GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate CA265_RS16405 CA265_RS16405 aconitate hydratase

Query= curated2:C1CVE0
         (181 letters)



>FitnessBrowser__Pedo557:CA265_RS16405
          Length = 759

 Score = 53.1 bits (126), Expect = 1e-11
 Identities = 50/144 (34%), Positives = 64/144 (44%), Gaps = 28/144 (19%)

Query: 41  RDFAKRVQPGDIIVAGADFGCGSSREHAVWALRGAGVGAVIAPNFARIYYRNSINNGFLA 100
           RD+ K    G I+V   ++G GSSREHA    R  GV AV+  +FARI+  N    G L 
Sbjct: 622 RDY-KAAGLGSIVVGDENYGEGSSREHAAMEPRHLGVRAVLVKSFARIHETNLKKQGMLG 680

Query: 101 LECDGIVEAFQDGDEANLDLKGGTI-----TNLRTGQTLTFV-----------PVPQF-- 142
           L        F D D+ +  L+  TI     T     Q LT V           PV     
Sbjct: 681 L-------TFADKDDYDKILEDDTIDILGLTEFTPDQPLTLVLHHADGTQESFPVNHSYN 733

Query: 143 --ALDVQKAGGWLEYMRAQVPAEA 164
              +D  KAGG L  +RA+  A+A
Sbjct: 734 AQQIDWFKAGGALNIIRAEAAAKA 757


Lambda     K      H
   0.319    0.136    0.414 

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: 368
Number of extensions: 17
Number of successful extensions: 2
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: 759
Length adjustment: 29
Effective length of query: 152
Effective length of database: 730
Effective search space:   110960
Effective search space used:   110960
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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