Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085773913.1 B1812_RS21530 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_002117405.1:WP_085773913.1 Length = 251 Score = 81.6 bits (200), Expect = 1e-20 Identities = 58/194 (29%), Positives = 97/194 (50%), Gaps = 15/194 (7%) Query: 18 IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQPLKGKKSF 77 + A++G+ E+ GE V ++GA+G+GK+T L + G L G I G+ + Sbjct: 33 VPALRGVSFEIERGEFVAIMGASGSGKSTLLNLL-GALDKPTA-GEIVIDGESVSAMGDD 90 Query: 78 ELV---KDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFAVFPRLKE-- 132 EL K+ V + + RMS EN+L+ S + G +DK RL E Sbjct: 91 ELAALRSRKIGFVFQQFNLLPRMSALENVLLPLNYSREVG-----LDKKALALARLAEMG 145 Query: 133 ---RAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRNVSAQ 189 R LSGG+QQ +A+ARAL++ P L+L DEP+ L ++I + + + Sbjct: 146 LEARVHHRPSQLSGGQQQRVAIARALVNGPSLVLADEPTGALDTQTSQEIMRLFSELHVK 205 Query: 190 GITILLVEQNAKLA 203 G+T++++ ++A Sbjct: 206 GLTVIVITHEPEVA 219 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: 144 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: 251 Length adjustment: 24 Effective length of query: 217 Effective length of database: 227 Effective search space: 49259 Effective search space used: 49259 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