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 WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_002899945.2:WP_103234822.1 Length = 416 Score = 171 bits (433), Expect = 3e-47 Identities = 97/281 (34%), Positives = 163/281 (58%), Gaps = 21/281 (7%) Query: 20 VAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVND------V 73 + + A+ + + EF V++G SG GK+T LR + L E T GK+YI+ + + Sbjct: 49 IGINKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKNNKELL 108 Query: 74 EPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRK 133 E + +++MVFQ + L PH T+ +N FGL++R K + + ++A I+G+ ++ Sbjct: 109 EVRRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFENQY 168 Query: 134 PRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYV 193 P QLSGG +QRV + RA+ +P+V L DE S LD ++ +M+ ++ +L + LQ TI+++ Sbjct: 169 PSQLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQKTIVFI 228 Query: 194 THDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGF---------IGSPPMNF 244 THD EA+ + D+IV+MKDG I+QIGT +I +PA+ +V F I + + F Sbjct: 229 THDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVDRKTIITARSLMF 288 Query: 245 VNARVVR-----GEGGL-WIQASGFKVKVPKEFEDKLANYI 279 A VVR EG L ++A+G + +F++K ++ Sbjct: 289 DKATVVRFRKDGPEGALRKMRATGLENLPVVDFQNKFLGFV 329 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: 349 Number of extensions: 14 Number of successful extensions: 2 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: 416 Length adjustment: 31 Effective length of query: 338 Effective length of database: 385 Effective search space: 130130 Effective search space used: 130130 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 24 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