Alignments for a candidate for drdehyd-beta in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Acidovorax sp. GW101-3H11

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Ac3H11_3700 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3700
          Length = 750

 Score =  400 bits (1028), Expect = e-115
 Identities = 278/759 (36%), Positives = 392/759 (51%), Gaps = 63/759 (8%)

Query: 21  ASTAVGALVIGFGLPLGAGRVQAAT---SAERGTQVPAFLEIRPDGTVRLLSPFMEGGQG 77
           A+TA GALVIG+G+     R+  A    +      +  +L++  D TV ++    E GQG
Sbjct: 6   AATA-GALVIGWGVMPPRQRLHPADPLPATPGQAALNGWLKVGTDNTVTVMMAKSEMGQG 64

Query: 78  THTAMAQIVGEELDADPATFIVEAAPPGEAY----------------------------- 108
           THT +A I+ EELDAD A   +  AP  + Y                             
Sbjct: 65  THTGLAAILAEELDADWAQVRLAMAPIDDIYNNLATVVDGLPFHPDNDGSMKAVAGWLTA 124

Query: 109 -VVMENGLRITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHA 167
             + E G+ +TGGS S++  +  MR  GA ARAML++A A QW V   E T   G V HA
Sbjct: 125 KTMREVGVMMTGGSSSIKDLWLPMREAGAHARAMLVRAAAAQWKVQAAECTANAGWVEHA 184

Query: 168 ASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDL 227
           A GR   +GELA+ A   P+  P  + L++P+QF+ IGKP+ R++A  K  G A++ ID 
Sbjct: 185 A-GRRATFGELAALAAQQPM--PGKVVLKEPAQFKLIGKPLTRIEAPSKLDGSAVFGIDA 241

Query: 228 KVDNMLHAAVQHAPRLGMTVG--SLRNQSQVEGMKGVHSV---HVLPGAVAVVAERWWHA 282
               + HA+V   P  G  V         ++ G+K V +V   H   G VAV+A+  WHA
Sbjct: 242 NPPGLQHASVVMCPTRGGKVARFDAAAAQKLPGVKQVLAVAPYHGGTGGVAVIADTPWHA 301

Query: 283 KRAVEAIQVDWQEAAADSALRVMPADFSSDKHREFLAAQQGPTR--DDENEGDVAGALKG 340
           K+A  A+ V+W    A        A  SSD     L      T+     + GDV  A++G
Sbjct: 302 KKAAAAVTVEWDHGPA--------ATLSSDTVMARLTQALDETKGFGYHSAGDVDQAMQG 353

Query: 341 AKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQ 400
           A T + A Y   YL HA LEP +   +   DG  ++W   Q P + R   AK  G+D  +
Sbjct: 354 AATSITADYRAPYLAHAALEPINCTVQVK-DGGAQVWTSTQVPGLARMAAAKALGMDEEK 412

Query: 401 ITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAV-SRPIKLIWSREEEFLRDVLRPLAVV 459
           +T+H  LLGG FGR    D      QA A+A+A    P++ +WSRE++   D  RP  + 
Sbjct: 413 VTVHQLLLGGGFGRRLEVDYV---AQAAAIAQAAGGAPVQTLWSREQDTQHDFYRPACMA 469

Query: 460 KFRAALDDKGLPVAIEAVSATEG-PTEALA---GKQGDKIDPTAVEGLSGKSYAIPNKRI 515
           +F+A  D +G  VA   +S  +    + LA   G  G   D TA EG   + Y  P+ RI
Sbjct: 470 RFKAGFDAQGQLVAWHNLSVGQAIVPQVLARTFGLPGAGPDKTASEGAFDQPYEWPHARI 529

Query: 516 AQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQ 575
           A   +     +G+WRSVG+S   FF ESF+DE A     DP   R  LL+ +PR   +LQ
Sbjct: 530 AHEIIDLPLPVGFWRSVGHSHQAFFKESFVDEAAHAAKKDPVAFRAALLQKHPRHLKVLQ 589

Query: 576 AAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGK-VKVHDIWQAID 634
            A EL+G  +  P  A  G +RARGVA+   FGS  A +AEVS+   K ++VH +   ID
Sbjct: 590 KAAELAGWGQPLPPDAL-GVQRARGVALHQSFGSIVAQVAEVSVGADKAIRVHRVVCVID 648

Query: 635 PGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRV 694
            G+ +NP ++  Q+  AV  GL+  L  E  + +G+ +  N+   P+L  A   RV   +
Sbjct: 649 CGAAINPNLIAQQMESAVVFGLTAALYGEVTFENGQVQQSNFHDVPLLRMADCPRVETHI 708

Query: 695 VESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           + S E   G+GEP +P +APAVANA+  LTGQR+R+LPL
Sbjct: 709 IASAEPPEGVGEPGVPPIAPAVANALFALTGQRLRALPL 747


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: 1398
Number of extensions: 68
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 739
Length of database: 750
Length adjustment: 40
Effective length of query: 699
Effective length of database: 710
Effective search space:   496290
Effective search space used:   496290
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