Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_011734654.1 PPRO_RS03480 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000015045.1:WP_011734654.1 Length = 267 Score = 147 bits (372), Expect = 3e-40 Identities = 88/211 (41%), Positives = 128/211 (60%), Gaps = 3/211 (1%) Query: 48 RTAFILECKKASPSKGVIRDDFDPARIAAIYK-HYASAISVLTDEKYFQGSFNFLPIVSQ 106 +TA I E KK SPS+G+IR DFDP IA IY+ + A+ +SVLTD+ +F G L + Sbjct: 56 QTAIIAEVKKGSPSRGLIRADFDPLEIARIYETNGATCLSVLTDQHFFMGRLENLTRIRG 115 Query: 107 IAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVS 166 P+L KDFI+DP+QIY AR ADA LL+ ++L+ Q +A L + +L EV Sbjct: 116 EVDLPLLRKDFILDPFQIYEARCAGADAILLITAILELPQMIDYITLARDLSLDILLEVH 175 Query: 167 NEEEQERAIALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRE 226 +E E + A+ ++G+NNR+LR + DL T LA L +++ESGI+T A + Sbjct: 176 DERELDVALRTDCTLIGVNNRNLRTFTTDLATTGRLASMLPPEHLLVAESGISTRADIER 235 Query: 227 L-SHFANGFLIGSALMAHDDLHAAVRRVLLG 256 L + A+ FLIG +LM D+ + + R+LLG Sbjct: 236 LAADGADAFLIGESLMRETDIGSQL-RILLG 265 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: 267 Number of extensions: 12 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