Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate WP_011779027.1 MVAN_RS08995 isochorismate synthase
Query= curated2:Q9HS66 (488 letters) >NCBI__GCF_000015305.1:WP_011779027.1 Length = 365 Score = 110 bits (276), Expect = 6e-29 Identities = 88/267 (32%), Positives = 132/267 (49%), Gaps = 14/267 (5%) Query: 215 SRVRRIQDAIRD---GDTFQANVSHRLDAPAAVHPVAVFEALRDTNPAPYSGIVE-FPGV 270 +R+R DA++ + RLDA ++ +A +A S E + G Sbjct: 101 ARLRDPDDALQKVVLARALRLTADGRLDARTLLNRLAANDAQATKYLVDLSAAGEGYSGA 160 Query: 271 DLVSASPELLLARRGRELTTEPIAGTRPRGATPAEDDAARAALRADDKERAEHAMLVDLE 330 L+ ASPELL+AR GR++ P AG+ PR PA D A AAL +K R EH ++VD Sbjct: 161 ALIGASPELLVARHGRQVICRPFAGSAPRLDDPAADAANGAALADSEKNRHEHQLVVDAL 220 Query: 331 RNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVTGRLRD-SCSLRDAIAAVFPGGTITG 389 R+ L + + + D ++ + V HL + ++G LR+ S + D A+ P + G Sbjct: 221 RSALEPLCT--DLQIADRPQLSRTAAVWHLYTPMSGVLREKSLTALDLAVALHPTPAVGG 278 Query: 390 APKPRTMALIDTVEATRRGPYTGSLAAIGFDGDATLSITIR----TLVRRAATYHLRVGA 445 +P +A I+ VE RG Y G++ GD ++IR + RR A H G Sbjct: 279 SPTDEAVAFINDVEGD-RGFYAGAVGWCDQRGDGRWVVSIRCAQLSADRRTAVAH--SGG 335 Query: 446 GIVHDSTPAAEYDETLAKARALVTALG 472 GIV +S P E DET K R +++ALG Sbjct: 336 GIVAESDPDDEVDETTTKFRTILSALG 362 Lambda K H 0.317 0.135 0.397 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: 453 Number of extensions: 32 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: 488 Length of database: 365 Length adjustment: 32 Effective length of query: 456 Effective length of database: 333 Effective search space: 151848 Effective search space used: 151848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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