Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_012384413.1 BIND_RS07200 indole-3-glycerol-phosphate synthase
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000019845.1:WP_012384413.1 Length = 278 Score = 159 bits (401), Expect = 1e-43 Identities = 103/261 (39%), Positives = 141/261 (54%), Gaps = 8/261 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQP--STRHFYDALQG----ARTAFILEC 55 M +L +I A K + KQ L + + + + R F AL R A I E Sbjct: 1 MADILKRIEAYKRQEIAQAKQSVSLDALRRQCESVEKPRGFIKALAAKQAEGRMALIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKG+IR DFDP +A Y+ +A +SVLTD FQGS FL I Q P L Sbjct: 61 KKASPSKGLIRADFDPPALARAYEEGGAACLSVLTDTPSFQGSPEFLTIARQAVSLPALR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF+ DPYQ++ AR + AD L++++ +DD+ L A L M L EV +E E RA Sbjct: 121 KDFLFDPYQVFEARAWGADCILIIMACVDDELAGALRDAARELGMDCLVEVHDEAELIRA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVREL-SHFANG 233 + L ++GINNRDLR ++ L + LA K+ + ++ ESGI T L +H Sbjct: 181 LRLETPLIGINNRDLRTFNVSLETSERLAAKIPDDRMIVGESGIFTAQDCARLKAHRIGT 240 Query: 234 FLIGSALMAHDDLHAAVRRVL 254 L+G +LM D+ AA RR+L Sbjct: 241 VLVGESLMREQDVTAATRRLL 261 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: 240 Number of extensions: 11 Number of successful extensions: 3 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: 278 Length adjustment: 29 Effective length of query: 424 Effective length of database: 249 Effective search space: 105576 Effective search space used: 105576 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