Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_008412392.1 DESHY_RS09800 amino acid ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000315365.1:WP_008412392.1 Length = 240 Score = 154 bits (390), Expect = 2e-42 Identities = 83/234 (35%), Positives = 142/234 (60%), Gaps = 4/234 (1%) Query: 8 DVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLV 67 +++K FG++ +R + L+VK+ E ++++GPSG GK+T LR + LEEP+ G+I I + Sbjct: 6 NIYKNFGQLQVLRGIDLQVKEQEVVVIIGPSGSGKSTFLRCLNLLEEPTSGEIIIDGMCL 65 Query: 68 ADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAF-PLKLRKVPRQEIDQRVREVAEL 126 D K + +++ MVFQ + L+PH T +NI P+K++ + + + R++ Sbjct: 66 TD--KSSDINKIRQNVGMVFQRFNLFPHKTALENITLAPVKVKGLTTEAAAEVARDLLAK 123 Query: 127 LGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQ 186 +GL + + P +LSGGQ+QRVA+ RA+ KP+V L DEP S LD ++ + A +K L Sbjct: 124 VGLQDKESAYPDQLSGGQQQRVAIARALAMKPKVMLFDEPTSALDPEMVGEVLAVMKDLA 183 Query: 187 RQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 R G+T + VTH+ A +GDR+ M+ G + + G+P++++ P N F+ Sbjct: 184 RD-GMTMVVVTHEMGFAREVGDRVLFMDEGRIIEQGTPEQIFGNPQNERTKSFL 236 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: 220 Number of extensions: 12 Number of successful extensions: 4 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: 240 Length adjustment: 27 Effective length of query: 345 Effective length of database: 213 Effective search space: 73485 Effective search space used: 73485 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: 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