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_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 287 bits (734), Expect = 4e-82 Identities = 164/364 (45%), Positives = 224/364 (61%), Gaps = 20/364 (5%) Query: 5 QVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIY 64 Q+ + +V K Y +V AV+ + VE+ + +V+LGPSGCGKTT LR+IAGLE +T G I+ Sbjct: 2 QIEIRDVRKDY-GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIH 60 Query: 65 IDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKIL 124 I G V + P R+I+MVFQ+YAL+PH+ V EN+ FGLK+RK P DEI+RR++ +L Sbjct: 61 IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLL 120 Query: 125 GIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHH 184 G+ LD KP +LSGG +QRVA+GRAI+ V L DEPLSNLDAKLR MR E+ L Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180 Query: 185 RLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNF 244 RL T+IYVTHDQVEAMTMAD+IV+M+DG+I Q +P Y PAN FVA FIG+PPMN Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240 Query: 245 VNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPE 304 V +G L G ++ P D+ +FGIRPE++ LA S + Sbjct: 241 VPLCPTQGGAAL---EPGGRLLFPGMDPDR--------YLFGIRPENL-----RLAESGQ 284 Query: 305 NTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKET 364 +V E LGS+T + ++ ++ R +E + L D ++ FD T Sbjct: 285 ---PAMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDART 341 Query: 365 EKAI 368 ++ + Sbjct: 342 QERV 345 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: 319 Number of extensions: 9 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: 365 Length adjustment: 30 Effective length of query: 339 Effective length of database: 335 Effective search space: 113565 Effective search space used: 113565 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 Apr 09 2024. 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