Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_012275875.1 SHAL_RS03825 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_000019185.1:WP_012275875.1 Length = 314 Score = 91.7 bits (226), Expect = 2e-23 Identities = 65/192 (33%), Positives = 104/192 (54%), Gaps = 7/192 (3%) Query: 6 LKVQQLSVAY-GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 L + L Y GG++AVKGI L VN+G+ L+G NGAGK+TT+ I+ + S G + Sbjct: 8 LVIDSLKKTYKGGVEAVKGISLTVNKGDFFALLGPNGAGKSTTIGVISSLVQKSA--GKV 65 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIA-ADIDKW 123 + K EL K + +VP+ ++ + ++ A K +A A +K+ Sbjct: 66 SVFEHDID--KELELAKLCIGLVPQEFNFNQFETVLQIVVNQAGYYGVKRDVALARAEKY 123 Query: 124 FAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVI 183 + L E+ A LSGG ++ L +ARALM PKLL+LDEP+ G+ + ++ + Sbjct: 124 LSQLD-LWEKRNSAARELSGGMKRRLMIARALMHEPKLLILDEPTAGVDIELRRSMWTFL 182 Query: 184 RNVSAQGITILL 195 ++AQG+TI+L Sbjct: 183 TELNAQGVTIIL 194 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: 166 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 241 Length of database: 314 Length adjustment: 25 Effective length of query: 216 Effective length of database: 289 Effective search space: 62424 Effective search space used: 62424 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: 47 (22.7 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