GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Echinicola vietnamensis KMM 6221, DSM 17526

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Echvi_0738 Echvi_0738 Acyl-CoA dehydrogenases

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Cola:Echvi_0738
          Length = 452

 Score =  369 bits (948), Expect = e-107
 Identities = 186/388 (47%), Positives = 248/388 (63%), Gaps = 1/388 (0%)

Query: 42  PPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVA 101
           PP   D+Y     L P EQ I  KVR+ MEKEV PI  EYW K  FP HI PK+  +G+A
Sbjct: 64  PPVNGDFYSLEKTLPPHEQEIVAKVRDFMEKEVRPIANEYWNKGHFPMHIIPKMAELGIA 123

Query: 102 GGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLP 161
           G + KGYGCPG S         E+ARVD S STF  V S L M +I +CGSE QK+++LP
Sbjct: 124 GLTYKGYGCPGHSALLEGFLAMEMARVDTSISTFFGVQSGLAMGSIYVCGSEEQKQEWLP 183

Query: 162 SLAQLNTVACWALTEPDNGSDASGLGTTATKVEGG-WKINGQKRWIGNSTFADLLIIFAR 220
            + +++ +  + LTEP  GS  +G  TT  K EG  W INGQK+WIGN+TF+D+ +I+AR
Sbjct: 184 KMQKMDVIGAFGLTEPKVGSGVAGGLTTTCKREGDEWVINGQKKWIGNATFSDITVIWAR 243

Query: 221 NTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDT 280
           +    Q+ GFIV+KD PG    KI NK+ LR VQN  I +++  VP+ DRL   NSF+DT
Sbjct: 244 DLDDQQVKGFIVRKDNPGFHPEKIENKMALRTVQNALITMKDCRVPESDRLQNANSFKDT 303

Query: 281 SKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAM 340
           S++L ++R  VAWQ +G   G Y+   RY  ERKQFG P+A FQL Q  LV MLG++ AM
Sbjct: 304 SEILRLTRAGVAWQAVGCGRGAYEAALRYTNERKQFGRPIAGFQLVQDLLVTMLGDLTAM 363

Query: 341 FLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCD 400
             M +RL K+ + G++    ASL K + + + R      REL GGNGIL ++ +A+   D
Sbjct: 364 QTMVYRLSKMQDAGELKDEHASLAKVFCTLRMRTIVDHSRELFGGNGILLEYDIARFVAD 423

Query: 401 LEPIYTYEGTYDINTLVTGREVTGIASF 428
            E IY+YEGT +IN+L+ GR +TG ++F
Sbjct: 424 AEAIYSYEGTKEINSLIVGRAITGHSAF 451


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: 461
Number of extensions: 13
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: 452
Length adjustment: 32
Effective length of query: 404
Effective length of database: 420
Effective search space:   169680
Effective search space used:   169680
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: 51 (24.3 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