Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_022948598.1 H035_RS0108695 aminodeoxychorismate synthase, component I
Query= curated2:O66849 (494 letters) >NCBI__GCF_000421465.1:WP_022948598.1 Length = 466 Score = 270 bits (690), Expect = 8e-77 Identities = 159/440 (36%), Positives = 251/440 (57%), Gaps = 18/440 (4%) Query: 48 ILLESAEGGEKWGRYSFIITGSSFYLRTRKDIGEIYERGKVNFFETKDPLSKIKEVVKKF 107 I L+S + GRY + S L TR ++ EI + +DP ++E++ + Sbjct: 30 IFLDSGRPRIEQGRYDILAARPSATLVTRGNLTEIRNSDGIRL-SPEDPFKLLREILGE- 87 Query: 108 IPYHDERLPR--FWGGLVGYFAYDVVKFYEPVEDKNPDPIHTYDIYLVLTDVVVIHDNLT 165 E +P F GG +GYF+YD+ + E + DP + ++ + + D V+ D+ Sbjct: 88 ---PAEGMPDLPFCGGALGYFSYDLARRLENLPQTTLDPGNIPEMAVGIYDWAVVVDHRE 144 Query: 166 GKIKVVVPIFAQNGIEEEYERAKNLIRDTVKKLKERGTTFLNVVEKEPDFKNWRSNFTKE 225 + +V + + + + +R ++ G + + RSN + + Sbjct: 145 RQTYLVAR--STPATRKIWPELQQSLRHPFPRISRTGFCLQSPI---------RSNLSWD 193 Query: 226 EFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFLNPSPYMYYLDFDQLK 285 + K + YI +GD QV +QRF + G+P +Y+ LR NP+P+ +L QL Sbjct: 194 AYAHAFAKIQHYIQEGDCYQVNFAQRFEAKAAGDPWRVYQDLRRENPAPFGSFLRLPQLG 253 Query: 286 VIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEHLMLVDLAR 345 ++ SSPE +R+ EG++ET+PI GTR R + EE+ L K+RAE+LM+VDL R Sbjct: 254 ILSSSPERFLRVREGKVETKPIKGTRARRLSPEENLFQIGALTESAKDRAENLMIVDLLR 313 Query: 346 NDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFPAGTVSGAP 405 ND+ + + GSV+V ++E ++ V H+VS VVGEL+E +LD+L+ FP G+++GAP Sbjct: 314 NDLSKTCQLGSVKVPELFQVESFATVHHLVSTVVGELKEDCHSLDLLRGCFPGGSITGAP 373 Query: 406 KVRAMQIIEELENERRGIYAGSVGYISFQGNMDMAIAIRTAVYRDRDIFVQAGAGIVADS 465 K+RAM+IIEELE+ RRGIY G++GYI F GNMD IAIRT V+ DR I AG GIVADS Sbjct: 374 KIRAMEIIEELESIRRGIYCGAIGYIGFDGNMDTNIAIRTLVHADRSIHFWAGGGIVADS 433 Query: 466 VPEKEWEETVNKAKALMKAI 485 ++E++E+ +KA AL++ + Sbjct: 434 DAKREYQESFDKASALIQVL 453 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: 524 Number of extensions: 25 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: 494 Length of database: 466 Length adjustment: 34 Effective length of query: 460 Effective length of database: 432 Effective search space: 198720 Effective search space used: 198720 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