Align MalF, component of Maltose/trehalose porter (characterized)
to candidate AZOBR_RS25885 AZOBR_RS25885 ABC transporter permease
Query= TCDB::O51924 (300 letters) >FitnessBrowser__azobra:AZOBR_RS25885 Length = 294 Score = 135 bits (341), Expect = 9e-37 Identities = 89/282 (31%), Positives = 154/282 (54%), Gaps = 16/282 (5%) Query: 23 YLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFV-GLRNYLRVLSAR-----EF 76 +L++LP+L +V ILP+M S+ TF + F G+ Y +L F Sbjct: 10 WLLVLPVLLIVAFSAILPLMTVVNYSVQD--TFGNNQFFWNGIGWYQELLDPSTDLGGRF 67 Query: 77 WYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWEL 136 + + + + FS + + +E LG++ AL + ++ +P +P + W++ Sbjct: 68 FDALWRNLLFSLLILLIEVPLGIAVALSMPRHGWRVAATLVVLALPLLIPWNVVGTIWQI 127 Query: 137 MYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQD 196 GL W ++ LG+ P N+ P+SA+ IV+ DVW T L+ LL AGL++IP Sbjct: 128 FAREDIGLLGWAVNRLGI-PYNYTADPLSAWVTIVVMDVWHWTSLVALLCYAGLRSIPDA 186 Query: 197 LYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTS 256 Y+AA IDGAS + F++I LP + VL++A++LR +D+ ++ +V+TGGGPG +TT Sbjct: 187 FYQAARIDGASRWAVFRNIQLPKMHRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTF 246 Query: 257 ISL----LAFNYYNLGDYGIGSAISILTFVLVLSFTIVYLKV 294 +S+ LA ++LG +A+SI+ +++L+ V+ V Sbjct: 247 VSIDLVKLALGQFDLGK---AAALSIVYNLIILAVCWVFYTV 285 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: 260 Number of extensions: 20 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: 294 Length adjustment: 26 Effective length of query: 274 Effective length of database: 268 Effective search space: 73432 Effective search space used: 73432 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