Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_083931640.1 A3OQ_RS0100395 aminodeoxychorismate synthase component I
Query= curated2:Q9Z4W7 (511 letters) >NCBI__GCF_000385335.1:WP_083931640.1 Length = 499 Score = 265 bits (676), Expect = 4e-75 Identities = 174/458 (37%), Positives = 245/458 (53%), Gaps = 42/458 (9%) Query: 76 DEAGF-LLESVPVSGGVARYSYVGHRPVPLEPT------------GGDPLTALRSHLAR- 121 + GF L+S + RYSY+G P + + PL ALR L + Sbjct: 57 ERPGFAFLDSALPHESLGRYSYIGIEPFGVFSSIAGQTTWNGTRLAEPPLEALRRLLTQF 116 Query: 122 SVAPVPGLPPFHGGVVGYLGYEAARHFEDLPLAAGP-PPGLPESAFLAADDLVVFDHATR 180 + PV G+PPF GG +G + Y+ + L L P P G F D ++ FDHA R Sbjct: 117 AFEPVAGVPPFRGGAIGAIPYDFGWRLDGLELRDRPHPEGRDPLHFSFYDLVLAFDHAER 176 Query: 181 RVLLMT--------LYRPARESYDDAVARIVRLNRALRRAPAPAAFSGRPLAAATPADHG 232 R + + L R AR AV R+ + AL +APA A G P + Sbjct: 177 RAFIFSSGFPETDLLKRQAR-----AVQRLDEILAALEKAPASAR--GLPPIS------- 222 Query: 233 TQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRA--RPTDLYRHLRATNP 290 GW +N T+A + V + R HI GD +Q +S+R + L Y LRA NP Sbjct: 223 --GWISNFTQAAYHAAVEQVRTHILDGDIYQANISQRFTTKLPDGFSAFAFYAALRAANP 280 Query: 291 SPYMYHLSLGGGRHVIGASPELLVKAEGRTVRTRPLAGTRPRHPDPAEDLRLERELRADE 350 +P+ +L+ G + +SPELL++ G + TRP+ GT R PD AED L A E Sbjct: 281 APFAAYLTCGD-IVIASSSPELLLRKRGGDIETRPIKGTIARSPDEAEDALRRESLLASE 339 Query: 351 KERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGRLAEGRDALDA 410 K+RAE++M+VDL RNDL RV+EP +V+V L +E ++ V HL S V G L+ G+DA+D Sbjct: 340 KDRAENIMIVDLLRNDLSRVSEPFSVQVPILCGLESYAGVHHLVSVVTGHLSPGKDAVDL 399 Query: 411 LRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAIALRTMVVADG 470 + + FP G+++GAPK RAM+IIA +E RG Y GA+G++G DG D IA+RT V+ DG Sbjct: 400 IATCFPGGSITGAPKRRAMQIIAAIEQIPRGYYCGAIGYLGFDGAMDLNIAIRTAVMKDG 459 Query: 471 HVHVQAGAGIVADSDPAAEFRETLHKSRAMLTAVRRAE 508 V +QAG GI S+P AE+ ET K + + A ++ Sbjct: 460 EVQIQAGGGITRLSEPQAEYDETFAKVKRLFAAFSESQ 497 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: 643 Number of extensions: 38 Number of successful extensions: 6 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: 499 Length adjustment: 34 Effective length of query: 477 Effective length of database: 465 Effective search space: 221805 Effective search space used: 221805 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 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