Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_069663042.1 BCR25_RS07715 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_001730305.1:WP_069663042.1 Length = 252 Score = 124 bits (310), Expect = 4e-33 Identities = 88/239 (36%), Positives = 126/239 (52%), Gaps = 9/239 (3%) Query: 6 LAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQG--ARTAFILECKKASPSKG 63 L KI+ +K + Q+ PL Q Q T FY+ ++ + I E K+ASPSKG Sbjct: 4 LEKIITEK----KQEIQKMPLEKLQPLRQ--TTSFYERVKKNPEKIHIIGEVKRASPSKG 57 Query: 64 VIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPY 122 I + A Y K +AISVLTD +F+GS L V+ P+LCKDFIID Sbjct: 58 AINLSVNVIEQAKAYEKAGVTAISVLTDPTFFKGSIEDLRQVAAEVSIPVLCKDFIIDEK 117 Query: 123 QIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKVV 182 Q+ AR A LL++S L + ++L A +L + VL EV +E+EQ A LGA ++ Sbjct: 118 QLIRARNAGATIVLLIVSALSRSRLKKLYEQARTLGLEVLVEVHDEQEQTIAEELGASLI 177 Query: 183 GINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALM 241 G+NNR+L+ + LN ++ L K + ISESG + QV ++ L+G LM Sbjct: 178 GVNNRNLKTFDVSLNVSQLLGEKQRTDAVYISESGFSDATQVEQVKDKYQAILVGEGLM 236 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: 220 Number of extensions: 15 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: 252 Length adjustment: 28 Effective length of query: 425 Effective length of database: 224 Effective search space: 95200 Effective search space used: 95200 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 Jul 26 2024. The underlying query database was built on Jul 25 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