GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Sinorhizobium meliloti 1021

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate SM_b21633 SM_b21633 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Smeli:SM_b21633
          Length = 263

 Score =  125 bits (315), Expect = 7e-34
 Identities = 76/246 (30%), Positives = 120/246 (48%)

Query: 17  LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENR 76
           L LTL+ P   NA + +M+ A     +    D  +RAV++TGA   F AG +L      +
Sbjct: 16  LRLTLNRPDKLNAFNEEMHLALRAGFERARSDDDVRAVMLTGAGRGFSAGQDLGDRDPRK 75

Query: 77  AKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136
              P +           +  +R   KPV+ AV+G AAGAG ++A ACD+ +AA  A+F+ 
Sbjct: 76  GGAPDLGRTIETFYNPLLRLIRSLEKPVVCAVNGVAAGAGANIAFACDITLAARSARFIQ 135

Query: 137 SYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAA 196
           ++A++GL PD GG+W L + +    A  + +  +P+ A      G++ +        D A
Sbjct: 136 AFAKIGLVPDSGGTWSLPRLVGEARAKALAMTAEPLDAETAASWGLIWRAVDDAALMDEA 195

Query: 197 VAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEK 256
            A A  L       +   K  + AA T    E L  ERD    +    +  EG++AFL+K
Sbjct: 196 SALAVRLAAGPTRGLGLTKRAIQAAATHSFDEQLDLERDLQREAGRSADYAEGVTAFLDK 255

Query: 257 RAPVYK 262
           R P ++
Sbjct: 256 RNPEFR 261


Lambda     K      H
   0.317    0.132    0.377 

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: 158
Number of extensions: 4
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: 262
Length of database: 263
Length adjustment: 25
Effective length of query: 237
Effective length of database: 238
Effective search space:    56406
Effective search space used:    56406
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