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 GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 207 bits (527), Expect = 4e-58 Identities = 125/343 (36%), Positives = 189/343 (55%), Gaps = 18/343 (5%) Query: 19 YSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRD 78 Y++ + H +GPSGCGKST L +I+GL +EG++ D K +N+ SP+DR+ Sbjct: 23 YAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQPSEGDVLFDGKRVNELSPRDRN 82 Query: 79 IAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSG 138 IA VFQ +Y M+VY+N+AF LK K I RVHE AE+L + + L +K +L+ Sbjct: 83 IAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARVHEIAEVLEIEDKLYKKAKNLTA 142 Query: 139 GQRQRVAMGRAIVR-DAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQT 197 ++Q+V+MGR +VR D L DEPL+ +D +L+ +R ++ +IH + T +YVTHDQ Sbjct: 143 DEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLRRKLKQIHEQFDITMVYVTHDQL 202 Query: 198 EAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVT 257 EA T AD+I +M G+I Q GTP EL+ +P + FV FIGSP MN EV Sbjct: 203 EASTFADKIAVMYG----------GQIVQFGTPTELFEQPNHTFVGFFIGSPGMNLIEVQ 252 Query: 258 VEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTA 317 R V ++L Q +L+ + +GIRPE + + + + A Sbjct: 253 -RCPRGVCFGSTVVSLESWQVDVLQRT--RSTNIKIGIRPEFVEVSSVASDD----TFEA 305 Query: 318 DILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360 ++L E LG+ ++ V+ + R + + S G KV L+F Sbjct: 306 EVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSF 348 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: 331 Number of extensions: 12 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: 366 Length adjustment: 30 Effective length of query: 347 Effective length of database: 336 Effective search space: 116592 Effective search space used: 116592 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