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_028312219.1 H566_RS0116000 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_000482785.1:WP_028312219.1
          Length = 801

 Score =  374 bits (960), Expect = e-107
 Identities = 274/779 (35%), Positives = 396/779 (50%), Gaps = 74/779 (9%)

Query: 12  VNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGTQVPA-------FLEIRPDGT 64
           V + RRRFL STA G+L++G      A   Q       G   P        F+ I  D +
Sbjct: 32  VRIDRRRFLLSTAAGSLMLGLAPLARAASEQTDKPQIWGAAPPPKALPPGPFISIGADDS 91

Query: 65  VRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSV 124
           V +    ++ GQG  TA+  ++ EELD D      E AP G+AY     G+++ GGS S+
Sbjct: 92  VTVQVNRLDFGQGVQTALPMLIAEELDCDWRKIKPELAPAGDAYKDPVFGIQMVGGSNSI 151

Query: 125 RMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALD 184
           + S+   R LGA ARA+L+ A A++W + V  L T  G V+ A  G+ L YGELA SA  
Sbjct: 152 KNSWLHYRTLGATARALLVNAAAQRWKLDVASLRTADGAVI-APDGKRLRYGELAESAAG 210

Query: 185 MPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLG 244
           + +P+  ++ L+ P QFR +GKP +RLDA  KS+G+  Y ID ++  +  A V H P  G
Sbjct: 211 IALPE--TVMLKKPEQFRLLGKPTRRLDATAKSSGRQSYGIDRQLPGLKVAVVAHPPVFG 268

Query: 245 MTVGSLRNQSQVEGMKGVHSVHVLPG-----AVAVVAERWWHAKRAVEAIQVDWQEAAAD 299
             V S+ + ++ + +KGV +V  +P      A+AVVA+ +W AK+A EA+ + W  +A +
Sbjct: 269 AKVASV-DDAKAKAVKGVRAVLRIPADRGGEAIAVVADGYWPAKQAREALDIKWDTSAVE 327

Query: 300 ----SALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQV---------- 345
               +AL     + +  K    +AA  GP       GD AGA  G  T V          
Sbjct: 328 KPDSAALLASYRERAKQKGTVAMAADMGPLTAPLGAGDRAGAAAGGMTTVAGTARATTVT 387

Query: 346 -------------------EATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMF 386
                              EA Y   YL HA +EP +       DG+ E+W  +Q   + 
Sbjct: 388 GAPSTAAVTEPLGATAKVIEAEYVFPYLAHAPMEPLNCTIALK-DGSAEVWCGSQFQTVD 446

Query: 387 RADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVS-----RPIKLI 441
           +  IAK   L+PA++  ++ + GG FGR  +  S++   +A  +A+A +      P+K+I
Sbjct: 447 QNAIAKTLDLEPAKVKFNTEMAGGGFGRRAV-PSSDYVVEAARIARAWAADGHAEPVKMI 505

Query: 442 WSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE----AVSATEGPT-EALAGKQGDKID 496
           WSRE++      RP+ V + R A+D  G  +A E      S  +G   E    K G  ID
Sbjct: 506 WSREDDIRGGYYRPMHVHRARIAVDAGGRVLAWEHRIVGQSIVKGTLFEGFLFKNG--ID 563

Query: 497 PTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDP 556
            T VEG+ G  YA+P +          P+L +WRSVG++   +  E+ +DELA   G DP
Sbjct: 564 GTMVEGM-GAPYAVPMELSVHNMDVNVPVL-WWRSVGSTHTAYVMETLVDELAANAGADP 621

Query: 557 YELRLHLLRDN-PRLTTLLQAAGELSG-GWKRGPFTAEDGTRRARGVAMASPFGSHTAAI 614
            E R  L+  N PR    L  A + SG G +R P         A GVA+   F S  A +
Sbjct: 622 VEYRRKLIGPNHPRHLAALDLAVQKSGYGKRRLP------AGHAWGVALHESFNSVVAYV 675

Query: 615 AEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYV-DGKPRA 673
            E S+ +GK K+H +W  +     VNP  V+AQV GA  + L  TL   A+ + DG    
Sbjct: 676 VEASVADGKPKLHHVWGGVHCNFAVNPLTVQAQVEGAALMALGTTLPGAAITLKDGAVEQ 735

Query: 674 RNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLP 732
            N+  Y +     M  V V +V S +   G+GEP LPA+APA+ANAVA+LTG+R+RSLP
Sbjct: 736 TNFHQYTVARMPDMPVVEVFIVPSVDAPTGMGEPGLPALAPALANAVAKLTGKRLRSLP 794


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: 1523
Number of extensions: 86
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 739
Length of database: 801
Length adjustment: 41
Effective length of query: 698
Effective length of database: 760
Effective search space:   530480
Effective search space used:   530480
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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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