GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Marinobacter adhaerens HP15

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase

Query= reanno::Marino:GFF3202
         (533 letters)



>lcl|FitnessBrowser__Marino:GFF3202 HP15_3144 NAD-dependent aldehyde
           dehydrogenase
          Length = 533

 Score = 1086 bits (2808), Expect = 0.0
 Identities = 533/533 (100%), Positives = 533/533 (100%)

Query: 1   MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG 60
           MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG
Sbjct: 1   MGIGVYIEWVNAKGRVALRQTQQEVEIMIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKG 60

Query: 61  QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA 120
           QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA
Sbjct: 61  QYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPAWGKTSPTERSNILLKIADRIEA 120

Query: 121 NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE 180
           NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE
Sbjct: 121 NLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHE 180

Query: 181 PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL 240
           PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL
Sbjct: 181 PLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILVLMEIIGDLLPPGVL 240

Query: 241 NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS 300
           NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS
Sbjct: 241 NIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENIIPSTVELGGKSPNIYFS 300

Query: 301 DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP 360
           DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP
Sbjct: 301 DVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNP 360

Query: 361 LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD 420
           LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD
Sbjct: 361 LDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGD 420

Query: 421 NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR 480
           NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR
Sbjct: 421 NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGR 480

Query: 481 VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF 533
           VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF
Sbjct: 481 VWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTKCMLTSYDTNPLGFF 533


Lambda     K      H
   0.319    0.136    0.412 

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: 1057
Number of extensions: 28
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: 533
Length of database: 533
Length adjustment: 35
Effective length of query: 498
Effective length of database: 498
Effective search space:   248004
Effective search space used:   248004
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 (21.7 bits)
S2: 52 (24.6 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