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 GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 214 bits (546), Expect = 2e-60 Identities = 137/349 (39%), Positives = 193/349 (55%), Gaps = 24/349 (6%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 + ++K ++ +AV N NL + E LLG SG GK+T LRM+AG E G I +DG Sbjct: 17 IRGISKSFDG-TLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLDG 75 Query: 68 KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127 + V + P R M+FQ+YAL+PHMTV +N+A GLK K PK EI RV K++ +E Sbjct: 76 QDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKME 135 Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187 RKP+QLSGGQ+QRVA+ R++ + PK+ L DEP+ LD KLR +M+ EL ++ + Sbjct: 136 PYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENVG 195 Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247 AT + VTHDQ EAMTMA +I +M G I QIG+P +IY SP + A FIGS +N A Sbjct: 196 ATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGS--VNIFEA 253 Query: 248 RVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEI---------IFGIRPEDIYDKLFA 298 + E V + + D +ID+ + + +RPE IY L Sbjct: 254 HIREDEAD--------SVTLTSDLLDAPV-FIDRGVTTPAESTATLVALRPEKIY--LTP 302 Query: 299 LAPSPENTIT-GVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQ 346 P EN + G VD + LG T +VK+ V + + + E+ Sbjct: 303 DKPDGENNWSCGTVDNIAYLGDITSYYVKLASGKRVQATMANVERRGER 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: 309 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: 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