GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudarthrobacter sulfonivorans Ar51

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_083510176.1 AU252_RS00745 enoyl-CoA hydratase-related protein

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



>NCBI__GCF_001484605.1:WP_083510176.1
          Length = 279

 Score =  153 bits (386), Expect = 4e-42
 Identities = 103/255 (40%), Positives = 145/255 (56%), Gaps = 12/255 (4%)

Query: 6   IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAG 64
           +  E+ G+V  +T+NRP+A NA+N   ++ +  A+    E   + AV+ITGSG KAF AG
Sbjct: 22  VTAEEIGHVFLVTINRPEARNAVNPDVIRGVGRALEHAEECPGIRAVVITGSGDKAFCAG 81

Query: 65  ADIAEMKDLTAVE-GRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIA 123
           AD+         E        G   F K  ++ KP IAAINGFALGGG E+ L+ D+ IA
Sbjct: 82  ADLKSAAVGAFGEIPEGMEQWGFAGFVK-HHISKPTIAAINGFALGGGTEIVLASDLAIA 140

Query: 124 SSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVE 183
           SS+A FG PEV LGI  G GG  R  + +   +A E++ TG+ + A+ AL IGLVN+VV 
Sbjct: 141 SSEAVFGLPEVKLGIFAGAGGAFRAGQQVPKKIAMEMLLTGQPLPAQRALEIGLVNRVVP 200

Query: 184 PDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVA------YEAEVFGECFA 237
           P+++L  A  L   I  NAP+AV+  K   N      +++  A      +EA+   +   
Sbjct: 201 PEEVLPAALELARQICENAPLAVQTTKRIANGITDGTVESDQADWARSEWEAQ---KLMR 257

Query: 238 TEDRVEGMTAFVEKR 252
           + D +EGM AF EKR
Sbjct: 258 STDFMEGMRAFAEKR 272


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: 168
Number of extensions: 13
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: 279
Length adjustment: 25
Effective length of query: 234
Effective length of database: 254
Effective search space:    59436
Effective search space used:    59436
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 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