Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate N515DRAFT_2823 N515DRAFT_2823 anthranilate synthase component 1
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Dyella79:N515DRAFT_2823 Length = 449 Score = 131 bits (330), Expect = 4e-35 Identities = 133/422 (31%), Positives = 185/422 (43%), Gaps = 40/422 (9%) Query: 48 YECDGQWVLAAGVQAMVEL----DSDELRVIRDGVTRRQQWSGRPGA---ALGEA--VDR 98 Y C Q V+ QA +L D L + DG Q + G AL A +R Sbjct: 25 YPCLLQSVVRGTPQARFDLLFAFPRDRLTLHADGRVLDGQGAEHAGGFLHALDAAWQAER 84 Query: 99 LLLETDQAF----GWVAFEFGVHRYGL------QQRLAPHTPLARVFS---PRTRIMVSE 145 L + D GWV F Y L + RLAPH L + P I+ E Sbjct: 85 LPRDADDGLPFHGGWVLFL----AYELAGEIEPRLRLAPHEVLPVALALRCPAAAIVDHE 140 Query: 146 KEIRLFDAGIRHREAIDRLLAT-----GVREVPQSRSVDVSDDPSGFRRRVAVAVDEIAA 200 +E + A + ++++ A + +P D DDP FR VA + + A Sbjct: 141 RERTVLIAEPGCEDLLEQMAADLEAQPPIAPLPAPLERD-EDDPQLFRDGVARIHEHLHA 199 Query: 201 GRYHKVILSRCVEVPFAIDFPLT---YRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAV 257 G +V LSR FA D P Y R N + LLQ + SPE + Sbjct: 200 GDIFQVNLSRAWRARFA-DAPTPASLYASLRMANPAPFAGLLQQPDWAVVSSSPERLVEA 258 Query: 258 RADGVVITEPLAGTRALGRGPAIDRLAR-DDLESNSKEIVEHAISVRSSLEEITDIAEPG 316 R GV T P+AGTR R PA D LAR +L ++ KE EH + + ++ + PG Sbjct: 259 RG-GVAQTRPIAGTRP--RTPADDELARIRELRTHPKERAEHVMLIDLERNDLGRVCVPG 315 Query: 317 SAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFR 376 S V + M V V H+ S +R +L P + A FP T +G PK +E I Sbjct: 316 SVQVDELMVVESYAHVHHIVSNVRGKLRPGVTPGQVIAATFPGGTITGCPKVRCMEIIHA 375 Query: 377 LDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETC 436 L++ PRG Y+GA+ L +G LD + +R G + LRAGAGI+ +S E+E +ET Sbjct: 376 LEDAPRGAYTGALGYLDRNGDLDLNILIRTLTLAGTQVSLRAGAGIVADSVAEKELDETR 435 Query: 437 EK 438 K Sbjct: 436 AK 437 Lambda K H 0.319 0.135 0.386 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: 461 Number of extensions: 29 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: 450 Length of database: 449 Length adjustment: 33 Effective length of query: 417 Effective length of database: 416 Effective search space: 173472 Effective search space used: 173472 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: 51 (24.3 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