Alignments for a candidate for drdehyd-beta in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Phaeobacter inhibens BS107

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate GFF977 PGA1_c09930 isoquinoline 1-oxidoreductase subunit beta

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



>FitnessBrowser__Phaeo:GFF977
          Length = 746

 Score =  365 bits (937), Expect = e-105
 Identities = 264/756 (34%), Positives = 370/756 (48%), Gaps = 60/756 (7%)

Query: 14  LSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLLSPFME 73
           ++RR FL  +A  A  + FG            + E G  V           V L++P  E
Sbjct: 7   IARRSFLIGSAAIAGGVAFGTYKYHQPAPNPLAQEDGRAVLNPFVFVDQSGVTLIAPRAE 66

Query: 74  GGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAY---VVMENGL--------------- 115
            GQG  +A A ++ EELD DPA   V   P  +AY    +M   L               
Sbjct: 67  MGQGVKSAWASLIAEELDVDPAKVTVLHGPAAKAYYNSAMMSEALPGRGYDGSALQHSLG 126

Query: 116 ------------RITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGR 163
                       ++TGGS S+R  +  MR  GA AR  L QA A Q G+   +LTT+ G 
Sbjct: 127 EIVGHMAKFLDLQVTGGSSSMRDGFERMRHAGASARETLKQAAADQLGISRDQLTTEDGH 186

Query: 164 VVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALY 223
           VV A  G  L Y  LA++A  +    P    LR  S++R IGK V R+D   KSTG A +
Sbjct: 187 VV-APDGTRLPYSALANAAASLA---PIEADLRPASEWRLIGKDVPRIDMVAKSTGTAEF 242

Query: 224 SIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAK 283
            +D+++  M  AA++  P  G+   +  + S  EGM GV  +  L  AVAVVA   W A+
Sbjct: 243 GVDVRLPGMKFAAIRQNPHFGVGKTAF-DASAAEGMAGVEKIIDLGDAVAVVASNTWLAQ 301

Query: 284 RAVEAIQVDWQEAAADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKT 343
           +AV+AI V W+ A        +  + +    R F AA     RDD   GDV  AL    T
Sbjct: 302 QAVDAIDVTWEAAPYPETTEAIFEEIA----RSFDAAPNSTMRDD---GDV-DALPDGAT 353

Query: 344 QVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITL 403
            +EA Y   YL HA +EP +A A ++ DG L+IW PNQ P + +   A   GLD   + +
Sbjct: 354 VIEAEYRLPYLAHATMEPMNATALYSGDG-LQIWAPNQGPTVVQKKAAALAGLDVDAVEV 412

Query: 404 HSPLLGGFFGRHFLYDSANPYPQAIALA-KAVSRPIKLIWSREEEFLRDVLRPLAVVKFR 462
           ++  LGG FGR    D  +   +A+ +A +    P++L WSREE+   DV RP A+ ++R
Sbjct: 413 NTTYLGGGFGRRIETDYTD---RAVQIAIQLQGTPVQLTWSREEDISHDVYRPGAIARYR 469

Query: 463 AALDDKGLPVAIEAVSATEGPTEALAGKQ----GDKIDPTAVEGLSGKSYAIPNKRIAQI 518
           AA+ D G  V +    A +  T   AG+         D   V+    +  AIPN R+   
Sbjct: 470 AAIKD-GKAVMVHGKIAAQSTTVEGAGRMLGLPMSGPDKGHVDAAFNQPLAIPNFRVEGY 528

Query: 519 YVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDN-PRLTTLLQAA 577
             K    +G+WRSVG S N FF +  +DE+A   G DP + RL L R        +L+  
Sbjct: 529 LAKPMLPVGFWRSVGASFNGFFSDCIIDEMAHAAGRDPLDFRLELARAEWEPAAKVLETV 588

Query: 578 GELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGS 637
            ++SG   + P    DG    RGVAMA  FG+  A + EV+ E+G++++ + W A D G 
Sbjct: 589 RDMSGWTGKTP----DGI--GRGVAMAYSFGTPVAQVIEVADEDGQIRMTNAWIAADLGR 642

Query: 638 IVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVES 697
           +++P    AQ+ G +  GLS     E     G     N+  Y  L    M  V V ++E+
Sbjct: 643 VIDPKNTRAQMFGGMVYGLSAACFGEITIDGGAVEQENFPDYDALRMHTMPTVQVELLEN 702

Query: 698 GEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
             +MGG GEP  P  APA+ANA+  LTG+R R LPL
Sbjct: 703 QPRMGGAGEPGTPPAAPALANALFDLTGKRARQLPL 738


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: 1413
Number of extensions: 74
Number of successful extensions: 9
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: 746
Length adjustment: 40
Effective length of query: 699
Effective length of database: 706
Effective search space:   493494
Effective search space used:   493494
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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