Aligments for a candidate for agx1 in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Aligments for a candidate for agx1 in Pseudomonas simiae WCS417

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF262 PS417_01335 hypothetical protein

Query= SwissProt::Q940M2
         (476 letters)



>lcl|FitnessBrowser__WCS417:GFF262 PS417_01335 hypothetical protein
          Length = 966

 Score =  301 bits (770), Expect = 9e-86
 Identities = 179/448 (39%), Positives = 253/448 (56%), Gaps = 19/448 (4%)

Query: 33  SIADAPPHIPPFVHQPRPYKGPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDE 92
           S+  +P  +        P   P A  +L +R      S  HYY  P  I  G   +L D 
Sbjct: 519 SLCPSPAALLGLACDAEPELDPEA--LLARRDASFARSQKHYYADPPRIERGWRNHLIDM 576

Query: 93  SGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPG 152
            GR YLD    +  +  GH HP +      Q  LL +  + + + A+ +F+E L A  P 
Sbjct: 577 QGRSYLDMLNNVAVL--GHGHPRMAAVAARQWSLL-NTNSRFHYAAVTEFSERLLALAPE 633

Query: 153 NLKVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQ 212
            +  V+ VNSG+EAN+LA+ +A  Y+G  +M+S+  AYHG S   +   A++T     PQ
Sbjct: 634 GMDRVFLVNSGTEANDLAIRLAWAYSGGRDMLSVLEAYHGWS---VAADAVSTSIADNPQ 690

Query: 213 GE------IHHVVNPDPYRGVFGSDGSL--YAKDVHDHIEY--GTSGKVAGFIAETIQGV 262
                   +H V  P+ YRG F    S   Y + V  ++     +  ++AGFI E + G 
Sbjct: 691 ALSSRPDWVHPVTAPNTYRGEFRGQDSAPDYVRSVEHNLAKIAASQRQLAGFICEPVYGN 750

Query: 263 GGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGI 322
            G + L PGYL+ VY +VR  GGVCIADEVQ G+GR G  +WGF+ Q VVPDI+TMAKG+
Sbjct: 751 AGGISLPPGYLQQVYGLVRAQGGVCIADEVQVGYGRMGHFFWGFEEQGVVPDIITMAKGM 810

Query: 323 GNGLPLGAVVTTPEIASVL-ASKILFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGS 381
           GNG PLGAV+T  EIA  L A    F++ GG+PV    G+AVL+V+++EK  E+   VG 
Sbjct: 811 GNGQPLGAVITRREIAEALEAEGYFFSSSGGSPVSCRIGMAVLDVMEEEKLWENARVVGG 870

Query: 382 HLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGK 441
           H   RL+++  RH ++G V G G  +G+ELV DR+   PA  ET++L ++LRELGI +  
Sbjct: 871 HFKARLEELIDRHPLVGAVHGSGFYLGLELVRDRQTLEPATEETTLLCDRLRELGIFMQP 930

Query: 442 GGLHGNVFRIKPPMCFTKDDADFLVDAL 469
            G + N+ +IKPPM  ++   DF VD L
Sbjct: 931 TGDYLNILKIKPPMVTSRHSVDFFVDML 958


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: 1051
Number of extensions: 53
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: 476
Length of database: 966
Length adjustment: 39
Effective length of query: 437
Effective length of database: 927
Effective search space:   405099
Effective search space used:   405099
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 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