Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Koxy:BWI76_RS06690 Length = 369 Score = 325 bits (833), Expect = 1e-93 Identities = 183/365 (50%), Positives = 236/365 (64%), Gaps = 15/365 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M+ + L ++ K + G T T+ NLDI+D EF VFVGPSGCGK+T LRMIAGLE+++EG Sbjct: 1 MSNIRLRNVTKRF-GSTV-TLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IGD +NDV P R +AMVFQ+YALYPHMTV +NM +GLK+ KVPK EI R+V+ A Sbjct: 59 EVLIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 K L ++HLLDRKPK LSGGQRQRVA+GRAIVR P+VF+ DEPLSNLDA+LRV+MR I K Sbjct: 119 KTLQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAK 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH L+TT++YVTHDQ EAMT+ D+IVVM G ++Q +P +Y P N FVAGFIGSP Sbjct: 179 LHHELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPK 238 Query: 241 MNFIRGEIV--QDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEV 298 MNF+ + Q G A +L L + + G V LG+RPE L + Sbjct: 239 MNFLPATVTAWQPGQLSVKMAQDHNLTL-----NITTSPLQPGAAVTLGIRPEHLSTDVN 293 Query: 299 FMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHV-YHVGSSVKLAIDLNK 357 T V++ Q EVVE +G+ YL + V + P V + + +A D Sbjct: 294 IGT-----VVEFQCEVVERLGNNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVAFDDRY 348 Query: 358 IHIFD 362 +FD Sbjct: 349 CMVFD 353 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: 397 Number of extensions: 15 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: 369 Length adjustment: 30 Effective length of query: 354 Effective length of database: 339 Effective search space: 120006 Effective search space used: 120006 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