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 AO356_28585 AO356_28585 ABC transporter
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 316 bits (809), Expect = 8e-91 Identities = 175/356 (49%), Positives = 236/356 (66%), Gaps = 12/356 (3%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 L+NV K + +++ +L + EFVV +GPSGCGK+T LR+IAGL+ I G + IDG Sbjct: 6 LDNVNKQLGGARI-LRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDG 64 Query: 68 KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127 + VND+EP++R + MVFQ+YALYPHM+VY+N++FGLKL K K + RV + A+IL ++ Sbjct: 65 RRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQLD 124 Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187 LL RKPR+LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA LRVQMR+E+ +LH RL Sbjct: 125 KLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRLG 184 Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247 +T+IYVTHDQVEAMT+ADKIVV+ G I+Q+G+P E+Y PA+ FVAGF+GSP MNF+ A Sbjct: 185 STMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFLAA 244 Query: 248 RV-VRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENT 306 + GE +P + AN ++ GIRPE I K + + T Sbjct: 245 FLHTPGETSQVESLVLGMTSLPFDSSGLAAN---TQLSLGIRPEHIALK------AAQGT 295 Query: 307 ITGVVDVVEPLGSETILHVKVG-DDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFD 361 V VE LGSET +H+ G DD +V + +++L LD+ +H FD Sbjct: 296 AGIAVSGVEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFD 351 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: 353 Number of extensions: 18 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: 379 Length adjustment: 30 Effective length of query: 339 Effective length of database: 349 Effective search space: 118311 Effective search space used: 118311 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: 50 (23.9 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