Align 2-keto-3-deoxy-L-lyxonate dehydratase (EC 4.2.1.43) (characterized)
to candidate GFF2612 PS417_13310 sugar transporter
Query= metacyc::MONOMER-18708 (331 letters) >FitnessBrowser__WCS417:GFF2612 Length = 290 Score = 92.0 bits (227), Expect = 2e-23 Identities = 69/243 (28%), Positives = 103/243 (42%), Gaps = 32/243 (13%) Query: 57 PGPDYAGLLEEGRVLPPLDHDDPAHCLVSGTGLTHLGSAATRDRMHQQNQGDETALTDTM 116 P P L +LP L DP +V G GLTH A Sbjct: 57 PAPLTVADLAGFELLPCLQPPDPRQGMVCGFGLTHQSKVA-------------------- 96 Query: 117 RIFRWGLEGGKPPAGQVGAQPEWFYKGDGGIVVRPGADFPLPAFAEDAGEEPELVGLYLI 176 +PP Q G +P +F KG + R G + A A EE E+V L+L+ Sbjct: 97 ----------EPP--QHGERPAFFIKGFADSLKRSGDVLRMNRGALSACEEAEVVALFLV 144 Query: 177 GDDRRPYRLGYALGNEFSDHLMERRNYLYLAHSKLRACCYGPELRVGELPRHLQGESRIL 236 D+ RP +GY GN+ +D + + YLA++KL+ L LP +QG++ I Sbjct: 145 ADNSRPTYIGYTFGNDLTDIALAKSKRNYLAYAKLQPSAISHLLYRQPLPELIQGKTSIY 204 Query: 237 RDGEVLWQQAFLSGEDNMCHSLENLEYHHFKYAQFLRPGDVHVHYFGTATLSFADGIKAA 296 R G++ W+Q F +G +C+ + L +++ PG + Y G S GI + Sbjct: 205 RAGDLHWEQGFSTGLSCLCYDADELFETLWQHPSLRLPGTLIYLYLGADRNSADAGIHLS 264 Query: 297 PGD 299 GD Sbjct: 265 HGD 267 Lambda K H 0.321 0.141 0.435 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: 320 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 331 Length of database: 290 Length adjustment: 27 Effective length of query: 304 Effective length of database: 263 Effective search space: 79952 Effective search space used: 79952 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: 48 (23.1 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