Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 132 bits (331), Expect = 2e-35 Identities = 80/240 (33%), Positives = 138/240 (57%), Gaps = 7/240 (2%) Query: 1 MTSVSVRDLSLNFGAVTV-LDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 M+ + V ++S + A ++ L+ +L + G + ++G SG GKS+LL IAGL S G Sbjct: 1 MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60 Query: 60 IFIKDRNVTWEE----PKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVK 115 + + D+ + P I ++ Q Y LYP TVE+N++ L + A ++R Sbjct: 61 VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERTA 118 Query: 116 RASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVE 175 E+L ++ +KP +LSGGQ+Q+VAIGRAL + +V L DEP S+LDA + +L E Sbjct: 119 EILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEE 178 Query: 176 IKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIG 235 +K + +L+ T+I+VTHD +AL +++ + +++ G + Q + ++ P + +VA G Sbjct: 179 LKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 Lambda K H 0.320 0.137 0.392 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: 246 Number of extensions: 12 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: 361 Length of database: 318 Length adjustment: 28 Effective length of query: 333 Effective length of database: 290 Effective search space: 96570 Effective search space used: 96570 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 Apr 09 2024. 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