GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Chryseobacterium arthrosphaerae CC-VM-7

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065397801.1 BBI00_RS05370 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001684965.1:WP_065397801.1
          Length = 379

 Score =  177 bits (448), Expect = 7e-49
 Identities = 114/367 (31%), Positives = 174/367 (47%), Gaps = 5/367 (1%)

Query: 62  IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSITANAI 120
           I +  +E  EK + P + E+ E   FP  +  +LG MG  G  + + YG  GL       
Sbjct: 12  IAETAKEFAEKNIRPNIMEWDESQTFPKDLFHQLGEMGFMGIVVPEQYGGSGLGYHEYVA 71

Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180
              EI++VD S    +  H+SL    I   G+E Q+ K+LP LA    +  W LTE + G
Sbjct: 72  ILDEISQVDPSIGLSVAAHNSLCTNHIYEFGNEEQRNKWLPQLATGKVIGAWGLTEHNTG 131

Query: 181 SDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGFIVKKDAP 237
           SD+ G+ TTA K    W ING K +I ++   D+ ++  R       N    F+++K   
Sbjct: 132 SDSGGMSTTAVKDGDEWIINGAKNFITHAISGDIAVVMTRTGEKGAKNNSTAFVLEKGML 191

Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRVMVAWQPI 296
           G  + K  NK+G+R  +  +++  NV VPD  RL  V   F+   K+L   R+ +A   +
Sbjct: 192 GFTSGKKENKLGMRASETAELIFDNVRVPDSHRLGEVGEGFKQAMKILDGGRISIAALSL 251

Query: 297 GISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQM 356
           G + G Y    +Y KER QFG  ++ FQ     L  M   + A  L+  R   L    Q 
Sbjct: 252 GTARGAYKAALKYAKERHQFGKSISEFQAINFMLADMATEIDAAELLIQRAATLKNAKQK 311

Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416
              + ++ K + S      ++   ++ GG G   DF   K + D +     EGT +I  L
Sbjct: 312 MTKEGAMAKLYASEACVRISNNAVQIFGGYGYTKDFPAEKFYRDSKLCTIGEGTSEIQRL 371

Query: 417 VTGREVT 423
           V GR++T
Sbjct: 372 VIGRDIT 378


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: 319
Number of extensions: 12
Number of successful extensions: 4
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: 379
Length adjustment: 31
Effective length of query: 405
Effective length of database: 348
Effective search space:   140940
Effective search space used:   140940
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