Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__PS:Dsui_2059 Length = 287 Score = 153 bits (386), Expect = 6e-42 Identities = 108/329 (32%), Positives = 166/329 (50%), Gaps = 60/329 (18%) Query: 22 LQSFGNAWVRIADLAL---LYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPH 78 ++ F + W + L ++ LLAL + + + GLL L AF VGAY+ AL+ H Sbjct: 1 MEWFNDFWSTYSTLVFSVGVHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTL-H 58 Query: 79 LADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEI 138 L +F + V+ + ++GAP L+L G YLA+ TL FGE+ Sbjct: 59 LEWSFGS---------------VLLAGGIAPTLVALIIGAPVLRLSGVYLAMATLAFGEV 103 Query: 139 IRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVV 198 +RI + NL+ +T GP+GL I L G+ I +++ Sbjct: 104 VRITVLNLE----ITGGPEGLNGIP------------LATEGWHI----------ALILA 137 Query: 199 VSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAF 258 V+V RL+ S++GRA+ AI+EDE+AA+ MGIN KLLAF +GA GV+GA+ F Sbjct: 138 VAVYGLARLRRSKVGRAFEAIKEDEVAARLMGINVDRYKLLAFSLGAFIAGVAGALNAHF 197 Query: 259 QGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGR 318 F+SP + +V I+ M VLGG + G +LG+ +L+ LPE+LR + Sbjct: 198 TFFISPREYGFENAVDILTMAVLGGTSSLIGPMLGSSILTLLPELLRSLQD--------- 248 Query: 319 LDSAILRQLLIALAMIIIMLLRPRGLWPS 347 R L+ +++++L P+GLW S Sbjct: 249 -----FRSLVNGAVLVLVVLFLPKGLWES 272 Lambda K H 0.328 0.144 0.430 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: 246 Number of extensions: 13 Number of successful extensions: 4 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: 358 Length of database: 287 Length adjustment: 28 Effective length of query: 330 Effective length of database: 259 Effective search space: 85470 Effective search space used: 85470 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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