Alignments for a candidate for agx1 in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Phaeobacter inhibens BS107

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF3422 PGA1_c34750 putative aminotransferase class 3

Query= SwissProt::Q940M2
         (476 letters)



>FitnessBrowser__Phaeo:GFF3422
          Length = 1009

 Score =  298 bits (764), Expect = 4e-85
 Identities = 177/453 (39%), Positives = 258/453 (56%), Gaps = 23/453 (5%)

Query: 39   PHIPPFVHQPRP---YKGPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGR 95
            P+  P ++ P     Y+      VL  R+   G +L   Y+ P+ ++ G   +L+DE GR
Sbjct: 562  PNPAPLLNLPAAQVSYQPTDKSTVLAGRRAHFGGNLSLTYRDPVMLLRGWKHHLFDEWGR 621

Query: 96   RYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLK 155
             YLDA+  +  V  GH HP I     +Q K + ++ T YLH A   FAE + +KMP +L+
Sbjct: 622  PYLDAYNNVPHV--GHAHPRIQAIAADQLKRM-NSNTRYLHPAQNAFAEKILSKMPDHLE 678

Query: 156  VVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPL----- 210
            V +FVNSG+EANELA+ +AR +TG+  M++  + YHG   NT G   ++ +K+       
Sbjct: 679  VCFFVNSGTEANELALRLARAHTGAKGMVTPDHGYHG---NTTGAIDISAYKFNAKGGVG 735

Query: 211  PQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIE------YGTSGKVAGFIAETIQGVGG 264
            P   +  V   D YRG +G D    A+   D ++        +   VAGFIAET   VGG
Sbjct: 736  PSDWVELVEVADDYRGTYGRDDPQRAQKYADLVDPAIAKLQASGHGVAGFIAETFPSVGG 795

Query: 265  AVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGN 324
             +    GYL +VYE +R AGG+CIADEVQTG GR G +Y+GF+ Q   PDIV + K IGN
Sbjct: 796  QIIPPKGYLPAVYEKIRAAGGICIADEVQTGLGRLGEYYFGFEHQGASPDIVVLGKPIGN 855

Query: 325  GLPLGAVVTTPEIASVLA-SKILFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHL 383
            G PLG +VTT  IA   A     F+TFGG+ +    G  VLN++D+E  QE+  + G+ L
Sbjct: 856  GHPLGVLVTTRAIADSFAQGPEFFSTFGGSTLSCRIGTEVLNIVDEEGLQENARQRGADL 915

Query: 384  IQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGG 443
            +  L+D+Q RH  IGDVRG GL +G+EL+  R D + A    + +  ++R+  IL+G  G
Sbjct: 916  LNGLRDLQSRHQAIGDVRGMGLFIGVELI--RTDGSEASEICAYVKNRMRDHRILIGSEG 973

Query: 444  LHGNVFRIKPPMCFTKDDADFLVDALDYSISRL 476
               N+ +I+PP+    +  + ++  LD  +S L
Sbjct: 974  PKDNILKIRPPLTIDAEGIEMILKTLDSILSEL 1006


Lambda     K      H
   0.320    0.138    0.412 

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: 1170
Number of extensions: 61
Number of successful extensions: 6
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: 476
Length of database: 1009
Length adjustment: 39
Effective length of query: 437
Effective length of database: 970
Effective search space:   423890
Effective search space used:   423890
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: 54 (25.4 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