Align D-lactate transporter, ATP-binding component (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 117 bits (294), Expect = 4e-31 Identities = 70/223 (31%), Positives = 115/223 (51%), Gaps = 8/223 (3%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 +L+ + +GKRFG AL V+L++R VHA++G NGAGKSTL+ L G PD GSV Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 DG+ + P E + GI V+Q + +LSV EN+ G + + Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYA-------GRYPRRRRLRMIDW 124 Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182 R + + A +L ++++ S ++ + I L R+L+LDEPT+ + Sbjct: 125 RQVRDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEG 184 Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225 + ++ Q++ ER + I + H + V++++DRITVL G Sbjct: 185 EVRELFRVIAQLR-ERGMAILFVTHFLDQVYAVSDRITVLRDG 226 Score = 47.0 bits (110), Expect = 8e-10 Identities = 50/212 (23%), Positives = 98/212 (46%), Gaps = 17/212 (8%) Query: 19 LSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFDGKSVLGRAPYEINQM 78 L V+L VR + + G G+G++ L L G + G + G+ V + P + Sbjct: 282 LHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVR 341 Query: 79 GIS---RVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQRDILEKAEHMLEE 135 G++ +T I +LSV EN+++ A++ A ++D E A +++ Sbjct: 342 GLALCPEERKTDGIVAELSVRENIVLALQARQGWRGMSRA------RQD--ELARQLVQA 393 Query: 136 MNM-ADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARADTNNTIDLLKQI 194 + + A +S G+++++ + L EPRLL+LDEPT G+ D +L+ ++ Sbjct: 394 LGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGI---DVAAKQELMAEV 450 Query: 195 --KSERDITIAIIEHDMHVVFSLADRITVLAQ 224 ++ + + I + + DRI V+ + Sbjct: 451 TRRAHAGMAVLFISAETGELTRWCDRIAVMRE 482 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: 284 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 505 Length adjustment: 29 Effective length of query: 222 Effective length of database: 476 Effective search space: 105672 Effective search space used: 105672 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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