Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_029936187.1 N746_RS0109875 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000711195.1:WP_029936187.1 Length = 504 Score = 135 bits (340), Expect = 3e-36 Identities = 122/413 (29%), Positives = 187/413 (45%), Gaps = 43/413 (10%) Query: 64 VELDSDELRVIRDGVTRRQQWSGRPGAALGEAVDRLLLETDQAF------GWVA-FEFGV 116 + +D ++RV+R G Q + P A L EA D A G V F + Sbjct: 72 IRVDGQQVRVLRAGEVVEHQVAADPLAWL-EAYQAQFKVLDSAELPKFCGGLVGYFGYDT 130 Query: 117 HRYGLQQRLAPHTPLA-RVFSPRTRIMVSEKEIRLFD--AGIRHR--------------- 158 RY ++ RLA P + +P +MVS +E+ +FD +G H Sbjct: 131 VRY-VEPRLAQSQPARDEIGTPDILLMVS-RELVVFDNLSGQVHVIIQADLSKPNAFKQA 188 Query: 159 ----EAIDRLLATGVREVPQSRSVDVSDDPSGFRRRVAV-----AVDE----IAAGRYHK 205 + +++ L E P S + D D + F+ AVD+ I +G + Sbjct: 189 QMRIDELEQQLGQSF-EKPDSFAADSQVDEADFKSSFGEQAFKDAVDKVKEYILSGDAMQ 247 Query: 206 VILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVIT 265 V+LS+ + + F YR R N F L L + +G SPE++ + D +V Sbjct: 248 VVLSQQMSIEFKQSSLDLYRALRYLNPSPYMFYLNLDDFQIVGSSPEILVRLE-DDLVTV 306 Query: 266 EPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMT 325 P+AGTR G DR DL ++ KE+ EH + + ++ IAE GS + + M Sbjct: 307 RPIAGTRRRGTDVEKDRALEQDLLNDPKEVAEHLMLIDLGRNDVGRIAEVGSVKLTEKMI 366 Query: 326 VRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLY 385 V V H+ S + L P + L A FPA T SG PK ++ I L+ RG+Y Sbjct: 367 VERYSHVMHIVSNVDGTLKPGLSPLEVLRATFPAGTVSGAPKIRAMQIIDELEPVKRGVY 426 Query: 386 SGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEK 438 +GAV L G +D A+ +R A R +++AGAGI+ +S P+ E++ET K Sbjct: 427 AGAVGYLGWHGNMDTAIAIRTAVVKNDRLYVQAGAGIVADSVPQSEWDETMNK 479 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: 493 Number of extensions: 27 Number of successful extensions: 2 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: 504 Length adjustment: 33 Effective length of query: 417 Effective length of database: 471 Effective search space: 196407 Effective search space used: 196407 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 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