Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_017597549.1 D471_RS0104620 aminodeoxychorismate synthase, component I
Query= curated2:Q9Z4W7 (511 letters) >NCBI__GCF_000341125.1:WP_017597549.1 Length = 447 Score = 229 bits (583), Expect = 2e-64 Identities = 169/457 (36%), Positives = 222/457 (48%), Gaps = 39/457 (8%) Query: 62 SVSPVTAFAQLCGPDEAGFLLESVPVSGGVARYSY------------VGHRPVPLEPTGG 109 +V AFA L G E F L+S G AR+S+ VG V + G Sbjct: 2 AVDTEAAFAHLYGAAEYAFWLDSSRPEGP-ARFSFLGAATGEILTYRVGDGEVRVRDVDG 60 Query: 110 ----DPLTALRSHLARSVAPVP-GLP-PFHGGVVGYLGYEAARHFEDLPLAAGPPPGLPE 163 +P T + R+ P GLP F GG VGY GYE D P+ Sbjct: 61 AERREPGTIFDALDRRTRPTAPTGLPFDFTGGHVGYFGYELKA---DCGADNAHTSPTPD 117 Query: 164 SAFLAADDLVVFDHATRRVLLMTLYRPARESYDDAVARIVRLNRALRRAPAPAAFSGRPL 223 + ++ D V DHA R ++ + D A A R AL P P Sbjct: 118 AVWMRCDRFVAVDHAEGRAYVV------HDDSDGARAWAGRTLDALSALPVPPP------ 165 Query: 224 AAATPADHGTQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRP--LRARPTDL 281 A P G + V H+ G++++I L+ R+ P DL Sbjct: 166 -PAPPGPAVDLGAHLERPHGDYVTDVKECLGHLTEGESYEICLTNRVRLPDDTSDDDLDL 224 Query: 282 YRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAEG-RTVRTRPLAGTRPRHPDPAEDL 340 YR LRA +P+PY L LG V+ ASPE ++ +G R +RP+ GT PRH DP D Sbjct: 225 YRRLRAASPAPYAALLRLGPVS-VLSASPERFLRVDGDRVAESRPIKGTAPRHADPDTDR 283 Query: 341 RLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGR 400 R ELR K RAE++M+VDL RNDLGRV E G+V+V M E ++ V L STVRGR Sbjct: 284 RAAEELRTGAKTRAENLMIVDLLRNDLGRVCEVGSVQVPAFMYTESYATVHQLVSTVRGR 343 Query: 401 LAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAI 460 L LDA+R+ FP G+++GAPK+R MEII LE RGVY GALG++ G D +I Sbjct: 344 LRPDVTTLDAVRACFPGGSMTGAPKLRTMEIIDRLESSARGVYSGALGYLSHAGTADLSI 403 Query: 461 ALRTMVVADGHVHVQAGAGIVADSDPAAEFRETLHKS 497 +RT V + G + + AG IV DSDP E+ E L K+ Sbjct: 404 VIRTAVRSGGELTIGAGGAIVLDSDPEDEYEEMLLKA 440 Lambda K H 0.319 0.134 0.394 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: 666 Number of extensions: 46 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: 511 Length of database: 447 Length adjustment: 34 Effective length of query: 477 Effective length of database: 413 Effective search space: 197001 Effective search space used: 197001 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: 51 (24.3 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