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 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 226 bits (576), Expect = 8e-64 Identities = 127/287 (44%), Positives = 187/287 (65%), Gaps = 17/287 (5%) Query: 21 VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDIA 80 + +L I++ EF+ +GPSGCGK+T LR+IAGLE + G + +D++ + ++R + Sbjct: 33 IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPAENRYVN 92 Query: 81 MVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSGGQ 140 VFQ+YAL+PHM+V+EN+AFGL+++K +I RV EA ++ L F +RKP LSGGQ Sbjct: 93 TVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQLSGGQ 152 Query: 141 RQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEAM 200 +QRVA+ RA+V ++ L+DE LS LD KLR M+ E+ + R++G T ++VTHDQ EA+ Sbjct: 153 QQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQEEAL 212 Query: 201 TLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVTVEK 260 T++DRIV+M GRIEQ GTP+E+Y EP N FVAGFIG +N F TV Sbjct: 213 TMSDRIVVMRD----------GRIEQDGTPREIYEEPKNLFVAGFIGE--INMFNATV-I 259 Query: 261 ERLVNQDGLSLALPQGQEKILEEKGYL--GKKVTLGIRPEDISSDQI 305 ERL Q A +G+E + + G+K+ + +RPED+ ++I Sbjct: 260 ERLDEQ--RVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEI 304 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: 363 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 347 Effective length of database: 348 Effective search space: 120756 Effective search space used: 120756 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