Align MalE2; aka Maltose ABC transporter, periplasmic maltose-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 BWI76_RS06695 BWI76_RS06695 ABC transporter substrate-binding protein
Query= TCDB::Q9S5Y1 (393 letters) >FitnessBrowser__Koxy:BWI76_RS06695 Length = 410 Score = 196 bits (498), Expect = 1e-54 Identities = 125/399 (31%), Positives = 206/399 (51%), Gaps = 16/399 (4%) Query: 6 LVLMLVVVSALVLSQT----KLTIWCSEKQVDILQKLGEEFKAKYGIPVEVQYVDFGSIK 61 L+L + LV Q +L +W K+ D ++ +F+ ++ + V VQ + + Sbjct: 9 LILTTLAAGQLVSLQAHAAGQLNVWEDIKKSDGIKAAVNDFEKQFNVKVNVQEMPYAQQL 68 Query: 62 SKFLTAAPQGQGADIIVGAHDWVGELAVNGLIEPIP-NFSDLKNFYDTALKAFSYGGKLY 120 K P G G D++V +D +G V GL+ P+ + + + F ++ AF LY Sbjct: 69 EKLRLDGPAGIGPDVLVIPNDQLGGAVVQGLLSPLTLDQAKQEAFTPASINAFHMDNVLY 128 Query: 121 GVPYAMEAVALIYNKDYVDSVPKTMDELIEKAKQIDEEYGGEVRGFIYDVANFYFSAPFI 180 GVP A+E + LIYNKD +D ++ + +K+ EE G+ G + Y+S I Sbjct: 129 GVPKAVETLVLIYNKDLIDKPLDSLQAWFDYSKKQREE--GKY-GLLAKFDQIYYSWGAI 185 Query: 181 LGYGGYVF-KETPQGLDVTDIGLANEGAVKGAKLIKRMIDEGVLTPG----DNYGTMDSM 235 GGY+F K G + D+GL GAV+ +K+ + V G + +DS+ Sbjct: 186 GPMGGYIFGKNDKGGFNPQDVGLNKPGAVEAVTFLKKFYTDKVFPAGILGDNGLNAIDSL 245 Query: 236 FKEGLAAMIINGLWAIKSYKDAGINYGVAPIPELEPGVPAKPFVGVQGFMINAKSPNKVI 295 F E AA +ING WA + Y+ AGI+YGVAP+P L G P F+GV+G++++ S +K + Sbjct: 246 FTEKKAAAVINGPWAFQPYEAAGIHYGVAPLPTLPDGKPMSSFLGVKGYVVSTWSKDKAL 305 Query: 296 AMEFLTNFIARKETMYKIYLADPRLPARKDVLE--LVKDNPDVVAFTQSASMGTPMPNVP 353 A +F+ FI + + + Y+A +P K +++ L+K++ A ++ T MP +P Sbjct: 306 AQQFI-EFINQPQYVKARYVATGEIPPLKAMIDDPLIKNDEKASAVAVQSARATAMPGIP 364 Query: 354 EMAPVWSAMGDALSIIINGQASVEDALKEAVEKIKAQIE 392 EM VW AL + + G+ + AL A ++IK QIE Sbjct: 365 EMGEVWGPANAALELSLTGKQEPKAALDNAEKQIKMQIE 403 Lambda K H 0.318 0.138 0.398 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: 403 Number of extensions: 23 Number of successful extensions: 5 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: 393 Length of database: 410 Length adjustment: 31 Effective length of query: 362 Effective length of database: 379 Effective search space: 137198 Effective search space used: 137198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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