Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate Synpcc7942_1197 Synpcc7942_1197 indole-3-glycerol-phosphate synthase
Query= uniprot:A0A560BXT3 (262 letters) >FitnessBrowser__SynE:Synpcc7942_1197 Length = 295 Score = 211 bits (538), Expect = 1e-59 Identities = 125/263 (47%), Positives = 169/263 (64%), Gaps = 5/263 (1%) Query: 2 SDVLTRICDDKRALVQARKSARPLSAVEDAARA-ADPARGFIRALRRTVDGGRYGLIAEI 60 S++L I K V A + PL +++ R R F+ ALR+ R +IAE+ Sbjct: 29 SNILEEIVWYKEREVNAWREQLPLQQLQNQVRGLTQTPRDFLAALRQAPT--RPAVIAEV 86 Query: 61 KKASPSKGLIRPDFDPPSLARAYREGGATCLSVLTDEPYFQGCDDYLLAARAAVDLPVLR 120 KKASPSKG++R DFDP ++A+AY GA C+SVLTDE +FQG + L RAAVD+P+L Sbjct: 87 KKASPSKGVLREDFDPVAIAQAYAANGAACISVLTDEKFFQGGFENLQRVRAAVDVPLLC 146 Query: 121 KDFMVDPYQIAESRALGADCILIIMAALSDAQAAEIEGAAIAWGLDVLVEVHNREELDRA 180 KDF++ PYQI ++R LGAD +L+I A LSDA A + GL+ LVEVH+ EL+R Sbjct: 147 KDFVIYPYQIYKARLLGADAVLLIAAILSDADLRYFLKIAHSLGLNALVEVHSLPELERV 206 Query: 181 LAL-KTPLLGVNNRNLKTLAVDIATTEELAAHV-PADRMLVAESGLYSPADLSRMAAVGA 238 LAL L+G+NNRNLKT D+A TE LAA D +LV+ESGL++ ADL R+ GA Sbjct: 207 LALDDLRLVGINNRNLKTFVTDLAVTEHLAAQCRDRDLLLVSESGLFTGADLDRVTQAGA 266 Query: 239 RCFLVGESLMRQEDVTAATRALL 261 + L+GESL++Q D A + L+ Sbjct: 267 QAVLIGESLVKQPDPGLALQQLV 289 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: 218 Number of extensions: 10 Number of successful extensions: 3 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: 295 Length adjustment: 25 Effective length of query: 237 Effective length of database: 270 Effective search space: 63990 Effective search space used: 63990 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 09 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