Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_035242625.1 Q366_RS19710 aminodeoxychorismate synthase, component I
Query= curated2:O66849 (494 letters) >NCBI__GCF_000745975.1:WP_035242625.1 Length = 749 Score = 231 bits (590), Expect = 5e-65 Identities = 143/397 (36%), Positives = 218/397 (54%), Gaps = 18/397 (4%) Query: 94 KDPLSKIKEVVKKFIPYHDE--RLPRFWGGLVGYFAYDVVKFYEPVEDK---NPDPIHTY 148 +DP + +VKK + + D+ +LP GL GYFAYD+ E + N P Sbjct: 87 QDPFDLVDTLVKK-LSFLDKAFKLP-VTAGLFGYFAYDLKDRIENLPRTCVGNGLP---- 140 Query: 149 DIYLVLTDVVVIHDNLTGKIKVVVPIFAQNGIEEEYERAKNLIRDTVKKLKERGTTFLNV 208 DI L VV+I D T + + +P+F ++ +E+ + +++ G Sbjct: 141 DICLYAPSVVLIQDRKTCENWLCLPVFDRDKGQEDVLAREEYFLKRLEQSWHPGAFCA-- 198 Query: 209 VEKEPDFKNWRSNFTKEEFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDNIYRVLR 268 D + S+F K E+ V + ++ QGD+ Q LSQRF F G+ ++ L Sbjct: 199 -----DGTGFVSSFAKPEYLSAVSQIIAHLRQGDIYQANLSQRFETGFNGDAYALFLKLF 253 Query: 269 FLNPSPYMYYLDFDQLKVIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLL 328 NP+P+ ++ +V+ +SPE +++E +E+RPI GT RG T E+D+ L Sbjct: 254 EKNPAPFFAFIQAGDHQVVSTSPERFLKVEGSTVESRPIKGTISRGNTPEQDRENAGTLS 313 Query: 329 SDEKERAEHLMLVDLARNDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDA 388 K+ AE M+VDL RND+ R+ + SV V R+E Y +V H+VS V G L+ Sbjct: 314 RSTKDDAELTMIVDLMRNDLSRITEHDSVDVTAHKRLEPYDNVFHLVSVVRGRLKADVSC 373 Query: 389 LDVLKATFPAGTVSGAPKVRAMQIIEELENERRGIYAGSVGYISFQGNMDMAIAIRTAVY 448 V++A FP G+++G PK+RAM+II+ LE +R +Y G++GY+SF G MD++IAIRTAV Sbjct: 374 AGVVRAAFPGGSITGCPKIRAMEIIDALEPVKRHVYTGAIGYLSFHGTMDLSIAIRTAVV 433 Query: 449 RDRDIFVQAGAGIVADSVPEKEWEETVNKAKALMKAI 485 D +F G G+V DS PEKE+EET+ K K LM + Sbjct: 434 HDGRLFFSVGGGVVYDSDPEKEFEETLAKGKTLMDTL 470 Lambda K H 0.318 0.138 0.390 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: 784 Number of extensions: 36 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 494 Length of database: 749 Length adjustment: 37 Effective length of query: 457 Effective length of database: 712 Effective search space: 325384 Effective search space used: 325384 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: 53 (25.0 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