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 PP_5179 PP_5179 spermidine/putrescine ABC transporter - ATP binding subunit
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Putida:PP_5179 Length = 380 Score = 235 bits (600), Expect = 1e-66 Identities = 138/340 (40%), Positives = 199/340 (58%), Gaps = 24/340 (7%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 V ++ VTK ++ + VAV + +L + E LLG SG GK+T LRM+AG E ++G+I++ Sbjct: 23 VKIDRVTKKFD-ETVAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFERPSEGRIFL 81 Query: 66 DGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILG 125 DG + D+ P +R I M+FQ+YAL+PHMTV +N+AFGL+ K PK EID RV E K++ Sbjct: 82 DGVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLQQDKMPKAEIDARVAEMLKLVH 141 Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185 + RKP QLSGGQRQRVA+ R++ + PK+ L DEP+ LD KLR QM+ EL ++ R Sbjct: 142 MTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIER 201 Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFV 245 + T + VTHDQ EAMTMA +I +M G I QIG+P +IY +P + V FIG+ Sbjct: 202 VGVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYETPTSRLVCEFIGN------ 255 Query: 246 NARVVRGEGGLWIQASGFKVKVPKEFEDKL-------ANYIDKEIIFGIRPEDIYDKLFA 298 V EG + A G+ + E E K+ + DK I + +RPE K+ Sbjct: 256 ---VNLFEGDVVDDAEGYAIIASPELERKIYVGHGITTSVEDKHITYALRPE----KMLV 308 Query: 299 LAPSP---ENTITGVVDVVEPLGSETILHVKVGDDLIVAS 335 P N G + + LG ++ +V++ +V S Sbjct: 309 TTQQPTCEHNWSRGKIHDIAYLGGHSVFYVELPSGKVVQS 348 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: 349 Number of extensions: 8 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: 380 Length adjustment: 30 Effective length of query: 339 Effective length of database: 350 Effective search space: 118650 Effective search space used: 118650 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