Alignments for a candidate for argD in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD in Burkholderia phytofirmans PsJN

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__BFirm:BPHYT_RS10155
          Length = 433

 Score =  208 bits (530), Expect = 2e-58
 Identities = 134/438 (30%), Positives = 224/438 (51%), Gaps = 24/438 (5%)

Query: 2   NSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPK 61
           N++    +   Q + R  G   P+  +RA+   V+D +GR  LDF  G      GH HP+
Sbjct: 4   NNDAVFWRNAKQHLIRYGGTFEPMIIERAQGSFVYDADGRAILDFTSGQMSAVLGHSHPE 63

Query: 62  VVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKI 121
           +V+ +     KL H  F  +   P ++L   + +  P D   + LL++TG+E+ E A+++
Sbjct: 64  IVSVINEYAGKLDHL-FSGMLSRPVVDLATRLAEITP-DGLDRALLLSTGAESNEAAIRM 121

Query: 122 ARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGM-GLMPGHVYRALYPCPL----- 175
           A+  T +   + F+ ++HG T    + T     YSAG  G+ P  V     P P      
Sbjct: 122 AKLVTGKYEIVGFAQSWHGMTAAAASAT-----YSAGRKGVGPAAVGSFAIPAPFLYRPR 176

Query: 176 ---HGISEDDAIASIHRIFK--NDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCD 230
              HG  + D +A +   F   +  +  ++AA + EP+   GG       +M  L+  C+
Sbjct: 177 FERHG--DYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPEGYMTALKRKCE 234

Query: 231 EHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVA 290
           E G++LI DE Q+G GRTGT+FA ++ GV PD+ T +K++  G PLA V   A++ +   
Sbjct: 235 ERGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAVVTSAQIEERAH 294

Query: 291 PGG--LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDV 348
             G     T+  +P+     L VL+V E++ L+ +AN +G +LK GLL + E+   IGD+
Sbjct: 295 ELGYLFYTTHVSDPLPAAVGLRVLEVVERDGLVARANLMGARLKRGLLDLMERFDCIGDI 354

Query: 349 RGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGLI--LLSCGPYYNVLRILVPLTIE 406
           RG G ++ +E+ +D    +P   L A+I     + GL   ++       V RI  PLT+ 
Sbjct: 355 RGRGLLLGMEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVH 414

Query: 407 DAQIRQGLEIISQCFDEA 424
           + +I  GL+++ Q  + +
Sbjct: 415 EDEIDLGLDLLGQAIERS 432


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: 471
Number of extensions: 23
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: 426
Length of database: 433
Length adjustment: 32
Effective length of query: 394
Effective length of database: 401
Effective search space:   157994
Effective search space used:   157994
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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