Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate Echvi_2508 Echvi_2508 Indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Cola:Echvi_2508 Length = 272 Score = 116 bits (291), Expect = 8e-31 Identities = 87/253 (34%), Positives = 128/253 (50%), Gaps = 11/253 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLAS------FQNEVQPSTRHFYDALQGARTAFILECKKA 58 +L KI+A K V RK P F+N+V ++ +T I E K+ Sbjct: 3 ILDKIIAHKKEEVAERKSLVPTKMLERSVFFENKVVSMKKY---VTLPTKTGIIAEFKRK 59 Query: 59 SPSKGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDF 117 SPSKG I + + Y ASA+SVLTD+++F GS L + PIL KDF Sbjct: 60 SPSKGAINSAAKVEKTSIGYMQAGASALSVLTDKEFFGGSNEDLITARKFNFCPILRKDF 119 Query: 118 IIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL 177 I+D YQI A+ AD LL+ + L+ + +LA AH L + VL EV ++EE +R++ Sbjct: 120 IVDEYQIVEAKSIGADCILLIAAALEPKRLEELAIFAHKLGLEVLMEVHDQEELDRSLND 179 Query: 178 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFA-NGFLI 236 +VG+NNR L+ + L+ + +L ++ ISESGI+ + +L +GFLI Sbjct: 180 HLDLVGVNNRSLKTFEVSLDTSYDLVGQIPDKFVKISESGISDPQTLVDLKKGGFDGFLI 239 Query: 237 GSALMAHDDLHAA 249 G M H A Sbjct: 240 GENFMKSIRPHQA 252 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: 280 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: 272 Length adjustment: 29 Effective length of query: 424 Effective length of database: 243 Effective search space: 103032 Effective search space used: 103032 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 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