GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Stenotrophomonas chelatiphaga DSM 21508

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001431535.1:WP_057509244.1
          Length = 387

 Score =  224 bits (570), Expect = 5e-63
 Identities = 130/387 (33%), Positives = 209/387 (54%), Gaps = 5/387 (1%)

Query: 43  PCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAG 102
           PC  D +    LL+ EE+A++  V   +++ V P++ + +++A FP  + P++ A+G+ G
Sbjct: 5   PC--DLFDVRSLLSDEERAVQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLG 62

Query: 103 GSIK-GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLP 161
            ++   YG  G+   A  +   E+ R D+   +F+ V SSL M  I   GSEAQ+ ++LP
Sbjct: 63  ATLPPAYGGGGMDAVAYGLICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLP 122

Query: 162 SLAQLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARN 221
           ++A+   + C+ LTE   GSD S + T A +    W+++G K WI N+  ADL I++A+ 
Sbjct: 123 AMARGERIGCFGLTEAHGGSDPSSMKTRAVREGDQWRLDGSKMWITNAPIADLAIVWAQ- 181

Query: 222 TTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTS 281
            T + + GFI+++   G    +I  K+ LR    G +    V VP+ +RL GV   +   
Sbjct: 182 -TEDGVQGFILERGMAGFSVQEIGRKMSLRASSTGALFFDQVQVPEANRLAGVVGMKGPL 240

Query: 282 KVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMF 341
             L  +R  ++W PIG ++        Y  +R+ FG PLAA Q  Q KL  M   +    
Sbjct: 241 GCLNQARFGISWGPIGAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQ 300

Query: 342 LMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDL 401
           L+  +L +L E G++ P Q SL K      A + A   R+LLG  GI  +    +   +L
Sbjct: 301 LLALQLGRLKEAGRLQPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNL 360

Query: 402 EPIYTYEGTYDINTLVTGREVTGIASF 428
           E + TYEGT  ++ LV GRE+TG+ +F
Sbjct: 361 ESVITYEGTETVHQLVIGRELTGLTAF 387


Lambda     K      H
   0.319    0.133    0.399 

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: 312
Number of extensions: 15
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: 436
Length of database: 387
Length adjustment: 31
Effective length of query: 405
Effective length of database: 356
Effective search space:   144180
Effective search space used:   144180
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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