Align D-lactate transporter, ATP-binding component (characterized)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Length = 290 Score = 155 bits (393), Expect = 7e-43 Identities = 91/247 (36%), Positives = 144/247 (58%), Gaps = 7/247 (2%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 IL ++++ F G +AL+++NL + + IIGPNGAGK+TL++ + GK P G F Sbjct: 49 ILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 108 Query: 63 -DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSG 121 + + + +I Q GI R FQ P +F LSV EN+ + K D + + + +SG Sbjct: 109 GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVWASLRARLSG 166 Query: 122 QRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMAR 181 ++ ++ +L+ + + + A +S G K+ LEIGM L Q+P+LLLLDEP AGM Sbjct: 167 EQK--DRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVAGMTD 224 Query: 182 ADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPK 241 A+T T +L K + + ++ ++EHDM V S+AD +TVL QG+ L E + ++ N + Sbjct: 225 AETEFTAELFKSLAGKH--SLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQDNER 282 Query: 242 VREAYLG 248 V E YLG Sbjct: 283 VIEVYLG 289 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: 203 Number of extensions: 8 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: 251 Length of database: 290 Length adjustment: 25 Effective length of query: 226 Effective length of database: 265 Effective search space: 59890 Effective search space used: 59890 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