GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Burkholderia phytofirmans PsJN

Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate BPHYT_RS17405 BPHYT_RS17405 indole-3-glycerol phosphate synthase

Query= uniprot:A0A166NT80_PSEFL
         (278 letters)



>FitnessBrowser__BFirm:BPHYT_RS17405
          Length = 261

 Score =  296 bits (757), Expect = 4e-85
 Identities = 155/260 (59%), Positives = 197/260 (75%), Gaps = 2/260 (0%)

Query: 6   VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65
           +L+ I+A K +EV        L EL   A + D  R F  AL  +      AVI+E+KKA
Sbjct: 4   ILDRIIAVKREEVRAAEQSAPLEELRLEASSRDI-RDFVGALRAKHTAGLAAVISEVKKA 62

Query: 66  SPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIRKDF 125
           SPSKGV+RE+FVPA+IA+SYEK GA CLSVLTD+ +FQG+ AYL++ARAAC LPV+RKDF
Sbjct: 63  SPSKGVLREHFVPAEIARSYEKHGAACLSVLTDVQFFQGSVAYLEEARAACNLPVLRKDF 122

Query: 126 MIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERALKT 185
           ++DPYQIVE+RA+GAD +LLI +AL+  +M +L A+A S+GL VLVEVHD DEL  +L T
Sbjct: 123 IVDPYQIVEARAMGADAILLIAAALETSQMQDLEALAHSLGLAVLVEVHDHDELMESL-T 181

Query: 186 LDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVYAFL 245
           L TPL+G+NNRNL TFE ++ETT+ +L  IP DR+V+TESGIL+RADVE +   DV+ FL
Sbjct: 182 LKTPLIGINNRNLRTFETSIETTIGMLEAIPDDRIVVTESGILSRADVERLRAMDVHTFL 241

Query: 246 VGEAFMRAESPGTELQRLFF 265
           VGEAFMRA  PG EL R+FF
Sbjct: 242 VGEAFMRANEPGVELARMFF 261


Lambda     K      H
   0.318    0.135    0.369 

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: 225
Number of extensions: 7
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: 278
Length of database: 261
Length adjustment: 25
Effective length of query: 253
Effective length of database: 236
Effective search space:    59708
Effective search space used:    59708
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 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