Aligments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E2

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf6N2E2_1204 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1204
          Length = 745

 Score =  358 bits (920), Expect = e-103
 Identities = 268/740 (36%), Positives = 379/740 (51%), Gaps = 38/740 (5%)

Query: 9   DAPVNLSRRRFLASTAVGALVIGF--GLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVR 66
           D+P  L RR FL    +G L +G    L L      AA   +   Q  AF++I P G V 
Sbjct: 24  DSPATLPRRSFLKIVGIGGLALGAFPHLALAQETNGAAVPLKPSQQPSAFVQIAPSGEVT 83

Query: 67  LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRM 126
           +    +E GQG  T +  I+ EELDAD +           AY+    G+ +TGGS S++ 
Sbjct: 84  VTINRLEFGQGVQTGLPMILAEELDADWSLVRSRNGNSDAAYMDPNFGIHLTGGSNSIKN 143

Query: 127 SYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMP 186
           SY   R LGA ARAMLL A A +W V V  L+TQ G V+  A GR   YGELA +A+ MP
Sbjct: 144 SYTQYRELGARARAMLLSAAAARWNVDVASLSTQAGMVLGPA-GRKASYGELAEAAMAMP 202

Query: 187 VPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMT 246
           VP+   ITL+DP  FR IG+   R+DA  KS+G+  + ID+ +   L A V   P  G  
Sbjct: 203 VPE--QITLKDPKDFRIIGQATTRIDAKAKSSGQQDFGIDMHLPGQLTAVVARPPVFGAR 260

Query: 247 VGSLRNQSQVEGMKGVHSVHVLP---GA--VAVVAERWWHAKRAVEAIQVDWQEAAADSA 301
           + SL + S     KGV +V  +P   GA  VAVVA+ +W AK A +A++V+W      SA
Sbjct: 261 IASL-DDSAARATKGVKAVLRVPLDGGAEGVAVVADSYWQAKLARDALKVEWDA----SA 315

Query: 302 LRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEP 361
           +  + ++    ++RE LA Q GP   D +   +A     A  Q++A +   YL HA +EP
Sbjct: 316 VEKVDSEKQLAQYRE-LANQPGPLHFDADMTPLA----SAPHQLDAEFVFPYLAHAPMEP 370

Query: 362 PSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSA 421
            +   +   DG  ++W+  Q P    A  AK  GL P QI ++    GG FGR  +  + 
Sbjct: 371 LNCTVQLAGDGA-QLWVGTQFPGGDGAAAAKVLGLKPEQIQVNVQTAGGGFGRRGV-PTN 428

Query: 422 NPYPQAIALAKA-----VSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE- 475
           +    A  +AKA     V+ PI+ +WSRE++      RP+ + + R   DD G  +A + 
Sbjct: 429 DFVVLACEVAKAARTAGVNAPIRTLWSREDDIKGGYYRPMHLHRARIGFDDSGKVLAWDH 488

Query: 476 -AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534
             V  +        G+  + IDPTA EGL    Y +P +          P+L +WRSVG+
Sbjct: 489 ALVGQSIITGTVFGGRVKNGIDPTATEGLR-NPYPLPMRLTVHHPKLNVPVL-WWRSVGS 546

Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRD-NPRLTTLLQAAGELSGGWKRGPFTAED 593
           +   F  E+ +DE+A     DP   R+ L  D +PR    LQ A + S   KR     + 
Sbjct: 547 THTAFVMETLIDEIARTTKQDPVAYRMKLFGDQSPRHREALQLAVDKSEYGKR-----QL 601

Query: 594 GTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVA 653
               A GVA+   F S  A + E S+++G+  +H++   +     VNP  VEAQV GA  
Sbjct: 602 PAGHAWGVAVHESFSSVVAYVVEASVQDGRPVLHNVTAGVHCNLAVNPRSVEAQVQGAAL 661

Query: 654 LGLSQTLLEEAVYV-DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAV 712
           +GLS  L   A+ + DG  +  N+  + +     M    V +V S E   G+GEP LPA+
Sbjct: 662 MGLSMCLPGGAITLKDGVVQQSNFADFSVPRITDMPTFAVHIVPSAEPPTGMGEPGLPAL 721

Query: 713 APAVANAVAQLTGQRVRSLP 732
           APA ANAVA LTG+ +R LP
Sbjct: 722 APAFANAVASLTGKPLRELP 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: 1390
Number of extensions: 84
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: 745
Length adjustment: 40
Effective length of query: 699
Effective length of database: 705
Effective search space:   492795
Effective search space used:   492795
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