Alignments for a candidate for drdehyd-beta in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Marinobacter adhaerens HP15

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate GFF1599 HP15_1560 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein

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



>FitnessBrowser__Marino:GFF1599
          Length = 777

 Score =  311 bits (798), Expect = 6e-89
 Identities = 247/781 (31%), Positives = 366/781 (46%), Gaps = 80/781 (10%)

Query: 13  NLSRRRFLASTAVG-ALVIGFGLPL---GAGRVQAATSAERGTQVP---AFLEIRPDGTV 65
           N+SRRRFL   A G ALV+     +   G  + Q    A  G  V     F+ I  DG V
Sbjct: 11  NVSRRRFLMGLAGGSALVLAARWDVALAGNEKAQFGAGAMPGGWVDDPNVFIHIDADGLV 70

Query: 66  RLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVR 125
            +++   E GQG  T++  +  +EL AD     VE A         +N    T GS S+R
Sbjct: 71  TIVNNRSEMGQGIRTSLVMVGADELGADWDQVRVEQAEGDHDKYGNQN----TDGSRSMR 126

Query: 126 MSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDM 185
             Y  MRR  A AR ML QA A +WGVPV E+      +VH  SG+ LG+GELA+ A ++
Sbjct: 127 HWYQPMRRAAAAARQMLEQAAANEWGVPVSEVQAGVHTIVHRPSGKELGFGELAAKAREL 186

Query: 186 PVPDPASITLRDPSQFRWIGKPV------------KRLDAYDKSTGKALYSIDLKVDNML 233
            VP   ++ L+   + R++GK              K +D  D  TGKA+Y  D+  + +L
Sbjct: 187 DVPGRNALVLKRDDELRFVGKETGLINGELKSAYPKAIDGEDIVTGKAVYGADVPFEGLL 246

Query: 234 HAAVQHAPRLGMTVGSLRNQS--QVEGMKGVHSVHVLP--------GAVAVVAERWWHAK 283
           +A +   P  G TVG   +    +V G++ V  V            G +AVVA   W A 
Sbjct: 247 YAVIARPPVYGATVGDFDDTEALKVPGVEKVLKVEGTGQPAGFSPLGGIAVVASNTWAAM 306

Query: 284 RAVEAIQVDWQ-EAAADSALRVMPADFSSDKHREFL-AAQQGPTRDDENEGDVAGALKGA 341
              +A+++DW  E A D+      A ++S  +RE L  A Q P +     GD+  AL+ A
Sbjct: 307 EGRKALKIDWNLEPAGDN------ASYTSATYRESLEKAAQQPGKVVRQHGDLDTALENA 360

Query: 342 KTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQI 401
             +V ATY+  ++  A +EPP A  R   DG  E+W P Q P   R  +A R GLD   +
Sbjct: 361 DKRVSATYYMPHMAQAPMEPPVATVRIK-DGKAEVWAPVQNPQATRDTVAGRLGLDAENV 419

Query: 402 TLHSPLLGGFFGRHFLYDSANPYPQAIALAKAV-SRPIKLIWSREEEFLRDVLRPLAVVK 460
           T+H  LLGG FGR    D A    +A ++A+A   RP++L WSRE++        ++V  
Sbjct: 420 TVHVTLLGGGFGRKSKPDFA---IEAASIAEAFKGRPVRLQWSREDDIHHAYYHAVSVDY 476

Query: 461 FRAALDDKGLPVAIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYV 520
             A LD+ G        + +       A     K +     G +   +++P  R+     
Sbjct: 477 LEAGLDNNGQATGWLHRTLSPSIGSLFAPDPKHKGEFELGMGFNTMPFSVPALRLENPPA 536

Query: 521 KGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGEL 580
                +G++RSV N  + +  +SF  E+A   G D  +  L LL  +  +  L      +
Sbjct: 537 PAHVRIGWFRSVYNLPHAWAIQSFAHEMAVAAGKDHRDYVLDLLGPDREIHNL-----TV 591

Query: 581 SGGWKRG------------------------PFTAEDGTRRARGVAMASPFGSHTAAIAE 616
             GW  G                         +    G  R  G+A    F S+TA + +
Sbjct: 592 GDGWNYGEDPDLYPIDIGRMRNVIERVTREADWGKSTGKNRGLGLAFHHSFVSYTAIVFD 651

Query: 617 VSIEN-GKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARN 675
           V +++ G++ +H    A D G   NP  + +Q+ GA+ +G+   L  E  + DG  +  N
Sbjct: 652 VEVDDQGELTIHRADIAFDCGPQANPERIRSQLEGAIVMGIGIALQSEVTFEDGVAQQGN 711

Query: 676 YDLY--PILAPA-QMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLP 732
           +D Y  P +  A +  RVH+ V    E MGG+GEP LP VAPA+ NA+   TG+R+R LP
Sbjct: 712 FDKYLIPRMPDAPKTLRVHL-VDNPDEAMGGVGEPGLPPVAPALCNAIYAATGKRIRRLP 770

Query: 733 L 733
           +
Sbjct: 771 V 771


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: 1476
Number of extensions: 80
Number of successful extensions: 12
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: 777
Length adjustment: 40
Effective length of query: 699
Effective length of database: 737
Effective search space:   515163
Effective search space used:   515163
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