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 GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 313 bits (801), Expect = 6e-90 Identities = 185/383 (48%), Positives = 243/383 (63%), Gaps = 38/383 (9%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 MT + L K+Y + + + + +L I D EF VFVGPSGCGKST LRMIAGLE+ + G Sbjct: 1 MTGVTLAKAVKKYGDVQ--VIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 N++I D+ + DR +AMVFQ+YALYPHM+V +NM FGLK+ + K+ I ++V EA+ Sbjct: 59 NIHIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEAS 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L ++L+RKP LSGGQRQRVA+GRAIVR +VFL DEPLSNLDA+LRV MR EIA+ Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+ IGAT IYVTHDQ EAMTLAD+IV++ A GR+EQ+G+P ELY P N+ Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRA----------GRVEQVGSPMELYANPDNR 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLV------NQDGLSLALPQGQEKILEEKGYLGKKVTLG 294 FVAGFIGSP+MNF E TV+ + +V + S+ALP G KV LG Sbjct: 229 FVAGFIGSPSMNFLEGTVQGDGVVVPALENRRVATSVALPAD-----------GSKVLLG 277 Query: 295 IRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSP-G 353 +RP+ +S T ++S+ D+ E LG S Y+ + E D P G Sbjct: 278 LRPQHLS------VTAADSSLVLDL--RERLGGVSYDYLSTPTGEKLIVETRGDEALPEG 329 Query: 354 EKVQLTFNIAKGHFFDLETEKRI 376 V L F+ A + FD TE+R+ Sbjct: 330 TAVALGFDDADAYIFDGATEQRL 352 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: 353 Number of extensions: 16 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: 353 Length adjustment: 30 Effective length of query: 347 Effective length of database: 323 Effective search space: 112081 Effective search space used: 112081 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