Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Burk376:H281DRAFT_04155 Length = 369 Score = 348 bits (892), Expect = e-100 Identities = 197/372 (52%), Positives = 245/372 (65%), Gaps = 25/372 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V L +I K Y TE ++D NLDI D EF VFVGPSGCGK+T +RMIAGLEDI+ G Sbjct: 1 MASVTLRNIRKAYD-DTE-VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +L I R+NDVPP R IAMVFQ+YALYPHMT+Y NMAFGLKL K EID V+ AA Sbjct: 59 DLTINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 KIL I HLLDRKPK LSGGQRQRVA+GRAI R+P+VFL DEPLSNLDA LRV+MR E + Sbjct: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH L+TT+IYVTHDQ EAMT+ D+IVV+ G ++Q +P ++Y P N FVAGFIGSP Sbjct: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 Query: 241 MNFIRG---EIVQDGDAFYFRAPSISLRLPEG---RYGVLKASGAIGKPVVLGVRPEDLH 294 MNF+ G + DG +++R G R V + G V +G+RPE LH Sbjct: 239 MNFMEGVVQSVTHDG---------VTVRYETGETQRVAVEPGAVKQGDKVTVGIRPEHLH 289 Query: 295 DEEVFMTTYPDSVLQMQVEVVEHMGSEVYLH--TSIGPNTIVARVNPRHVYHVGSSVKLA 352 V MT D + + VE +G YL+ +S+ P+ ++AR+ P + G + KL Sbjct: 290 ---VGMT---DDGVSARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHAKGETQKLG 343 Query: 353 IDLNKIHIFDAE 364 H+FD+E Sbjct: 344 ATPEHCHLFDSE 355 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: 449 Number of extensions: 17 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: 369 Length adjustment: 30 Effective length of query: 354 Effective length of database: 339 Effective search space: 120006 Effective search space used: 120006 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