Align 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) (characterized)
to candidate Pf6N2E2_1679 SUGAR TRANSPORTER
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3317 (330 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1679 Length = 259 Score = 83.2 bits (204), Expect = 6e-21 Identities = 56/184 (30%), Positives = 83/184 (45%), Gaps = 2/184 (1%) Query: 132 AGVQPEWFYKGDGGIVVRPGQPFPLPPFAEDAGEEPEIAGLYVIGHDGKPYRLGFAVGNE 191 A + W+YKG+G ++ G P +P ++ EP I LY + G +GF +GN+ Sbjct: 46 AKTEQAWYYKGNGRLLKTDGDPLQVPYHSQSISSEPCIVCLYWVDPFGALRFIGFTLGND 105 Query: 192 FSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRILRDGEVLWQNEFLSGEA 251 DHV+ ++ + H+ LR+C+ P L VGEL LA +I RDG+ L + Sbjct: 106 IHDHVLHSRDAISSTHAHLRTCAIAPALIVGELQADLAINVQIERDGQPLTASHHRMSLH 165 Query: 252 NMCHSLANLEFHHFKYSQFLRPGDVHIHFFGTATLSFADGIRTQPGDVFEITQAEFGAPL 311 E K+ QFL PG VH F + + + Q GD I E + Sbjct: 166 RWQSLRRYSEEFLEKHEQFLEPGLVHYVFHSLSHRT--ANVPLQHGDWLSIDCPELELAM 223 Query: 312 INGI 315 N I Sbjct: 224 SNQI 227 Lambda K H 0.319 0.138 0.415 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: 222 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 330 Length of database: 259 Length adjustment: 26 Effective length of query: 304 Effective length of database: 233 Effective search space: 70832 Effective search space used: 70832 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 (21.7 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