Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__Koxy:BWI76_RS01840 Length = 369 Score = 377 bits (967), Expect = e-109 Identities = 196/362 (54%), Positives = 255/362 (70%), Gaps = 1/362 (0%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA+++++N+ K + + K I+LE+ D EFVVFVGPSGCGKSTLLR+IAGLE V+ G + Sbjct: 1 MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 + + +V PA+R + MVFQ+YALYPH+SV +NMSF L LAG K+L+ +V++ A + Sbjct: 61 LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L+L LLERKPK LSGGQRQRVAIGR +V P++FL DEPLSNLDAALRVQMR+E++RLH Sbjct: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 K L TMIYVTHDQVEAMTLADK+VVL++GR+ QVG PLELYH PA+ FVAGF+G+PKM Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 FLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTV 300 FL KVT + +V+L + LP+ A + VG+ ++LGIRPEHL + TL Sbjct: 241 FLPVKVTATAIEQVQVELPNRQQVWLPVDSARVQVGANMSLGIRPEHLLPSDIADVTLEG 300 Query: 301 TADVGERLGSDTFCHV-ITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359 V E+LG +T H+ I + + L R + + G T + L P CHLF DG A Sbjct: 301 EVQVVEQLGHETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTAC 360 Query: 360 AR 361 R Sbjct: 361 RR 362 Lambda K H 0.319 0.136 0.384 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: 413 Number of extensions: 15 Number of successful extensions: 2 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: 367 Length of database: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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: 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