GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Burkholderia phytofirmans PsJN

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 BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS22435 BPHYT_RS22435
           4-aminobutyrate aminotransferase
          Length = 427

 Score =  589 bits (1519), Expect = e-173
 Identities = 295/421 (70%), Positives = 338/421 (80%)

Query: 1   MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60
           M N E   R+ +ATPRGVGVMC+F+A+ AENA L DVEG  +IDFAAGIAV NTGHRHP 
Sbjct: 1   MKNAELKSRKDAATPRGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPK 60

Query: 61  LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120
           ++AA+  QL  FTHTAYQIVPY SYV LAEK+N  AP     KTAFFTTGAEAVENA+KI
Sbjct: 61  ILAAIRDQLDHFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKI 120

Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180
           ARA TGRPGVIAF+GGFHGRT M MALTGKVAPYKIGFGPFP  V+H P+P+ LHG++T 
Sbjct: 121 ARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTA 180

Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240
           DSL AIE LFK+DI+ K+VAAIIFEPVQGEGGF  AP E V A+R+LC+EHGI++IADEV
Sbjct: 181 DSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEV 240

Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300
           Q+GFARTGKLFAM HY   PDLMT+AKSLAGGMPLSGV+G A++MDA APGGLGGTYAGN
Sbjct: 241 QTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGN 300

Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360
           PLAVAAAHAVL+IID+E LCERA  LG R+K  LI  +  VP IA VRG G M+AVEF  
Sbjct: 301 PLAVAAAHAVLDIIDEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCK 360

Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
               EP A   +++Q RAL +GLLLL CG Y NV+RFL+PLTI DA FD AM IL+D + 
Sbjct: 361 AGGTEPDAEFTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIK 420

Query: 421 D 421
           D
Sbjct: 421 D 421


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: 673
Number of extensions: 23
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: 421
Length of database: 427
Length adjustment: 32
Effective length of query: 389
Effective length of database: 395
Effective search space:   153655
Effective search space used:   153655
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 Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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