Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_2057 Dsui_2057 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__PS:Dsui_2057 Length = 237 Score = 257 bits (656), Expect = 2e-73 Identities = 127/234 (54%), Positives = 174/234 (74%) Query: 8 VLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67 VLL+V L VAYG I+AVKG+DF + EGE+ +L+G+NGAGK+TT+ A++G + G IE Sbjct: 3 VLLRVHDLAVAYGHIEAVKGLDFHLNEGEITALVGANGAGKSTTLLALSGLIKPTRGKIE 62 Query: 68 YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFT 127 + G+ I A +V+ GLV V EGR + +T+ ENLQ+GAY R+DK GI A +E+++ Sbjct: 63 FQGEDISRLPAHQIVERGLVQVAEGRAILTTLTVEENLQLGAYTRQDKEGIPASMEEVYQ 122 Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187 +FPRL+ER Q AG +SGGEQQMLA+GRALM++PK+LLLDEPSMGL+PI+V +IF ++ + Sbjct: 123 LFPRLKERSQQFAGNLSGGEQQMLAIGRALMAKPKLLLLDEPSMGLAPIVVQEIFRILVE 182 Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 + G+TI+LVEQN +AL IA GYV+E+G I + G LL +PKV AYLG Sbjct: 183 INRRGLTILLVEQNVRQALKIAKHGYVIETGKIVLADSGANLLANPKVEEAYLG 236 Lambda K H 0.317 0.136 0.373 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: 179 Number of extensions: 4 Number of successful extensions: 1 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: 242 Length of database: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 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 (21.7 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