GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Methylocystis bryophila S285

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_085771307.1 B1812_RS09075 ornithine--oxo-acid transaminase

Query= SwissProt::P50457
         (421 letters)



>NCBI__GCF_002117405.1:WP_085771307.1
          Length = 413

 Score =  195 bits (495), Expect = 2e-54
 Identities = 135/399 (33%), Positives = 195/399 (48%), Gaps = 41/399 (10%)

Query: 32  ATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVT--LA 89
           A L DV G  YID  +  + ++ GH HP ++A + +Q  +        VP  +Y    L 
Sbjct: 28  AYLWDVAGRRYIDMMSAYSAVSLGHAHPRILAKLSEQAHRLA------VPSRAYYNDRLG 81

Query: 90  EKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGR------PGVIAFSGGFHGRTYM 143
             + AL  ++G        +GAEAVE A+K AR    R      P +I   G FHGRT  
Sbjct: 82  PFLEALCMLTGLDAALPMNSGAEAVETAIKAARRWGQRVKGVASPEIIVAEGNFHGRTTT 141

Query: 144 TMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAII 203
            ++ + +   Y+ GFGPF      VP+  DL       S              ++  A++
Sbjct: 142 VISFSSE-QEYRDGFGPFTPGFRAVPF-GDLEATRAAIS--------------ERTVAVL 185

Query: 204 FEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLM 263
            EP+QGE G  V P+  +A +RRLCDE  I+++ DE+QSG  RTG  FA  H    PD +
Sbjct: 186 VEPIQGEAGVIVPPRGWLAGLRRLCDEARILLLLDEIQSGLGRTGAWFAYQHENVLPDGV 245

Query: 264 TMAKSLAGG-MPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCER 322
           T+ K+L GG +P+S  V    +MD   PG  G T+ GN LA A     LN+I +E+L ER
Sbjct: 246 TLGKALGGGVLPVSAFVARREVMDVFTPGSHGSTFGGNALAAAVGLEALNVIREENLVER 305

Query: 323 ANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQG 382
           +  LG  L + L   K   P +A VRGLG     E       +P  + A+   +R L +G
Sbjct: 306 SRTLGAHLFDRLHAIKS--PVLADVRGLGLWAGAEI------QPRFSSARTFCERLLEKG 357

Query: 383 LLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421
             +L+   +  V+R   PL I  A  D A+   ++ L +
Sbjct: 358 --VLSSATHHTVVRLAPPLVISKADLDWALDRFEEVLRE 394


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: 404
Number of extensions: 22
Number of successful extensions: 7
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: 413
Length adjustment: 31
Effective length of query: 390
Effective length of database: 382
Effective search space:   148980
Effective search space used:   148980
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 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