Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 266 bits (681), Expect = 5e-76 Identities = 146/296 (49%), Positives = 201/296 (67%), Gaps = 8/296 (2%) Query: 1 MADLKLTGVEKAYGDV--KVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGG 58 M+ L+L + K Y V + L I++DI GE ++ VGPSGCGKSTL+ IAGLE IT G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 TLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAA 118 ++ +DG ++ + P R IAMVFQSYALYP M+VREN++F LKI + EID VE A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178 + LQ+ +++ P LSGGQ+QRVA+GR++ R P++YLFDEPLSNLDA LRV R EI + Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSP 238 L + + ++T+VYVTHDQ+EAMTLA RI VL G + Q+G+P E+Y++PEN FVA F+GSP Sbjct: 181 LHQRL-KTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSP 239 Query: 239 KMNLLPGKI-IGTGAQTTVEMTDGGRAVSDYPSDDSL---MGAAVNVGVRPEDMVE 290 M+ +P + G G + GR+V P + L +G V +G+RPE + + Sbjct: 240 AMSFVPVTVEQGEGGLQAEVRGNDGRSVK-LPVPEFLADRVGKKVILGIRPEHITQ 294 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: 404 Number of extensions: 23 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: 373 Length of database: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 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