Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 3608115 Dshi_1520 ABC transporter related (RefSeq)
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__Dino:3608115 Length = 277 Score = 202 bits (514), Expect = 5e-57 Identities = 98/217 (45%), Positives = 148/217 (68%), Gaps = 1/217 (0%) Query: 17 LHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYMGEELVGQDSSHIMRK 76 LH + V +GEI ++G NGAGKST + + G H+GS+R GE++ G + K Sbjct: 62 LHDCTLAVDRGEIAVIVGPNGAGKSTAMKAVFGMLNIHTGSVRLDGEDITGLSPQARVAK 121 Query: 77 SIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLFPRLKERFTQRGGTMSG 136 +A VP+ +F +TVEENL MG F + D E M++V LFP L+E+ Q G +SG Sbjct: 122 GMAFVPQVNNIFTTMTVEENLEMGAFLR-RDDISETMEQVYELFPILREKRRQAAGELSG 180 Query: 137 GEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLRKDGVTVFLVEQNANQA 196 G++Q +A+GRALM++P++L+LDEP+ G++PI++ ++FD I ++ + G+++ +VEQNA QA Sbjct: 181 GQRQQVAVGRALMTRPQVLMLDEPTAGVSPIVMDELFDRIIEVARTGISILMVEQNARQA 240 Query: 197 LKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLGG 233 L+IAD+ YVL GR TG+ALL DP VR+++LGG Sbjct: 241 LEIADKGYVLVQGRNRYTDTGQALLADPDVRKSFLGG 277 Lambda K H 0.320 0.137 0.381 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: 202 Number of extensions: 9 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: 233 Length of database: 277 Length adjustment: 24 Effective length of query: 209 Effective length of database: 253 Effective search space: 52877 Effective search space used: 52877 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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