Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_084058689.1 B9A12_RS13775 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_900176285.1:WP_084058689.1 Length = 268 Score = 214 bits (544), Expect = 2e-60 Identities = 117/260 (45%), Positives = 164/260 (63%), Gaps = 7/260 (2%) Query: 12 ILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPA---VIAEI 68 IL +I++ K E+ E +R+ ++ L+ +A++ P AR F R+ PA VIAEI Sbjct: 3 ILSKILEVKRREVQEARRREPLSRLQRRAQEAPPARPFVE----RLSAPGPAGANVIAEI 58 Query: 69 KKASPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPVIR 128 K+ASPSKG +R +P A +Y++ GAA LSVLTDR FFQG E L +AR A SLPV+R Sbjct: 59 KRASPSKGTIRSHLDPPSHAWAYQRAGAAALSVLTDRSFFQGSEQDLQSARTAVSLPVLR 118 Query: 129 KDFMVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELDDA 188 KDF++ YQ+YE+RA+GAD +LLI ++ +++ + E+GL LVEVHD EL+ A Sbjct: 119 KDFVIDEYQIYEARAMGADAVLLIVRAVSPSFLRDALSLCRELGLGALVEVHDERELETA 178 Query: 189 LTLTTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGIYG 248 L PLVG+NNR+L TF + T+ L + + ESGI +R DVE + GI+ Sbjct: 179 LACDAPLVGVNNRDLATFRTDIQTSIRLKTLLPAHTPLVAESGIGSRQDVETLLEAGIFN 238 Query: 249 FLVGESFMRAEEPGQKLQEL 268 FLVG S +RA +P + LQ L Sbjct: 239 FLVGTSLVRAPDPERALQSL 258 Lambda K H 0.320 0.136 0.387 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: 192 Number of extensions: 6 Number of successful extensions: 1 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: 273 Length of database: 268 Length adjustment: 25 Effective length of query: 248 Effective length of database: 243 Effective search space: 60264 Effective search space used: 60264 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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