Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_022390118.1 NSB1T_RS20210 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000473955.1:WP_022390118.1 Length = 219 Score = 107 bits (266), Expect = 4e-28 Identities = 73/218 (33%), Positives = 110/218 (50%), Gaps = 13/218 (5%) Query: 4 LKLTGVEKAYG----DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 ++L V K + + + L +I L I E + +GPSGCGKSTLL +I L++ T GT Sbjct: 2 IELKSVSKVFQTKDIETRALDDICLKINSSEFVSIMGPSGCGKSTLLNLIGLLDQPTAGT 61 Query: 60 LEIDGTVVNDVPPAQ------RGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAA 113 + I T V+ + + + + VFQ++ L P + V +N+ L + + E Sbjct: 62 ILIHDTDVSRMSDREAARFRNKSLGFVFQNFHLVPSLNVMDNVELPLLYGRVAAVERKER 121 Query: 114 VEAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATR 173 V+ + L + P LSGGQ QRVAI R+IV P++ L DEP NLD+ + Sbjct: 122 VKEVLNMVGLSHRMKHFPSQLSGGQCQRVAIARAIVGHPEIILADEPTGNLDSRMGEEIM 181 Query: 174 LEIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGG 211 + +L E T+V VTHD+ + RIV L G Sbjct: 182 DILLELNEL--GVTVVMVTHDE-HIASKTGRIVRLLDG 216 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: 173 Number of extensions: 15 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: 219 Length adjustment: 26 Effective length of query: 347 Effective length of database: 193 Effective search space: 66971 Effective search space used: 66971 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: 47 (22.7 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