Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_012282978.1 HM1_RS08630 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000019165.1:WP_012282978.1 Length = 288 Score = 112 bits (280), Expect = 2e-29 Identities = 82/220 (37%), Positives = 116/220 (52%), Gaps = 12/220 (5%) Query: 52 ILECKKASPSKGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQ 110 I E K+ASPSKG + + +AA Y+ ASAIS+LT+EKYF G + L + Sbjct: 66 IAEVKRASPSKGPLFPEAKAGDLAARYEQAGASAISILTEEKYFLGCLDDLQEAKEQVSL 125 Query: 111 PILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEE- 169 P++ KDF+IDPYQI AR ADACLL+ ++L + ++ A A + L EV EE Sbjct: 126 PVMRKDFLIDPYQIAEARLCGADACLLIAAMLGPSRLDEMCAAALEFGIHTLIEVHGEED 185 Query: 170 --------EQERAIALG-AKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINT 220 E+ RA G VVGIN R+L L +D + L L V ++ESGI Sbjct: 186 LAWAAEAVEKNRAQRPGWLPVVGINARNLATLKVDKEQALRLGAALPEGVVKVAESGIGG 245 Query: 221 YAQ-VRELSHFANGFLIGSALMAHDDLHAAVRRVLLGENK 259 + R L+ + L+G AL+ D A+R ++ EN+ Sbjct: 246 ASDGQRALAAGFDAILVGEALVTAADPGKALRDLIGLENR 285 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: 289 Number of extensions: 16 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: 288 Length adjustment: 29 Effective length of query: 424 Effective length of database: 259 Effective search space: 109816 Effective search space used: 109816 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 09 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