Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 145 bits (367), Expect = 1e-39 Identities = 88/236 (37%), Positives = 134/236 (56%), Gaps = 5/236 (2%) Query: 8 DVWKVF--GEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYI-GD 64 DV K + G A+ +SL VK GE ++G SG GK+T +R+I GLE PS GQ+ + GD Sbjct: 6 DVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGD 65 Query: 65 KLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVA 124 + A G+ R + M+FQ + L TV N+AFPLKL P E+ R E+ Sbjct: 66 DVAALGVAGLRA--LRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAELL 123 Query: 125 ELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKK 184 E +GL+ + P +LSGGQ+QRV + RA+ P+V L DE S LD + ++ + Sbjct: 124 ERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLIAG 183 Query: 185 LQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 L R+LG+T + +TH+ + DR+AV++ G + + G+ +EV+ PA+ F+ Sbjct: 184 LNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239 Lambda K H 0.323 0.142 0.406 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: 270 Number of extensions: 12 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: 372 Length of database: 332 Length adjustment: 29 Effective length of query: 343 Effective length of database: 303 Effective search space: 103929 Effective search space used: 103929 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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