Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_038204075.1 Q392_RS07780 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000745855.1:WP_038204075.1 Length = 267 Score = 150 bits (378), Expect = 6e-41 Identities = 98/257 (38%), Positives = 144/257 (56%), Gaps = 13/257 (5%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPS--TRHFYDALQG----ARTAFILEC 55 M +L KIVA K V A +++ PL + + + + TR F A++ + A I E Sbjct: 1 MSDILNKIVAVKHEEVAAARKRVPLEAIRADAESRVLTRDFVGAMRAKIAAGQAAVIAEI 60 Query: 56 KKASPSKGVIRD-DFDPARIAAIYKH-----YASAISVLTDEKYFQGSFNFLPIVSQIAP 109 KKASPSKGVIR +F PA +A Y A+ +SVLTD ++FQGS ++L Sbjct: 61 KKASPSKGVIRSGEFIPADLAQSYAEGDGAISAACLSVLTDRQFFQGSIDYLKQARASCG 120 Query: 110 QPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEE 169 P+L KDF++D +Q+Y +R AD LL+ + LDD Q R A+A SL M VL EV + Sbjct: 121 LPVLRKDFMVDAWQVYESRAIGADCILLIAACLDDAQMRDFEAIALSLGMAVLVEVHDAA 180 Query: 170 EQERAIALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSH 229 E ERA+ L +VG+NNR+LR + L T +L + + +++ESGI T V+ L Sbjct: 181 EMERALKLRTPLVGVNNRNLRSFEVSLQTTLDLRSSVPADRLLVTESGIATRQDVKTLRD 240 Query: 230 F-ANGFLIGSALMAHDD 245 + FL+G + M ++ Sbjct: 241 AGVDAFLVGESFMRAEE 257 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: 249 Number of extensions: 10 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: 267 Length adjustment: 29 Effective length of query: 424 Effective length of database: 238 Effective search space: 100912 Effective search space used: 100912 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