Alignments for a candidate for dopDH in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Halomonas desiderata SP1

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_086510671.1 BZY95_RS14765 aldehyde dehydrogenase (NADP(+))

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>NCBI__GCF_002151265.1:WP_086510671.1
          Length = 525

 Score =  721 bits (1861), Expect = 0.0
 Identities = 363/524 (69%), Positives = 418/524 (79%)

Query: 1   MPLTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRE 60
           M L G +LIG+  V+GS   I A+DP TG+ L PAY GGT   V +AC LA AAF  YRE
Sbjct: 1   MTLLGKMLIGREAVSGSSTPIHAVDPATGERLAPAYAGGTQAEVERACQLAEAAFGVYRE 60

Query: 61  TSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAG 120
           T+LEQRA FL+ +A +IEA+GD LI+RA+ ETGLP+AR++GERGRTC QLR FA  VRAG
Sbjct: 61  TTLEQRAAFLDTVAGEIEAIGDELIERAMAETGLPRARLEGERGRTCGQLRLFASVVRAG 120

Query: 121 EWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180
           EWLD+R+D ALPER+PLPRADLRQR + LGPVAVFGASNFPLAFSVAGGDTASALAAGCP
Sbjct: 121 EWLDLRLDPALPEREPLPRADLRQRHIPLGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180

Query: 181 VVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFT 240
           V+VKAHSAHPGTSELVG+AV +AV++  LPEGVFSLL+GSGREVG ALV+DPRI+AVGFT
Sbjct: 181 VIVKAHSAHPGTSELVGRAVQRAVEKSDLPEGVFSLLFGSGREVGQALVADPRIQAVGFT 240

Query: 241 GSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQ 300
           GSR GG AL + AQARP+PIPVYAEMSSINPVFL   AL+AR   LA+GFVASL  GAGQ
Sbjct: 241 GSRGGGTALMRTAQARPQPIPVYAEMSSINPVFLLPEALKARGAQLAEGFVASLNMGAGQ 300

Query: 301 FCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAI 360
           FCTNPGLVI  +G  L  F+  A G V Q A QTMLTPGI  AYQ G+  L+ N   +  
Sbjct: 301 FCTNPGLVIGVKGAELGAFVETAGGAVTQSAGQTMLTPGIHDAYQQGVKRLSSNGKVREA 360

Query: 361 TSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420
             GQ G+  + CQA LFVT A+ FLA+P LQ EVFGA SLV+ C D  ++RQVA  LEGQ
Sbjct: 361 ARGQVGETAHACQAGLFVTTAQDFLAEPELQEEVFGATSLVIECADQNEMRQVASQLEGQ 420

Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480
           LTATLQ+D+ D+D+AR LL  LERKAGRIL NGWPTGVEVC AMVHGGPFPATSD+RTTS
Sbjct: 421 LTATLQMDDGDLDAARQLLLILERKAGRILANGWPTGVEVCHAMVHGGPFPATSDSRTTS 480

Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGKRE 524
           VG+AAI RFLRPVCYQ +P  LLP+ L+ GNP  + RL+DGKRE
Sbjct: 481 VGSAAIFRFLRPVCYQALPQGLLPEPLRDGNPWGVSRLVDGKRE 524


Lambda     K      H
   0.319    0.134    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: 925
Number of extensions: 31
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: 525
Length of database: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources