Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_041100205.1 SUTH_RS14350 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000828635.1:WP_041100205.1 Length = 268 Score = 159 bits (402), Expect = 1e-43 Identities = 106/264 (40%), Positives = 145/264 (54%), Gaps = 8/264 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQN--EVQPSTRHFYDALQG----ARTAFILEC 55 M +L +I+A K V A +PLA + E TR F A++ TA I E Sbjct: 1 MSDILNRILAVKREEVAAASAAKPLAGIRAVAEALAPTRDFVGAMKARVGAGETAIIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKGVIR DF P IAA Y KH A+ +SVLTD ++FQGS +L P+L Sbjct: 61 KKASPSKGVIRPDFHPTEIAADYEKHGATCLSVLTDRQFFQGSEAYLREARAACSLPVLR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF++D YQ+Y AR ADA LL+++ L Q +++ A+AHSL M VL E + E + A Sbjct: 121 KDFLVDNYQVYEARAMGADAILLIVAALSLAQMQEMEAIAHSLGMAVLVESHDAAELDVA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVREL-SHFANG 233 + L ++GINNR+LR + L+ T ++ + V++ESGI T V L N Sbjct: 181 LQLKTPLIGINNRNLRSFEVSLDTTLSQLDRIPADRIVVTESGIVTPDDVALLRGRGVNA 240 Query: 234 FLIGSALMAHDDLHAAVRRVLLGE 257 FL+G A M A + R+ E Sbjct: 241 FLVGEAFMRAPSPGAELARLFSPE 264 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: 245 Number of extensions: 9 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: 268 Length adjustment: 29 Effective length of query: 424 Effective length of database: 239 Effective search space: 101336 Effective search space used: 101336 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