GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Desulfacinum infernum DSM 9756

Align BadI (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein

Query= metacyc::MONOMER-892
         (260 letters)



>NCBI__GCF_900129305.1:WP_073037062.1
          Length = 263

 Score =  143 bits (360), Expect = 4e-39
 Identities = 94/260 (36%), Positives = 139/260 (53%), Gaps = 6/260 (2%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           M F+++++E+R+GVA I  NRP  +NA    T +EL +A+  A  D  V  +VL GAGD+
Sbjct: 1   MDFQNILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDK 60

Query: 61  AFCTGGD-QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119
           AF  G D       N           +++  ++ D+PKPVIA V G+A+GGG  LA  CD
Sbjct: 61  AFVAGADITELQKMNPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCD 120

Query: 120 LTICSEKAIFGQVGPKMGSVDPGY-GTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178
               S+KA FGQ    +G + PG+ GT  LAR+VG  KA+E+    +    ++A+ +GL 
Sbjct: 121 FIYASDKAKFGQPEINLGII-PGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLV 179

Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN--MDTAHQAGIAGMGMYALKLYYD 236
               PH+ L  E  K    +  +S TAL   K   +  MD   + G A +   A  + + 
Sbjct: 180 AKVFPHEALLEETLKAATAMAAKSCTALRAIKHVVDRGMDADLKTGCA-LEAEAFGVCFA 238

Query: 237 TDESREGVKALQEKRKPEFR 256
             +++EG  A  EKRKP F+
Sbjct: 239 GQDAKEGTTAFLEKRKPVFK 258


Lambda     K      H
   0.319    0.138    0.418 

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: 188
Number of extensions: 11
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: 260
Length of database: 263
Length adjustment: 25
Effective length of query: 235
Effective length of database: 238
Effective search space:    55930
Effective search space used:    55930
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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