Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 371 bits (952), Expect = e-107 Identities = 200/372 (53%), Positives = 258/372 (69%), Gaps = 19/372 (5%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA+V L+ + K YP V + + +I D E V VGPSGCGKTT LRMIAGLE I+ G Sbjct: 1 MAKVRLDKLRKVYPNG-HVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 L IG+R VND+ PKDRDIAMVFQNYALYPHMTV +N+ FGLKLR PKAEI+RRV EAA Sbjct: 60 TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 ++L++ LD +P ALSGGQRQRVALGRA+VR+P+VFL+DEPLSNLDAKLR+ MR EI + Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 +HQRL+ T++YVTHDQ EAMT+G RIVV+ GVIQQ DTP +Y P N+FVAGF+GSPA Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGR--YGVLKASGAI----GKPVVLGVRPEDLH 294 MN +RG + +DG L +P+G G L A+ + +V+G+RPEDL Sbjct: 240 MNLLRGILYRDG--------GWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDL- 290 Query: 295 DEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAID 354 + + L Q+EVVE +G+EV+L+ G +V+R+ PR + GS++ Sbjct: 291 ---LLCADAAGAALAAQLEVVEPVGNEVFLNLRHGELALVSRMPPRELPAPGSTLHFGFA 347 Query: 355 LNKIHIFDAETE 366 ++H FDA+ E Sbjct: 348 PERLHFFDAKGE 359 Lambda K H 0.321 0.138 0.395 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: 447 Number of extensions: 18 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: 384 Length of database: 364 Length adjustment: 30 Effective length of query: 354 Effective length of database: 334 Effective search space: 118236 Effective search space used: 118236 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: 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