Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_059150071.1 V474_RS03155 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:A0A560BXT3 (262 letters) >NCBI__GCF_001046635.1:WP_059150071.1 Length = 263 Score = 293 bits (751), Expect = 2e-84 Identities = 160/261 (61%), Positives = 189/261 (72%), Gaps = 1/261 (0%) Query: 1 MSDVLTRICDDKRALVQARKSARPLSAVEDAARAADPARGFIRALRRTVDGGRYGLIAEI 60 M+D LT ICD KR V ARK+A + ++ A RGF ALR G + LIAEI Sbjct: 1 MTDKLTEICDTKRLEVAARKAAATTADLDSRAARQSAPRGFEAALRAKAQTG-FALIAEI 59 Query: 61 KKASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLR 120 KKASPSKGLIRPDF P AR Y +GGA CLS+LTD PYFQG +DYL+ ARAA LPV+R Sbjct: 60 KKASPSKGLIRPDFRPADHARHYEKGGAACLSILTDAPYFQGHEDYLIEARAACTLPVIR 119 Query: 121 KDFMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRA 180 KDFM+DP+Q+AE+RA+GAD ILII+AAL DA AEIE AA+ G+D LVEVHN E++RA Sbjct: 120 KDFMIDPWQVAEARAIGADAILIIVAALDDALMAEIESAALERGMDCLVEVHNELEMERA 179 Query: 181 LALKTPLLGVNNRNLKTLAVDIATTEELAAHVPADRMLVAESGLYSPADLSRMAAVGARC 240 LK+ L+GVNNR+LK A DIATTE LA P +LV+ESG+ S DL R+A GAR Sbjct: 180 SRLKSRLIGVNNRDLKRFATDIATTERLAPLAPDGTLLVSESGINSHNDLLRLAPCGART 239 Query: 241 FLVGESLMRQEDVTAATRALL 261 FLVGESLMR+ DV AATR LL Sbjct: 240 FLVGESLMREADVEAATRMLL 260 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: 226 Number of extensions: 10 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: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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 Jul 26 2024. The underlying query database was built on Jul 25 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