GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Pseudomonas fluorescens FW300-N2E3

Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate AO353_28215 AO353_28215 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_28215 AO353_28215
           4-aminobutyrate aminotransferase
          Length = 430

 Score =  432 bits (1110), Expect = e-125
 Identities = 209/417 (50%), Positives = 282/417 (67%)

Query: 1   MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60
           ++    L+++R Q +PRG+   HP+  DRA+   +WDV+G+ YLDF GGI VLN GH HP
Sbjct: 5   VDETPHLLRQRDQFVPRGLVTAHPLVIDRAQGAELWDVDGKRYLDFVGGIGVLNIGHNHP 64

Query: 61  KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120
           KVVAAV+AQL+K+SH CFQV+AY+PYL+L + + + + G+ A K    T+G+EAVENAVK
Sbjct: 65  KVVAAVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGNEAYKAAFFTSGAEAVENAVK 124

Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180
           IARA T RS  IAF G +HGRT     LTG   PY    G     V+   YP    G+S 
Sbjct: 125 IARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVSS 184

Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240
           + A+ ++  +     APE +AAI+IEPVQG+GGF ++   F+Q LRAL ++HGI+LI DE
Sbjct: 185 EMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQALRALTEKHGIVLILDE 244

Query: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300
           +Q+G GRTG  F  +  G+ PDL T AKS+AGG PL+GV G+A +MDA  PGGLGGTY G
Sbjct: 245 IQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAGIMDAPLPGGLGGTYGG 304

Query: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF 360
           N ++C AAL V+  +EQE LL + + LG++L+ GLL +  +H +IGDVRG G M+AIEL 
Sbjct: 305 NALSCAAALAVIDAYEQEQLLARGDALGERLRQGLLRLQARHRQIGDVRGSGFMLAIELI 364

Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417
           +D D   PDA L   ++  AR  GL+++ CG Y NVLR L PL   + QI + L+I+
Sbjct: 365 KDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTTEDQIDEALQIL 421


Lambda     K      H
   0.320    0.137    0.401 

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: 561
Number of extensions: 20
Number of successful extensions: 1
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: 426
Length of database: 430
Length adjustment: 32
Effective length of query: 394
Effective length of database: 398
Effective search space:   156812
Effective search space used:   156812
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 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