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 GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 356 bits (914), Expect = e-103 Identities = 185/374 (49%), Positives = 257/374 (68%), Gaps = 13/374 (3%) Query: 3 MAQVVLENVTKVYENKVV-AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDG 61 M+Q+ L ++ K Y +K ++ + EF++L+GPSGCGK+T + IAGLE ITDG Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 62 KIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAA 121 I +DGK ++ +EPKDRDIAMVFQ+YALYP M+V EN+AFGLK+R PK EID+ V A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 122 KILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKK 181 +L I L+++KP LSGGQ+QRVA+GRA+ R P+++LFDEPLSNLDAKLRV+MR+E+KK Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 182 LHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPP 241 LH RL+ TI+YVTHDQ+EAMT+AD+I V+KDGE+QQ+GTP E+Y+ P N+FVAGF+GSP Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 242 MNFVNARVVRGEGGLWIQA---SGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFA 298 M+FV V +GEGGL + G VK+P + LA+ + K++I GIRPE I Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLP--VPEFLADRVGKKVILGIRPEHITQ---P 295 Query: 299 LAPSPENTITG----VVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDM 354 + T+ ++V EP G + I +++ D + ++P + +L+ DM Sbjct: 296 QDQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDM 355 Query: 355 TRMHAFDKETEKAI 368 ++ FD ETEK I Sbjct: 356 KKVVFFDPETEKRI 369 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: 412 Number of extensions: 13 Number of successful extensions: 3 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: 372 Length adjustment: 30 Effective length of query: 339 Effective length of database: 342 Effective search space: 115938 Effective search space used: 115938 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