GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Thioalkalivibrio paradoxus ARh 1

Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_006746920.1 THITH_RS15380 indole-3-glycerol phosphate synthase TrpC

Query= uniprot:A0A166NT80_PSEFL
         (278 letters)



>NCBI__GCF_000227685.2:WP_006746920.1
          Length = 275

 Score =  309 bits (791), Expect = 5e-89
 Identities = 163/265 (61%), Positives = 199/265 (75%), Gaps = 1/265 (0%)

Query: 3   VPTVLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEI 62
           VP +L+ ILARK +E+  RSA + L EL + A+ AD PRGF  AL  + +   PAVIAEI
Sbjct: 8   VPDILQRILARKQEEIRARSATLPLPELASRARDADPPRGFRAALAARIRRGLPAVIAEI 67

Query: 63  KKASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVIR 122
           KKASPSKGV+R +F P  IA SY + GA CLSVLTDID+FQGAD YLQ+ARAAC LPV+R
Sbjct: 68  KKASPSKGVLRADFDPVAIAGSYARHGAACLSVLTDIDFFQGADGYLQKARAACDLPVLR 127

Query: 123 KDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELERA 182
           KDF++DPYQ+ E+RALGADC+LLIV+ALDD +M  L  +A  +G+DVLVEVHD DEL RA
Sbjct: 128 KDFVVDPYQVHEARALGADCILLIVAALDDEQMRALYRLALDLGMDVLVEVHDRDELGRA 187

Query: 183 LKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDVY 242
           L  LD  L+G+NNR+L +FE  LETTLDL  ++P   L++TESGI   +DV  M  + V 
Sbjct: 188 L-ALDAGLIGINNRDLRSFETRLETTLDLCAQVPEGVLLVTESGIHRPSDVARMRAAGVE 246

Query: 243 AFLVGEAFMRAESPGTELQRLFFPE 267
           AFLVGEAFMRA  PG  L+RLF PE
Sbjct: 247 AFLVGEAFMRAPDPGEALERLFGPE 271


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: 236
Number of extensions: 6
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: 275
Length adjustment: 25
Effective length of query: 253
Effective length of database: 250
Effective search space:    63250
Effective search space used:    63250
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