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 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 325 bits (832), Expect = 2e-93 Identities = 186/378 (49%), Positives = 242/378 (64%), Gaps = 24/378 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M LKL + K + + K ++ LD+ D EFIV VGPSGCGKST LRM+AGLE +TEG Sbjct: 1 MAGLKLQAVTKSW-DGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEG 59 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +++I+D+ + + PKDR IAMVFQNYALYPHMSV ENMA+GLK+R K I +RV EAA Sbjct: 60 DIWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAA 119 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L L+R+P +LSGGQRQRVAMGRAIVRD VFL DEPLSNLDAKLRV MR E+ + Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +HRR+ T++YVTHDQ EAMTLA R+++M+ G EQIGTP E+Y +PA+ Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNG----------GVAEQIGTPVEVYEKPASL 229 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILE--EKGYLGKKVTLGIRPE 298 FVA FIGSPAMN VN +G L G E L + Y G+K+TLGIRPE Sbjct: 230 FVASFIGSPAMNLL------TGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPE 283 Query: 299 DISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQL 358 I+ P T E+LG++++ + ++G + R+ ++ + G + L Sbjct: 284 HIALSSQAEGGVPMVMDTL-----EILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWL 338 Query: 359 TFNIAKGHFFDLETEKRI 376 + H FD ET +R+ Sbjct: 339 HLAENQLHLFDGETGQRV 356 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: 336 Number of extensions: 11 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: 356 Length adjustment: 30 Effective length of query: 347 Effective length of database: 326 Effective search space: 113122 Effective search space used: 113122 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