Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 152 bits (383), Expect = 1e-41 Identities = 87/250 (34%), Positives = 147/250 (58%), Gaps = 9/250 (3%) Query: 1 MAKIQFSNIKKSFGSADV-LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 M+ ++ S + K + + + L+ L + G + +VG SG GKS+LLR +AGLE +G Sbjct: 1 MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60 Query: 60 ISIDGKKI----NDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVN 115 + + +KI + P +I ++ Q Y LYP+ TV EN+ L L + A + +R Sbjct: 61 VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQK--ERTA 118 Query: 116 EISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLE 175 EI ELL ++ D+KP++LSGGQ+Q+VA+GRALS + V+L DEP S+LDA + + E Sbjct: 119 EILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEE 178 Query: 176 IKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIG 235 +K + + T+I+VTHD +A + + + +++ G + Q G E++ +P + ++A G Sbjct: 179 LKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 Query: 236 SPEMNFLEGA 245 +N + GA Sbjct: 239 --YLNLIPGA 246 Lambda K H 0.318 0.136 0.383 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: 189 Number of extensions: 7 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: 347 Length of database: 318 Length adjustment: 28 Effective length of query: 319 Effective length of database: 290 Effective search space: 92510 Effective search space used: 92510 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 (21.7 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