Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate HSERO_RS19450 HSERO_RS19450 indole-3-glycerol-phosphate synthase
Query= uniprot:A0A166NT80_PSEFL (278 letters) >FitnessBrowser__HerbieS:HSERO_RS19450 Length = 266 Score = 263 bits (671), Expect = 4e-75 Identities = 148/263 (56%), Positives = 183/263 (69%), Gaps = 5/263 (1%) Query: 6 VLENILARKVQEVAERSARVSLAEL----ENLAKAADAPRGFAKALIDQAKTKQPAVIAE 61 +L IL K +EV LA L E ++ R F ++L + Q VIAE Sbjct: 4 ILNKILDVKAEEVRIAKKERDLASLRRDVETDSELRSELRNFEESLRGKIANGQAGVIAE 63 Query: 62 IKKASPSKGVIRENFVPADIAKSYEKGGATCLSVLTDIDYFQGADAYLQQARAACKLPVI 121 +KKASPSKGVIR +F PA+IA SY + GA CLSVLTD +FQG+ YL+QARAAC LPV+ Sbjct: 64 VKKASPSKGVIRPDFKPAEIAVSYAEHGAACLSVLTDEQFFQGSPDYLKQARAACALPVL 123 Query: 122 RKDFMIDPYQIVESRALGADCVLLIVSALDDVKMAELAAVAKSVGLDVLVEVHDGDELER 181 RKDFM+D YQI ++R+ GAD +LLIV+ALD MA+L A A +G+ VLVEVHD EL+ Sbjct: 124 RKDFMMDHYQIYQARSWGADAILLIVAALDHGLMADLEACAHELGMSVLVEVHDQAELDA 183 Query: 182 ALKTLDTPLVGVNNRNLHTFEVNLETTLDLLPRIPRDRLVITESGILNRADVELMEISDV 241 ALK L T L+G+NNRNL TFE L+TTL+LLPRIP ++LV+TES I DV+ M +DV Sbjct: 184 ALK-LKTRLLGINNRNLRTFETTLDTTLNLLPRIPPEKLVVTESAIATPDDVKRMRDADV 242 Query: 242 YAFLVGEAFMRAESPGTELQRLF 264 +AFLVGEAFMRA PG EL RLF Sbjct: 243 HAFLVGEAFMRAPEPGVELARLF 265 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: 215 Number of extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 253 Effective length of database: 241 Effective search space: 60973 Effective search space used: 60973 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