Alignments for a candidate for deoxyribonate-transport in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoxyribonate-transport in Azohydromonas australica DSM 1124

Align 2-deoxy-D-ribonate transporter (characterized)
to candidate WP_029001265.1 H537_RS0132785 MFS transporter

Query= reanno::BFirm:BPHYT_RS04765
         (447 letters)



>NCBI__GCF_000430725.1:WP_029001265.1
          Length = 448

 Score =  667 bits (1720), Expect = 0.0
 Identities = 328/448 (73%), Positives = 386/448 (86%), Gaps = 1/448 (0%)

Query: 1   MTTQSAGPAGNALHRIATHKAMLRLIPLMCVIYFMSYLDRTNVSLAKARLATDLGISAAA 60
           M T+S     +  HR+AT KAM RLIPL+C IYFMSY+DRTNVSLAKA LA DLGISAAA
Sbjct: 1   METRSIESGVDETHRVATQKAMTRLIPLLCAIYFMSYIDRTNVSLAKAHLAADLGISAAA 60

Query: 61  YGLGAGIFFIGYALLEVPSNLVAHRVGPRRWIARIAITWGALSASMMFVQGEWSFYAIRV 120
           YGLGAGIFF+GYALLEVPSNL+AHR+GPR WIARIA+TWGALS +MMFVQGE SFY +RV
Sbjct: 61  YGLGAGIFFLGYALLEVPSNLLAHRIGPRPWIARIAVTWGALSVAMMFVQGEASFYLLRV 120

Query: 121 LLGIAEAGLFPALMYMVTMWFAPQDRSVAVGWIYTAPALALVIGNPLGGAFMQMDGLGGL 180
           LLGIAEAGLFPALMYMVT+WFAP+DR V VGWIYTAPAL L++GNPLGGA MQ+DGL GL
Sbjct: 121 LLGIAEAGLFPALMYMVTLWFAPKDRPVVVGWIYTAPALGLLLGNPLGGALMQLDGLAGL 180

Query: 181 HGWQWLFLLEGLPTIFVGVLLWFKLPEKPSDARWLSADEARALEARAVPD-AAHPGMFSQ 239
            GWQW+F+LEGLPTI VG+LL+FKL E+PSDA+WLS +EA+ALE+RAV D A H  + SQ
Sbjct: 181 RGWQWMFMLEGLPTIAVGILLYFKLAERPSDAKWLSREEAQALESRAVIDQAGHANLSSQ 240

Query: 240 DWVAALKRPATVLIGLIYFLNQVAFVGLVFFTPAMIQQMHVKSPLMIGVLSSSVGIGFLL 299
           DW+AA+KRP+TVL GLIYFLNQVAFVGLVFFTPAMIQQM V+SP ++GV+SSSVG+GFLL
Sbjct: 241 DWMAAIKRPSTVLTGLIYFLNQVAFVGLVFFTPAMIQQMKVESPFLVGVMSSSVGLGFLL 300

Query: 300 GVLVLPRIHRRVTNDCLYLGVLTLGLVTSAILFMSTSVLSTQLLLFVATAFFAGGVLPLY 359
           GVL LPRIHRRV +D ++LG LT GL+ SA  F++T   + Q+ LFVATAFF GG+LP Y
Sbjct: 301 GVLTLPRIHRRVKSDFVFLGALTAGLLLSACAFLATERPAVQIALFVATAFFGGGILPSY 360

Query: 360 WAIAMKRLHGIQAAAGLAFINTIGLIGGFVGPYLFGLAESASGHSASGFSVVVGASVLGL 419
           WAIAMKRL GIQAAAGLAFINTIGL+GGFVGPYLFG+ E+A+G S++GFSV++GA+ LGL
Sbjct: 361 WAIAMKRLQGIQAAAGLAFINTIGLLGGFVGPYLFGMVETATGRSSAGFSVILGAAALGL 420

Query: 420 VLVPLLAKAIQSEGRAASLAEPLLNTES 447
           +LVP LAKA +SE +A  LA+P++   S
Sbjct: 421 LLVPALAKASRSERQAPELADPVIKPVS 448


Lambda     K      H
   0.327    0.140    0.431 

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: 718
Number of extensions: 29
Number of successful extensions: 3
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: 447
Length of database: 448
Length adjustment: 33
Effective length of query: 414
Effective length of database: 415
Effective search space:   171810
Effective search space used:   171810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

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 2024 update 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