Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 8501596 DvMF_2315 Chorismate binding-like protein (RefSeq)
Query= curated2:Q9Z4W7 (511 letters) >FitnessBrowser__Miya:8501596 Length = 547 Score = 146 bits (369), Expect = 2e-39 Identities = 141/411 (34%), Positives = 186/411 (45%), Gaps = 36/411 (8%) Query: 118 HLARSVAPVPGLPPFHGGVV-------GYLGYEAARHFEDLPLA-AGPPPGLPESAFLAA 169 H ++A GLPP G L ++ AR D+ L GLP +A Sbjct: 132 HTDAALAAFLGLPPPFGAHSTTPPRDGAPLPWQPARADHDIALGFLAYTYGLPRFGIRSA 191 Query: 170 DDLVVFDHATRRVLLMTLYRPARES-----YDDAVARIV-RLNRALRRAPAPAAFSGRPL 223 V+ RR + + PA + + DA + R +R L AP PAAF+ Sbjct: 192 KPRVLPHALLRRYHAVARWNPATGALTLSVHPDAPPDLTARCSRLLADAPPPAAFTAPNG 251 Query: 224 AAATPADHGTQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTD--- 280 A G ++L A +T V I AGD +Q LS R L A D Sbjct: 252 CAVFTPSGGCTALPSSLDRAGYTAGVREVLRRIHAGDTYQCNLSTRFG--LHAPGLDSAA 309 Query: 281 LYRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAE------GRTVRTRPLAGTR---P 331 L HL T P+P+ + L GGRHV+ ASPE ++ + GR V ++P+ GT P Sbjct: 310 LSLHLWRTRPAPF-HGLFRIGGRHVVSASPERFLRVDAPGGGPGR-VLSQPIKGTLAFGP 367 Query: 332 RHPDPAEDLRLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERF---- 387 P P L L A KERAE M+VDL RND+ G+V V R R Sbjct: 368 GTPHPVWHPGLPGLLAATPKERAELSMIVDLVRNDISADCAHGSVAVARHCATFRVGGAA 427 Query: 388 SHVMHLSSTVRGRLAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGAL 447 S ++ + S V G L R LD L SAFP G+++G PK R + II EP R VY G+L Sbjct: 428 SGLVQMYSDVTGTLRPERTCLDLLLSAFPGGSVTGCPKRRTLAIIEAGEPHSREVYCGSL 487 Query: 448 GFVGADGLTDFAIALRT--MVVADGHVHVQAGAGIVADSDPAAEFRETLHK 496 + D +IA+RT A G AG+GIV DSDP +E+ ET K Sbjct: 488 LAIADARTMDASIAIRTGWHDAATGRFEHCAGSGIVVDSDPESEYEETWAK 538 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: 784 Number of extensions: 45 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: 547 Length adjustment: 35 Effective length of query: 476 Effective length of database: 512 Effective search space: 243712 Effective search space used: 243712 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 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