Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000009985.1:WP_011384263.1 Length = 273 Score = 131 bits (330), Expect = 2e-35 Identities = 88/252 (34%), Positives = 135/252 (53%), Gaps = 8/252 (3%) Query: 12 AYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVP 71 ++G + + +L+I+ GE + +GPSGCGKST L +AG + G + +DG V P Sbjct: 25 SFGAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVDGVEVTG-P 83 Query: 72 PAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLP 131 +RG MVFQ ++L+P TV EN++F ++ K++AE + + LG R P Sbjct: 84 GPERG--MVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGLGGSAQRYP 141 Query: 132 KALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYV 191 ALSGG QRV I R++V P V L DEP LDA R + + +L + +T+++V Sbjct: 142 AALSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQI-GNTVLFV 200 Query: 192 THDQVEAMTLATRIVVL-AGGGIAQVGSPLEL-YEKPENEFVAQFIGSPKMNLLPGKIIG 249 THD EA+ LA R+VV+ A G + L+L +PE+ F K L ++I Sbjct: 201 THDIDEALFLADRVVVMSAAPGRVLLDLRLDLPRPRPEDVFATPQFAEHKRQCL--RLIR 258 Query: 250 TGAQTTVEMTDG 261 ++ + DG Sbjct: 259 QESRRAFDFIDG 270 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: 253 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: 373 Length of database: 273 Length adjustment: 28 Effective length of query: 345 Effective length of database: 245 Effective search space: 84525 Effective search space used: 84525 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: 48 (23.1 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