GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Pseudomonas putida KT2440

Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate PP_0422 PP_0422 Indole-3-glycerol phosphate synthase

Query= uniprot:A0A166NT80_PSEFL
         (278 letters)



>FitnessBrowser__Putida:PP_0422
          Length = 277

 Score =  464 bits (1193), Expect = e-135
 Identities = 240/268 (89%), Positives = 252/268 (94%)

Query: 1   MSVPTVLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIA 60
           MSVPTVLE I+ARK QEVAERSA VSLAELE LAKAADAPRGFA ALI+QAK KQPAVIA
Sbjct: 1   MSVPTVLERIIARKFQEVAERSAHVSLAELEGLAKAADAPRGFANALIEQAKRKQPAVIA 60

Query: 61  EIKKASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPV 120
           EIKKASPSKGVIRE+FVPA+IA SYEKGGATCLSVLTD+DYFQGAD YLQQARAA  LPV
Sbjct: 61  EIKKASPSKGVIREHFVPAEIAVSYEKGGATCLSVLTDVDYFQGADEYLQQARAAVSLPV 120

Query: 121 IRKDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELE 180
           IRKDFM+DPYQIVE+RALGADCVLLIVSALDDVKMAELAA AK VGLDVLVEVHDGDELE
Sbjct: 121 IRKDFMVDPYQIVEARALGADCVLLIVSALDDVKMAELAATAKDVGLDVLVEVHDGDELE 180

Query: 181 RALKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISD 240
           RALKTLDTPLVGVNNRNLHTFEV+LETTLDLLPRIPRDRL ITESGILNRADVELM I++
Sbjct: 181 RALKTLDTPLVGVNNRNLHTFEVSLETTLDLLPRIPRDRLAITESGILNRADVELMAINE 240

Query: 241 VYAFLVGEAFMRAESPGTELQRLFFPER 268
           VY+FLVGEAFMRAE PG ELQRLFFPE+
Sbjct: 241 VYSFLVGEAFMRAEQPGLELQRLFFPEQ 268


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: 332
Number of extensions: 7
Number of successful extensions: 1
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: 277
Length adjustment: 25
Effective length of query: 253
Effective length of database: 252
Effective search space:    63756
Effective search space used:    63756
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