Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 301 bits (772), Expect = 2e-86 Identities = 177/374 (47%), Positives = 241/374 (64%), Gaps = 17/374 (4%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M ++ L K Y +A + N +LDI + EF VF+GPSGCGKST LR IAGLED+T G Sbjct: 1 MASITLRAAQKAYGDAPPV-IRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSG 59 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +L+I K +ND R +AMVFQ+YAL+PHM+VYENM+FGL L K K +I ++V EAA Sbjct: 60 DLFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAA 119 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L E L+RKP +LSGGQRQRVA+GRAIVR VFL DEPLSNLDA LR R EIA+ Sbjct: 120 RILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIAR 179 Query: 181 IHRRI-GATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239 +HR+ A+ +YVTHDQ EAMTLADRIV++ A + + GSI Q+GTP ELY+ P N Sbjct: 180 LHRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIA---QVGTPMELYHHPRN 236 Query: 240 KFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKIL-EEKGYL--GKKVTLGIR 296 +FVAGFIGSP MNF V V ++G+ + L +E +L +G L G+ VT+G+R Sbjct: 237 RFVAGFIGSPRMNFLPAQVAG---VQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVR 293 Query: 297 PEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSH-SPGEK 355 PE + + + ++++ E LG ++ +++ + + A D+ + GE+ Sbjct: 294 PEHMEIG-----SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAAGDARITRGER 348 Query: 356 VQLTFNIAKGHFFD 369 V++ A + FD Sbjct: 349 VRVAIAPACAYLFD 362 Lambda K H 0.318 0.135 0.379 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: 353 Number of extensions: 20 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: 377 Length of database: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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