Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 335 bits (859), Expect = 1e-96 Identities = 194/369 (52%), Positives = 244/369 (66%), Gaps = 14/369 (3%) Query: 1 MADLKLTGVEKAYGD-VKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA + L GV+KAYGD V+ +++L+I + E VF+GPSGCGKSTLLRMIAGLE +T G Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 L I G V+NDVP AQRG+AMVFQSYAL+PHMTV ENM+F LK+AK + EID V AA Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 LQL L+R PKALSGGQRQRVAIGR+IVR P V+LFDEPLSNLDA LR TR+EIA+L Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVL-AG------GGIAQVGSPLELYEKPENEFVA 232 + ++++VYVTHDQ+EAMTLA +IV+L AG G IAQ+G+PLELY +P + FVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 233 QFIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLM--GAAVNVGVRPEDMVE 290 FIGSP+MN LPG+I AQ V D P+D + + AV +GVRPE + Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300 Query: 291 A---APGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAE 347 A + D V V++ E LGE + ++ + P G I K G + G L Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGV-ALIAKAPGDTRLAPGDRANLRVP 359 Query: 348 PAKVHVFKD 356 H+F + Sbjct: 360 RHATHLFTE 368 Lambda K H 0.316 0.135 0.379 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: 449 Number of extensions: 25 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: 373 Length of database: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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