Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_0626 Dsui_0626 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__PS:Dsui_0626 Length = 238 Score = 292 bits (748), Expect = 4e-84 Identities = 146/234 (62%), Positives = 188/234 (80%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 LL V+GL++AYGGIQAVKG+ F V GE V+LIG+NGAGKT+T+KA+ L G++ Y Sbjct: 5 LLIVEGLRIAYGGIQAVKGITFHVDPGETVALIGANGAGKTSTLKALARQLDAAGGSVRY 64 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 G+ I +LV +G+ +VPEGRGVFAR+T+TENL+MGAY R DKA I D+E++F + Sbjct: 65 QGREISALAPHELVGQGIALVPEGRGVFARLTVTENLEMGAYCRHDKAEIADDLERIFAL 124 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 PRL+ER QLAGT+SGGEQQMLAMGRALMS+P++LLLDEPSMGL+PIMV K+FEVV++V Sbjct: 125 LPRLKERHGQLAGTLSGGEQQMLAMGRALMSRPRLLLLDEPSMGLAPIMVQKVFEVVQEV 184 Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242 + G+TI+LVEQNA AL ++ RGYVMESG IT+T LL++P+V+AAYLGE Sbjct: 185 ASQGMTILLVEQNARLALQVSRRGYVMESGDITLTDAAGTLLDNPRVKAAYLGE 238 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: 204 Number of extensions: 1 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: 238 Length adjustment: 23 Effective length of query: 219 Effective length of database: 215 Effective search space: 47085 Effective search space used: 47085 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