GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Pseudomonas putida KT2440

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate PP_2216 PP_2216 short-chain acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Putida:PP_2216
          Length = 375

 Score =  166 bits (421), Expect = 9e-46
 Identities = 112/374 (29%), Positives = 182/374 (48%), Gaps = 5/374 (1%)

Query: 54  LLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPG 112
           L+  E+Q I   VR   ++ + P   ++ +   FP     ++  +G+ G  + + +G   
Sbjct: 2   LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61

Query: 113 LSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACW 172
               A A+A  EIA  D +CST + VH+S+G + I   G+E QKE++L  LA    +  +
Sbjct: 62  TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121

Query: 173 ALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA---RNTTTNQING 229
           ALTEP  GSDAS L T A      + +NG K++I +   A ++I+FA          I+ 
Sbjct: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181

Query: 230 FIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSR 288
           FIV  D+PG +  ++ +K+G        I+  NV VP  +RL      ++     L   R
Sbjct: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241

Query: 289 VMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLC 348
           + +A Q +G++   +++   Y  ER+ FG PL   Q    +L  M   +     M     
Sbjct: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301

Query: 349 KLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYE 408
            L + G+    +AS+ K + S  A +  S   + LGG G L+DF + + + D+     YE
Sbjct: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361

Query: 409 GTYDINTLVTGREV 422
           GT DI  +V  R +
Sbjct: 362 GTSDIQRMVIARNL 375


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: 316
Number of extensions: 15
Number of successful extensions: 4
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: 375
Length adjustment: 31
Effective length of query: 405
Effective length of database: 344
Effective search space:   139320
Effective search space used:   139320
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