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 AO353_07265 AO353_07265 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07265 Length = 374 Score = 242 bits (617), Expect = 1e-68 Identities = 141/325 (43%), Positives = 191/325 (58%), Gaps = 12/325 (3%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 V V K Y+ + + VK+ NL + EF+ LLGPSG GKTT+L M+AG E T G+I + Sbjct: 15 VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILL 74 Query: 66 DGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILG 125 G+ +N+V P RDI MVFQNYAL+PHMTV EN+AF L +R K ++ RV+ ++ Sbjct: 75 AGRAINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKSDVSDRVKRVLSMVQ 134 Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185 ++ R P QLSGGQ+QRVA+ RA+V P++ L DEPL LD +LR M+ E+K LH R Sbjct: 135 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 194 Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFV 245 L T++YVTHDQ EA+TM+D++ V GEIQQI P E+Y P N FVA FIG N + Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRELYEKPKNTFVANFIGE--NNRL 252 Query: 246 NARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDK---EIIFGIRPEDIYDKLFALAPS 302 N R+ G + G KV + LA + K + IRPE + L + S Sbjct: 253 NGRLHSHTGDRCVVELGRGEKV-----EALAVNVGKTGEPVTLSIRPERV--SLNGSSES 305 Query: 303 PENTITGVVDVVEPLGSETILHVKV 327 N +G V LG + ++V Sbjct: 306 CVNRFSGRVAEFIYLGDHVRVRLEV 330 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: 313 Number of extensions: 12 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: 374 Length adjustment: 30 Effective length of query: 339 Effective length of database: 344 Effective search space: 116616 Effective search space used: 116616 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