GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_28215
          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:

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