GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Phaeobacter inhibens BS107

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Phaeo:GFF1551
          Length = 406

 Score =  224 bits (570), Expect = 5e-63
 Identities = 131/384 (34%), Positives = 204/384 (53%), Gaps = 2/384 (0%)

Query: 47  DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105
           D    +D L+ +E+ I    R   ++++ P +   +E  E    I  ++G MG+ G +I 
Sbjct: 22  DPLRLDDQLSEDERMIAASARSYAQEKLQPRVLNAYENEETDPEIFREMGEMGLLGTTIP 81

Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165
           + YG  G    +  +   E+ RVD+   + + V SSL M  I   GSE Q++KYLP L+ 
Sbjct: 82  EQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVMYPIYAYGSEEQRQKYLPKLSS 141

Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225
              + C+ LTEPD GSD +G+ T A K +GG+++ G K WI N+  AD+ +++A++    
Sbjct: 142 GEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKMWISNAPIADVFVVWAKSEAHG 201

Query: 226 -QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284
            +I GF+++K   GL A KI NK  LR    G+I++  V V D+  LP V   +     L
Sbjct: 202 GKIRGFVLEKGMKGLSAPKIANKASLRASITGEIVMDGVEVGDDALLPHVEGLKGPFGCL 261

Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344
             +R  ++W  +G +   +    +Y  +RKQFG PLA  QL Q KL  M   +       
Sbjct: 262 NRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPLANTQLFQLKLANMQTEITLGLQAS 321

Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404
            R+ +L +     P   S+ K     KA E A   R++ GGNGI  +F V +   +LE +
Sbjct: 322 LRVGRLMDEANAAPEMISIVKRNNCGKALEIARHARDMHGGNGISLEFGVIRHMVNLETV 381

Query: 405 YTYEGTYDINTLVTGREVTGIASF 428
            TYEGT+D++ L+ GR  TG+ +F
Sbjct: 382 NTYEGTHDVHALILGRAQTGLQAF 405


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: 335
Number of extensions: 19
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: 406
Length adjustment: 32
Effective length of query: 404
Effective length of database: 374
Effective search space:   151096
Effective search space used:   151096
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