Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 328 bits (840), Expect = 2e-94 Identities = 191/383 (49%), Positives = 248/383 (64%), Gaps = 23/383 (6%) Query: 1 MAKVRLEHVWKRF-GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59 MA + L + K F G ++D NLE + EF VF+GPSGCGK+T LR++AGLE+ ++G+ Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 60 IYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR 119 + IG R +N VP +R +AMVFQ+YAL+PHM VYENMAFGL+L R PK EIDR+V+EAA Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179 +L+++ LL RKPRELSGGQRQRVA+GRAIVREP VFL DEPLSNLDA LR + R EIA+L Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 180 -QRRLGVTTIYVTHDQVEAMTLGHRIVVM-------KDGEIQQVDTPLNLYDFPANRFVA 231 QR + +YVTHDQ+EAMTL +IV++ + G I Q+ PL LY P ++FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 232 GFIGSPSMNFVRAGVE-VQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLG 290 GFIGSP MNF+ VE + + V + PG +R V G LKP G+ V LG+RPEH+ Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSMPGTALRV-LVDGRRLKP--GQRVTLGIRPEHVR 297 Query: 291 LKGYTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLAD 350 G T L + E LG + +H G L+AK G V+ G+++ L Sbjct: 298 FDGGT------QTLAVNALLTEQLGEHSYLHADHAGGTLIAKAPGDLHVRNGERLALHLP 351 Query: 351 TQRLHAFD---LETDRTI-GHAQ 369 H FD + RTI G+AQ Sbjct: 352 ADACHLFDEDGIALHRTIVGNAQ 374 Lambda K H 0.320 0.139 0.400 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: 428 Number of extensions: 18 Number of successful extensions: 5 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: 376 Length of database: 381 Length adjustment: 30 Effective length of query: 346 Effective length of database: 351 Effective search space: 121446 Effective search space used: 121446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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