Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate Ga0059261_0256 Ga0059261_0256 anthranilate synthase component I, non-proteobacterial lineages
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__Korea:Ga0059261_0256 Length = 508 Score = 137 bits (345), Expect = 8e-37 Identities = 100/297 (33%), Positives = 142/297 (47%), Gaps = 6/297 (2%) Query: 145 EKEIRLFDAGIRHREAIDRLLATGVREVPQSRSVDVSDDPS----GFRRRVAVAVDEIAA 200 + E RL DA R RL + +++++ P+ + VA A + I A Sbjct: 190 DPEARLADAAERIDATAARLATAPLPPKVAGDALEIAARPTLADGDYAAMVARAKEYITA 249 Query: 201 GRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRAD 260 G +V+L++ PFA+ YR RR N + L L G G SPE++ VR D Sbjct: 250 GDIFQVVLAQRFTAPFALPPIELYRALRRVNPSPFLYFLDLPGFALTGSSPEILVRVRDD 309 Query: 261 GVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAV 320 V I P+AGTR G+ A D R L ++ KE EH + + + +A+ G+ V Sbjct: 310 EVTI-RPIAGTRPRGKTAAEDEANRTSLLADPKERAEHLMLLDLGRNDTGRVAQAGTVRV 368 Query: 321 IDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDEC 380 D TV V H+ S + +L P +D + AL A FPA T SG PK E I L+ Sbjct: 369 TDSYTVEFYSHVMHIVSNVVGKLRPDADALDALFAGFPAGTVSGAPKVRACEIIAELERE 428 Query: 381 PRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCE 437 RG Y+G V S DG +D+ + LR A G + AGAGI+ +S+ E E CE Sbjct: 429 QRGPYAGGVGYFSPDGSMDSCIVLRTAIVKDGTMHVTAGAGIVADSDAAYEQRE-CE 484 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: 483 Number of extensions: 28 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: 508 Length adjustment: 34 Effective length of query: 416 Effective length of database: 474 Effective search space: 197184 Effective search space used: 197184 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