Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_017597380.1 D471_RS0103705 anthranilate synthase component I
Query= BRENDA::P00897 (519 letters) >NCBI__GCF_000341125.1:WP_017597380.1 Length = 457 Score = 172 bits (437), Expect = 2e-47 Identities = 130/407 (31%), Positives = 201/407 (49%), Gaps = 25/407 (6%) Query: 54 IDSALPITALGHTVSVQALTANGPALLPVLDEALPPEVRNQARPNGRE---LTFPAIDAV 110 +D L + A G V+ AL A G LLPV+ +AL Q R + +T P DA Sbjct: 64 VDPCLEVIARGRRVTATALNARGRVLLPVVADALVSVGAGQDREADADHVAVTVPEPDAG 123 Query: 111 Q--DEDARLRSLSVFDALRTLLTLVDSPADEREAVMLGGLFAYDLVAGFENLPA-VRQDQ 167 + E+ R R SVF A+R ++ + SP D + L G F YDL FE + A + +D Sbjct: 124 EFFTEEERSRRPSVFTAVRAVIAAMSSPEDAN--LGLYGAFGYDLAFQFEPIEAHIDRDP 181 Query: 168 RCPDFCFYLAETLLVLDHQRGSARLQASVFSEQASEAQRLQHRLEQLQAELQQPPQPIPH 227 D +L + ++V D +R + F+ A + R + + L+ + P+ + Sbjct: 182 GDRDLVLHLPDAIVVRDRKRETCVRYTYEFTVPA-DGDRPEASTDGLERVTEPTPRVVAA 240 Query: 228 QKLENMQLSCNQSDEEYGAVVSELQEAIRQGEIFQVVPSRRFSLPCPAPLGPYQTLKDNN 287 + E + Y VV+E +E R+G++F+VVP R C +P Y+ L++ N Sbjct: 241 EVPEGPEPG------SYARVVAEAKEKFRRGDLFEVVPGHRTYARCSSPARFYELLRERN 294 Query: 288 PSPYMFFMQ-DDDFTLFGASPESALKYDAG---NRQIEIYPIAGTRPRGRRADGSLDLDL 343 P+PY FF + L GASPE ++ +++E PI+GT RG A G Sbjct: 295 PAPYEFFFNLGEGEYLVGASPEMFVRVTGEPGTGQRVETCPISGTISRGEDALG------ 348 Query: 344 DSRIELEMRTDHKELAEHLMLVDLARNDLARICQAGSRYVADLTKVDRYSFVMHLVSRVV 403 D+ E+ + KE +E M D+ RND +R+C+ GS V +++ YS ++H V + Sbjct: 349 DAENIQELLSSVKEKSELTMCTDVDRNDKSRVCEPGSVRVIGRRQIEMYSRLIHTVDHIE 408 Query: 404 GTLRADLDVLHAYQACMNMGTLSGAPKVRAMQLIAALRSTRRGSYGG 450 GTLR D D L A+ M T++GAPK AM+ I ++ R YGG Sbjct: 409 GTLRRDFDALDAFLTHMWAVTVTGAPKTWAMRFIERHETSPRRWYGG 455 Lambda K H 0.320 0.135 0.387 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: 491 Number of extensions: 26 Number of successful extensions: 4 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: 519 Length of database: 457 Length adjustment: 34 Effective length of query: 485 Effective length of database: 423 Effective search space: 205155 Effective search space used: 205155 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: 52 (24.6 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