Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 5209432 Shew_1903 para-aminobenzoate synthase, subunit I (RefSeq)
Query= curated2:P05378 (462 letters) >FitnessBrowser__PV4:5209432 Length = 477 Score = 233 bits (595), Expect = 8e-66 Identities = 154/444 (34%), Positives = 228/444 (51%), Gaps = 23/444 (5%) Query: 30 PVSFLLESVERGR-QSRFSIVGVGARRTFRLKDGVF-----------------TVNGERV 71 P + LL+S +R+ I+ T +DGV + +G + Sbjct: 31 PWAILLDSAGADHIDARYDIISFDPLATITSQDGVTHTRHLRPTAASATEENQSKDGVEI 90 Query: 72 ETRDPLRALYERV--YAPLERHPDLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDL 129 DPL L + Y P + +LP F GG +G +YDL R E+LP++ D+ LP++ Sbjct: 91 SQDDPLSILQAAIADYFPTQHACELP-FSGGALGTFSYDLGRRIEKLPTIAAQDIELPEM 149 Query: 130 LFVEPEVVAVFDHLKNLLHLVAPGRDPEEAEARLFWAERRLKGPL-PGVPGERAGGRARF 188 + +F + LV R + RL E RL P GE+ + Sbjct: 150 NIGLYDWALLFCYQSQTWSLVHY-RGETALKERLADLEARLSSPSNEKANGEKFALSRDW 208 Query: 189 QADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPSPYMGY 248 Q ++ Y + R DY+ +GD +Q+ L+ R + + Y LR+ N +P+ + Sbjct: 209 QPQITKGEYRDKFDRVQDYLHSGDCYQINLTQRFEAEYRGDEWQAYLKLRASNKAPFSAF 268 Query: 249 LDLGEVVLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHV 308 + L ++S SPE ++ G + T+PI GT R D DK AE L EK+ AE++ Sbjct: 269 IRLDMHAILSISPERFIKLKGDAIETKPIKGTMARSSDATADKAAAEALAASEKDRAENL 328 Query: 309 MLLDLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPM 368 M++DL RNDIG+VA+ G+VRV +E + V HLVSTV LA +P D L + P Sbjct: 329 MIVDLLRNDIGKVASPGSVRVPHLFAIESFPAVHHLVSTVTANLAAPNSPCDLLRAAFPG 388 Query: 369 GTVSGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAG 428 G+++GAPKIRAMEIIEELEP RR Y GS GY++ D MD ++T+RT V ++ AG Sbjct: 389 GSITGAPKIRAMEIIEELEPSRRSLYCGSIGYISQDRQMDTSITIRTLVAEPPRLYCWAG 448 Query: 429 AGIVADSVPEREYEECWNKARALL 452 GIVADS + EY+E ++K +L Sbjct: 449 GGIVADSQVDAEYQESYDKVSKIL 472 Lambda K H 0.321 0.139 0.408 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: 499 Number of extensions: 18 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: 462 Length of database: 477 Length adjustment: 33 Effective length of query: 429 Effective length of database: 444 Effective search space: 190476 Effective search space used: 190476 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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