Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate Ac3H11_772 Indole-3-glycerol phosphate synthase (EC 4.1.1.48)
Query= uniprot:A0A166NT80_PSEFL (278 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_772 Length = 283 Score = 270 bits (691), Expect = 2e-77 Identities = 149/263 (56%), Positives = 191/263 (72%), Gaps = 5/263 (1%) Query: 6 VLENILARKVQEVAERSARVSLAELENLAKAADAPRGFAKALIDQAKTKQPAVIAEIKKA 65 +L I+A K +EVA R+ L+ + A++ R F AL + Q AVIAE+KKA Sbjct: 21 ILNKIVAVKHEEVAAAKKRLPLSAMRADAESRVLTRDFEGALRAKIAKGQAAVIAEVKKA 80 Query: 66 SPSKGVIRENFVPADIAKSYEKG----GATCLSVLTDIDYFQGADAYLQQARAACKLPVI 121 SPSKGV+R +F PADIA+SY +G A CLSVLTD +FQG YL+QARA+ LPV+ Sbjct: 81 SPSKGVLRADFEPADIAQSYMEGDGKVSAACLSVLTDRQFFQGQPDYLKQARASTLLPVL 140 Query: 122 RKDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELER 181 RKDFM+D YQI ESRA+GAD +LLI ++LDD +MA+ A+A+S+ + VLVEVHD ELER Sbjct: 141 RKDFMVDAYQIYESRAMGADAILLIAASLDDAQMADFEAIARSLDMAVLVEVHDRAELER 200 Query: 182 ALKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDV 241 AL+ L T LVG+NNRNL TFEV L+TTL +L +P+DRL++TESGIL ADV+ M + V Sbjct: 201 ALQ-LKTRLVGINNRNLRTFEVTLDTTLGMLKDVPQDRLLVTESGILKPADVKTMRDAGV 259 Query: 242 YAFLVGEAFMRAESPGTELQRLF 264 +AFLVGEAFMRA+ PG L +LF Sbjct: 260 HAFLVGEAFMRADDPGLALAKLF 282 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: 244 Number of extensions: 9 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: 278 Length of database: 283 Length adjustment: 26 Effective length of query: 252 Effective length of database: 257 Effective search space: 64764 Effective search space used: 64764 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 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