GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Sedimenticola selenatireducens DSM 17993

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000428045.1:WP_029134232.1
          Length = 397

 Score =  248 bits (634), Expect = 2e-70
 Identities = 143/376 (38%), Positives = 210/376 (55%), Gaps = 1/376 (0%)

Query: 55  LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLS 114
           LT EE+ +R   ++  ++++ P + E      F   I  ++G +G+ G +I GY C GL+
Sbjct: 23  LTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTIDGYDCAGLN 82

Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174
             +  +   E+ RVD+   + + V SSL M  I   G+E Q+EKYLP LA    V C+ L
Sbjct: 83  YVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGCFGL 142

Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKK 234
           TEPD+GSD +G+ T A  V+GG+ ++G K WI NS  AD+ I++A++     I GFI++K
Sbjct: 143 TEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKD-DEGVIRGFILEK 201

Query: 235 DAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQ 294
              GL A KI  K  LR    G+I++  VFVP E+ LP V         L  +R  +AW 
Sbjct: 202 GMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNVKGLAGPFGCLNRARYGIAWG 261

Query: 295 PIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETG 354
            +G +   +     Y  +RKQFG PLAA QL Q KL  M   +        +L +L++ G
Sbjct: 262 VLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCLQLGRLFDAG 321

Query: 355 QMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDIN 414
           Q  P   SL K   + KA + A + R++ GGNGI  +F V +   +LE + TYEGT+D++
Sbjct: 322 QAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVNTYEGTHDVH 381

Query: 415 TLVTGREVTGIASFKP 430
            L+ GR  TGI +F P
Sbjct: 382 ALILGRAQTGIQAFAP 397


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: 356
Number of extensions: 16
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: 397
Length adjustment: 31
Effective length of query: 405
Effective length of database: 366
Effective search space:   148230
Effective search space used:   148230
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 Apr 09 2024. 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