Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 350 bits (897), Expect = e-101 Identities = 187/343 (54%), Positives = 241/343 (70%), Gaps = 13/343 (3%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA V L + K YEN AV +L + D EF+V +GPSGC K+TTLRMIAGLE+I+ G+ Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 IYI + VND+ PKDR IAMVFQNYALYPH TV++NMAFGLK++K PKDEI RRV +AA+ Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 L I LL RKP+++SGGQRQRVAVGRAIVR P VFLFDEPLSNLDAKLRV MR ++ +L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 183 HHRLQ-----ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237 H L+ AT+IYVTHDQ EA+T+ D+I V+ G I Q+ TP ++YN P N FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 238 GSPPMNFVNARVVRGEGGLWIQ-ASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKL 296 GSP +N ++ + + L+++ A G ++ +P + L YI+K + FGIRPE I Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHI---- 296 Query: 297 FALAPSPE--NTITGVVDVVEPLGSETILHVKVGDDLIVASVN 337 +LA + NT GV+ VVE +GSE L+ VG ++A V+ Sbjct: 297 -SLASDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVD 338 Lambda K H 0.319 0.138 0.387 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: 385 Number of extensions: 15 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: 369 Length of database: 376 Length adjustment: 30 Effective length of query: 339 Effective length of database: 346 Effective search space: 117294 Effective search space used: 117294 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