Alignments for a candidate for drdehyd-beta in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Derxia gummosa DSM 723

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_084544860.1 H566_RS23550 molybdopterin-dependent oxidoreductase

Query= metacyc::MONOMER-20833
         (739 letters)



>NCBI__GCF_000482785.1:WP_084544860.1
          Length = 747

 Score =  400 bits (1028), Expect = e-115
 Identities = 278/739 (37%), Positives = 382/739 (51%), Gaps = 40/739 (5%)

Query: 9   DAPVNLSRRRFL--ASTAVGALVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVR 66
           +AP + +RRRFL  A+ A G+LV+GF L   A    +A  AE      AFL I PDGTV 
Sbjct: 31  NAPASRARRRFLTGATLAGGSLVLGFSLDAAARPAASAPPAEADFAPDAFLRIAPDGTVT 90

Query: 67  LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA-YVVMENGLRITGGSMSVR 125
           +  P++E GQGT+T++  ++ EEL+ D A   VE APP +A Y     G ++TGGS ++R
Sbjct: 91  MTMPYVEMGQGTYTSIPMLLAEELEVDLARVRVEHAPPDDARYANPLLGFQVTGGSTTIR 150

Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185
            ++  MRR GA AR ML+ A A +WGV       + G V+H  SGR L YG L + A   
Sbjct: 151 AAFEPMRRAGASARRMLVGAAAARWGVAPDSCRAEHGAVLHPPSGRRLAYGALLAEAARQ 210

Query: 186 PVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGM 245
           P+PD  S+ L+  S FR IG P +RLD   K  G ALY ID +   +  AA+  AP +G 
Sbjct: 211 PLPD--SVALKPASAFRLIGTPARRLDTPAKVNGTALYGIDARPPGLRVAALMQAPAIG- 267

Query: 246 TVGSLR--NQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQE---AAADS 300
             G LR  + +    M+GV  V VL   VAVVA     A++ + A++ DW +   A  DS
Sbjct: 268 --GRLRGVDPAPALAMRGVSQVVVLDDCVAVVAAHMGAARKGLAALRPDWDDGPNAGLDS 325

Query: 301 ALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLE 360
           A   +  D ++   R  + A     RDD   GDV  AL GA  +++A Y   +L HA +E
Sbjct: 326 A--AIWRDMAAASARGGVKA-----RDD---GDVDAALAGAAQRLDAVYQLPFLIHAAME 375

Query: 361 PPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDS 420
           P +       D   E+W+  Q     RA  A+ +GL   ++T+H+ LLGG FGR    DS
Sbjct: 376 PLNCTVDVRADAC-EVWVGTQVLTRARAAAAEASGLPVERVTVHNHLLGGGFGRRLEIDS 434

Query: 421 ANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE-AVSA 479
                 A+ +A+ V  P+K++WSREE+   D+ RP      R  LD  G  VA    ++ 
Sbjct: 435 V---ALAVRIARQVKGPLKVVWSREEDIRHDMYRPAFHDVVRGGLDADGRVVAWHHRITG 491

Query: 480 TEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPML--GYWRSVGNSLN 537
           +            D +DP  ++G     YA+ + R+   Y    P L   +WR VG + N
Sbjct: 492 SSVIRRWAPPLYRDGLDPEVIDGADRPPYALASVRVE--YQNHEPPLPTAFWRGVGPTHN 549

Query: 538 DFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRR 597
            F  ESF+DELA   G DP   RL    D      L +AA E   GW + P  A  G   
Sbjct: 550 LFVVESFIDELAVLAGRDPLRFRLDQAPDPRARAVLERAAAE--AGWGQ-PLPARAG--- 603

Query: 598 ARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGL 656
            RGVA+   FGS  A + EV +  +G V+   +  A+D G +VNP  V AQ+ G    GL
Sbjct: 604 -RGVALGFAFGSWIAMVCEVEVASDGSVRARRVTTAVDCGVVVNPDTVRAQIEGGAIFGL 662

Query: 657 SQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAV 716
           S  L  +A   DG+    N+   P+L   ++ R    ++ S    GG+GEP    VAPA+
Sbjct: 663 SAALHGQATVRDGRIEQSNFHDAPVLRMNELPRFSTHLLPSEAAPGGVGEPGTAIVAPAL 722

Query: 717 ANAVAQLTGQRVRSLPLSR 735
           ANAV   TG R R LPL R
Sbjct: 723 ANAVRAATGVRTRRLPLDR 741


Lambda     K      H
   0.317    0.134    0.394 

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: 1458
Number of extensions: 85
Number of successful extensions: 13
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: 739
Length of database: 747
Length adjustment: 40
Effective length of query: 699
Effective length of database: 707
Effective search space:   494193
Effective search space used:   494193
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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:

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