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 PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 232 bits (592), Expect = 1e-65 Identities = 131/317 (41%), Positives = 196/317 (61%), Gaps = 27/317 (8%) Query: 2 TTLKLDNIYKRYPNAKHYS--VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITE 59 T +++ N+ KRY + + ++N ++DI D EF +GPSGCGK+T LR IAG E +++ Sbjct: 5 TAIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSD 64 Query: 60 GNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEA 119 G + + + +ND P R + VFQ+YAL+PHMSV +N+AFGL+++ + I +RV E Sbjct: 65 GEIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEM 124 Query: 120 AEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIA 179 ++ + +RKPA+LSGGQ+QRVA+ RA+ KV L+DEPLS LD KLR M+ E+ Sbjct: 125 LALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELK 184 Query: 180 KIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239 ++ + G T I+VTHDQ EA+TL+DRI +MSA G+I QIG+P E+Y P + Sbjct: 185 RVQKEAGITFIFVTHDQEEALTLSDRIAVMSA----------GKILQIGSPNEIYERPQH 234 Query: 240 KFVAGFIGSPAMNFFEVTVEK----ERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGI 295 +FVA FIG +NF +++ E+L +G+ + +P +G+ G KV L Sbjct: 235 QFVAQFIGD--INFLPGHIKRGQQNEKLFVPNGMPVEIP------CPAQGFDGSKVQLAF 286 Query: 296 RPEDISSDQIVHETFPN 312 RPE Q+V T P+ Sbjct: 287 RPE---RSQLVEPTQPH 300 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: 324 Number of extensions: 7 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: 377 Length of database: 361 Length adjustment: 30 Effective length of query: 347 Effective length of database: 331 Effective search space: 114857 Effective search space used: 114857 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: 49 (23.5 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