Align D-lactate transporter, ATP-binding component (characterized)
to candidate RR42_RS11135 RR42_RS11135 branched-chain amino acid ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Cup4G11:RR42_RS11135 Length = 257 Score = 187 bits (474), Expect = 2e-52 Identities = 97/245 (39%), Positives = 157/245 (64%), Gaps = 4/245 (1%) Query: 4 LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63 LE+ +V K+FG + + VNLS+ + HA+IGPNGAGKST N + G+ P +G+V + Sbjct: 5 LELNDVRKKFGQTEIIRGVNLSIPKGERHALIGPNGAGKSTTFNLISGRFAPSSGTVRLN 64 Query: 64 GKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQR 123 G+ + G P+ IN+MG+SR FQ IF LSV EN+ C ++ + +S R Sbjct: 65 GQEIGGLQPFVINRMGLSRSFQITNIFHRLSVFENLR--CAVLWSLGYKYSFWHRLSELR 122 Query: 124 DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARAD 183 D E+A+ +LE + + + A+ ++ ++R LEIG+ ++ ++LLDEPTAGM+R++ Sbjct: 123 DARERADEVLELIGLQHRHSTQASLLTYAEQRALEIGITIAGGAEVILLDEPTAGMSRSE 182 Query: 184 TNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKVR 243 +++ ++L++++ + T+ ++EHDM VVF LADRI+VL G + D P+ I+ N KV+ Sbjct: 183 SDHAVELIRRVTVGK--TLVMVEHDMSVVFGLADRISVLVYGEVIATDTPEAIRANRKVK 240 Query: 244 EAYLG 248 EAYLG Sbjct: 241 EAYLG 245 Lambda K H 0.318 0.135 0.379 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: 174 Number of extensions: 10 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: 251 Length of database: 257 Length adjustment: 24 Effective length of query: 227 Effective length of database: 233 Effective search space: 52891 Effective search space used: 52891 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: 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