Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_013010469.1 DACET_RS05910 indole-3-glycerol-phosphate synthase
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000025725.1:WP_013010469.1 Length = 254 Score = 132 bits (333), Expect = 1e-35 Identities = 91/243 (37%), Positives = 132/243 (54%), Gaps = 10/243 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAFILECKKASPSKGV 64 VL +I+++K RK+ + L+ E F A+ + FI E KKASPS G Sbjct: 6 VLERILSNK------RKEIELLSESVEERTKPLLDFRQAIIDRQ--FICEVKKASPSLGA 57 Query: 65 IRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPYQ 123 I D ++AA+Y+ A +SVLTD+++F GSF+ L V+ P+LCKDFII Q Sbjct: 58 INTGADVEKVAAVYESIGAGCVSVLTDKEFFGGSFDDLRKVTAKVSIPVLCKDFIITEKQ 117 Query: 124 IYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKVVG 183 I +A ADA LLM + L + Y +L + M L E+ EE E + ++G Sbjct: 118 IDVAYSMGADAVLLMATSLSREDYERLYSYVKGKGMQALVEIHELEELEIVKGMEPDILG 177 Query: 184 INNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANGFLIGSALMA 242 +N+R+L+ L IDLN+ E+ L I+ESG+ A +R +S A GFL+GS+LM Sbjct: 178 VNSRNLKTLEIDLNKGAEIIRSLPEYEVKIAESGMKAEADIRLMSQAGAKGFLVGSSLMG 237 Query: 243 HDD 245 DD Sbjct: 238 ADD 240 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: 226 Number of extensions: 9 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: 254 Length adjustment: 28 Effective length of query: 425 Effective length of database: 226 Effective search space: 96050 Effective search space used: 96050 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