Align ABC transporter related (characterized, see rationale)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000166355.1:WP_013403450.1 Length = 343 Score = 169 bits (428), Expect = 7e-47 Identities = 95/253 (37%), Positives = 150/253 (59%), Gaps = 16/253 (6%) Query: 9 LSVKNIHKSFGDHHV----LKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 + +KN+ K + + + L ++L+ +GD+ I+G SG+GKST +RC+N+LE P GS Sbjct: 2 IRIKNLTKIYHSNGIDIKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGS 61 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ 124 + + G E+ KL P++ +++ R ++G++FQ+FNL S TV N + P+ + Sbjct: 62 IEIDGVEMT-------KLSPTELKEM---RKKVGIIFQHFNLLSSRTVKGN-VAFPLEIA 110 Query: 125 KRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSA 184 + + LL VGL K YP+ LSGGQ+QRV IARALA +PKV+L DE TSA Sbjct: 111 GLDKKTIDNRVKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNPKVLLCDEATSA 170 Query: 185 LDPELVGEVLRVMRSLAEE-GRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFV 243 LDPE +L +++ + E G T++VVTHEM + + N+V + +GQ+ G E+F Sbjct: 171 LDPETTLSILNLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFA 230 Query: 244 ECKSDRFRQFVSS 256 K+ + F+ S Sbjct: 231 NPKTKIAQNFLRS 243 Lambda K H 0.318 0.133 0.377 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: 182 Number of extensions: 11 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: 263 Length of database: 343 Length adjustment: 27 Effective length of query: 236 Effective length of database: 316 Effective search space: 74576 Effective search space used: 74576 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 (21.7 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