Align MalE1; 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::Q9X0T1 (391 letters) >FitnessBrowser__Koxy:BWI76_RS06695 Length = 410 Score = 211 bits (537), Expect = 3e-59 Identities = 135/408 (33%), Positives = 219/408 (53%), Gaps = 22/408 (5%) Query: 1 MKKFLVIALLV--------VSLVVLAQPKLTIWCSEKQVDILQKLGEEFKAKYGVEVEVQ 52 MKK + AL++ VSL A +L +W K+ D ++ +F+ ++ V+V VQ Sbjct: 1 MKKNTLAALILTTLAAGQLVSLQAHAAGQLNVWEDIKKSDGIKAAVNDFEKQFNVKVNVQ 60 Query: 53 YVNFQDIKSKFLTAAPEGQGADIIVGAHDWVGELAVNGLIEPIP-NFSDLKNFYETALNA 111 + + K P G G D++V +D +G V GL+ P+ + + + F ++NA Sbjct: 61 EMPYAQQLEKLRLDGPAGIGPDVLVIPNDQLGGAVVQGLLSPLTLDQAKQEAFTPASINA 120 Query: 112 FSYGGKLYGIPYAMEAIALIYNKDYVPEPPKTMDELIEIAKQIDEEFGGEVRGFITSAAE 171 F LYG+P A+E + LIYNKD + +P ++ + +K+ EE G+ G + + Sbjct: 121 FHMDNVLYGVPKAVETLVLIYNKDLIDKPLDSLQAWFDYSKKQREE--GKY-GLLAKFDQ 177 Query: 172 FYYIAPFIFGYGGYVFKQTEKG-LDVNDIGLANEGAIKGVKLLKRLVDE-----GILDPS 225 YY I GGY+F + +KG + D+GL GA++ V LK+ + GIL Sbjct: 178 IYYSWGAIGPMGGYIFGKNDKGGFNPQDVGLNKPGAVEAVTFLKKFYTDKVFPAGILG-D 236 Query: 226 DNYQIMDSMFREGQAAMIINGPWAIKAYKDAGIDYGVAPIPDLEPGVPARPFVGVQGFMV 285 + +DS+F E +AA +INGPWA + Y+ AGI YGVAP+P L G P F+GV+G++V Sbjct: 237 NGLNAIDSLFTEKKAAAVINGPWAFQPYEAAGIHYGVAPLPTLPDGKPMSSFLGVKGYVV 296 Query: 286 NAKSPNKLLAIEFLTSFIAKKETMYRIYLGDPRLPSRKDVLE--LVKDNPDVVGFTLSAA 343 + S +K LA +F+ FI + + + Y+ +P K +++ L+K++ + +A Sbjct: 297 STWSKDKALAQQFI-EFINQPQYVKARYVATGEIPPLKAMIDDPLIKNDEKASAVAVQSA 355 Query: 344 NGIPMPNVPQMAAVWAAMNDALNLVVNGKATVEEALKNAVERIKAQIQ 391 MP +P+M VW N AL L + GK + AL NA ++IK QI+ Sbjct: 356 RATAMPGIPEMGEVWGPANAALELSLTGKQEPKAALDNAEKQIKMQIE 403 Lambda K H 0.319 0.139 0.404 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: 406 Number of extensions: 21 Number of successful extensions: 6 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: 391 Length of database: 410 Length adjustment: 31 Effective length of query: 360 Effective length of database: 379 Effective search space: 136440 Effective search space used: 136440 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 (21.7 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