GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Marinobacter adhaerens HP15

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase

Query= uniprot:A1S8Y2
         (425 letters)



>lcl|FitnessBrowser__Marino:GFF3915 HP15_3855 2,4-diaminobutyrate
           4-transaminase
          Length = 422

 Score =  184 bits (467), Expect = 4e-51
 Identities = 128/407 (31%), Positives = 215/407 (52%), Gaps = 19/407 (4%)

Query: 25  PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEK--FSHTCFMVL 82
           PV   RA+NA ++  +G+EY+DF  G   LN GH +  +K A+ E +E    S    M  
Sbjct: 19  PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78

Query: 83  GYESYVAVCEKLNQLVPGDFAKKSALFT--SGSEAVENAIKVARAYTKRAGVIAFTSGYH 140
             +       K + L P     K   FT  +G+  VE A+K+AR    R+G+I+FT+G+H
Sbjct: 79  TAKHDFMESYKKHILDPRGLDYKMQ-FTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137

Query: 141 GRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSED-DAMASIERIFKNDAEPS 199
           G TM A+A TG    +  G+G    NV   +F      + +D D +A ++++  + +   
Sbjct: 138 GVTMGAVATTGN-KHHRGGVGTPLGNV---DFMFYDGYLGDDVDTLAIMDKLLSDGSSGF 193

Query: 200 DI-AAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQM 258
           ++ AA+I+E VQGEGG  A    ++K L ELC +  I+LI D++Q G GRTG FF+ E  
Sbjct: 194 ELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFA 253

Query: 259 GVAADITTFAKSIAG-GFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIE-VF 316
           G+  DI T +KS++G G P++ +  + E +D   PG   GT+ G+ +A   A A +E  +
Sbjct: 254 GIKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFITARAAVENYW 312

Query: 317 EEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLT 376
           +++       A  + +  A+  +  +YP   +++G G M  IE        P     +  
Sbjct: 313 KDDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLMRGIEAKHADITGP-----ITK 367

Query: 377 EARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423
            A   GLI+ + G    V++ L+P+T  +E +++G  ++A+  + ++
Sbjct: 368 RAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEIM 414


Lambda     K      H
   0.319    0.136    0.391 

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: 440
Number of extensions: 23
Number of successful extensions: 4
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: 425
Length of database: 422
Length adjustment: 32
Effective length of query: 393
Effective length of database: 390
Effective search space:   153270
Effective search space used:   153270
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