +      A  SE +   L GD  + FFT  G
Sbjct: 77  SSVGRCNPRVVEAIRKQSESLMHSMEVNSSKRTELAAKISEIMPDGLRGDC-ITFFTQGG 135

Query: 166 TEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSMWK--FNVVQNSVHHALNP 223
           ++A E A+  AK  TG   I+A   GYHG   A+   T  + ++  F      V HA  P
Sbjct: 136 SDALEAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGTAYRKGFGPFMGGVIHAPYP 195

Query: 224 DPYRGVFGSD---GEKYAKDLQDLI---QYGTTGHIAGFICEAIQGVGGIVELAPGYLSA 277
             YR  F +     E+ A +  D +    Y     +A  I E +QG GG V  +P +L  
Sbjct: 196 YAYRFPFDTSHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQI 255

Query: 278 AYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPE 337
                 ++G L I DEVQ+G  RTG  W  E   V PD++T  KGIG   P+  +V   +
Sbjct: 256 LRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSD 315

Query: 338 IAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQ--ENAAMVGSYLKEKLTQLKEKH 395
           +A  +   S  NTF  NS+S    L  +++++  +L     A  +G   +E++       
Sbjct: 316 LAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSFNSPW 375

Query: 396 EIIGDVRGRGLMLGVELVSDRKLKTPATAETL-HIMDQMKELGVLIGKGGYFGNVFRITP 454
             +G+VRGRGLM+G+ELV +R+ + P + E L  +MD +   GVL+   G + NV R+ P
Sbjct: 376 --VGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVVGHGVLMIPCGRYTNVMRVMP 433

Query: 455 PL 456
            L
Sbjct: 434 SL 435


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: 544
Number of extensions: 21
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: 477
Length of database: 456
Length adjustment: 33
Effective length of query: 444
Effective length of database: 423
Effective search space:   187812
Effective search space used:   187812
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 Apr 09 2024. The underlying query database was built on Apr 09 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:

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
the source code
instructions for running GapMind on your computer
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