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 HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 335 bits (860), Expect = 9e-97 Identities = 183/369 (49%), Positives = 238/369 (64%), Gaps = 9/369 (2%) Query: 3 MAQVVLENVTKVY---ENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEIT 59 MA + L+ V K Y V + + + D EF+V++GPSGCGK+T LRM+AGLEEI+ Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 60 DGKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVRE 119 G+I I +VVND+EPK+RDIAMVFQNYALYPHMTVY+NMA+GLK++ K EID RV+ Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 120 AAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSEL 179 AA IL + LL+R PRQLSGGQRQRVA+GRAIVR P VFLFDEPLSNLDAKLRVQMR E+ Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 180 KKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGS 239 +KLH L+ T +YVTHDQVEAMT+ +++VM G +QIGTP E+Y PA FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 240 PPMNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFAL 299 PPMN + ++ G + S L +E I G+RPE + L Sbjct: 241 PPMNLLQGKL--SADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDGS 298 Query: 300 APSPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHA 359 A ++ V++VE LG+E ++H + G +V Q + Q+I +H Sbjct: 299 AAQ----LSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHW 354 Query: 360 FDKETEKAI 368 FD ++ + I Sbjct: 355 FDVKSTRRI 363 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: 350 Number of extensions: 13 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: 364 Length adjustment: 30 Effective length of query: 339 Effective length of database: 334 Effective search space: 113226 Effective search space used: 113226 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: 49 (23.5 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