Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_011734654.1 PPRO_RS03480 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_000015045.1:WP_011734654.1 Length = 267 Score = 230 bits (586), Expect = 3e-65 Identities = 119/263 (45%), Positives = 165/263 (62%) Query: 6 LDKTPTILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPAVI 65 ++ TP L++IV K+EE+ + K ++ +L+ +ARD GF ALR + Q A+I Sbjct: 1 MNNTPDTLKKIVAHKYEELRDLKAHTALGELRVRARDMAPTHGFEAALRRKKGQGQTAII 60 Query: 66 AEIKKASPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLP 125 AE+KK SPS+G++R F+P IA YE GA CLSVLTD+ FF G + L R LP Sbjct: 61 AEVKKGSPSRGLIRADFDPLEIARIYETNGATCLSVLTDQHFFMGRLENLTRIRGEVDLP 120 Query: 126 VIRKDFMVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEEL 185 ++RKDF++ P+Q+YE+R GAD ILLI A L QM + +A ++ LD+L+EVHD EL Sbjct: 121 LLRKDFILDPFQIYEARCAGADAILLITAILELPQMIDYITLARDLSLDILLEVHDEREL 180 Query: 186 DDALTLTTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARG 245 D AL L+G+NNRNL TF L TT L + + L + ESGI TR+D+E + A G Sbjct: 181 DVALRTDCTLIGVNNRNLRTFTTDLATTGRLASMLPPEHLLVAESGISTRADIERLAADG 240 Query: 246 IYGFLVGESFMRAEEPGQKLQEL 268 FL+GES MR + G +L+ L Sbjct: 241 ADAFLIGESLMRETDIGSQLRIL 263 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: 211 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: 267 Length adjustment: 25 Effective length of query: 248 Effective length of database: 242 Effective search space: 60016 Effective search space used: 60016 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