GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Dyadobacter tibetensis Y620-1

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_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  177 bits (449), Expect = 5e-49
 Identities = 126/337 (37%), Positives = 171/337 (50%), Gaps = 33/337 (9%)

Query: 29  AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQ--FTHTAYQIVPYESYV 86
           A+ + L D  G EY+D   G AV++ GH HPD VA + +QL +  F   + QI   E   
Sbjct: 18  AQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEELA 77

Query: 87  TLAEKINALAPVSGQAKTAFF--TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144
           T       L  +SG      F   +GAEA ENA+K+A  HTGR  V+AF+  FHGRT   
Sbjct: 78  T------KLGTLSGYPDYKLFLCNSGAEANENALKLASFHTGRKKVVAFTKAFHGRTAGA 131

Query: 145 MALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIF 204
           +A T             P  V  V Y   +  +   D    IE L     E  +VAA+I 
Sbjct: 132 VAATDN-----------PSIVAPVNYNEHVSFLPFND----IEALQAGITE--EVAAVIV 174

Query: 205 EPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMT 264
           E +QG GG  V   E + A+R+ CDE G  +I D VQ G+ RTGK F+       PD+MT
Sbjct: 175 EGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMT 234

Query: 265 MAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERAN 324
           MAK +  G P++GV+         + G LG T+ GN LA AA  AVL+I+  E L + A 
Sbjct: 235 MAKGMGNGFPIAGVLIAPQF--KASFGLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNAT 292

Query: 325 QLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP 361
           ++G  L + +    E +     +RG G MI +EF+ P
Sbjct: 293 KIGAYLFHEI----EELGGYKDLRGRGLMIGIEFDFP 325


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: 433
Number of extensions: 25
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: 421
Length of database: 384
Length adjustment: 31
Effective length of query: 390
Effective length of database: 353
Effective search space:   137670
Effective search space used:   137670
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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