Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_012565349.1 RC1_RS00475 anthranilate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000016185.1:WP_012565349.1 Length = 509 Score = 146 bits (369), Expect = 1e-39 Identities = 96/305 (31%), Positives = 153/305 (50%), Gaps = 16/305 (5%) Query: 152 DAGIRHREAIDRLLATGVRE----VPQSRSVDVSDDP----------SGFRRRVAVAVDE 197 DA + +R A +RL A V + VP + D+ P + + V A + Sbjct: 185 DADVAYRRATERL-AEAVADLEGPVPAALGTDLDLQPLPEPASNTSRAEYHALVERAKEY 243 Query: 198 IAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAV 257 I AG +V+ S+ VPF++ YR RR N F L G + +G SPE++ + Sbjct: 244 IRAGDIFQVVPSQRFSVPFSLPPFALYRALRRLNPSPFLFFLDFGHVSVVGSSPEILVRL 303 Query: 258 RADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGS 317 R D V P+AGTR G+ A D+ DL S+ KE+ EH + + ++ +A+ G+ Sbjct: 304 R-DNTVTIRPIAGTRRRGKDAAEDKELAADLLSDPKELAEHLMLLDLGRNDVGRVAQVGT 362 Query: 318 AAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRL 377 V + T+ V H+ S + ++ P+ + AL A FPA T SG PK +E I L Sbjct: 363 VKVTERFTIEYYSHVMHIVSNVEGQVAPTFTAIDALIAGFPAGTVSGAPKIRAMEIIDEL 422 Query: 378 DECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCE 437 ++ RG+Y G + +A+G +D + LR A G +++AG G++ +S+PE E++ET Sbjct: 423 EKTRRGIYGGCIGYFAANGTMDTCIALRTAVIKDGMMYVQAGGGVVADSDPEAEYQETVN 482 Query: 438 KLSTL 442 K L Sbjct: 483 KSKAL 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: 465 Number of extensions: 25 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: 509 Length adjustment: 34 Effective length of query: 416 Effective length of database: 475 Effective search space: 197600 Effective search space used: 197600 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