Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate WP_011883360.1 anthranilate synthase
Query= curated2:Q9HS66 (488 letters) >NCBI__GCF_000016205.1:WP_011883360.1 Length = 714 Score = 176 bits (445), Expect = 3e-48 Identities = 102/255 (40%), Positives = 141/255 (55%), Gaps = 11/255 (4%) Query: 194 GPPPADSPAPFESVAGRAAFESRVRRIQDAIRDGDTFQANVSHRLDAPAAVHPVAVFEAL 253 GPP A R AF++ + + DA+R GD++Q N ++RL+ P+A++ L Sbjct: 109 GPPSIAGVAHVAKSVSRDAFDAAIAAVHDALRAGDSYQINYTYRLNFDMFGTPLALYRRL 168 Query: 254 RDTNPAPYSGIVEFP-GVDLVSASPELLLARRGRELTTEPIAGTRPRGATPAEDDAARAA 312 R P Y ++ P G +VS SPEL + + G L P+ GT PR A P ED AA A Sbjct: 169 RARQPVRYGALIALPDGGWVVSCSPELFVEKHGDVLRARPMKGTAPRSADPHEDAAAAAF 228 Query: 313 LRADDKERAEHAMLVDLERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVTGRLRDSC 372 L D K RAE+ M+VDL RND+ +++ GSV VP V+ Y+ V + S V RD Sbjct: 229 LANDPKNRAENVMIVDLLRNDVSRIARTGSVKVPALFSVEPYASVWQMTSTVEAGWRDGT 288 Query: 373 SLRDAIAAVFPGGTITGAPKPRTMALIDTVEATRRGPYTGSLAAIGFD----------GD 422 + + A+FP G+ITGAPK +TM LID +EAT RG YTG++ + GD Sbjct: 289 TFAQMLRALFPCGSITGAPKHKTMELIDAIEATPRGLYTGAIGWLDAPHGASSGAAGCGD 348 Query: 423 ATLSITIRTLVRRAA 437 LS+ IRTL+ AA Sbjct: 349 FCLSVAIRTLMIEAA 363 Score = 29.6 bits (65), Expect = 4e-04 Identities = 17/28 (60%), Positives = 17/28 (60%) Query: 443 VGAGIVHDSTPAAEYDETLAKARALVTA 470 VGAGIV DS A EY E KAR L A Sbjct: 472 VGAGIVLDSVAADEYAECELKARFLTDA 499 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: 961 Number of extensions: 61 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 488 Length of database: 714 Length adjustment: 37 Effective length of query: 451 Effective length of database: 677 Effective search space: 305327 Effective search space used: 305327 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: 53 (25.0 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