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 350388 BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Btheta:350388 Length = 224 Score = 133 bits (334), Expect = 5e-36 Identities = 79/214 (36%), Positives = 122/214 (57%), Gaps = 8/214 (3%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 L+ + K E + A+ N ++ V+ EFV ++GPSGCGK+T L ++ L+ T G+ Y++G Sbjct: 7 LQKIFKTEEVETWALNNVSIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGGEYYLNG 66 Query: 68 KVVNDVEPKDRD------IAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAA 121 V+ R I VFQ++ L + VYEN+ L E +RV A Sbjct: 67 TEVSKYTESQRTSLRKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKKRVETAM 126 Query: 122 KILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKK 181 + + I + P+QLSGGQ+QRVA+ RA+V NPK+ L DEP NLD+K ++ L + Sbjct: 127 ERMAITHRSKHFPQQLSGGQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEVMGLLSE 186 Query: 182 LHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEI 215 L ++ TI+ VTH Q +A AD+I+ + DG++ Sbjct: 187 L-NKEGTTIVMVTHSQHDA-GYADRIINLFDGQV 218 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: 173 Number of extensions: 9 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: 224 Length adjustment: 26 Effective length of query: 343 Effective length of database: 198 Effective search space: 67914 Effective search space used: 67914 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: 47 (22.7 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