Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_087412571.1 BUB52_RS05180 phosphate ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_900129655.1:WP_087412571.1 Length = 250 Score = 93.2 bits (230), Expect = 4e-24 Identities = 72/238 (30%), Positives = 122/238 (51%), Gaps = 13/238 (5%) Query: 4 NILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAIT---GTLPASRV 60 N ++ + ++ YG A+KGI +++ E +V IG +G GK+T L+ + +P +R+ Sbjct: 2 NKIETRDVNFWYGDFHALKGISMDIAEKSVVAFIGPSGCGKSTFLRLLNRMNDLIPDTRL 61 Query: 61 EGHIEYLGQPL--KGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSD--DKGQI 116 G I GQ + KG + EL K+ + MV + F + SI EN+ G + D I Sbjct: 62 TGEILIDGQDIYKKGVQVDELRKN-VGMVFQRPNPFPK-SIFENVAYGLRVNGVTDNAFI 119 Query: 117 AADID---KWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSP 173 ++ K A++ +K++ A LSGG+QQ L +ARA+ P +LL+DEP+ L P Sbjct: 120 RRRVEETLKGAALWDEVKDKLKVSAYALSGGQQQRLCIARAMAVSPSVLLMDEPASALDP 179 Query: 174 IMVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDP 231 I K+ E+I + Q TI++V N + A + G + G +++ +P Sbjct: 180 ISTAKVEELIHELKKQ-YTIVIVTHNMQQAARVSDSTAFFYMGEMVEFGDTKKIFTNP 236 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: 112 Number of extensions: 6 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: 250 Length adjustment: 24 Effective length of query: 217 Effective length of database: 226 Effective search space: 49042 Effective search space used: 49042 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 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