GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucA in Pantoea rwandensis LMG 26275

Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate WP_084932211.1 HA51_RS04040 aldolase

Query= BRENDA::Q58813
         (181 letters)



>NCBI__GCF_002095475.1:WP_084932211.1
          Length = 212

 Score = 85.9 bits (211), Expect = 4e-22
 Identities = 62/179 (34%), Positives = 93/179 (51%), Gaps = 11/179 (6%)

Query: 8   KICR---KLYDRKYVVGSGGNVSVKEGDKIYLTPTGSILGFLKEDDIAEMDLDGNVIK-G 63
           +IC+    L+ R Y VGS GN+S K  D   +TPT   LG L+ D IA+++L+G  +  G
Sbjct: 10  EICQTGHSLHRRGYTVGSSGNISAKLEDGWLITPTDVCLGSLRPDMIAKVNLEGEWVNGG 69

Query: 64  KPTSEKNLHLMIYRKRNDINAIIHTHS--LISTFLSTINKEIELLTPEGKIFLKKIG--- 118
           KP+    LH  IY   + +  I+HTHS  L++  L  +  +  +L P     + K+G   
Sbjct: 70  KPSKTLKLHRTIYENNDAVRGIVHTHSTHLVAMTLGEVWSKESILPPITPYQVMKVGRIP 129

Query: 119 YVDYYEAGSLKLAEETAKRDEDV--IILKNHGVVCLGKDLIDAYIKVEVLEEQAKLTLL 175
            + Y   GS  +A +  +   DV  I+L+  G V  G  +  A   +E LEE AKL L+
Sbjct: 130 LISYCRPGSPDVAVQAGELAHDVKGIMLERLGPVIWGTSVTKAAEILEELEETAKLWLM 188


Lambda     K      H
   0.318    0.139    0.385 

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: 101
Number of extensions: 5
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: 181
Length of database: 212
Length adjustment: 20
Effective length of query: 161
Effective length of database: 192
Effective search space:    30912
Effective search space used:    30912
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 (21.6 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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