Align Anthranilate synthase component I (characterized, see rationale)
to candidate 14729 b0593 isochorismate synthase (NCBI)
Query= uniprot:Q8AAD3_BACTN (468 letters) >FitnessBrowser__Keio:14729 Length = 391 Score = 91.3 bits (225), Expect = 5e-23 Identities = 72/246 (29%), Positives = 107/246 (43%), Gaps = 3/246 (1%) Query: 220 VFQIVLSRRF--IQPYAGDDFKVYRALRSINPSPYLFYFDFG-GYRIFGSSPETHCKIED 276 V ++VLSR A D + L + NP Y F+ G + G+SPE + + Sbjct: 145 VDKVVLSRLIDITTDAAIDSGVLLERLIAQNPVSYNFHVPLADGGVLLGASPELLLRKDG 204 Query: 277 GRAYIDPIAGTTRRTGDTVKDRELAEALLADPKENAEHVMLVDLARNDLSRNCHDVRVLF 336 R P+AG+ RR D V DRE LLA K+ EH ++ + L ++ V Sbjct: 205 ERFSSIPLAGSARRQPDEVLDREAGNRLLASEKDRHEHELVTQAMKEVLRERSSELHVPS 264 Query: 337 YKEPQYYSHVIHLVSRVSGQLNEGADKIKTFIDTFPAGTLSGAPKVRAMQLISEIEPHNR 396 + + HL + G+ N + + P LSG P A Q+I+E+EP +R Sbjct: 265 SPQLITTPTLWHLATPFEGKANSQENALTLACLLHPTPALSGFPHQAATQVIAELEPFDR 324 Query: 397 GAYGGCIGFIGLNGELNQAITIRTFVSRNNELWFQAGGGIVARSQDEYELQEVNNKLGAL 456 +GG +G+ G +TIR R N++ AG GIV S E +E KL + Sbjct: 325 ELFGGIVGWCDSEGNGEWVVTIRCAKLRENQVRLFAGAGIVPASSPLGEWRETGVKLSTM 384 Query: 457 KKAIDL 462 L Sbjct: 385 LNVFGL 390 Lambda K H 0.318 0.136 0.396 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: 330 Number of extensions: 17 Number of successful extensions: 2 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: 468 Length of database: 391 Length adjustment: 32 Effective length of query: 436 Effective length of database: 359 Effective search space: 156524 Effective search space used: 156524 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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