Alignments for a candidate for drdehyd-beta in Marinobacter guineae M3B

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Marinobacter guineae M3B

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_099616143.1 CLH62_RS00125 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_002744735.1:WP_099616143.1
          Length = 776

 Score =  324 bits (830), Expect = 1e-92
 Identities = 252/780 (32%), Positives = 376/780 (48%), Gaps = 79/780 (10%)

Query: 13  NLSRRRFLASTAVG-ALVIG--FGLPLGAGRVQAATSAERGTQVP---AFLEIRPDGTVR 66
           N+SRRR L   A G ALV+   + +PL +   Q    A  G  V     F++I  DGTV 
Sbjct: 11  NVSRRRLLMGMAGGSALVLAARWDMPLASENAQFGAGAMPGGWVDDPNVFIQIDSDGTVT 70

Query: 67  LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRM 126
           +++   E GQG  T++  +  +EL AD     V  A    +    +N    T GS S+R 
Sbjct: 71  IVNNRSEMGQGIRTSLVMVGADELGADWDQVKVRQAEGDHSKYGNQN----TDGSRSMRH 126

Query: 127 SYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMP 186
            Y  MRR  A AR ML QA A QWGVPV E+ TQ  +VVH  SG+ LG+GELAS A ++ 
Sbjct: 127 WYEPMRRAAAAARLMLEQAAASQWGVPVHEVKTQVHKVVHQPSGKELGFGELASRARELE 186

Query: 187 VPDPASITLRDPSQFRWIGKPV------------KRLDAYDKSTGKALYSIDLKVDNMLH 234
           VPD  ++ L+  ++ R+IGK              K +D  D  TG+A+Y  D+  D++L+
Sbjct: 187 VPDRNALVLKQDNELRFIGKETGLINGKLESPHPKAIDGEDIVTGRAVYGADVPFDDLLY 246

Query: 235 AAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAK 283
           A +   P  G TV S  + ++   ++GV  V  +            G VAVVA   W A 
Sbjct: 247 AVIARPPVYGATVRSF-DDAEALKVRGVEKVLKVEGTGQPAGFSPLGGVAVVASNTWAAM 305

Query: 284 RAVEAIQVDWQ-EAAADSALRVMPADFSSDKHREFL-AAQQGPTRDDENEGDVAGALKGA 341
              +A+++DW  E+A ++      A ++S  +R+ L  A Q P +   + GD+  AL+ A
Sbjct: 306 EGKKALKIDWNLESAGEN------AGYTSIAYRQSLEKAAQSPGKVVRHHGDLDRALESA 359

Query: 342 KTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQI 401
             ++ ATY+  ++  A +EPP A  R   DG  E+W P Q P   R  +A+R GLD   +
Sbjct: 360 DKRISATYYMPHMAQAPMEPPVATVRIK-DGKAEVWAPVQNPQATRDTVAQRLGLDTENV 418

Query: 402 TLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVS-RPIKLIWSREEEFLRDVLRPLAVVK 460
           T+H  LLGG FGR    D AN   +A ++A+  + RP++L WSRE++        ++V  
Sbjct: 419 TVHVTLLGGGFGRKSKPDFAN---EAASIAELFNGRPVRLQWSREDDIHHAYFHAVSVDH 475

Query: 461 FRAALDDKGLPVAIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYV 520
             A LD  G        + +       A     K +     G +   + +P  R+     
Sbjct: 476 LEAGLDGDGNATGWLHRTLSPSIGSLFAPDPKHKGEFELGMGFNTMPFDVPALRLENPPA 535

Query: 521 KGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGEL 580
                +G++RSV N  + +  +SF  ELA   G D  +  L LL  +  +  L      +
Sbjct: 536 PAHVRIGWFRSVYNLPHAWAIQSFAHELAVAAGRDHRDYVLDLLGPDREIHNL-----TV 590

Query: 581 SGGWKRGP------------------FTAEDG------TRRARGVAMASPFGSHTAAIAE 616
             GW  G                    T+E G        R  G+A    F S+TA + E
Sbjct: 591 GDGWNYGENPDLYPIDIGRMRAVIERATSEAGWGKSVQEGRGLGLAFHHSFVSYTAIVFE 650

Query: 617 VSIEN-GKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARN 675
           V +++ G + +     A D G   NP  + +Q+ GA  +G+   L  E  + DG  +  N
Sbjct: 651 VEVDDQGGLTILQADIAFDCGKQANPERIRSQLEGACVMGIGIALQSEVTFKDGVAQQDN 710

Query: 676 YDLYPI-LAPAQMARVHVRVVES-GEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           +D Y I   P     + V +V++  E MGG+GEP LP VAPA+ NA+   TG+R+R LP+
Sbjct: 711 FDNYLIPRMPDAPKSIRVHLVDNPQEAMGGVGEPGLPPVAPALCNAIYAATGKRIRRLPV 770


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: 1361
Number of extensions: 85
Number of successful extensions: 11
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: 776
Length adjustment: 40
Effective length of query: 699
Effective length of database: 736
Effective search space:   514464
Effective search space used:   514464
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 24 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