Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_085770681.1 B1812_RS05440 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_002117405.1:WP_085770681.1 Length = 270 Score = 166 bits (419), Expect = 1e-45 Identities = 103/264 (39%), Positives = 149/264 (56%), Gaps = 10/264 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDALQGA----RTAFILEC 55 M +L KI K + K + P ++ + ++Q R F A++ R A I E Sbjct: 1 MTDILHKIETYKRTEISEAKVRMPRSTLERKIQDHDPPRGFVHAIEQKHNERRIALIGEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKGVIR DFDP +A ++ +A +SVLTD FQGS ++L + + P L Sbjct: 61 KKASPSKGVIRADFDPPNLAKAFQAGGAACLSVLTDGPSFQGSLDYLELARKATHLPALR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF+ DPYQ+Y AR + AD L++++ + D + + L AH L M VL EV +E E ERA Sbjct: 121 KDFMFDPYQVYEARAFGADCILIIMAAVSDSEAKALNTAAHDLSMDVLVEVHDERELERA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVREL--SHFAN 232 +AL +++GINNR+L D I L + LA + +++ESGI T+ L SH Sbjct: 181 LALETRLIGINNRNLHDFRIALETSERLAELAPKDKILVAESGIETHEDCLRLERSHIFT 240 Query: 233 GFLIGSALMAHDDLHAAVRRVLLG 256 FL+G +LM ++ AA R +L G Sbjct: 241 -FLVGESLMRRPNVEAATRELLHG 263 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: 13 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: 270 Length adjustment: 29 Effective length of query: 424 Effective length of database: 241 Effective search space: 102184 Effective search space used: 102184 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