Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate WP_004325644.1 C665_RS18035 anthranilate synthase component I family protein
Query= curated2:Q9HS66 (488 letters) >NCBI__GCF_000310185.1:WP_004325644.1 Length = 510 Score = 189 bits (479), Expect = 3e-52 Identities = 138/327 (42%), Positives = 166/327 (50%), Gaps = 30/327 (9%) Query: 173 EAGRDRVQSL--AAAIRDGDPAVGPPPADSPAPFESVAGRAAFESRVRRIQDAIRDGDTF 230 EA R R ++ +A D DP GP PA SV RAAFE + RI AI +G+T+ Sbjct: 135 EAQRQRRPAIGTSATAPDPDPDTGPAPAGVLGLRASV-DRAAFEDAIARIHAAIAEGETY 193 Query: 231 QANVSHRLDAPAAVHPVAVFEALRDTNPAPYSGIVEFP------GVDLV-SASPELLLAR 283 Q N S+RLD P+A++ LR P + ++ P G D V S SPEL L Sbjct: 194 QVNYSYRLDFDTFGSPLALYRRLRARQPVAFGALIRLPADADEGGPDWVLSCSPELFLRH 253 Query: 284 RGRELTTEPIAGTRPRGATPAEDDAARAALRADDKERAEHAMLVDLERNDLGKVSEYGSV 343 L P+ GT R A D A L AD K RAE+ M+VDL RNDLG+V GSV Sbjct: 254 HDGVLQARPMKGTAARSGDDAADALAARRLAADAKNRAENLMIVDLLRNDLGRVVTTGSV 313 Query: 344 AVPDYRRVDAYSEVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTITGAPKPRTMALIDTVE 403 VP V+ Y VL + S V L D+ + A+FP G+ITGAPK RTM LID +E Sbjct: 314 RVPALFEVERYPTVLQMTSTVEAELSDATEFPALLRALFPCGSITGAPKHRTMQLIDGLE 373 Query: 404 ATRRGPYTGSLAAIGFD------GDATLSITIRTLVRRAA-------------TYHLRVG 444 +T RG YTGSL I GD LS+ IRTL AA + VG Sbjct: 374 STPRGLYTGSLGWIDAPPAGRACGDFCLSVAIRTLTLTAAGAAGAATLAGPLHRGRMGVG 433 Query: 445 AGIVHDSTPAAEYDETLAKARALVTAL 471 AGIV DS A EY E KA L TAL Sbjct: 434 AGIVIDSRAADEYAECRLKAHFL-TAL 459 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: 646 Number of extensions: 38 Number of successful extensions: 4 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: 510 Length adjustment: 34 Effective length of query: 454 Effective length of database: 476 Effective search space: 216104 Effective search space used: 216104 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: 52 (24.6 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