GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Rhodococcus qingshengii djl-6-2

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_003939770.1 C1M55_RS24690 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_002893965.1:WP_003939770.1
          Length = 390

 Score =  233 bits (594), Expect = 8e-66
 Identities = 136/394 (34%), Positives = 212/394 (53%), Gaps = 9/394 (2%)

Query: 40  TFPPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFH-ITPKLGAM 98
           T P   S+ +  + LL  EE AIR  VR+ ++  + P + E++E A  P   +  +LGA+
Sbjct: 2   TTPQSLSELFAIDTLLDAEEIAIRDTVRKMVDDRIRPHVGEWFEAAALPARELAKELGAL 61

Query: 99  GVAGGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEK 158
           GV G  ++GYGC G+S TA  +A  E+  VD+   + + V  SL M  I   GSE QKE+
Sbjct: 62  GVLGMHLEGYGCAGMSATAYGLACQELEAVDSGIRSLVSVQGSLAMFAIHHNGSEEQKEE 121

Query: 159 YLPSLAQLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIF 218
           +LP +A    + C+ LTEPD GS+  G+ T A +    W +NG K WI N + AD+ +++
Sbjct: 122 WLPRMAAGEAIGCFGLTEPDFGSNPGGMRTNAKRDGDDWILNGTKMWITNGSIADVAVVW 181

Query: 219 ARNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQ 278
           AR  T + + GF+V  D PG  A +I NK+ LR     +++L++V +P    LP      
Sbjct: 182 AR--TDDGVRGFVVPTDTPGFSAPEIKNKMSLRASVTSELVLEDVRLPASAMLPKARGLS 239

Query: 279 DTSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQ 338
                L  +R  + +  +G +    +    Y ++RK F   LAA+Q+ Q K+  M   + 
Sbjct: 240 GPLGCLNEARFGIIFGAMGAARDCLETAISYARDRKVFDKSLAAYQITQAKIADMAVELG 299

Query: 339 AMFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRE---LLGGNGILADFLVA 395
              L+   L +L + G + P Q S GK    +  RE   + RE   +LG NGI  ++ V 
Sbjct: 300 KGQLLAIHLGRLKDAGTVRPEQVSTGKL---NNVREAIKIARECRTILGANGITLEYPVI 356

Query: 396 KAFCDLEPIYTYEGTYDINTLVTGREVTGIASFK 429
           +   +LE + TYEGT +++ LV GR +TG  +F+
Sbjct: 357 RHANNLESVLTYEGTSEVHQLVIGRALTGEEAFR 390


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: 333
Number of extensions: 13
Number of successful extensions: 2
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 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