Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 309 bits (791), Expect = 9e-89 Identities = 180/372 (48%), Positives = 238/372 (63%), Gaps = 26/372 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M+ + L K Y G+T+ V +L I D EF VFVGPSGCGK+T LRMIAGLE+ +EG Sbjct: 1 MSGITLRGAVKRY-GETQ-VVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +++IG R V + P +R +AMVFQ YALYPHMTV +NM FGLK+ VPKAEI +V A+ Sbjct: 59 SIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAAS 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL + L RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV+MR EI + Sbjct: 119 EILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+ + T+IYVTHDQ EAMT+ D+IVV+R G ++Q P +Y P N+FVAGFIGSPA Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPA 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGK--PVVLGVRPEDLHDEEV 298 MNF+ G I + DA + LP L GA G+ PV +GVRP + + Sbjct: 239 MNFLDGRI--ENDAVHLAG------LPP-----LPVPGAAGRSGPVTVGVRP-----QHI 280 Query: 299 FMTTYPDSVLQMQVEVVEHMGSEVYLH-TSIGPNTIVARVNPRHVYHVGSSVKLAIDLNK 357 + D L VE+ E +G YL+ + + G+ V L++ ++ Sbjct: 281 ALEPGGDGYL---VELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDR 337 Query: 358 IHIFDAETEESI 369 + +F+AET + + Sbjct: 338 VMLFEAETGQRL 349 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: 394 Number of extensions: 14 Number of successful extensions: 1 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: 351 Length adjustment: 30 Effective length of query: 354 Effective length of database: 321 Effective search space: 113634 Effective search space used: 113634 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