Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate GFF1663 PGA1_c16860 anthranilate synthase component 1
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Phaeo:GFF1663 Length = 503 Score = 119 bits (299), Expect = 2e-31 Identities = 81/262 (30%), Positives = 123/262 (46%), Gaps = 11/262 (4%) Query: 186 GFRRRVAVAVDEIAAGRYHKVILSR-----CVEVPFAIDFPLTYRLGRRHNTPVRSFLLQ 240 G+ V A D I AG +V+ ++ + PFA+ YR RR N F Sbjct: 232 GYMAAVEKAKDYIRAGDIFQVVPAQRWTQTFRQPPFAL-----YRSLRRTNPSPFMFYFN 286 Query: 241 LGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAI 300 GG + +G SPE++ V V I P+AGTR G P D+ DL ++ KE+ EH + Sbjct: 287 FGGFQVVGASPEILVRVFGQEVTI-RPIAGTRPRGATPEEDKALELDLLADKKELAEHLM 345 Query: 301 SVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAV 360 + + +A+ G+ + + V H+ S + L D + A A PA Sbjct: 346 LLDLGRNDTGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELAEDKDALDAFFAGMPAG 405 Query: 361 TASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGA 420 T SG PK +E I L+ RG+Y G V SA G +D + LR A +++AG Sbjct: 406 TVSGAPKVRAMEIIDELEPEKRGVYGGGVGYFSAGGDMDMCIALRTAIVKDQNLYIQAGG 465 Query: 421 GIIEESEPEREFEETCEKLSTL 442 G++ +S+PE E+ ET K + + Sbjct: 466 GVVYDSDPEAEYMETVHKSNAI 487 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: 442 Number of extensions: 19 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: 503 Length adjustment: 33 Effective length of query: 417 Effective length of database: 470 Effective search space: 195990 Effective search space used: 195990 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