Align D-lactate transporter, ATP-binding component (characterized)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__PV4:5210167 Length = 265 Score = 148 bits (373), Expect = 1e-40 Identities = 85/254 (33%), Positives = 142/254 (55%), Gaps = 12/254 (4%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 IL V + FGG++AL+DV+ V V +IIGPNGAGK+++LN + G+ P G++ F Sbjct: 5 ILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTIHF 64 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAIS----- 117 D + V P +GI R FQ +FG +SVL+N+M+ R + N ++ Sbjct: 65 DNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMV----GRHHLMKNNWLTGPLYW 120 Query: 118 AVSGQRDIL---EKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDE 174 A Q++ L + E +++ ++++ R A ++S G ++R+E+ ++ P+L+LLDE Sbjct: 121 ASPAQKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDE 180 Query: 175 PTAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQ 234 P AGM + + + + E IT+ +IEHDM VV ++ + VL G L+ P+ Sbjct: 181 PMAGMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPE 240 Query: 235 NIKGNPKVREAYLG 248 + + VR+AYLG Sbjct: 241 AVMADEHVRQAYLG 254 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: 182 Number of extensions: 15 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: 251 Length of database: 265 Length adjustment: 24 Effective length of query: 227 Effective length of database: 241 Effective search space: 54707 Effective search space used: 54707 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