GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Limnohabitans curvus MWH-C5

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_108401500.1 B9Z44_RS01330 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_003063475.1:WP_108401500.1
          Length = 258

 Score =  334 bits (856), Expect = 1e-96
 Identities = 162/257 (63%), Positives = 205/257 (79%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60
           M+   +L E +GRVG++TLNRP+ LNALND LMD LGAAL   DADD IGAIV+TGS+KA
Sbjct: 1   MSQPTVLSERQGRVGVLTLNRPEQLNALNDTLMDALGAALLALDADDGIGAIVITGSDKA 60

Query: 61  FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120
           FAAGADI  M+ + YMDV+   +ITRNWET+R +RKP+IAAVAGFA+GGGCELA+ CD+I
Sbjct: 61  FAAGADIAAMADWGYMDVFSSAFITRNWETIRQVRKPVIAAVAGFAMGGGCELALACDLI 120

Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180
            AA++AKF  PE+KL ++PGAGGTQRLPRA+ KAKAMD+CL+AR + A EA+R GLVSRV
Sbjct: 121 VAAESAKFALPEVKLAMLPGAGGTQRLPRAIGKAKAMDMCLSARMLSAEEADRYGLVSRV 180

Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240
           +P+ +L+ E +  A TIA F  PA++ +KESVNRA+E +L EGV FER   ++ FA+ D 
Sbjct: 181 VPSDALMAETLKLANTIAGFSLPALIAIKESVNRAWEGSLTEGVKFERHALYARFASADA 240

Query: 241 KEGMAAFVEKRKPVFKH 257
            EGM AF+EKRKP F+H
Sbjct: 241 HEGMHAFLEKRKPTFQH 257


Lambda     K      H
   0.321    0.134    0.380 

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: 235
Number of extensions: 5
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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