Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 350 bits (898), Expect = e-101 Identities = 189/355 (53%), Positives = 250/355 (70%), Gaps = 11/355 (3%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 M+ + ++ K + ++ G+DL + D EF VFVGPSGCGKSTLLR+IAGLEE SEG+I Sbjct: 1 MSGITLRGAVKRYGETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 + RD+T + P++R +AMVFQTYALYPHM+V +NM F L + GV K +++KV+ A+ I Sbjct: 61 HIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L+L L RKPK LSGGQRQRVAIGRAIVR P++FLFDEPLSNLDA LRV+MR+E+ARLH Sbjct: 121 LKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 KE+ ATMIYVTHDQVEAMTLADK+VVL +GR+EQVG+PLELY P N+FVAGF+G+P M Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMN 240 Query: 241 FLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTV 300 FL G R+E+ + + AG L LP+ GA G VT+G+RP+H+ + G L Sbjct: 241 FLDG---RIENDAVHL---AG-LPPLPVPGAAGRSG-PVTVGVRPQHIALEPGGDGYL-- 290 Query: 301 TADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTD 355 ++ E LG ++ ++ A+G LT+ + G + L L P LF+ + Sbjct: 291 -VELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFEAE 344 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: 412 Number of extensions: 14 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: 367 Length of database: 351 Length adjustment: 29 Effective length of query: 338 Effective length of database: 322 Effective search space: 108836 Effective search space used: 108836 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