GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Shewanella amazonensis SB2B

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__SB2B:6938693
          Length = 391

 Score =  221 bits (563), Expect = 3e-62
 Identities = 135/383 (35%), Positives = 203/383 (53%), Gaps = 3/383 (0%)

Query: 47  DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105
           D  +FN LLT EE+ IR  V E  + ++   +        F   I  +LG +G+ G ++ 
Sbjct: 10  DPLNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLP 69

Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165
           + YGC   +  +  +   EI RVD+   + + V SSL M  I   G+EAQ+ KYLP LA 
Sbjct: 70  EEYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLAT 129

Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225
              V C+ LTEPD GSD +G+ T A +++GG++I G K WI NS  AD+ +++A+     
Sbjct: 130 GEWVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAK--LDG 187

Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285
            I GF+++K   GL A KI  K  LR    G+I++ NV V ++  LP V   +     L 
Sbjct: 188 AIRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALLPNVEGLKGPFGCLN 247

Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345
            +R  +AW  +G +   +    +Y  +R QF  PLAA QL Q+KL  M   +        
Sbjct: 248 KARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFACL 307

Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405
           +  +L +   +     SL K     KA + A + R++ GGNGI  +F V +   +LE + 
Sbjct: 308 QAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEAVN 367

Query: 406 TYEGTYDINTLVTGREVTGIASF 428
           TYEGT+DI+ L+ GR  T + +F
Sbjct: 368 TYEGTHDIHALILGRAQTDLQAF 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: 326
Number of extensions: 13
Number of successful extensions: 3
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: 391
Length adjustment: 31
Effective length of query: 405
Effective length of database: 360
Effective search space:   145800
Effective search space used:   145800
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