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_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 136 bits (343), Expect = 1e-36 Identities = 80/220 (36%), Positives = 127/220 (57%), Gaps = 10/220 (4%) Query: 6 VVLENVTKVY---ENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 V V K+Y + + V +L + EF+ L+G SGCGK+T L M AGL ++++G Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 + +DG+ V++ P D A+VFQ +L+P +T +N+A G+ R YP R+ + Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408 Query: 123 IL---GIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSEL 179 L G+ + +D+K +S G RQRV + RA +PK+ L DEP LD+ R +++ L Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468 Query: 180 KKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIG 219 ++ R + T I VTHD EA+ +ADK+V+M +G +IG Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIG 508 Score = 135 bits (339), Expect = 4e-36 Identities = 77/208 (37%), Positives = 127/208 (61%), Gaps = 6/208 (2%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 L+ V K Y V +++ +L +ED EF+ +LG SG GKTT + ++AGL + G++ + G Sbjct: 6 LKGVAKSYGASSV-LRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLLRG 64 Query: 68 KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKI--LG 125 K V+ D +VFQ+Y+L P +TV N+A + + +R+ R A I +G Sbjct: 65 K---PVDGPGADRGVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIGMVG 121 Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185 + + +R+P +LSGG RQRVAV RA+ +P + L DEPLS LDA R +++ E++ + + Sbjct: 122 LSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIWEQ 181 Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDG 213 + T+I +T+D EA+ +AD+I+ + G Sbjct: 182 EKKTVILITNDVDEALLLADRIIPLNPG 209 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: 454 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 369 Length of database: 553 Length adjustment: 33 Effective length of query: 336 Effective length of database: 520 Effective search space: 174720 Effective search space used: 174720 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: 51 (24.3 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