GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Streptacidiphilus oryzae TH49

Align indole-3-glycerol-phosphate synthase (EC 4.1.1.48) (characterized)
to candidate WP_037581605.1 BS73_RS29020 indole-3-glycerol phosphate synthase TrpC

Query= BRENDA::A1KJ27
         (272 letters)



>NCBI__GCF_000744815.1:WP_037581605.1
          Length = 269

 Score =  320 bits (820), Expect = 2e-92
 Identities = 167/263 (63%), Positives = 203/263 (77%), Gaps = 1/263 (0%)

Query: 5   TVLDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALR-EPGIGVIAEVKRASP 63
           +VLD I+EGVR D+A R+A VSL E+K  AA AP   D +AALR + G+ VI EVKR+SP
Sbjct: 2   SVLDEIIEGVREDLAERQARVSLDELKEQAAKAPAAKDGVAALRGDDGVKVICEVKRSSP 61

Query: 64  SAGALATIADPAKLAQAYQDGGARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVV 123
           S GALA IADPA LA  Y+ GGA  +SV+TEQRRF GSL DLDAVRA V + VLRKDF+V
Sbjct: 62  SKGALAAIADPASLAADYEAGGAAAISVLTEQRRFGGSLADLDAVRAKVDVAVLRKDFIV 121

Query: 124 QPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKAGA 183
             YQ+ EARAHGAD+ LLIVAAL+Q  LVS+++R ES+G+T LVEVH E E  RA+ AGA
Sbjct: 122 TSYQLWEARAHGADIALLIVAALDQPALVSLIERAESIGLTPLVEVHDEDEVTRAVDAGA 181

Query: 184 KVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGE 243
           ++IGVNAR+L TL V+RD FA +AP +P  ++++AESGVRG  DL+ YA  GADAVLVGE
Sbjct: 182 RIIGVNARNLKTLQVNRDTFAEVAPAIPKGIVKVAESGVRGPHDLITYANDGADAVLVGE 241

Query: 244 GLVTSGDPRAAVADLVTAGTHPS 266
            LVT  DP+ AVADLV AG HP+
Sbjct: 242 SLVTGRDPKTAVADLVAAGAHPA 264


Lambda     K      H
   0.317    0.131    0.358 

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: 248
Number of extensions: 11
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: 272
Length of database: 269
Length adjustment: 25
Effective length of query: 247
Effective length of database: 244
Effective search space:    60268
Effective search space used:    60268
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 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