GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Xanthobacter autotrophicus Py2

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000017645.1:WP_012116241.1
          Length = 390

 Score =  171 bits (432), Expect = 5e-47
 Identities = 114/366 (31%), Positives = 176/366 (48%), Gaps = 5/366 (1%)

Query: 62  IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLSITANAI 120
           +R  VR   + E+AP   E     +FP  + PKLGA+G+ G + +  YG  GL    + I
Sbjct: 20  LRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGGSGLGYLEHVI 79

Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180
           A  EI+R  AS       HS+L +  I+  G+  QK KYLP L     V   A++EP  G
Sbjct: 80  AMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVGALAMSEPGAG 139

Query: 181 SDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQINGFIVKKDAP 237
           SD   + T A K    + +NG K WI N   A+ L+++A+         +  F+V++D P
Sbjct: 140 SDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGMTAFLVERDFP 199

Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRVMVAWQPI 296
           G    +  +K+G+R    G+++ Q+  VP+E+ L  V          L   R ++A  P 
Sbjct: 200 GFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDYERAVLAGGPT 259

Query: 297 GISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQM 356
           GI     D+   Y+ ERKQFG P+  FQL Q K+  M   + A     + + K  + G  
Sbjct: 260 GIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYAVAKACDRGAT 319

Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416
           T   A+    + + KA   A    + LGGNG + D+   +   D +      GT +I  +
Sbjct: 320 TREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEIGAGTSEIRRM 379

Query: 417 VTGREV 422
           + GR++
Sbjct: 380 LIGRQL 385


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: 384
Number of extensions: 18
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: 390
Length adjustment: 31
Effective length of query: 405
Effective length of database: 359
Effective search space:   145395
Effective search space used:   145395
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 Apr 09 2024. 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