Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate PfGW456L13_4123 Para-aminobenzoate synthase, aminase component (EC 2.6.1.85)
Query= curated2:P67002 (516 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4123 Length = 447 Score = 262 bits (669), Expect = 2e-74 Identities = 167/452 (36%), Positives = 234/452 (51%), Gaps = 33/452 (7%) Query: 49 PGTFLLESAENGRSWSRWSFIGAGAPTALTVREGQAVWLGAVPKDAPTGGDPLRALQVTL 108 PG LL+S R+ + A LTV ++ G L+ L+ L Sbjct: 26 PGAVLLDSGRPSADRGRYDLLSAWPLEQLTVSPDES------------GDAFLQRLRNNL 73 Query: 109 ELLATADRQSEPGLPPLSGGMVGFFAYDMVRRLERLPERAVDDLCLPDMLLLLATDVAAV 168 L A + LP +GG++G+ +YD R LERLP +A DDL LPD L Sbjct: 74 TRLGEAILPEDYELP-FAGGLIGYLSYDFGRHLERLPSQASDDLHLPDARFGLYGWALIS 132 Query: 169 DHHEGTITLIANAVNWNGTDERVDWAYDDAVARLDVMTAALGQPLPSTVATFSRPEPRHR 228 DH T L+ + + +R + QP P V F P Sbjct: 133 DHLSRTSQLVFHPTLPDSERQR--------------LIELFSQPAPEVVTPFKLLTPM-T 177 Query: 229 AQRTVEEYGAIVEYLVDQIAAGEAFQVVPSQRFEMDTDVDPIDVYRILRVTNPSPYMYLL 288 A + +EY +E + I AG+ +QV +QRF DP Y LR P+P+ Sbjct: 178 ADLSADEYQQAIERIQQYIQAGDCYQVNFAQRFRAPCLGDPWAAYCALRAACPTPFSGFQ 237 Query: 289 QVPNSDGAVDFSIVGSSPEALVTVHEGWATTHPIAGTRWRGRTDDEDVLLEKELLADDKE 348 +P+ D +++ SPE V V +G T PI GTR RG T ++D ELLA K+ Sbjct: 238 NLPDGD-----AVLSLSPERFVKVSQGHVETRPIKGTRPRGLTPEQDAANAAELLASPKD 292 Query: 349 RAEHLMLVDLGRNDLGRVCTPGTVRVEDYSHIERYSHVMHLVSTVTGKLGEGRTALDAVT 408 RAE+LM+VDL RNDLGR C G+VRV + +E Y +V HLVS+VTG+L + R ALD + Sbjct: 293 RAENLMIVDLLRNDLGRTCRTGSVRVPELFSLESYPNVHHLVSSVTGELADERDALDLIA 352 Query: 409 ACFPAGTLSGAPKVRAMELIEEVEKTRRGLYGGVVGYLDFAGNADFAIAIRTALMRNGTA 468 FP G+++GAPK+RAM++I+E+E TRRGLY G + YLD G D +IAIR+ L+++G Sbjct: 353 GSFPGGSITGAPKIRAMQIIDELEPTRRGLYCGSLLYLDVRGEMDSSIAIRSLLVKDGQV 412 Query: 469 YVQAGGGVVADSNGSYEYNEARNKARAVLNAI 500 GGG+VADS EY E+ K + +L+ + Sbjct: 413 CCWGGGGIVADSQWQAEYQESITKVKVLLDTL 444 Lambda K H 0.318 0.134 0.395 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: 574 Number of extensions: 29 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: 516 Length of database: 447 Length adjustment: 34 Effective length of query: 482 Effective length of database: 413 Effective search space: 199066 Effective search space used: 199066 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 09 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