Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Burk376:H281DRAFT_03749 Length = 360 Score = 351 bits (901), Expect = e-101 Identities = 189/358 (52%), Positives = 241/358 (67%), Gaps = 8/358 (2%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M + L I K YG V+HGIDL I +GEFVV VGPSGCGKSTL+RM+AGLEEI+GGD+ Sbjct: 1 MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I G R N++ P +R I+MVFQSYALYPH++VY+N+AFG RI +ES R+ AA M Sbjct: 61 MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L L YLDRLP+ALSGGQRQRVA+GRA+ R P +FLFDEPLSNLDA LRV R EI L Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 +R+ + T+IYVTHDQ+EAMT+ADRIVV++AG IEQ+G PLELY+ PANLFVA F+GSP+M Sbjct: 181 QRLKN-TVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSM 239 Query: 241 NVIPATIT--ATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLR-VTEADDFL 297 N + G A+ LA G + L+ ++ G + GVRPE + +T+ D Sbjct: 240 NFAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTPDVT 299 Query: 298 FEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDT 355 + V +VE G T LY G + + ++V G++V A +HLFDT Sbjct: 300 MQ--VEVVEPTGAETHLY--GKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDT 353 Lambda K H 0.320 0.137 0.387 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: 382 Number of extensions: 15 Number of successful extensions: 4 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: 362 Length of database: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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