Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_041456890.1 AVA_RS17560 aminodeoxychorismate synthase component I
Query= SwissProt::P20579 (493 letters) >NCBI__GCF_000204075.1:WP_041456890.1 Length = 711 Score = 229 bits (584), Expect = 2e-64 Identities = 141/377 (37%), Positives = 203/377 (53%), Gaps = 19/377 (5%) Query: 115 FNGGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVD 174 FN G VGYFGY+ K S P PD +L++SD ++ FD+ + + L Sbjct: 327 FNCGFVGYFGYEL-----KAESGSGLEHPSSCPDAILLLSDRLIAFDHQEQTTYLVYLAP 381 Query: 175 PAE----EQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAV 230 E + FE + RL+ L P+ P S P FR S + + Y++ + Sbjct: 382 VGETAPAKDWFEITEKRLRTL-----PPLPPLVPSTTSHPVT----FRLSRSYQTYKDDI 432 Query: 231 GRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSP 290 R + I G+ QV + ++ D P+ YR LR NP PY F FG+ + SSP Sbjct: 433 SRCLKEIREGETYQVCLTNQLRTDTTTDPLTFYRRLRQVNPAPYSAFLRFGEMAIACSSP 492 Query: 291 EVLVRVE-DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGR 349 E ++++ V +PI GT RG T E D L + L S +KE AE+LM++DL RND+GR Sbjct: 493 ERFLQIDRQGWVETKPIKGTVRRGETPEEDFLLRESLRSSEKEQAENLMIVDLLRNDLGR 552 Query: 350 VSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAM 409 V GS+ + + M +E Y+ V +VS + G L + A D +R P G+++GAPK+R M Sbjct: 553 VCQVGSIHVPKLMDVESYATVHQLVSTIRGFLSPDMDATDCIRMAFPGGSMTGAPKLRTM 612 Query: 410 EIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALE 469 EIID+LE RGVY GA+G+ NG D I IRTAV+ + + GGGIVA S +E Sbjct: 613 EIIDQLEQEARGVYSGAIGFLGVNGAADLNIVIRTAVLTPNQTSIGIGGGIVALSEVEME 672 Query: 470 WEETINKRRAMFRAVAL 486 ++ETI K A+ +A+ L Sbjct: 673 FQETILKADALIQAMLL 689 Lambda K H 0.320 0.138 0.403 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: 816 Number of extensions: 60 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: 493 Length of database: 711 Length adjustment: 37 Effective length of query: 456 Effective length of database: 674 Effective search space: 307344 Effective search space used: 307344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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