Alignments for a candidate for drdehyd-beta in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Sinorhizobium meliloti 1021

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate SMa1488 SMa1488 oxidoreductase

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



>FitnessBrowser__Smeli:SMa1488
          Length = 747

 Score =  919 bits (2374), Expect = 0.0
 Identities = 466/729 (63%), Positives = 559/729 (76%), Gaps = 6/729 (0%)

Query: 11  PVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSA-ERGTQVPAFLEIRPDGTVRLLS 69
           P  L RR FL ++ +GALV+G  LP G  R QAA +A   GT++ AFLEI P+ TV   S
Sbjct: 19  PFKLPRRGFLGAS-LGALVLGVTLPAGRARAQAAAAAITPGTRISAFLEILPNETVLFRS 77

Query: 70  PFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYP 129
            F+EGGQG  TAMAQIVGEELD DP  F+VE APPG  Y++   G R TGGSMSVRMSY 
Sbjct: 78  AFIEGGQGIFTAMAQIVGEELDVDPMQFVVEGAPPGPDYLLTGGG-RFTGGSMSVRMSYD 136

Query: 130 TMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPD 189
            MR+LGA AR ML+QA A +  VPV EL+T+PGRVVH ASGR+L YGE+A +A  +P+P 
Sbjct: 137 AMRKLGASARHMLIQAAAVRLRVPVSELSTEPGRVVHGASGRTLPYGEIADAAAGLPLP- 195

Query: 190 PASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249
             ++ LRD + FRWIGKPV RLD  DKSTGKA Y+IDLKVD MLHAAVQH+PRLG   G+
Sbjct: 196 -TNVVLRDRADFRWIGKPVARLDVRDKSTGKARYAIDLKVDRMLHAAVQHSPRLGGEPGA 254

Query: 250 LRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPADF 309
           L+N++ V GM GVHS+H LPG VAVVA+ WW A+ A EA+QV W E    +A  VMPADF
Sbjct: 255 LQNEADVRGMPGVHSIHSLPGTVAVVADSWWRARMAAEALQVTWTEPTRGTA-HVMPADF 313

Query: 310 SSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFN 369
           S++ H   L A  G     E  G+ A AL  A   VEATY   YL H QLEPPSALAR+N
Sbjct: 314 STEAHMAMLKATPGEGVAYETVGNAATALGDAARVVEATYDAPYLVHGQLEPPSALARWN 373

Query: 370 PDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIA 429
            DG+L++W+PNQAP+MF+A+ AK  G+ P ++T+HSP+LGGFFGRHFLY +ANP+PQAI 
Sbjct: 374 DDGSLDLWVPNQAPEMFQAEAAKVAGIAPEKVTIHSPMLGGFFGRHFLYQTANPFPQAIL 433

Query: 430 LAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAG 489
           LAKAV+RP+KLIWSREEEFLRD LRP+  V+FRA LD +GLPVA+EAV+  EGPT    G
Sbjct: 434 LAKAVARPVKLIWSREEEFLRDTLRPMGAVRFRAGLDAEGLPVALEAVAVGEGPTGRWFG 493

Query: 490 KQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELA 549
           +Q DK+D ++VEG++GK YAIPN+ I Q++V    ++G+WRSVG+S+NDFFYE+F DE+A
Sbjct: 494 RQPDKVDSSSVEGIAGKVYAIPNRHIGQVHVDDPAIIGFWRSVGHSMNDFFYETFFDEMA 553

Query: 550 DKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGS 609
           D G  DPYELR  LL D+PR  TLL+A  ELSGGW+RGPF A+DGTRRARGVAMASPFGS
Sbjct: 554 DAGQQDPYELRRRLLADSPRHRTLLEAVAELSGGWRRGPFIADDGTRRARGVAMASPFGS 613

Query: 610 HTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDG 669
             A IAEVS+ +G+V VHD+W AIDPGSIVNPAI+EAQVN AVALGLS  LLEE VYVDG
Sbjct: 614 EVATIAEVSLRSGEVVVHDVWVAIDPGSIVNPAIIEAQVNSAVALGLSSALLEEVVYVDG 673

Query: 670 KPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVR 729
            P+ARNYD YPIL P +M RVHVR+VESG  MGGIGEP LP V PA+ANAV+ L G+RVR
Sbjct: 674 MPQARNYDGYPILTPDRMPRVHVRIVESGAPMGGIGEPGLPGVPPAIANAVSVLAGRRVR 733

Query: 730 SLPLSRHTF 738
           SLPLS+H F
Sbjct: 734 SLPLSKHDF 742


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: 1669
Number of extensions: 76
Number of successful extensions: 5
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 Sep 17 2021. 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 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