Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_083441807.1 NITAL_RS26705 hypothetical protein
Query= curated2:Q9Z4W7 (511 letters) >NCBI__GCF_000969705.1:WP_083441807.1 Length = 806 Score = 249 bits (637), Expect = 2e-70 Identities = 175/412 (42%), Positives = 214/412 (51%), Gaps = 21/412 (5%) Query: 99 HRPVPLEPTGGDPLTALRSHLA-RSVAP----VPGLPPFHGGVVGYLGYEAARHFEDLPL 153 HR +EP G DP L A V P GLP F GG+VG Y+ AR E LP Sbjct: 404 HRDGRVEPLGDDPFDVLERWCATHGVTPDAPREAGLPAFTGGLVGAFAYDLARRVERLPT 463 Query: 154 AAGPPPGLPESAFLAADDLVVFDHATRRVLLMTLYRPARESYDDAVARIVRLNRALRRAP 213 A P + A+ +V R LL L RP A L Sbjct: 464 RATIDRQGPHLSLRIAELIVAVGPDRDRALL--LVRPLTTDPATLAADADEL-------- 513 Query: 214 APAAFSGRPLAAATPADHGTQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRP 273 A GR A A P+ + T +L + V EHIAAGD FQ+ L++RL+ Sbjct: 514 -VARLGGRAAAPAEPSAPSPRPVTTSLPRPAYLAAVESVLEHIAAGDCFQVNLTQRLTTR 572 Query: 274 LRARPTDLYRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAEGRTVRTRPLAGTRPRH 333 +A LYR LR +P+P H +L V SPE + +GR V TRP+ GTRPR Sbjct: 573 WQAPVEHLYRRLRDISPAP---HGALLPDVGVASVSPETFLTVDGRDVATRPIKGTRPRD 629 Query: 334 PDPAEDLRLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHL 393 PDP D +L K+RAE+VM+VDL RNDLGRV PG+VR RL VE V HL Sbjct: 630 PDPDLDAAHADDLATSAKDRAENVMVVDLERNDLGRVCVPGSVRAPRLCVVEAHPTVWHL 689 Query: 394 SSTVRGRLAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGAD 453 S V GRL EG LR+ FP G+++GAPK+RAMEII LEP +RG Y GA+GF+ A Sbjct: 690 VSDVVGRLREGIGYGQLLRATFPCGSITGAPKVRAMEIIETLEPVRRGWYCGAVGFL-AP 748 Query: 454 GLTDFAIALRTMV-VADGHVHVQAGAGIVADSDPAAEFRETLHKSRAMLTAV 504 G ++A+RT ADG V G GIVADSDPAAE E+L K+ A L AV Sbjct: 749 GAASLSVAIRTATRHADGTVDHGVGGGIVADSDPAAEHAESLDKAAAFLRAV 800 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: 1314 Number of extensions: 91 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: 511 Length of database: 806 Length adjustment: 38 Effective length of query: 473 Effective length of database: 768 Effective search space: 363264 Effective search space used: 363264 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: 54 (25.4 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