Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate Ac3H11_2391 L-asparaginase (EC 3.5.1.1)
Query= reanno::BFirm:BPHYT_RS08815 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2391 Length = 317 Score = 266 bits (681), Expect = 4e-76 Identities = 159/317 (50%), Positives = 200/317 (63%), Gaps = 16/317 (5%) Query: 22 RIVVLATGGTIAGAAASATNTSGYQAGVIGVEQLLAVVPALSTVA--RMEREQIASVDSK 79 +IVVL TGGTIAG +A A + GY A +GVEQLLA VP L +A + EQ+A VDSK Sbjct: 5 KIVVLGTGGTIAGTSAQAGDNIGYTAAQVGVEQLLAAVPGLQALAGGTLVVEQVAQVDSK 64 Query: 80 DMAMPLWTTLAQRINTLLADDEIDGVVVTHGTDTLEETAYLLHLTIKSDKPVVLTAAMRP 139 DM +W LAQR LAD ++ G+V+THGTDTLEETA+ LH + + KPVVLT AMRP Sbjct: 65 DMDDGVWRALAQRCAHHLADPDVRGLVITHGTDTLEETAWFLHEVLDTTKPVVLTCAMRP 124 Query: 140 ASALSADGPLNLLNAVTVAAQASARGQGVLVAFNNRIHSARDVVKTSTYAVDAFHSPEIG 199 A+AL+ DGP NLL+AV V A GV+ +H+AR+V K Y V AF+S + G Sbjct: 125 ATALTPDGPQNLLDAVAVVLAPGA--TGVVAVAAGELHAARNVQKVHPYRVHAFNSGDAG 182 Query: 200 ALGWVQDGRVEFQRG-----VVRPHTLATEFVIGAQWPHVEIVLSYAGVSRIAVDALVAA 254 LGWV++GRV F + V R T + A+WP VE+VLS+AG VDALV A Sbjct: 183 PLGWVEEGRVRFVQNWPLPPVGRAFTAIKTGIESAEWPWVEVVLSHAGARAQTVDALVHA 242 Query: 255 GVRGIVVAGTGNGSIHASVQQALADAASQGVAVVRASRVGSGHVM-RNGAAADDALGFVS 313 GVRG+VVA TGNG+IH ++ AL A GV VVRA+R G V+ + G D+ G Sbjct: 243 GVRGLVVACTGNGTIHHALDAALLRAQQAGVRVVRATRCAEGQVLPKPGDVLPDSRG--- 299 Query: 314 AGSLNPYKARVLLMLAL 330 L+P KARV L+L L Sbjct: 300 ---LSPVKARVALLLDL 313 Lambda K H 0.317 0.129 0.360 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: 241 Number of extensions: 16 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: 347 Length of database: 317 Length adjustment: 28 Effective length of query: 319 Effective length of database: 289 Effective search space: 92191 Effective search space used: 92191 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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