GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Cupriavidus basilensis 4G11

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Cup4G11:RR42_RS28565
          Length = 377

 Score =  163 bits (412), Expect = 1e-44
 Identities = 111/369 (30%), Positives = 172/369 (46%), Gaps = 7/369 (1%)

Query: 58  EEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSIT 116
           ++  IR   R    + +AP   E+    + P  +  ++GA+G+ G  + + +G       
Sbjct: 8   QQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGTYTDYI 67

Query: 117 ANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTE 176
           A A+A  EIA   A+C+T + VH+S+G   I   G++AQKE+YLP LA    +  + LTE
Sbjct: 68  AYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLASGEIIGAFCLTE 127

Query: 177 PDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQINGFIVK 233
           P  GS+A  L T A   + GW ++G K+++ N   A + I+FA          ++ F+V 
Sbjct: 128 PQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGLSAFVVP 187

Query: 234 KDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL--PGVNSFQDTSKVLAVSRVMV 291
            D PG        K+G+R      I L +  VP +  L  PG    +     L   R+ +
Sbjct: 188 TDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPG-EGLRIALSNLEGGRIGI 246

Query: 292 AWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLY 351
           A Q +GI+   ++   RY  ER QFG PL         L  M   + A  L+  R   + 
Sbjct: 247 AAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHRAAHMR 306

Query: 352 ETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTY 411
             GQ    +AS  K + S  A    S   ++ GG G L D+ V + + D      YEGT 
Sbjct: 307 TAGQPCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARITQIYEGTS 366

Query: 412 DINTLVTGR 420
           +I  ++  R
Sbjct: 367 EIQRMLIAR 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: 329
Number of extensions: 11
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: 377
Length adjustment: 31
Effective length of query: 405
Effective length of database: 346
Effective search space:   140130
Effective search space used:   140130
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