Align Maltose/maltodextrin 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::P19566 (369 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 151 bits (381), Expect = 3e-41 Identities = 102/320 (31%), Positives = 173/320 (54%), Gaps = 35/320 (10%) Query: 1 MASVQLRNVTKAW-GDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59 M+ +++ V+K + + +D +L + G V VG SG GKS+LLR+IAGLE ++G Sbjct: 1 MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60 Query: 60 LFIGETRM----NDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVN 115 + +G+ ++ + P + ++ Q Y LYP+ +V EN++ L L K +R Sbjct: 61 VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYD--KAYQKERTA 118 Query: 116 QVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIE 175 ++ E+L L ++KP+ LSGGQ+Q+VAIGR L EP V LLDEP S+LDA + + E Sbjct: 119 EILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEE 178 Query: 176 ISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIG 235 + + L T+I+VTHD +A+ ++++++++ G++ Q G E++ PA +VA G Sbjct: 179 LKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 Query: 236 SPKMNFLP-----------VKVT------ATAIEQ--------VQVELPNRQQIW-LPVE 269 +N +P VK+T A ++Q + V+L + + W + Sbjct: 239 --YLNLIPGAEEAYVRPSEVKITSKTSIKAEVVKQQFLIHYNLLTVKLEDSELFWKVDDP 296 Query: 270 SRGVQVGANMSLGIRPEHLL 289 SR V VG + L + E L+ Sbjct: 297 SRSVNVGDEVFLDYQKEQLI 316 Lambda K H 0.321 0.138 0.396 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: 199 Number of extensions: 6 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: 369 Length of database: 318 Length adjustment: 29 Effective length of query: 340 Effective length of database: 289 Effective search space: 98260 Effective search space used: 98260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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