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 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >MicrobesOnline__882:209027 Length = 368 Score = 234 bits (598), Expect = 2e-66 Identities = 139/366 (37%), Positives = 217/366 (59%), Gaps = 27/366 (7%) Query: 7 DNIYKRYPNAKHY----SVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNL 62 DNI + K++ +++N +L+I + EF+ +GPSGCGK+T LR+I+G E G + Sbjct: 5 DNIIELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVI 64 Query: 63 YIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEI 122 + + M+DA P+ R + VFQNYAL+PHMSV EN+ FGL++++ KD+I +RVH+A + Sbjct: 65 TLKGQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRM 124 Query: 123 LGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIH 182 + L +R+P LSGGQ+QRVA+ RA+V + V L+DEP S LD KLR M+ EI + Sbjct: 125 VHLEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQ 184 Query: 183 RRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFV 242 R++G T ++VTHDQ EA ++DR+V+M+ G+IEQIG+PQE+Y EPAN +V Sbjct: 185 RQLGITFVFVTHDQEEAFAMSDRVVVMND----------GKIEQIGSPQEIYEEPANLYV 234 Query: 243 AGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQE-KILEEKGYL-GKKVTLGIRPEDI 300 A F+G +N + + DGL A+ +G I ++ + G KV + +RPED+ Sbjct: 235 ARFVGE--INILNAVIAAN---HGDGLYDAVIEGVTFPIRSQRTFAPGDKVNVLLRPEDL 289 Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYV------KFGSTEFTARVNARDSHSPGE 354 + + +T I S G+ L V + + EF + +++PGE Sbjct: 290 RVYTLTEDRPAGPHLTGRIEESVYKGATVDLIVTLSDGRRLMAAEFFNEDDVDINYNPGE 349 Query: 355 KVQLTF 360 V +++ Sbjct: 350 TVTVSW 355 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: 352 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: 377 Length of database: 368 Length adjustment: 30 Effective length of query: 347 Effective length of database: 338 Effective search space: 117286 Effective search space used: 117286 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