GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sphingomonas koreensis DSMZ 15582

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Ga0059261_2902 Ga0059261_2902 Enoyl-CoA hydratase/carnithine racemase

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



>FitnessBrowser__Korea:Ga0059261_2902
          Length = 273

 Score =  145 bits (367), Expect = 7e-40
 Identities = 91/259 (35%), Positives = 143/259 (55%), Gaps = 7/259 (2%)

Query: 8   LEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67
           +E+DG +  +T++ P   NAL+    +E+ AA + I  D +V  VI+T +G  F AG ++
Sbjct: 15  VERDGPLVILTIDDPGTRNALSPLLTRELVAACDAINADMSVGCVILTAAGDVFCAGGNL 74

Query: 68  AEMKDLT------AVEGRKFSVLG-NKIFRKLENLEKPVIAAINGFALGGGCELSLSCDI 120
            +M          A E R+  + G   I R L +LE P IAA+NG A+G G + +  C +
Sbjct: 75  KDMYARANHFAGNAAEIRRTYLAGVQTIARALHDLEVPSIAAVNGAAMGAGMDFATMCTM 134

Query: 121 RIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNK 180
           RIAS +AKF +  + LG+T   GG   L RAIG   A E+  TG  ++AE+AL IGLV++
Sbjct: 135 RIASDRAKFAESFIKLGLTSAAGGAWFLTRAIGQSAAAEMALTGDTLDAEQALAIGLVSR 194

Query: 181 VVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATED 240
           VV+ D LL+EA+ L   I  +   ++R+    +    + D+ T +   A +      T+D
Sbjct: 195 VVQHDALLDEARTLAARITRHPMHSIRLNTRLLRDSARLDLHTALEIAAGMQAIVQQTDD 254

Query: 241 RVEGMTAFVEKRDKAFKNK 259
           + E + A +E+R  AF  +
Sbjct: 255 QHEAVAAVMERRIPAFTGR 273


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: 150
Number of extensions: 7
Number of successful extensions: 1
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: 273
Length adjustment: 25
Effective length of query: 234
Effective length of database: 248
Effective search space:    58032
Effective search space used:    58032
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: 47 (22.7 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