GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme

Query= SwissProt::P50457
         (421 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03179 H281DRAFT_03179
           4-aminobutyrate aminotransferase apoenzyme
          Length = 429

 Score =  583 bits (1503), Expect = e-171
 Identities = 291/421 (69%), Positives = 337/421 (80%)

Query: 1   MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60
           + N E   R+ +ATPRGVGVMC+F+A+ A+NA L DVEG  +IDFAAGIAV NTGHRHP 
Sbjct: 3   LKNAELKSRKDAATPRGVGVMCDFYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPK 62

Query: 61  LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120
           +VAA+  QL +FTHTAYQIVPY SYV LAEK+N  AP     KTAFFTTGAEAVENA+KI
Sbjct: 63  IVAAIRDQLDRFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKI 122

Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180
           ARA TGRPGVIAF+GGFHGRT M MALTGKVAPYK GFGPFP  V+H P+P+ LHG+ST 
Sbjct: 123 ARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVSTA 182

Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240
           DSL AIE LFK+DI+ K+VAAIIFEPVQGEGGF  AP E V A+R+LC+EHGI++IADEV
Sbjct: 183 DSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEV 242

Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300
           Q+GFARTGKLFAM HY   PDLMT+AKSLAGGMPLSGV+G A++MDA APGGLGGTYAGN
Sbjct: 243 QTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGN 302

Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360
           PLAVAAA AVL+IID+E LCERA  LG R+K  LI  +   P IA VRG G M+AVEF  
Sbjct: 303 PLAVAAALAVLDIIDEEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEFCK 362

Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
           P + EP A   +++Q RAL +GLLLL CG Y NV+RFL+PLTI D  FD A+ IL+D + 
Sbjct: 363 PGSTEPDAEFTKRVQTRALKRGLLLLVCGVYSNVVRFLFPLTIEDTVFDEALAILEDVIK 422

Query: 421 D 421
           D
Sbjct: 423 D 423


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: 664
Number of extensions: 25
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: 429
Length adjustment: 32
Effective length of query: 389
Effective length of database: 397
Effective search space:   154433
Effective search space used:   154433
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 paper from 2022 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