Align Anthranilate synthase; EC 4.1.3.27 (characterized, see rationale)
to candidate WP_027721082.1 H589_RS0105320 anthranilate synthase component I family protein
Query= uniprot:B8DM47_DESVM (520 letters) >NCBI__GCF_000425265.1:WP_027721082.1 Length = 471 Score = 540 bits (1392), Expect = e-158 Identities = 279/456 (61%), Positives = 328/456 (71%), Gaps = 1/456 (0%) Query: 53 EIVLRQTGRWLEADVDTPISVFLGMVGSGQGILLESAEVDGRWGRFSVIAFNFLLRLGCR 112 +I L Q G+WL AD TPIS++LG+VG GILLESAEVDGR GR+S+IA++F L+L Sbjct: 2 KIELTQYGKWLPADTQTPISLYLGLVGDAPGILLESAEVDGRLGRYSLIAWDFRLKLSPV 61 Query: 113 DGKLEVAVRDPRLAPLRRFDGMGFIEGTRAVMRALRIEPDAAFADQPPITRALYGYFGYG 172 GKL V D RLA L + GM F++G RAVM+AL I P + P +TR LYG GYG Sbjct: 62 SGKLSVECADSRLAGLATYSGMDFLDGMRAVMKALHINPQPEVGELPSLTRGLYGTMGYG 121 Query: 173 VSGLFEPKLAKVLPTSSAEACLALPGTVVLFDHLYNRLCQLSLTDLPGGRVDRSQVDRTP 232 ++G+ EPKL LP AE LALPG VVLFDHL + C LSL + Sbjct: 122 IAGMLEPKLKDKLPAEDAEVRLALPGRVVLFDHLKHSCCFLSLDKDATPQFTPPVFGAEC 181 Query: 233 EPPEVGPVVNVPEQAVYTRAVARVKDMIRQGEAIQVVLSTRFQASFSGDPFTLYRRLRRI 292 EP +VG V VP + Y V +VKD+I GE IQVVLSTRF A FSGD F LYRRLR+ Sbjct: 182 EPTKVGEPVAVPGKEKYMSGVRKVKDLIADGECIQVVLSTRFSAPFSGDSFDLYRRLRQA 241 Query: 293 NPSPYMFFMRLPGVS-LLGSSPEVMVRCRADKLQVSPIAGTRPRGTDDAHDAALARELLE 351 NPSP+MF+M+ LLGSSPE+M RC +L+V PIAGTRPRG D A D A EL+ Sbjct: 242 NPSPFMFYMKFSREEILLGSSPEMMARCEKGRLEVRPIAGTRPRGKDAAGDRKYAEELMA 301 Query: 352 DPKERAEHVMLVDLGRNDLGRIAAPGTVQVERFMDVEKFSHVMHLTSRVTAQIEPGRDAL 411 DPKERAEHVMLVDLGRNDLGRIA PG+V VE+FM +E FSHVMH+TS V A + DAL Sbjct: 302 DPKERAEHVMLVDLGRNDLGRIAKPGSVSVEKFMQIEYFSHVMHITSYVEADLRDDHDAL 361 Query: 412 DVLAATFPAGTVSGAPKVRAMEIISEAEGLARGPYAGAIGWLGLDRDSVNLDTGITIRSL 471 DVL ATFPAGT+SGAPK+RAMEIISE E + RGPY G IG++GLD+DSVNLDTGITIRS+ Sbjct: 362 DVLQATFPAGTLSGAPKIRAMEIISEIEDVPRGPYGGCIGFIGLDKDSVNLDTGITIRSM 421 Query: 472 WVRDGQVHWQAGAGIVFDSVPEMEWKECNNKAAVIR 507 W+RDG+ HWQAGAGIV+DS EMEW ECNNKA V+R Sbjct: 422 WIRDGKCHWQAGAGIVYDSDLEMEWLECNNKARVLR 457 Lambda K H 0.320 0.137 0.413 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: 717 Number of extensions: 18 Number of successful extensions: 3 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: 520 Length of database: 471 Length adjustment: 34 Effective length of query: 486 Effective length of database: 437 Effective search space: 212382 Effective search space used: 212382 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: 52 (24.6 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