Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_028950337.1 Q385_RS0103490 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000619805.1:WP_028950337.1 Length = 225 Score = 104 bits (259), Expect = 3e-27 Identities = 67/204 (32%), Positives = 103/204 (50%), Gaps = 13/204 (6%) Query: 1 MADLKLTGVEKAYG----DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKIT 56 M+ + L V+K Y +V L I+L ++ G++I +GPSG GKSTLL +I G++ T Sbjct: 1 MSSVLLENVKKVYKNAQEEVWALKGISLKVENGQMIAVMGPSGSGKSTLLHIIGGIDYPT 60 Query: 57 GGTLEIDGTVVNDVPPAQ------RGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEI 110 G + I+G +N++ Q I VFQ + L P T EN+ ++I K + + Sbjct: 61 EGKVLINGLQINNLNDKQLSKFRNENIGFVFQFHYLLPEFTALENVMIPMEI--KGEKNV 118 Query: 111 DAAVEAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRV 170 K L L+ P LSGG++QRVAI R++ P + + DEP NLD+ Sbjct: 119 KEKAIEILTKFNLQHRLNHKPPQLSGGEQQRVAIARAVANQPSLLIADEPTGNLDSQNAK 178 Query: 171 ATRLEIAQLKEAMPESTMVYVTHD 194 + +L E T++ THD Sbjct: 179 NVIMLFKELNE-KKGMTIIIATHD 201 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: 186 Number of extensions: 9 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: 225 Length adjustment: 26 Effective length of query: 347 Effective length of database: 199 Effective search space: 69053 Effective search space used: 69053 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 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