Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_052669275.1 NITAL_RS02255 isochorismate synthase
Query= curated2:Q9YGB3 (433 letters) >NCBI__GCF_000969705.1:WP_052669275.1 Length = 407 Score = 135 bits (341), Expect = 2e-36 Identities = 90/267 (33%), Positives = 140/267 (52%), Gaps = 21/267 (7%) Query: 172 FVEIVRAGKEYIYSGDVFQVVLSREYRV--RTDLDALEIYKRLVELNPSPYTFILEFEKT 229 ++E V + + +GD+ +VVL+R++ V + D L++ +RL PS +TF++E Sbjct: 151 WLEAVAIAVDRLQAGDLDKVVLARDHAVWSQETFDPLDLARRLTARFPSCHTFVVE---G 207 Query: 230 VVGASPETMGSVEGRTFKINPIAGTAPRGRTGEEDRELEKALLSDEKERAEHVMLVDLAR 289 +VGA+PE + + +G +AGT R ED L ALL+ +K+R EH + D R Sbjct: 208 LVGATPELLLARDGDRVTSRVLAGTTGRSTDEAEDAALGAALLASDKDRHEHQLAADSVR 267 Query: 290 N-------DVRRVSKPGSVRLTRFFDVLKYSHVQHIESEVVGELDEGKNAFDAMEAAFPA 342 D++ +P +RL +VQH+ + G LD + + + P Sbjct: 268 EVLAARCADLQHDPEPRLLRL---------DNVQHLATLFGGHLDRSASVLEVVAELHPT 318 Query: 343 GTLTGAPKIRAMEIIDELERSRRKVYGGAVGYFSLTGDADMAIAIRMAEIEGRKASVRAG 402 + G P+ RA+E+I ELE R Y VG+ GD + AIA+R AE+ G +A + AG Sbjct: 319 AAVGGTPRDRALEVIAELEGMDRGRYAAPVGWIDAAGDGEWAIALRCAELAGARARLFAG 378 Query: 403 AGIVADSVPEKEFFETENKMRAVLKAL 429 GIVA S+PE E ET K+ A+ AL Sbjct: 379 VGIVAASLPEDELEETRLKLLAMQAAL 405 Lambda K H 0.318 0.137 0.384 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: 441 Number of extensions: 27 Number of successful extensions: 4 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: 433 Length of database: 407 Length adjustment: 32 Effective length of query: 401 Effective length of database: 375 Effective search space: 150375 Effective search space used: 150375 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: 50 (23.9 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