Align ABC transporter related (characterized, see rationale)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000015985.1:WP_172599875.1 Length = 249 Score = 238 bits (608), Expect = 7e-68 Identities = 125/255 (49%), Positives = 169/255 (66%), Gaps = 11/255 (4%) Query: 1 MNATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETP 60 M + VA+ + ++K +G HVL+ +++ H+G+ I I G SGSGKST +RC+N LE Sbjct: 1 MQVSDEVAIQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEH 60 Query: 61 DDGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGP 120 G + + G EL SD + +D+VRS++GMVFQ+FNL+ H+T+LEN P Sbjct: 61 QSGQIVVDGIELT-----------SDLKNIDKVRSEVGMVFQHFNLFPHLTILENCTLAP 109 Query: 121 MRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDE 180 + V+K + E+ E A L KV + E+ YP LSGGQQQRVAIAR+L M P++MLFDE Sbjct: 110 IWVRKTPKKEAEEVAMHYLKKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDE 169 Query: 181 PTSALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDE 240 PTSALDPE++ EVL M LAEEG TML VTHEMGFA+ V+NRV+F+ QGQ+ P E Sbjct: 170 PTSALDPEMIKEVLDTMIELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGE 229 Query: 241 VFVECKSDRFRQFVS 255 F KS+R + F+S Sbjct: 230 FFRNPKSERTKLFLS 244 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: 181 Number of extensions: 7 Number of successful extensions: 2 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: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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: 47 (22.7 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