Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate N515DRAFT_2111 N515DRAFT_2111 indole-3-glycerol phosphate synthase
Query= uniprot:E4PQZ8_MARAH (273 letters) >FitnessBrowser__Dyella79:N515DRAFT_2111 Length = 264 Score = 292 bits (747), Expect = 6e-84 Identities = 146/258 (56%), Positives = 191/258 (74%) Query: 12 ILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPAVIAEIKKA 71 IL+RI+ RK EEI ER ++ +A+LKA+ D R FA+A+ ++IE PAVIAE+KKA Sbjct: 4 ILQRILTRKTEEIAERSARLPLAELKARLADAAQTRPFADAVEAKIEADLPAVIAEVKKA 63 Query: 72 SPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPVIRKDF 131 SPSKG++R F+PA IA SYE+ GAACLSVLTD+DFFQG E++L AR AC+LPV+RKDF Sbjct: 64 SPSKGVIRADFDPASIARSYERAGAACLSVLTDKDFFQGSEEFLRQAREACALPVLRKDF 123 Query: 132 MVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELDDALTL 191 ++ PYQVYE+RAIGADCILLI A L ++++L A E+ +DVL EVHD EEL+ A L Sbjct: 124 VIHPYQVYEARAIGADCILLIVAALEDSELEDLSMQAAELDMDVLCEVHDAEELERAQAL 183 Query: 192 TTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGIYGFLV 251 L+G+NNRNL TF+ +LDT+ +L E + R+ + ESGI T DVE + GI FLV Sbjct: 184 PVRLIGVNNRNLRTFETTLDTSIELRELMDYHRILVAESGIHTPDDVERLRDAGINAFLV 243 Query: 252 GESFMRAEEPGQKLQELF 269 GE+FMRA +PG +L+ LF Sbjct: 244 GEAFMRAPDPGAELKRLF 261 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: 252 Number of extensions: 8 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: 264 Length adjustment: 25 Effective length of query: 248 Effective length of database: 239 Effective search space: 59272 Effective search space used: 59272 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 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