Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens GW456-L13

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate PfGW456L13_3352 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3352
          Length = 722

 Score =  381 bits (978), Expect = e-110
 Identities = 271/737 (36%), Positives = 380/737 (51%), Gaps = 43/737 (5%)

Query: 14  LSRRRFLASTAV--GALVIGFGLPLGAGRVQAATSAERGTQVP-AFLEIRPDGTVRLLSP 70
           LSRR FL  +A+  G LV+ F +P GA R       +     P AFL I  D +V +L  
Sbjct: 7   LSRRGFLKGSAMLGGGLVVAFAMP-GAHRFAMGAENQGNVFAPNAFLRIGNDNSVTVLLG 65

Query: 71  FMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMEN--GLRITGGSMSVRMSY 128
             E GQG  T +  ++ EELDAD     VE AP   A   +    G++ITGGS S  M +
Sbjct: 66  HSEMGQGIWTGLTMLIAEELDADWTKIRVEHAPASAADYGLPGFGGMQITGGSTSTWMEF 125

Query: 129 PTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVP 188
              R+ GA AR ML+ A AK++ V   E+ T+ G VV A   R+  YGELA  A  +P P
Sbjct: 126 DRYRQAGAAARLMLIDAAAKRFNVAPSEIHTESG-VVMAGEHRAT-YGELADEAGQLPRP 183

Query: 189 DPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVG 248
           DPASI L+D   ++ IGKP +RLD  +K TG+A + +D++ D ++ A V  +P  G +V 
Sbjct: 184 DPASIKLKDAKDWKLIGKPTQRLDTPEKITGRAKFGMDVQFDGLMTAMVARSPTFGGSVK 243

Query: 249 SLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQ---EAAADSALRVM 305
           S    ++   + GVH V  +P  +AV+A+ +W AK   +A++++W     A  DS  + +
Sbjct: 244 SFEG-AEALAIPGVHKVVQVPTGIAVIADHFWAAKLGRDALKIEWNPGPNAGLDS--QAL 300

Query: 306 PADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSAL 365
             +F        LA  QG        GD   AL  A  +++  Y   YL HA +EP +  
Sbjct: 301 LENFRK------LATTQGLNAGQA--GDTQAALAKAAKKIDVEYSVPYLAHAPMEPLNCT 352

Query: 366 ARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANP-- 423
                D   EIW   Q   + +    K TGL P Q+ +H+  LGG FGR      ANP  
Sbjct: 353 VSITKD-KCEIWTGTQFQTLDQMVAGKITGLKPEQVVIHTEFLGGGFGRR-----ANPTS 406

Query: 424 --YPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATE 481
               +A+ +AKA   P+K +W+RE++      R   +   R  L   GLP+A + V   +
Sbjct: 407 DFVSEAVYVAKAAGAPVKTVWAREDDIRGGYYRSAFLHHARIGLGADGLPLAWKHVMVGQ 466

Query: 482 G---PTEALAGKQGDKIDPTAVEGLSGKSY--AIPNKRIAQIYVKGAPMLGYWRSVGNSL 536
                T   A    D ID T+VEG++   Y   + N +I     +    + + RSVG++ 
Sbjct: 467 SIMAGTSLEASMVKDGIDKTSVEGVADSPYLEGLANHQIELHSPQTGISVLWLRSVGHTH 526

Query: 537 NDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTR 596
             F  ES +DELA   G DP E R  LL+D+PR   +L  A +    WK       DG  
Sbjct: 527 TAFVMESLIDELATAAGKDPVEYRRTLLKDHPRHLGVLNLAVQ-KANWKA---PLPDG-- 580

Query: 597 RARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGL 656
            A GVA+   FGS+ A +AEVS +N  ++VH +  A+D G  VNP  + AQ+   +  GL
Sbjct: 581 HALGVAVHESFGSYVAQVAEVSQDNLAIRVHRVVCAVDCGIAVNPQSIAAQMESCITFGL 640

Query: 657 SQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAV 716
           S  L  +    DG+    NY  Y +L   +M  V V +V S +K GGIGE  +P +APAV
Sbjct: 641 SFALHSKLTLKDGQVVQSNYHDYRVLRLNEMPLVEVHIVPSSDKPGGIGEAGVPPMAPAV 700

Query: 717 ANAVAQLTGQRVRSLPL 733
           ANAV  LTGQR+R LPL
Sbjct: 701 ANAVFALTGQRLRELPL 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: 59
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