Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 172 bits (437), Expect = 9e-48 Identities = 96/224 (42%), Positives = 148/224 (66%), Gaps = 4/224 (1%) Query: 18 AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVP 77 A+ + SL+VK G + ++G SG GK++ LR+IAGLE S G +++GD+ + +P + + VP Sbjct: 19 ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKL-VP 77 Query: 78 PKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLNRKP 137 D +I ++ Q Y LYP+ TV +NIA PL L Q+ +R E+ ELL L ++KP Sbjct: 78 GYD-EIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQK--ERTAEILELLSLRAFKDKKP 134 Query: 138 RELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVT 197 R+LSGGQ+Q+VA+GRA+ +P+V L+DEP S+LDA + + ELK++ L VT I+VT Sbjct: 135 RQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVTVIFVT 194 Query: 198 HDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIG 241 HD +A+ M + + ++ +G L Q G+ EV+ KPA+ +VA G Sbjct: 195 HDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 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: 274 Number of extensions: 18 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: 372 Length of database: 318 Length adjustment: 29 Effective length of query: 343 Effective length of database: 289 Effective search space: 99127 Effective search space used: 99127 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