GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_001592305.1:WP_068170823.1
          Length = 428

 Score =  518 bits (1334), Expect = e-151
 Identities = 256/420 (60%), Positives = 322/420 (76%), Gaps = 3/420 (0%)

Query: 2   SNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDL 61
           +N  +HQRRL ATPRGVGVM +FF   A+NA L D+EG  +IDFA GIAVLNTGH HP +
Sbjct: 9   TNAAWHQRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKV 68

Query: 62  VAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIA 121
            AA+  QLQ+FTH+ YQ+VPY  YV+LAE+INA+ P+ G+AKTAFF+TGAEA+ENA+KIA
Sbjct: 69  QAAIAAQLQRFTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIA 128

Query: 122 RAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQD 181
           R+ TGR GVIAF G FHGR+   ++LTGKV PYK GFGPFP  +YHVP+P++  G S  +
Sbjct: 129 RSSTGRSGVIAFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPAE--GASLDE 186

Query: 182 SLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQ 241
           +  A++ +FK DIE  +VAAI+FEPVQGEGGFN   K+ V  +R LCD+HGI++IADEVQ
Sbjct: 187 TKRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQ 246

Query: 242 SGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNP 301
           +GFARTG++FAM+HY   PDLMTMAKS+AGG  LS V G A IMD PAPGGLGGTYAGNP
Sbjct: 247 TGFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNP 306

Query: 302 LAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP 361
           LA+AA+HAVL+++ +E L ERA +LG +L   L  AK   P I  VRGLG+M+A EF D 
Sbjct: 307 LAIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVD- 365

Query: 362 QTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421
             G P A   +++Q  AL +GLLLLTCG YGNVIR+L+PLTI D+ F  A+ +L  A+++
Sbjct: 366 AAGAPDADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425


Lambda     K      H
   0.319    0.134    0.388 

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: 621
Number of extensions: 26
Number of successful extensions: 3
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: 421
Length of database: 428
Length adjustment: 32
Effective length of query: 389
Effective length of database: 396
Effective search space:   154044
Effective search space used:   154044
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 Sep 17 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