Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Burk376:H281DRAFT_01057 Length = 517 Score = 306 bits (785), Expect = 9e-88 Identities = 188/504 (37%), Positives = 281/504 (55%), Gaps = 11/504 (2%) Query: 1 MNGQMSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSIL 60 MNG S+ ++E + +TK F +L+ VS+ V GE HALVG NGAGKSTL I+ Sbjct: 1 MNGHAD--ISAGDLLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIM 58 Query: 61 TGLRKPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQP-LRG 119 G+ PD+GE+RF+G + DA R + ++Q + +VAEN+F +P R Sbjct: 59 AGVYAPDSGEIRFAGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRI 118 Query: 120 GVIDWQAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTA 179 GV+D M RDA+ALL + + R G+LSV +Q+VEIA+A++ R +ILDEPTA Sbjct: 119 GVLDHGRMNRDAQALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTA 178 Query: 180 QLDGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPR 239 + G E++ LF R+ L+ +GV ++ISH L E++E+C VTV++D R + + V+ R Sbjct: 179 VIAGKEVQLLFARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTR 238 Query: 240 EQLIEAMTGERGGLAVADAAARGALPADTAVALELKEL-TGADYEGVSFTVKRGEVVGLT 298 +QL+ M G D + L LE+ L G S TV+ GE+VG+ Sbjct: 239 DQLVRLMVGREMKDIYPD---KPILAPGVPNVLEVNGLCVGNRVVDASLTVRAGEIVGIA 295 Query: 299 GATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLT 358 G SGRT +A I G A RGT+ + G ++ G+G V +DR +GL++ Sbjct: 296 GMVGSGRTELAAGIFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLML 355 Query: 359 QSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVV 418 VA+N + T + +FG+ PA + A Q I+ I P V+ LSGGNQQKV+ Sbjct: 356 LDVAQNVTATTLAQVSRFGLMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVL 415 Query: 419 MARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRV 477 ++R + VL+L +PT GVDV +K + V+ + G +L++S EL + + DRV Sbjct: 416 ISRWVRVCKRVLILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRV 475 Query: 478 LVMFRGRVAAEFPAGWQ--DHDLI 499 LVM GR+ E +G Q +HD++ Sbjct: 476 LVMREGRINGEV-SGEQMTEHDIM 498 Lambda K H 0.318 0.134 0.377 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: 626 Number of extensions: 34 Number of successful extensions: 8 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: 510 Length of database: 517 Length adjustment: 35 Effective length of query: 475 Effective length of database: 482 Effective search space: 228950 Effective search space used: 228950 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: 52 (24.6 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