Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2C3

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AO356_26900 AO356_26900 carbon monoxide dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_26900
          Length = 747

 Score =  353 bits (905), Expect = e-101
 Identities = 265/741 (35%), Positives = 379/741 (51%), Gaps = 38/741 (5%)

Query: 9   DAPVNLSRRRFLASTAVGALVIGF--GLPLGAGRVQAATSAERGTQVP-AFLEIRPDGTV 65
           D P  L RR FL    +G L +G    L L      A  +  + TQ P AF++I P+G V
Sbjct: 24  DGPAALPRRSFLKIVGIGGLALGAFPHLALAQEANGAVAAPLKPTQQPSAFVQIAPNGEV 83

Query: 66  RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVR 125
            +    +E GQG  T +  I+ EELDAD +           AY+    G+ +TGGS +++
Sbjct: 84  TVTINRLEFGQGVQTGLPMILAEELDADWSLVRSRNGSNDAAYMDPAFGIHLTGGSNTIK 143

Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185
            SY   R LGA ARAMLL A A +W V V  L+TQ G V+  A GR   YGELA +A+ M
Sbjct: 144 NSYTQYRELGARARAMLLSAAAARWNVDVASLSTQAGMVLGPA-GRKASYGELAQAAMAM 202

Query: 186 PVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGM 245
           PVP+   ITL+DP  FR IG+   R+DA  KS+G+  + ID+ +   L A V   P  G 
Sbjct: 203 PVPE--QITLKDPKDFRIIGQATTRIDAKAKSSGQQDFGIDMHLPGQLTAVVARPPVFGA 260

Query: 246 TVGSLRNQSQVEGMKGVHSVHVLP---GA--VAVVAERWWHAKRAVEAIQVDWQEAAADS 300
            + +L + S     KGV +V  +P   GA  VAVVA+ +W AK A +A++V+W      S
Sbjct: 261 RIAAL-DDSAARATKGVKAVLRVPLDGGAEGVAVVADSYWQAKLARDALKVEWNA----S 315

Query: 301 ALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLE 360
           A+  + ++    ++RE LA+Q GP   D +   +A     A  ++EA +   YL HA +E
Sbjct: 316 AVEKLDSEKQLAQYRE-LASQPGPLHFDADMTPLA----TAPHRLEAEFLFPYLAHAPME 370

Query: 361 PPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDS 420
           P +   +       ++W+  Q P    A  AK   L P QI ++    GG FGR  +  +
Sbjct: 371 PLNCTVQLAGKNGAQLWVGTQFPGGDAAAAAKVLDLKPEQIQVNVQTAGGGFGRRGV-PT 429

Query: 421 ANPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE 475
            +    A  +AKA     V  PI+ +WSRE++      RP+ + + R   DD G  +A +
Sbjct: 430 NDFVVLACEVAKAARTAGVDAPIRTLWSREDDIKGGYYRPMHLHRARIGFDDSGKVLAWD 489

Query: 476 --AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVG 533
              V  +        G+  + IDPTA EGL    Y +P +          P+L +WRSVG
Sbjct: 490 HALVGQSIITGTVFGGRVKNGIDPTATEGLR-DPYPLPMRLTVHHPKLNVPVL-WWRSVG 547

Query: 534 NSLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKRGPFTAE 592
           ++   F  E+ +DE+A     DP   R+ L  D +PR    LQ A + S   KR     +
Sbjct: 548 STHTAFVMETLIDEIARTTKQDPVAYRMKLFGDQSPRHRAALQLAVDKSEYGKR-----Q 602

Query: 593 DGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAV 652
               RA GVA+   F S  A + E S+++G+  +H++   +     VNP  VEAQV GA 
Sbjct: 603 LPAGRAWGVAVHESFSSVVAYVVEASVQDGRPVLHNVTAGVHCNLAVNPRSVEAQVQGAA 662

Query: 653 ALGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPA 711
            +GLS  L   A+ + DG  +  N+  + +     M    V +V S E   G+GEP LPA
Sbjct: 663 LMGLSMCLPGGAITLKDGVVQQSNFADFSVPRITDMPEFAVHIVPSAEPPTGMGEPGLPA 722

Query: 712 VAPAVANAVAQLTGQRVRSLP 732
           +APA ANAVA LTG+ +R LP
Sbjct: 723 LAPAFANAVASLTGKPMRELP 743


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: 1440
Number of extensions: 85
Number of successful extensions: 12
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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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, or view the source code.

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