GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Pseudomonas fluorescens FW300-N1B4

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Pf1N1B4_1733 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::pseudo3_N2E3:AO353_11510
         (425 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 5-aminovalerate
           aminotransferase (EC 2.6.1.48) /
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 425

 Score =  818 bits (2112), Expect = 0.0
 Identities = 413/425 (97%), Positives = 422/425 (99%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLH 60
           MSKTNASLMKRREAAVPRGVGQIHPIFA+ AKN+TVTDVEGREFIDFAGGIAVLNTGH+H
Sbjct: 1   MSKTNASLMKRREAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60

Query: 61  PKVIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSI 120
           PK+IAAVTEQLNKLTHTCFQVLAYEPYVE+CEKINAKVPGDFAKKTLLVTTGSEAVENSI
Sbjct: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSI 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD
Sbjct: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEE 420
           F +GDSHKPNAAAVA VVAKARDKGLILLSCGTYGNVLRVLVPLT+PDEQLDKGLAI+EE
Sbjct: 361 FVDGDSHKPNAAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 420

Query: 421 CFSEL 425
           CF+EL
Sbjct: 421 CFAEL 425


Lambda     K      H
   0.320    0.137    0.395 

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: 835
Number of extensions: 20
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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