GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pontibacter ramchanderi LP43

Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_101443452.1 BD749_RS06200 aconitate hydratase

Query= curated2:Q9WYC8
         (166 letters)



>NCBI__GCF_002846395.1:WP_101443452.1
          Length = 759

 Score = 52.4 bits (124), Expect = 2e-11
 Identities = 41/139 (29%), Positives = 64/139 (46%), Gaps = 29/139 (20%)

Query: 14  STDHIA-PGRYFHLRNNLEELAKHVLEDAMEDFAKKVQK--------------------- 51
           +TDHI+  G +   R +L+ ++ ++L  A+  F  +  K                     
Sbjct: 567 TTDHISMAGPWLKYRGHLDNISNNMLIGAINAFNGEANKVYNDMTRGYDTVPATARTYKA 626

Query: 52  ---GDIIVAGKNFGLGSSREHAARIIKIAGVSCIVAKSFARIFYRNAIN---VGLPVIEL 105
              G ++V  +N+G GSSREHAA   +  GV  ++ KSFARI   N      +GL     
Sbjct: 627 AGIGTVVVGDENYGEGSSREHAAMEPRHLGVRAVIVKSFARIHETNLKKQGMLGLTFANK 686

Query: 106 KEVDEINQGDELEI-DLEN 123
            + D I + D ++I  LEN
Sbjct: 687 ADYDLIEENDTIDILGLEN 705


Lambda     K      H
   0.321    0.141    0.408 

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: 306
Number of extensions: 17
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: 166
Length of database: 759
Length adjustment: 29
Effective length of query: 137
Effective length of database: 730
Effective search space:   100010
Effective search space used:   100010
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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