Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 211 bits (536), Expect = 3e-59 Identities = 128/341 (37%), Positives = 186/341 (54%), Gaps = 34/341 (9%) Query: 3 SVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI 62 S++++N+ K +G V D++L I GE V +GPSGCGK+TLLR+IAG+ET G + Sbjct: 2 SIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMF 61 Query: 63 GEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEV----INQRVNQVA 118 ER VG VFQ YAL+ H++V EN++FGL++ K+ I +RV + Sbjct: 62 EGSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLL 121 Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 ++QL L DR P LSGGQRQR+A+ R L EP V LLDEP LD +R ++R + R Sbjct: 122 SLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRR 181 Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238 LH + + ++VTHDQ EA+ +AD++VV++ GR+ QVG P E+Y PA FV F+G+ Sbjct: 182 LHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN-- 239 Query: 239 MNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIA-D 297 +N +V W V DV G IRP + +A Sbjct: 240 VNVFHSRV-----------------HGAWAEVARDDVPAGQEAVAFIRPHDIDIDTVATP 282 Query: 298 VILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVE 338 LE +V V+ +G P +R +++ Q ++V VE Sbjct: 283 ESLEAKVSYVQTIG---------PLVRVEVIH-QGELVEVE 313 Lambda K H 0.320 0.137 0.393 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: 317 Number of extensions: 11 Number of successful extensions: 2 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: 371 Length of database: 360 Length adjustment: 30 Effective length of query: 341 Effective length of database: 330 Effective search space: 112530 Effective search space used: 112530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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