Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 294 bits (753), Expect = 2e-84 Identities = 175/364 (48%), Positives = 222/364 (60%), Gaps = 34/364 (9%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + ++ I K Y T + D NLDI+D EF VFVGPSGCGK+T LR +AGLE ++ G Sbjct: 1 MAGIKIDKINKFYG--TTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG R V V P DRD+AMVFQ+YALYPHMTV +NM FG+K+ R+ EAA Sbjct: 59 RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 ++L + LDRKP LSGGQRQRVA+GRAIV+ P VFL DEPLSNLDAKLRVQMR E+ Sbjct: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH++L T+IYVTHDQ EAMTM D+IVV+ G I+Q +P +Y +P + FVA FIGSPA Sbjct: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238 Query: 241 MNFIRGEI-VQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MN ++ +QD IS L AS A +G RPE + Sbjct: 239 MNVFSSDVGLQD----------IS----------LDASAAF-----VGCRPEHIE----- 268 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSI-GPNTIVARVNPRHVYHVGSSVKLAIDLNKI 358 + D + V V E +G E L+ + G IVARV VG++V L +++ Sbjct: 269 IVPDGDGHIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRL 328 Query: 359 HIFD 362 H FD Sbjct: 329 HQFD 332 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: 382 Number of extensions: 15 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: 338 Length adjustment: 29 Effective length of query: 355 Effective length of database: 309 Effective search space: 109695 Effective search space used: 109695 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