GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Methanosarcina acetivorans C2A

Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_011022932.1 MA_RS15690 indole-3-glycerol-phosphate synthase

Query= BRENDA::P84126
         (254 letters)



>NCBI__GCF_000007345.1:WP_011022932.1
          Length = 268

 Score =  143 bits (361), Expect = 3e-39
 Identities = 94/216 (43%), Positives = 131/216 (60%), Gaps = 12/216 (5%)

Query: 46  LSVIAEVKRQSPSEGLIREVDPVEAA-LAYA--RGGARAVSVLTEPHRFGGSLLDLKRVR 102
           + VIAEVK  SP +   RE+ P EAA LA+     GA A+SVLTEP  F GSL +LK+VR
Sbjct: 50  MPVIAEVKPASPGKSF-REIPPAEAAELAWEMEEAGAVAISVLTEPGVFRGSLENLKQVR 108

Query: 103 EAVDLPLLRKDFVVDPFMLEEARAFGASAALLIVALLGELTGAYLEEARRLGLEALVEVH 162
           + V LP+LRKDF++D   LEE    G+   LLI  +LG    A+++ A   G E LVEVH
Sbjct: 109 KTVCLPVLRKDFIIDRRQLEET---GSDLILLIAGILGPELDAFVDLALEKGFEPLVEVH 165

Query: 163 TERELEIALEAGAEVLGINNRDLATLHINLETAPRLGRLARK----RGFGGVLVAESGYS 218
              ELE+ALE   +++GINNR+  TL I+L T   L  L R+     G   ++++ESG +
Sbjct: 166 NSEELELALETDTKLIGINNRNFETLKIDLATTEALAPLIREYDLDHGTSHIIISESGMN 225

Query: 219 RKEEL-KALEGLFDAVLIGTSLMRAPDLEAALRELV 253
              ++ + +E   DAVLIG++LM +  +    +E V
Sbjct: 226 SPADVRRVIEAGADAVLIGSALMESDSVFEKTKEFV 261


Lambda     K      H
   0.318    0.138    0.379 

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: 166
Number of extensions: 10
Number of successful extensions: 4
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: 254
Length of database: 268
Length adjustment: 25
Effective length of query: 229
Effective length of database: 243
Effective search space:    55647
Effective search space used:    55647
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 Jul 25 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