Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N1B4

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf1N1B4_4584 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4584
          Length = 722

 Score =  386 bits (992), Expect = e-111
 Identities = 269/735 (36%), Positives = 379/735 (51%), Gaps = 39/735 (5%)

Query: 14  LSRRRFLASTAV--GALVIGFGLPLGAGRVQAATSAERGTQVP-AFLEIRPDGTVRLLSP 70
           +SRR FL  +AV  G LV+ F +P GA R       +     P AFL I  D ++ +L  
Sbjct: 7   VSRRGFLKGSAVLGGGLVVAFVIP-GANRFAHGAENQGNVFAPNAFLRIGNDNSITVLLG 65

Query: 71  FMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVME--NGLRITGGSMSVRMSY 128
             E GQG  T +  ++ EELDAD +   VE AP   A   +    G++ITGGS S  M +
Sbjct: 66  HSEMGQGIWTGLTMLIAEELDADWSKIRVEHAPASAADYGLPAFGGIQITGGSTSTWMEF 125

Query: 129 PTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVP 188
              R+ GA AR ML++A AK++ V   ++ T+ G V+  A  +   YGELA  A  +PVP
Sbjct: 126 DRYRQAGAAARLMLIEAAAKRFDVAPSQIRTESGVVM--AGDKRATYGELADDAGKLPVP 183

Query: 189 DPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVG 248
           DPASI  ++   ++ IGKP KRLD  +K TG+A + +D++ D ++ A V   P  G +V 
Sbjct: 184 DPASIKFKEAKDWKIIGKPTKRLDTPEKITGQAKFGMDVQFDGLMTAMVARPPVFGGSVK 243

Query: 249 SLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPAD 308
           S    ++   + GVH V  +P  VAV+A+ +W AK   +A++V+W             A 
Sbjct: 244 SFEG-AEALAVPGVHKVVQVPTGVAVIADHYWAAKLGRDALKVEWDLGPN--------AG 294

Query: 309 FSSDKHRE-FLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALAR 367
             S K  E F      P       GD    L  A   +EA Y   YL HA +EP +   +
Sbjct: 295 LDSQKLLESFRKLAATPGTSASQAGDATATLGKAAKTIEAEYSVPYLAHAPMEPLNCTVK 354

Query: 368 FNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANP---- 423
            + D   EIW   Q   + +    K TGL P Q+ +H+  LGG FGR      ANP    
Sbjct: 355 ISKD-KCEIWTGTQFQTLDQMIAGKITGLKPEQVEIHTQFLGGGFGRR-----ANPTSDF 408

Query: 424 YPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEG- 482
             +A+ +AKA   P+K +W+RE++      R   + + R  L   G+P+A + V   +  
Sbjct: 409 VSEAVYVAKAAGGPVKTVWAREDDIRGGYYRSAFLHQARIGLGADGMPMAWKHVLVGQSI 468

Query: 483 --PTEALAGKQGDKIDPTAVEGLSGKSY--AIPNKRIAQIYVKGAPMLGYWRSVGNSLND 538
              T   A    D ID T+VEG++   Y   + N ++     +    + + RSVG++   
Sbjct: 469 LTGTSFAATMVKDGIDKTSVEGVADSPYLEGLANHQVELHSPQTGISVLWLRSVGHTHTA 528

Query: 539 FFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRA 598
           F  ES +DELAD  G DP E R  LL+ +PR   +L  A E    WK       DG   A
Sbjct: 529 FVMESLIDELADAAGKDPVEYRRALLKAHPRHLGVLNLAVE-KANWKA---PLPDG--HA 582

Query: 599 RGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQ 658
            GVA+   FGS+ A +AEVS +N  ++VH +  A+D G  VNP  + AQ+   +  GLS 
Sbjct: 583 LGVAVHESFGSYVAQVAEVSQDNLAIRVHRVVCAVDCGIAVNPQSIAAQMESGITFGLSF 642

Query: 659 TLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVAN 718
           TL  +  + DG+    NY  Y +L   +M  V V +V S +K GGIGE  +P VAPAVAN
Sbjct: 643 TLHSKLTFKDGQVEQSNYHDYQVLRLNEMPVVEVHIVPSSDKPGGIGEVGVPPVAPAVAN 702

Query: 719 AVAQLTGQRVRSLPL 733
           AV  LTGQR+R LPL
Sbjct: 703 AVFALTGQRLRELPL 717


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: 1298
Number of extensions: 64
Number of successful extensions: 8
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: 722
Length adjustment: 40
Effective length of query: 699
Effective length of database: 682
Effective search space:   476718
Effective search space used:   476718
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