Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_019557130.1 F612_RS0107430 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000381085.1:WP_019557130.1 Length = 264 Score = 163 bits (412), Expect = 7e-45 Identities = 101/246 (41%), Positives = 143/246 (58%), Gaps = 8/246 (3%) Query: 4 TVLAKIVADKAIWVEARKQQQPLASFQNE--VQPSTRHFYDALQG----ARTAFILECKK 57 T+L KI+ K ++ + PL + + P T+ F A+Q ++A I E KK Sbjct: 5 TILKKIILRKLEEIQDGCDKIPLREMKRRALLAPETKSFVGAMQAKLDAGQSAVIAEIKK 64 Query: 58 ASPSKGVIRDDFDPARIAAIYK-HYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKD 116 ASPSKGV+R+ FDP IA Y + A+ +SVLTD+ +FQGS +L V + PI+ KD Sbjct: 65 ASPSKGVLRESFDPVEIAKSYAANGAACLSVLTDKDFFQGSNEYLQQVREAVDLPIIRKD 124 Query: 117 FIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIA 176 FI+D YQ+Y AR AD LL+ + + D Q +L VA +L+M VL EV N+EE ERA+ Sbjct: 125 FIVDDYQVYEARAIGADCILLIAAAIGDAQMSELTQVALTLDMDVLIEVHNKEELERALH 184 Query: 177 LGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQV-RELSHFANGFL 235 L ++GINNRDL + L+ T E+ + + VI+ESGI T V R + + FL Sbjct: 185 LPLPMIGINNRDLHSFEVSLDTTIEMLEMIPEDRIVITESGILTKGDVARMRACHVDAFL 244 Query: 236 IGSALM 241 +G A M Sbjct: 245 VGEAFM 250 Lambda K H 0.320 0.135 0.389 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: 257 Number of extensions: 14 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: 453 Length of database: 264 Length adjustment: 29 Effective length of query: 424 Effective length of database: 235 Effective search space: 99640 Effective search space used: 99640 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: 49 (23.5 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