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 Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 329 bits (843), Expect = 8e-95 Identities = 184/370 (49%), Positives = 239/370 (64%), Gaps = 44/370 (11%) Query: 3 MAQVVLENVTKVYENKVVA---VKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEIT 59 MA + L N+TK Y + A + N V+D EFVV++GPSGCGK+T LRM+AGLEEI+ Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 60 DGKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVRE 119 G++ I +VVND+EP RDIAMVFQNYALYPHMT +ENMA+GLK+ K PKDEI RV + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 120 AAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSEL 179 AAKIL + +LL+RKPR+LSGGQRQRVA+GRAIVR P+VFLFDEPLSNLDAKLR Q R E+ Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 180 KKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGS 239 +KLH L T ++VTHDQVEAMT+A +++VM G ++Q GTP E+Y++PA FVA FIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 240 PPMNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPE--DIYDKLF 297 PPMN + K A I GIRPE D+ + + Sbjct: 241 PPMNLL----------------------------KNAPGAQPGTILGIRPEHLDVRSEGW 272 Query: 298 ALAPSPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMT-R 356 A+ V+ VE LG+E +++ ++ + ++ V T + E + V R Sbjct: 273 AV----------TVETVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADR 322 Query: 357 MHAFDKETEK 366 +HAFD T K Sbjct: 323 LHAFDAATGK 332 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: 360 Number of extensions: 11 Number of successful extensions: 1 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: 334 Length adjustment: 29 Effective length of query: 340 Effective length of database: 305 Effective search space: 103700 Effective search space used: 103700 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