Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q88GX0 (260 letters) >NCBI__GCF_000015985.1:WP_172599875.1 Length = 249 Score = 332 bits (851), Expect = 5e-96 Identities = 161/241 (66%), Positives = 195/241 (80%) Query: 19 VLIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQ 78 V I+I +NK YG+FHVLRD+++ V +GERIV+CGPSGSGKSTLIRCINRLE Q G I Sbjct: 7 VAIQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQSGQIV 66 Query: 79 VDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARM 138 VDGI+L + + +VRS++GMVFQHFNLFPH+++L+NC LAP VR +K+AEE A Sbjct: 67 VDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEEVAMH 126 Query: 139 YLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVL 198 YL KV I QAHKYP QLSGGQQQRVAIAR+LCMKPRIMLFDEPTSALDPEM+ EVLD + Sbjct: 127 YLKKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPTSALDPEMIKEVLDTM 186 Query: 199 VQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQI 258 ++LA GMTMLCVTHEMGFA+ VA RV+F++ GQI+E + P FF P++ER K FL+QI Sbjct: 187 IELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFFRNPKSERTKLFLSQI 246 Query: 259 L 259 L Sbjct: 247 L 247 Lambda K H 0.322 0.137 0.395 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: 234 Number of extensions: 5 Number of successful extensions: 1 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: 260 Length of database: 249 Length adjustment: 24 Effective length of query: 236 Effective length of database: 225 Effective search space: 53100 Effective search space used: 53100 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 (21.9 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