Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085771991.1 B1812_RS13095 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_002117405.1:WP_085771991.1 Length = 252 Score = 82.8 bits (203), Expect = 6e-21 Identities = 67/226 (29%), Positives = 110/226 (48%), Gaps = 11/226 (4%) Query: 6 LKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIE 65 L ++ L +YGG V +D E+ +G + L+G NGAGKTTT+ + G + S G I Sbjct: 10 LSLRGLCKSYGGKLVVGPLDFELEKGAVTALLGGNGAGKTTTIGMVMGLIQPS--SGSIH 67 Query: 66 YLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGA--YTSDDKGQIAADIDKW 123 LG + + E V ++ + R+S++ENL + A Y D + A + K Sbjct: 68 ALGADMATNR--ESVLGRMNFESPYVDLPHRLSVRENLRVFAMLYGVADAKEKIARLAKD 125 Query: 124 FAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVI 183 FA L++ + G LS G++ +A+A+AL++ P+LLLLDEP+ L P + + + Sbjct: 126 FA----LEDFLDRPNGRLSAGQKTRVALAKALINDPELLLLDEPTASLDPDTADWVRARL 181 Query: 184 RNV-SAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQML 228 TILL N R ++ G++ G+ +L Sbjct: 182 ETQREKHDCTILLASHNMGEVERLCDRVLMLRKGVLVDDGKPAALL 227 Lambda K H 0.317 0.134 0.365 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: 132 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: 241 Length of database: 252 Length adjustment: 24 Effective length of query: 217 Effective length of database: 228 Effective search space: 49476 Effective search space used: 49476 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 (21.6 bits) S2: 46 (22.3 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