Alignments for a candidate for pco in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for pco in Pseudarthrobacter sulfonivorans Ar51

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_058932486.1 AU252_RS21750 acyl-CoA dehydrogenase

Query= BRENDA::Q33DR0
         (703 letters)



>NCBI__GCF_001484605.1:WP_058932486.1
          Length = 715

 Score = 1165 bits (3015), Expect = 0.0
 Identities = 594/709 (83%), Positives = 631/709 (88%), Gaps = 13/709 (1%)

Query: 1   MTEVVDRASSPASPGSTTA----AADGAKV---------AVEPRVDVAALGEQLLGRWAD 47
           MTEVVDR + P +  + TA    AA G  V         AV+P VDVAALGEQLLG+WAD
Sbjct: 1   MTEVVDRPTGPDAAVTNTAVTNTAAAGPAVTSPSANYGSAVQPAVDVAALGEQLLGKWAD 60

Query: 48  IRLHARDLAGREVVQKVEGLTHTEHRSRVFGQLKYLVDNNAVHRAFPSRLGGSDDHGGNI 107
            R  +R LA    + K+EGLTHTEHR+R FGQLKYLVDN+AVHRAFPS LGGSDDHGGNI
Sbjct: 61  SRRQSRVLASDPALHKIEGLTHTEHRTRAFGQLKYLVDNSAVHRAFPSALGGSDDHGGNI 120

Query: 108 AGFEELVTADPSLQIKAGVQWGLFGSAVMHLGTREHHDKWLPGIMSLEIPGCFAMTETGH 167
           A FEELVTADPSLQIKAGVQWGLFGSAVMHLGT++HH KWLPGIMSLEIPGCFAMTETGH
Sbjct: 121 AAFEELVTADPSLQIKAGVQWGLFGSAVMHLGTQQHHTKWLPGIMSLEIPGCFAMTETGH 180

Query: 168 GSDVASIATTATYDEETQEFVIDTPFRAAWKDYIGNAANDGLAAVVFAQLITRKVNHGVH 227
           GSDVASIATTATYD ETQEFV+ TPFRAAWKDYIGNAA DGL AVVFAQL+T  VNHGVH
Sbjct: 181 GSDVASIATTATYDAETQEFVVHTPFRAAWKDYIGNAAIDGLGAVVFAQLVTNGVNHGVH 240

Query: 228 AFYVDLRDPATGDFLPGIGGEDDGIKGGLNGIDNGRLHFTNVRIPRTNLLNRYGDVAVDG 287
           AFYVDLRDP T +F+PGIGGEDDG+KGGLNGIDNGRLHF NVRIPRTNLLNRYGDVA DG
Sbjct: 241 AFYVDLRDPQTKEFMPGIGGEDDGVKGGLNGIDNGRLHFDNVRIPRTNLLNRYGDVAPDG 300

Query: 288 TYSSTIESPGRRFFTMLGTLVQGRVSLDGAAVAASKVALQSAIHYAAERRQFNATSPTEE 347
           TY+S+I SPGRRFFTMLGTLVQGRVSLDGAAVAASKVAL +AI YA ERRQFNA+S T+E
Sbjct: 301 TYTSSIASPGRRFFTMLGTLVQGRVSLDGAAVAASKVALTAAIRYATERRQFNASSHTDE 360

Query: 348 EVLLDYQRHQRRLFTRLATTYAASFAHEQLLQKFDDVFSGAHDTDADRQDLETLAAALKP 407
           EVLLDYQRHQRRLFTRLATTYAA FAHEQLLQKFDDVFSGAHDTD DRQDLETLAAALKP
Sbjct: 361 EVLLDYQRHQRRLFTRLATTYAAGFAHEQLLQKFDDVFSGAHDTDEDRQDLETLAAALKP 420

Query: 408 LSTWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKRLLADY 467
           LSTWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKRLLADY
Sbjct: 421 LSTWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKRLLADY 480

Query: 468 AKEFRGANFGVLARYVVDQAAGVALHRTGLRQVAQFVADSGSVQKSALALRDEEGQRTLL 527
           AKEFR  +FGVLARYVV QA GVA+HRTGLRQVAQFVAD+GSVQK+A+ALRDEEGQR LL
Sbjct: 481 AKEFRNVDFGVLARYVVAQATGVAIHRTGLRQVAQFVADTGSVQKAAIALRDEEGQRALL 540

Query: 528 TDRVQSMVAEVGAALKGAGKLPQHQAAALFNQHQNELIEAAQAHAELLQWEAFTEALAKV 587
           TDRVQ+MVA+VG+ALKGA +LP  + AALFNQHQNELI+AAQAHAELLQWEAFT AL  V
Sbjct: 541 TDRVQTMVADVGSALKGANRLPVEKGAALFNQHQNELIDAAQAHAELLQWEAFTAALEDV 600

Query: 588 DDAGTKEVLTRLRDLFGLSLIEKHLSWYLMNGRLSMQRGRTVGTYINRLLVKIRPHALDL 647
            D GTK VLT LRDLFGLSLIEK+LSWYLMNGRLSMQR RTVG YINRLLVKIRPHALDL
Sbjct: 601 TDPGTKRVLTWLRDLFGLSLIEKNLSWYLMNGRLSMQRARTVGDYINRLLVKIRPHALDL 660

Query: 648 VDAFGYGAEHLRAAIATGAEATRQDEARTYFRQQRASGSAPADEKTLLA 696
           VDAFGYG EH+RA+IATGAE TRQDEAR Y R QRASG+AP DEK LLA
Sbjct: 661 VDAFGYGDEHVRASIATGAEKTRQDEARAYVRAQRASGNAPVDEKVLLA 709


Lambda     K      H
   0.319    0.134    0.387 

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: 1459
Number of extensions: 44
Number of successful extensions: 3
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: 703
Length of database: 715
Length adjustment: 39
Effective length of query: 664
Effective length of database: 676
Effective search space:   448864
Effective search space used:   448864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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