Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039 Length = 367 Score = 326 bits (835), Expect = 7e-94 Identities = 170/368 (46%), Positives = 242/368 (65%), Gaps = 17/368 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + ++++ K + G + +K +L++ DKEF VFVGPSGCGK+T LR+IAGLE+++ G Sbjct: 1 MANLKIKNLQKGFEGFS--IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + + R + +V P RD+AMVFQ YALYPHM+V +NM+F L L V KAE++++V EAA Sbjct: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL++ +L+RKPK LSGGQRQRVA+GRAIVR P++FL DEPLSNLDA LRVQMR E+ + Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+ LQ T+IYVTHDQ EAMTM D++VV+ G I+Q +P +Y QP N+FVAGF+G+P Sbjct: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASG---AIGKPVVLGVRPEDLHDEE 297 M F++G+I + + ++L G L G ++G V LG+RPE L Sbjct: 239 MGFLKGKITR------VDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLE--- 289 Query: 298 VFMTTYPDSVLQMQVEVVEHMGSEVYLHT-SIGPNTIVARVNPRHVYHVGSSVKLAIDLN 356 + D LQ+ +V E +GS+ + H + + RV G ++ L +D Sbjct: 290 --LAKPGDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQ 347 Query: 357 KIHIFDAE 364 H+FDA+ Sbjct: 348 HCHLFDAD 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: 406 Number of extensions: 16 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: 367 Length adjustment: 30 Effective length of query: 354 Effective length of database: 337 Effective search space: 119298 Effective search space used: 119298 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