Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_049992151.1 LT39_RS19510 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000784335.1:WP_049992151.1 Length = 395 Score = 264 bits (675), Expect = 3e-75 Identities = 160/385 (41%), Positives = 225/385 (58%), Gaps = 28/385 (7%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MA +KL + K Y DV + +++++I+ GE + FVGPSGCGKST + +AGL + T G + Sbjct: 1 MARVKLENITKRYDDVTAVDDVSMEIEDGEFVTFVGPSGCGKSTTMETVAGLTQPTEGQV 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 I V ++ P RG+AMVFQ+ AL+PHM V EN+SF L++ K EI VE AA+ Sbjct: 61 YIGNDDVTNLAPKDRGVAMVFQNIALFPHMNVFENISFGLRLRKYDDEEIQRRVEQAADI 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 +QL LDR+P +SGGQRQRVAI R+IVR+P V+L DEPL+NLDA LRV R E+ +L Sbjct: 121 VQLEGMLDRMPDEMSGGQRQRVAIARAIVRNPDVFLMDEPLANLDAKLRVHMRTELQRLH 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + + ++T++YVTHDQ EAMT++ RI VL G + Q+ PL Y +P N FVA FIGSP M Sbjct: 181 KEL-DTTIIYVTHDQAEAMTMSNRIAVLNKGRLQQLAPPLVCYNEPANLFVAGFIGSPSM 239 Query: 241 NLLPGKIIGTGAQT---TVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM-----VEAA 292 N + G+++ G +T TVE + P D +G AV +GVRPED+ ++ Sbjct: 240 NFVEGELVENGLETNNFTVEFDP-----THVP--DVSVGDAVTLGVRPEDVHLVQYADSL 292 Query: 293 PGGDYVFEGKVAITEALGE---VTLLYFEAPSG---EDPTIGK---LQGIHKDL---KGQ 340 + + + E +G+ V LL EA G EDP L + D Q Sbjct: 293 SSPTDPIDAQTDVIEPMGDEVFVYLLLSEAAVGSMEEDPATSPNQLLMSVTPDTDIEADQ 352 Query: 341 VTRLTAEPAKVHVFKDGVSLHYPHG 365 + + +K+H+F HG Sbjct: 353 SVNVVLDRSKIHLFDTASGDALVHG 377 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: 368 Number of extensions: 16 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: 373 Length of database: 395 Length adjustment: 30 Effective length of query: 343 Effective length of database: 365 Effective search space: 125195 Effective search space used: 125195 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 24 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