Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate BPHYT_RS03600 BPHYT_RS03600 anthranilate synthase
Query= curated2:Q9Z4W7 (511 letters) >FitnessBrowser__BFirm:BPHYT_RS03600 Length = 638 Score = 191 bits (486), Expect = 5e-53 Identities = 127/340 (37%), Positives = 177/340 (52%), Gaps = 27/340 (7%) Query: 180 RRVLLMTLYRPARESYDDAVARIVRLNRA--LRRAPAPAAFSGRPLAAATPADHGTQGWT 237 R +L L R + DA R + R L R A R AA P+ GT Sbjct: 70 RHLLDGDLNRSLKTQRGDATLRFLLFERCENLSREEVDAWLMARDEGAAEPSVAGTMNVR 129 Query: 238 ANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTDLYRHLRATNPSPYMYHL 297 A++ A+F + + AGD++Q+ + RL + PT LYR LRA P PY + Sbjct: 130 ASVDPAEFNAAIDAIHSALRAGDSYQVNYTYRLGFDVFGSPTALYRRLRARQPVPYGALI 189 Query: 298 SLGGGRHVIGASPELLVKAEGRTVRTRPLAGTRPRHPDPAEDLRLERELRADEKERAEHV 357 +L G + V+ SPEL ++ +G T+R RP+ GT PR DPA D R L D K RAE+V Sbjct: 190 ALPGRQWVLSCSPELFIEKQGATLRARPMKGTAPRSDDPAVDRRAAEFLGNDPKNRAENV 249 Query: 358 MLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGRLAEGRDALDALRSAFPA 417 M+VDL RNDL RV + G+V+V L VE ++ V ++STV L LR+ FP Sbjct: 250 MIVDLLRNDLSRVAQTGSVKVPALFSVEPYASVWQMTSTVEAALKPATSFAQTLRALFPC 309 Query: 418 GTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVG--------ADGLT---------DF-- 458 G+++GAPK R M++I ELE RG+Y GA+G++ AD T DF Sbjct: 310 GSITGAPKHRTMQLIDELESTPRGLYTGAIGWLDAPSSSADTADATTCDANHTACGDFCL 369 Query: 459 AIALRTMVVA----DGHVH--VQAGAGIVADSDPAAEFRE 492 ++A+RT+ + GH+ + GAGIV DS A E+ E Sbjct: 370 SVAIRTLTLGPSTQTGHLEGKMGVGAGIVLDSVAADEYAE 409 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: 722 Number of extensions: 32 Number of successful extensions: 1 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: 638 Length adjustment: 36 Effective length of query: 475 Effective length of database: 602 Effective search space: 285950 Effective search space used: 285950 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: 53 (25.0 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