GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS22435
          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:

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