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 5207485 Shew_0019 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

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



>FitnessBrowser__PV4:5207485
          Length = 716

 Score =  140 bits (352), Expect = 1e-37
 Identities = 83/193 (43%), Positives = 113/193 (58%), Gaps = 6/193 (3%)

Query: 11  DGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEM 70
           + N+A +  N   ++N  +  TL  ++ A++ +A+   V  +++T    AF+ GADI E 
Sbjct: 14  EDNIARLCFNAEGSVNKFDRETLNSLNDALDALAQTQGVKGLMLTSGKDAFIVGADITEF 73

Query: 71  KDLTAVEGRKFSVL---GNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKA 127
             L A +           NK+F KLE+L  P I+AI GFALGGGCE  L+ D+RIA + A
Sbjct: 74  LGLFAQDDNVLQGWLEDANKVFNKLEDLPFPTISAIKGFALGGGCETILATDLRIADTSA 133

Query: 128 KFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKL 187
           + G PE  LGI PGFGGT RL R IG   A E I TGK    E AL++G ++ VV P+ L
Sbjct: 134 RIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEAALKVGAIDAVVAPE-L 192

Query: 188 LEEA--KALVDAI 198
           LE A  + L DAI
Sbjct: 193 LETAACQMLQDAI 205


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: 422
Number of extensions: 17
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: 259
Length of database: 716
Length adjustment: 32
Effective length of query: 227
Effective length of database: 684
Effective search space:   155268
Effective search space used:   155268
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: 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