Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Dsui_0841 Dsui_0841 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__PS:Dsui_0841 Length = 251 Score = 223 bits (568), Expect = 3e-63 Identities = 116/240 (48%), Positives = 165/240 (68%), Gaps = 6/240 (2%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L+V L VAYG ++A+ + L + EGE+VT+IG NGAGKTT L A+ G LP G + Sbjct: 10 VLEVSDLCVAYGKVEALHKVSLRIREGEIVTVIGPNGAGKTTLLSALMGLLP---YRGEV 66 Query: 65 EYLGQPLKGKKSFE-LVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKG--QIAADID 121 Y+ L E V L +VPE R +F MS+++NLL+GA+ G A ++ Sbjct: 67 AYVSHNLDAHVEVEERVGQGLTLVPEKRELFAEMSVEDNLLLGAFHRYRSGLRDHAQTME 126 Query: 122 KWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFE 181 + FA+FPRLKER Q AGTLSGGE+QMLAM RALM+ PKLL+LDEPS+GL+P+++++IF Sbjct: 127 EVFALFPRLKERRTQAAGTLSGGERQMLAMGRALMAKPKLLMLDEPSLGLAPLIIKEIFR 186 Query: 182 VIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGEG 241 ++ + G++ILLVEQNA+ AL+ A GYV+E+G ++++G + ++ DDPRV YLG G Sbjct: 187 IVAELKQTGVSILLVEQNARAALQVADYGYVLETGEVSLEGPSHELADDPRVIETYLGLG 246 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: 194 Number of extensions: 7 Number of successful extensions: 3 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 Sep 17 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