Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 312 bits (800), Expect = 8e-90 Identities = 184/371 (49%), Positives = 232/371 (62%), Gaps = 21/371 (5%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M V L K Y G + + D +L I D EF VFVGPSGCGK+T LRMIAGLE+ + G Sbjct: 1 MTGVTLAKAVKKY-GDVQ-VIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 N++IGDR V + DR +AMVFQ+YALYPHMTV NM FGLK+ PK +I +V EA+ Sbjct: 59 NIHIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEAS 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL + L RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV MR EI + Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIAR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+ + T+IYVTHDQ EAMT+ D+IVV+R G ++Q +P +Y+ P N FVAGFIGSP+ Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPS 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MNF+ G + DG P++ R R A A G V+LG+RP+ L Sbjct: 239 MNFLEGTVQGDGVV----VPALENR----RVATSVALPADGSKVLLGLRPQHL------S 284 Query: 301 TTYPDSVLQMQVEVVEHMG--SEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKI 358 T DS L + + E +G S YL T G IV G++V L D Sbjct: 285 VTAADSSLVLDLR--ERLGGVSYDYLSTPTGEKLIV-ETRGDEALPEGTAVALGFDDADA 341 Query: 359 HIFDAETEESI 369 +IFD TE+ + Sbjct: 342 YIFDGATEQRL 352 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: 384 Number of extensions: 13 Number of successful extensions: 2 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: 353 Length adjustment: 30 Effective length of query: 354 Effective length of database: 323 Effective search space: 114342 Effective search space used: 114342 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