GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Marinobacter adhaerens HP15

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Marino:GFF2
          Length = 389

 Score =  159 bits (403), Expect = 1e-43
 Identities = 113/383 (29%), Positives = 186/383 (48%), Gaps = 6/383 (1%)

Query: 46  SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105
           S Y   N  L      +R+++      E+AP   E     EFP  +  K+G MG+ G ++
Sbjct: 3   SQYSELNFGLGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITV 62

Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164
            + YG   +   A+ IA  EI+R  AS       HS+L +  I   G+E QK+KYLP L 
Sbjct: 63  SEEYGGSDMGYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLV 122

Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTT- 223
               +   A++EP+ GSD   +  TA      + +NG K WI N   A+  +I+A+  T 
Sbjct: 123 SGEHIGALAMSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTS 182

Query: 224 --TNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDT 280
             +  +  FIV++DAPG    +  +K+G+R     +++ Q+  VP E+ L GV N  +  
Sbjct: 183 AGSRGVTAFIVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVL 242

Query: 281 SKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAM 340
              L   R++++  P+GI     D+   Y++ERKQFG  +  F+L Q K+  M   +   
Sbjct: 243 MSGLDYERLVLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTA 302

Query: 341 FLMGWRLCKLYETGQMTPGQASLGKAWISSK-ARETASLGRELLGGNGILADFLVAKAFC 399
               + +    + G  T  + + G    S++ A + A    +LLGGNG + ++   +   
Sbjct: 303 KSYVYMVAMSADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLR 362

Query: 400 DLEPIYTYEGTYDINTLVTGREV 422
           D +      GT +I  ++ GRE+
Sbjct: 363 DAKLYEIGAGTSEIRRMLIGREL 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: 373
Number of extensions: 25
Number of successful extensions: 5
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: 389
Length adjustment: 31
Effective length of query: 405
Effective length of database: 358
Effective search space:   144990
Effective search space used:   144990
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