Align Anthranilate synthase; EC 4.1.3.27 (characterized, see rationale)
to candidate WP_017600087.1 D471_RS0119075 isochorismate synthase
Query= uniprot:B8DM47_DESVM (520 letters) >NCBI__GCF_000341125.1:WP_017600087.1 Length = 431 Score = 148 bits (373), Expect = 4e-40 Identities = 117/333 (35%), Positives = 159/333 (47%), Gaps = 22/333 (6%) Query: 186 PTSSAEACLALPGTVVLFDHLYNRLCQLSLTDLPGGRVDRSQVDRTP--EPPEVGPVVNV 243 PTS A L +P VL R ++TD P R D V +P +P VGP+ Sbjct: 106 PTSGGSA-LVVPR--VLIGRRNGRAWVTTVTDAPNARPD---VPSSPAFDPRPVGPLSWG 159 Query: 244 PEQAV---YTRAVARVKDMIRQGEAIQVVLSTRFQASFSG--DPFTLYRRLRRINPSPYM 298 P +T VA D IR G + VL+ A D TL RLR PS + Sbjct: 160 PGSLTGREWTDTVADTVDRIRSGPLDKAVLARDIVAEAESPIDVRTLLERLRLRYPSCFT 219 Query: 299 FFMRLPGVSLLGSSPEVMVRCRADKLQVSPIAGTRPRGTDDAHDAALARELLEDPKERAE 358 F + ++G++PE+++R D+L +AGTRPRG D D LA EL K+ E Sbjct: 220 FSVD----GMVGATPELLLRREGDRLSSLVLAGTRPRGRDAVEDRRLAEELRASAKDLEE 275 Query: 359 HVMLVDLGRNDLGRIAAPGTVQVERFMDVEKFSHVMHLTSRVTAQIEPGRDALDVLAATF 418 H + VD R L +A + V + ++V HL +R A++ PG ALD +AA Sbjct: 276 HALAVDSLRIALEPLARE--LSVPSSPALLALANVQHLATRAHARLAPGVSALDAVAALH 333 Query: 419 PAGTVSGAPKVRAMEIISEAEGLARGPYAGAIGWLGLDRDSVNLDTGITIRSLWVRDGQV 478 P V G P AM +I+E EG+ RG YAG +GWL + N + GI +RS V + Sbjct: 334 PTAAVGGTPTAAAMRLIAEVEGMDRGGYAGPVGWLD---GAGNAEWGIALRSARVEGRRA 390 Query: 479 HWQAGAGIVFDSVPEMEWKECNNKAAVIRAAVT 511 AG GIV S P E E +K +R A+T Sbjct: 391 RLFAGCGIVAGSDPAAELAETESKFRAVREALT 423 Lambda K H 0.320 0.137 0.413 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: 567 Number of extensions: 31 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: 520 Length of database: 431 Length adjustment: 33 Effective length of query: 487 Effective length of database: 398 Effective search space: 193826 Effective search space used: 193826 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