Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= TCDB::O25788 (407 letters) >FitnessBrowser__Koxy:BWI76_RS22920 Length = 436 Score = 238 bits (606), Expect = 3e-67 Identities = 149/404 (36%), Positives = 216/404 (53%), Gaps = 24/404 (5%) Query: 13 LTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVISKIGY 72 L +LFFL LNDIL+P + F LT F+A LIQ F+ YF++ G ++ K+ Y Sbjct: 29 LCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFVIPIPAGILMKKLSY 88 Query: 73 PFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLLSKGKE 132 G++ G + A G ALF+PAA +Y FL LFI+A+G+ CL+TA NPFVT+L Sbjct: 89 KAGIITGLFLYAFGAALFWPAAEVMNYTLFLIGLFIIAAGLGCLETAANPFVTVLGPESG 148 Query: 133 AR-NLVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDKLADAK----------SVQ 181 L L Q FNS G + +FG LI S + ++DK+A + SVQ Sbjct: 149 GHFRLNLAQTFNSFGAIIAVVFGQSLILSNVP-HQSQDVLDKMAPEQLSAYKHSLVLSVQ 207 Query: 182 MPYLGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKS-------LFSHKHFVFGALGIFF 234 PY+ + LL+AL++ L K P ++ + + TQ S L +H+ + L F Sbjct: 208 TPYMIIVAVVLLVALLIMLTKFPALQSDDHSDATQSSFSASLARLVRVRHWRWAVLAQFC 267 Query: 235 YVGGEVAIGSFLV-LSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMNKIAPNKYLA 293 YVG + A S+L+ + E++ + +A+YL +GRF G+ L+++ AP+K LA Sbjct: 268 YVGAQTACWSYLIRYAIEEIPGMTPGFAANYLTGTMVCFFIGRFSGTWLISRFAPHKVLA 327 Query: 294 FNALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLTSKASGVISM 353 AL S++L ++ GG + L ALT F SI +PTIFSL NLG T S I M Sbjct: 328 AYALLSMILCLISAFTGGHVGLLALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFIVM 387 Query: 354 AIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCYFYILFFA 397 I+GG ++ P+ G V+D N+ A VP LC+ I FA Sbjct: 388 TIIGGGIVTPVMGFVSD----AAGNIPTAELVPALCFAVIFIFA 427 Lambda K H 0.328 0.144 0.423 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: 463 Number of extensions: 31 Number of successful extensions: 5 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: 407 Length of database: 436 Length adjustment: 32 Effective length of query: 375 Effective length of database: 404 Effective search space: 151500 Effective search space used: 151500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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