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 353142 BT3616 fucose permease (NCBI ptt file)
Query= TCDB::O25788 (407 letters) >FitnessBrowser__Btheta:353142 Length = 418 Score = 210 bits (535), Expect = 5e-59 Identities = 133/418 (31%), Positives = 210/418 (50%), Gaps = 19/418 (4%) Query: 1 MQKTSNTLALGSLTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMG 60 M+K + T+ L + +LFFL + L +I L +L FEAS + ++ AYFI Sbjct: 1 MKKNTYTIPLALVFSLFFLWAISSNLLPTMIRQLMKTCELNTFEASFTETAYWLAYFIFP 60 Query: 61 GVFGNVISKIGYPFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAG 120 + + Y G++ G ++ A G LF+PAA Y +L FI+A+G+ L+TA Sbjct: 61 IPIAMFMKRYSYKAGIIFGLLLAAVGGLLFFPAAMLKEYWAYLCIFFIIATGMCFLETAA 120 Query: 121 NPFVTLLSKGKEA-RNLVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDKLA---- 175 NP+VT+L + A R L L Q+FN LG + +F S LI S T +D Sbjct: 121 NPYVTVLGAPETAPRRLNLAQSFNGLGAFIAAMFLSKLILSGTHYTRETLPVDYPGGWQA 180 Query: 176 ----DAKSVQMPYLGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKS-------LFSHKH 224 + ++++PYL LA+ L +A++ KLP + E + + K + H Sbjct: 181 YIQLETDAMKLPYLILALLLLAIAVVFVFSKLPKIGDEGAEPASGKKEKLIDFDVLKRSH 240 Query: 225 FVFGALGIFFYVGGEVAIGSFLVLSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMN 284 +G + FFY GG+ AI S ++ L ++ + Y ++GR++G+ LM Sbjct: 241 LRWGVIAQFFYNGGQTAINSLFLVYCCTYAGLPEDTATTFFGLYMLAFLLGRWIGTGLMV 300 Query: 285 KIAPNKYLAFNALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLT 344 K P L AL +I+L + ++ GG I L+A+ + FF SIM+PT FSLA LG+ T Sbjct: 301 KFRPQGMLLVYALMNILLCGVVMLWGGMIGLYAMLAISFFMSIMYPTQFSLALKGLGNQT 360 Query: 345 SKASGVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCYFYILFFALKGYK 402 S + MAIVG A +P + + E AYG+P++C+ + ++ KGYK Sbjct: 361 KSGSAFLVMAIVGNACLPQL---TAYFMHVNEHIYYVAYGIPMICFAFCAYYGWKGYK 415 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: 468 Number of extensions: 20 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: 407 Length of database: 418 Length adjustment: 31 Effective length of query: 376 Effective length of database: 387 Effective search space: 145512 Effective search space used: 145512 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 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