Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_010962065.1 MCA_RS14050 aminodeoxychorismate synthase, component I
Query= curated2:O66849 (494 letters) >NCBI__GCF_000008325.1:WP_010962065.1 Length = 468 Score = 279 bits (714), Expect = 1e-79 Identities = 171/442 (38%), Positives = 254/442 (57%), Gaps = 17/442 (3%) Query: 48 ILLESAEGGEKWGRYSFIITGSSFYLRTRKDIGEIYERGKVNFFETKDPLSKIK-EVVKK 106 + L+S + GRY I L TR I EI RG +DP S ++ E+ + Sbjct: 28 VFLDSGFPHCRHGRYDIIAADPLATLVTRGHISEIRRRGGEVALSPEDPFSLLRRELGTR 87 Query: 107 FIPYHDERLPRFWGGLVGYFAYDVVKFYEPVEDKNPDPIHTYDIYLVLTDVVVIHDNLTG 166 P + LP F GG VGYF YD+ + E + ++ D + D+ + + D VI D+L G Sbjct: 88 ADPVGE--LP-FSGGAVGYFGYDLGRRLEKLPERAVDAENMADMAVGIYDWAVIVDHLQG 144 Query: 167 KIKVVVPIFAQNGIEEEYERAKNLIRD--TVKKLKERGTTFLNVVEKEPDFKNWRSNFTK 224 + +V +Q R +L+R ++ L + T F + R+N + Sbjct: 145 RSWLV----SQGRSPATAARWPHLVRSFSQIQTLGWQRTGFDVLAPV-------RANMNR 193 Query: 225 EEFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFLNPSPYMYYLDFDQL 284 ++ ++ + YI +GD QV L+QRF +G+ +Y+ LR NP+P+ +++ Q Sbjct: 194 RDYVAAFERIQHYIREGDCYQVNLAQRFAAPCRGSAWTLYQTLRQTNPAPFSAFINGPQA 253 Query: 285 KVIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEHLMLVDLA 344 +V+ SSPE +R+ +GR+ET+PI GTR R ED+R EE L EK+RAE+LM+VDL Sbjct: 254 RVLSSSPERFLRVLDGRVETKPIKGTRPRSTDPLEDRRQEETLRHSEKDRAENLMIVDLL 313 Query: 345 RNDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFPAGTVSGA 404 RND+G+ + GSVRV IE Y+ V H+VS V G L G+DA+ +L+ +FP G+++GA Sbjct: 314 RNDLGKHCQPGSVRVPKLFEIESYTTVHHLVSTVTGTLARGHDAIGLLRDSFPGGSITGA 373 Query: 405 PKVRAMQIIEELENERRGIYAGSVGYISFQGNMDMAIAIRTAVYRDRDIFVQAGAGIVAD 464 PK+RAM+IIEELE RRG+Y G++GY+ F GNMD IAIRT V + + AG GIVAD Sbjct: 374 PKIRAMEIIEELEPHRRGVYCGAIGYVGFDGNMDTNIAIRTLVQSEGTVRFWAGGGIVAD 433 Query: 465 SVPEKEWEETVNKAKALMKAIE 486 S E++E +KA AL+ +E Sbjct: 434 SSAASEYQECFDKAAALLNLLE 455 Lambda K H 0.318 0.138 0.390 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: 542 Number of extensions: 19 Number of successful extensions: 3 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: 494 Length of database: 468 Length adjustment: 34 Effective length of query: 460 Effective length of database: 434 Effective search space: 199640 Effective search space used: 199640 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: 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