Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= BRENDA::P68187 (371 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein Length = 364 Score = 317 bits (811), Expect = 4e-91 Identities = 182/374 (48%), Positives = 239/374 (63%), Gaps = 23/374 (6%) Query: 1 MASVQLQNVTKAW--GEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 MA V+L + K + G V V+ + + +I +GE +V VGPSGCGK+TLLRMIAGLE+I+ G Sbjct: 1 MAKVRLDKLRKVYPNGHVGVA-EASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59 Query: 59 DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118 L IGE+ +ND P +R + MVFQ+YALYPH++VAEN+ FGLKL G K I +RV + A Sbjct: 60 TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119 Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 +L+L LD +P ALSGGQRQRVA+GR LV +P VFLLDEPLSNLDA LR+ MR+EI+R Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238 +H+RL TM+YVTHDQ+EAMTL +IVVL+ G + Q+ P+ LY PA+ FVAGF+GSP Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 239 MNFL--------PVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEH- 289 MN L K+ + V ELP + W RD+ V G+RPE Sbjct: 240 MNLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAW---RDRDIVV------GLRPEDL 290 Query: 290 LLPSDIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPP 349 LL +D A L +++VVE +GNE ++++ + LV R L G+T G P Sbjct: 291 LLCADAAGAALAAQLEVVEPVGNEVFLNLRHGELA--LVSRMPPRELPAPGSTLHFGFAP 348 Query: 350 ERCHLFREDGTACR 363 ER H F G R Sbjct: 349 ERLHFFDAKGEGAR 362 Lambda K H 0.320 0.137 0.393 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: 393 Number of extensions: 19 Number of successful extensions: 3 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: 371 Length of database: 364 Length adjustment: 30 Effective length of query: 341 Effective length of database: 334 Effective search space: 113894 Effective search space used: 113894 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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