GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas stutzeri RCH2

Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF2033 Psest_2076 Enoyl-CoA hydratase/carnithine racemase

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



>FitnessBrowser__psRCH2:GFF2033
          Length = 270

 Score =  134 bits (336), Expect = 3e-36
 Identities = 84/266 (31%), Positives = 136/266 (51%), Gaps = 11/266 (4%)

Query: 2   EFKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAF 61
           E+K   +E    +A + +NRP+ +NA++AA   EI    N +   D V  V+++G+G+ F
Sbjct: 3   EYKAFRVELADKIARVVINRPEKINAMDAAFWSEIIDIFNWVDATDEVRVVVLSGAGEHF 62

Query: 62  VAGADIAEMKDLTAVEGRKFSVLGNKIFRKLENLE----------KPVIAAINGFALGGG 111
            +G D+  +  + +  G        ++ RK+ +L+          KPVIAAI G+ LGG 
Sbjct: 63  SSGIDLQLLASVGSQLGNDVGRNAERLRRKILSLQASFNAVDHCRKPVIAAIQGYCLGGA 122

Query: 112 CELSLSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEE 171
            +L  +CD+R +++ AKF   E+ +G+    G  QRL R IG GM +EL +TG+ I+ EE
Sbjct: 123 IDLISACDMRYSTASAKFSIKEIDMGMAADVGTLQRLPRIIGDGMMRELAFTGRTIDGEE 182

Query: 172 ALRIGLVNKV-VEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAE 230
           A  IGLVN+   +   L++    L   I   +P+A+R  K  I       +D G+ Y A 
Sbjct: 183 ARSIGLVNRTYADQQALMDGVLELARDIARKSPVAIRGTKEMIRYMRDHRVDDGLEYIAT 242

Query: 231 VFGECFATEDRVEGMTAFVEKRDKAF 256
                  + D    + A + K+   F
Sbjct: 243 WNAAMLQSADIKVAIAAHMSKQKPDF 268


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: 138
Number of extensions: 7
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: 270
Length adjustment: 25
Effective length of query: 234
Effective length of database: 245
Effective search space:    57330
Effective search space used:    57330
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