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 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 177 bits (448), Expect = 5e-49 Identities = 113/340 (33%), Positives = 182/340 (53%), Gaps = 35/340 (10%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M+TL + ++ Y + + NL + E +GPSGCGK+T LR IAGL+DI+ G Sbjct: 1 MSTLSIQGLHSDYRGEQ--VLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAG 58 Query: 61 NLYIDDKLMND----ASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRV 116 ++ I+ K ++ +P+ R I M+FQ+YAL+PH++V +N+ FG+ R+ K + R+ Sbjct: 59 SIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGV--RQLDKQSRSVRL 116 Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176 E ++ L +R P +LSGGQ+QRV++ RA+ + + L+DEP SN+DA++R A+ Sbjct: 117 EEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALML 176 Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236 EI I + + ++VTH + EA AD + + A GRI Q G P+ LY Sbjct: 177 EIRAILKARNVSAVFVTHSKDEAFAFADTLALFEA----------GRIVQHGIPETLYQS 226 Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296 P +VA F+G A N+ +V +E +L++ G + LPQ + E +L +R Sbjct: 227 PNTPYVADFLG--ASNYLDVRLEAGQLISTLG-AFPLPQDFKAASETGRWL-------LR 276 Query: 297 PEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFG 336 PE + + A +IL LG+ V+ G Sbjct: 277 PEQLLIE-------ARADGAGEILERRFLGNGCHYLVRLG 309 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: 265 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: 341 Length adjustment: 29 Effective length of query: 348 Effective length of database: 312 Effective search space: 108576 Effective search space used: 108576 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