Alignments for a candidate for IGPS in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for IGPS in Pseudomonas stutzeri RCH2

Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate GFF3580 Psest_3647 Indole-3-glycerol phosphate synthase

Query= uniprot:A0A166NT80_PSEFL
         (278 letters)



>FitnessBrowser__psRCH2:GFF3580
          Length = 280

 Score =  413 bits (1061), Expect = e-120
 Identities = 210/268 (78%), Positives = 237/268 (88%), Gaps = 1/268 (0%)

Query: 1   MSVPTVLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIA 60
           MSVPTVLE I+ARK +EVA+RS +V L ELE  A AAD  RGFA AL  + ++K+PAVIA
Sbjct: 1   MSVPTVLEKIIARKFEEVAQRSRQVGLGELEQRAAAADPVRGFAAALERRVRSKEPAVIA 60

Query: 61  EIKKASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPV 120
           E+KKASPSKGVIR+ F+PA+IA SYE GGA CLSVLTDID+FQGAD YLQQARAAC LPV
Sbjct: 61  EVKKASPSKGVIRDPFLPAEIAASYETGGAACLSVLTDIDFFQGADEYLQQARAACSLPV 120

Query: 121 IRKDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELE 180
           IRKDFMIDPYQ++E+RALGADC+LLIV+ALDD +M ELAAVAK  GLDVLVEVHD  ELE
Sbjct: 121 IRKDFMIDPYQVIEARALGADCILLIVAALDDARMHELAAVAKQQGLDVLVEVHDATELE 180

Query: 181 RALKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISD 240
           RAL+ L+TPLVG+NNRNLHTFEVNLETTLDLLPRIP+DRLV+TESGI NRADVELMEI+ 
Sbjct: 181 RALR-LETPLVGINNRNLHTFEVNLETTLDLLPRIPKDRLVVTESGIFNRADVELMEINQ 239

Query: 241 VYAFLVGEAFMRAESPGTELQRLFFPER 268
           VYAFLVGEAFMRAE PG ELQRLF+P+R
Sbjct: 240 VYAFLVGEAFMRAEQPGVELQRLFYPDR 267


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: 302
Number of extensions: 5
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: 280
Length adjustment: 26
Effective length of query: 252
Effective length of database: 254
Effective search space:    64008
Effective search space used:    64008
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 Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis