Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_011938634.1 GURA_RS08800 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_000016745.1:WP_011938634.1 Length = 268 Score = 235 bits (600), Expect = 6e-67 Identities = 134/263 (50%), Positives = 173/263 (65%), Gaps = 7/263 (2%) Query: 3 DVLTRICDDKRALVQARKSARPLSAVEDA-ARAADPARGFIRALRRTVDGGRYG---LIA 58 D+L +I K + A K+ARPLS V+ A D RGF RALR D GR G +IA Sbjct: 6 DILKKIVAYKDGELAAVKAARPLSEVKARLAGLEDHPRGFARALR---DAGRSGWTPVIA 62 Query: 59 EIKKASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPV 118 E+KK SPSKG+IRPDFDP ++A Y+E GA CLSVLTDE +F G YL R + LP+ Sbjct: 63 EVKKGSPSKGVIRPDFDPLAIAETYQENGAVCLSVLTDEHFFLGHLSYLALIRERITLPL 122 Query: 119 LRKDFMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELD 178 LRKDF+ DPYQI E+RA GAD +L+I A L Q + A LDVL+EVH+ EL+ Sbjct: 123 LRKDFIFDPYQIYEARAAGADAVLLIAAMLDLHQLRDFAALAGELSLDVLLEVHDEAELE 182 Query: 179 RALALKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGA 238 AL L+G+NNR+L++ D+ATTE LA +PA+R++VAESG+ + AD+ R+ GA Sbjct: 183 TALETDCELIGINNRDLRSFVCDLATTERLARLIPAERLIVAESGINTRADIIRLQDAGA 242 Query: 239 RCFLVGESLMRQEDVTAATRALL 261 FL+GESLMR+ D+ A R LL Sbjct: 243 GAFLIGESLMREPDMGAKLRELL 265 Lambda K H 0.321 0.135 0.382 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: 202 Number of extensions: 8 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: 262 Length of database: 268 Length adjustment: 25 Effective length of query: 237 Effective length of database: 243 Effective search space: 57591 Effective search space used: 57591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 12 2024. The underlying query database was built on Apr 09 2024.
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:
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