GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella loihica PV-4

Align crotonase (EC 4.2.1.150) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__PV4:5209977
          Length = 706

 Score =  131 bits (330), Expect = 3e-35
 Identities = 79/186 (42%), Positives = 117/186 (62%), Gaps = 5/186 (2%)

Query: 11  DGNVASITLNRP-KALNALNAATLKEIDAAINDIAEDDNVYAV-IITGSGKAFVAGADIA 68
           D  +A +T++ P + +N L A    EI   + +I  D  +  V II+G   +FVAGADI+
Sbjct: 11  DNGIAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADIS 70

Query: 69  EMKDL-TAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIA--SS 125
            +    TA + R+ S  G+++F  LE+L  PV+AAING  LGGG EL+L+C  R+   S+
Sbjct: 71  MLDACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSN 130

Query: 126 KAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPD 185
           K   G PEV LG+ PG GGTQRL R +G+  + +++ TGK + A++AL++GLV+ VV   
Sbjct: 131 KTMLGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPES 190

Query: 186 KLLEEA 191
            LL+ A
Sbjct: 191 ILLQTA 196


Lambda     K      H
   0.318    0.136    0.376 

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: 410
Number of extensions: 17
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: 259
Length of database: 706
Length adjustment: 32
Effective length of query: 227
Effective length of database: 674
Effective search space:   152998
Effective search space used:   152998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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