Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 314 bits (804), Expect = 3e-90 Identities = 183/367 (49%), Positives = 238/367 (64%), Gaps = 19/367 (5%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L ++ KTY G E ++D NLDI+ E VFVGPSGCGK+T LRMIAGLE I+ G Sbjct: 1 MANLKLTNVAKTYGGGVE-VLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 L I + +ND+PP R IAMVFQ+YALYPHMTV NMAF LK+ K K EID + AA Sbjct: 60 TLEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 KIL + LDR PKALSGGQRQRVA+GR+IVR+P+V+L DEPLSNLDA LRV R EI + Sbjct: 120 KILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQ 179 Query: 181 LHQRL-QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSP 239 L + + +T+IYVTHDQ EAMT+ RIVV+ D I Q TP +Y +P+N FVA FIGSP Sbjct: 180 LKEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSP 239 Query: 240 AMNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLK---ASGAIGKPVVLGVRPEDLHDE 296 AMN I G +V G P ++RL G V + G V +GVRPEDL +E Sbjct: 240 AMNLIPGTVVATG-------PRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEE 292 Query: 297 EVFMTTYPDSVLQMQVEVVEHMG--SEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAID 354 +++ +V++VE +G + +Y+ G + ++A++ H GSSV+L D Sbjct: 293 GT-----GGALIDSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYAD 347 Query: 355 LNKIHIF 361 ++H+F Sbjct: 348 PARLHLF 354 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: 383 Number of extensions: 19 Number of successful extensions: 4 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: 363 Length adjustment: 30 Effective length of query: 354 Effective length of database: 333 Effective search space: 117882 Effective search space used: 117882 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