Align MalF, component of Maltose/trehalose porter (characterized)
to candidate Ac3H11_793 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= TCDB::O51924 (300 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_793 Length = 298 Score = 134 bits (336), Expect = 3e-36 Identities = 82/264 (31%), Positives = 141/264 (53%), Gaps = 3/264 (1%) Query: 23 YLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFWYSTFV 82 + +ILP++ V ILP+M S+ +D+ + FVG + V+ E + + Sbjct: 13 WFLILPVIICVAFSAILPLMTVVNYSV-QDIISPERRVFVGTEWFAAVMRDEELHAALWR 71 Query: 83 TVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSY 142 ++FS +++E LG+ AL + + + +V + +P + W++ Sbjct: 72 QLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQIYGRADI 131 Query: 143 GLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLYEAAL 202 GL +L +G+ ++ G A+ +++ DVW TPL+ LL AGL++IP Y+AA Sbjct: 132 GLMGRMLQEMGIE-YSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQAAR 190 Query: 203 IDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSIS-LLA 261 IDGAS F F+ I LP ++ VL++A++LR +D+ ++ +VLTGGGPG ATT +S L Sbjct: 191 IDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFLSQYLT 250 Query: 262 FNYYNLGDYGIGSAISILTFVLVL 285 D G +A S++ F ++L Sbjct: 251 TKAVGQFDLGPAAAFSLIYFFIIL 274 Lambda K H 0.329 0.145 0.436 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: 264 Number of extensions: 17 Number of successful extensions: 3 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: 300 Length of database: 298 Length adjustment: 27 Effective length of query: 273 Effective length of database: 271 Effective search space: 73983 Effective search space used: 73983 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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