GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Pedobacter sp. GW460-11-11-14-LB5

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Pedo557:CA265_RS22715
          Length = 379

 Score =  179 bits (454), Expect = 1e-49
 Identities = 118/378 (31%), Positives = 188/378 (49%), Gaps = 7/378 (1%)

Query: 50  HFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGY 108
           HF   L+ E+  IR+  R+  ++E+ P + E  E  +FP     KLG +G  G  + + Y
Sbjct: 2   HFE--LSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKY 59

Query: 109 GCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNT 168
              GL   +  +   E++++DAS S  + V++SL    +   GSEAQKEKYL  LA    
Sbjct: 60  NGSGLDAISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEK 119

Query: 169 VACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTN 225
           +  + L+EP+ GSDA+   TTA      + +NG K WI N + A   ++ A+        
Sbjct: 120 IGAFCLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHK 179

Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVN-SFQDTSKVL 284
            IN FIV+K   G       NK+G+R      ++  +V VP E+R+      F+   K L
Sbjct: 180 GINAFIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTL 239

Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344
              R+ +A Q +GI+ G +++  +Y KERK FG P++  Q    KL  M   ++A  L+ 
Sbjct: 240 EGGRIGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLV 299

Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404
           ++   L + G       S+ K + S  A +      ++ GG G + ++ V +   D +  
Sbjct: 300 YKAAWLKDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKIT 359

Query: 405 YTYEGTYDINTLVTGREV 422
             YEGT +I  +V  REV
Sbjct: 360 QIYEGTSEIQKMVISREV 377


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: 325
Number of extensions: 11
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 17 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