GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Algoriphagus aquaeductus T4

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_111395068.1 CLV31_RS21080 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_003253485.1:WP_111395068.1
          Length = 452

 Score =  362 bits (929), Expect = e-104
 Identities = 181/388 (46%), Positives = 253/388 (65%), Gaps = 1/388 (0%)

Query: 42  PPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVA 101
           P    D+Y     L  EE+ I+ KVRE ME+E+ PI  +YW +AEFP HI PK+  + +A
Sbjct: 64  PAINGDFYELGKSLPKEEREIQLKVREFMEREIKPIANDYWNRAEFPMHIIPKMAELNIA 123

Query: 102 GGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLP 161
           G + +GYGCPG S         E+ARVD S STF  V S L M ++ LCGSEAQK+++LP
Sbjct: 124 GLTYQGYGCPGHSALLEGFIAMEMARVDTSISTFFGVQSGLAMGSVYLCGSEAQKQEWLP 183

Query: 162 SLAQLNTVACWALTEPDNGSDASGLGTTATKVEGG-WKINGQKRWIGNSTFADLLIIFAR 220
           ++ +L  +  + LTEP+ GS A+G  TT  K EG  W +NGQK+WIGN+TF+D+ +I+AR
Sbjct: 184 AMQKLEKIGAFGLTEPEVGSGAAGGLTTTCKREGDVWILNGQKKWIGNATFSDMTVIWAR 243

Query: 221 NTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDT 280
           +   NQ+ GFIV+K  PG +A K+ +K+ LR VQN  I L N  VP+ DRL   NSF+DT
Sbjct: 244 DLDDNQVKGFIVRKGNPGFQAEKLKDKMALRTVQNALITLTNCEVPESDRLQSANSFKDT 303

Query: 281 SKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAM 340
           +KVL ++R  VAWQ +G + G Y++   Y  ER+QFG P+A+FQL Q  LV MLG++ AM
Sbjct: 304 AKVLRMTRAGVAWQAVGCARGAYELALAYTNERQQFGRPIASFQLVQDLLVTMLGDLTAM 363

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

Query: 401 LEPIYTYEGTYDINTLVTGREVTGIASF 428
            E +Y+YEGT +IN+L+ GR +TG ++F
Sbjct: 424 AEAVYSYEGTKEINSLIVGRAITGHSAF 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: 462
Number of extensions: 16
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 24 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