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) >FitnessBrowser__Dyella79:N515DRAFT_4212 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:
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