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 CA265_RS08675 CA265_RS08675 glucose/galactose MFS transporter
Query= TCDB::O25788 (407 letters) >FitnessBrowser__Pedo557:CA265_RS08675 Length = 428 Score = 192 bits (488), Expect = 2e-53 Identities = 131/415 (31%), Positives = 202/415 (48%), Gaps = 36/415 (8%) Query: 13 LTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVISKIGY 72 + ALFF+ GF+T N LIP K F L+ +A + F + AYF + ++ K+G+ Sbjct: 19 ICALFFIFGFVTWANGTLIPFFKLSFGLSNLQAFFVTFASYMAYFFLALPSSWILKKVGF 78 Query: 73 PFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLLSKGKE 132 G+VLG VI G +F PAA ++G FL +F+ + + LQTA NP++T++ + Sbjct: 79 KNGIVLGLVILGLGSLIFIPAAQTRTFGLFLTGIFVQGAALALLQTASNPYLTIIGPIES 138 Query: 133 ARNLVLVQAF-NSLGTTLGP-IFGSLLIFSTTKMGDNASLIDKLADAKS----------- 179 A + + N + P I GSL + NAS ++K A + Sbjct: 139 AAKRISIAGICNKFAGMIVPLIMGSLFL-------KNASEVEKQIKAATGAVHEQLLNDV 191 Query: 180 ---VQMPYLGLAVFSLLLALIMYLLKLPDVEKE-------MPKETTQKSLFSHKHFVFGA 229 V MPY+ LA+ L A+ + LP+VE E + KS+F H GA Sbjct: 192 LGRVNMPYIVLAIVFCLFAIFIKFTNLPEVEVEEDVIDESKGEVVKHKSIFQFPHLFLGA 251 Query: 230 LGIFFYVGGEVAIGSFLVLSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMNK-IAP 288 L IF YVG EV G + + + + L + + S ++G +G V + K I+ Sbjct: 252 LCIFVYVGAEVMAGDIIGI-YGRELGISPEISGKLTSITLFSMLIGYIIGIVTIPKYISQ 310 Query: 289 NKYLAFNALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLTSKAS 348 K L A+ I+ L+ +I A+ + +G NS+M+P IF L +LG T S Sbjct: 311 QKALRICAILGIIFTILSFVISSWFAVIFVALLGLANSLMWPAIFPLGISHLGKFTKIGS 370 Query: 349 GVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLL-CYFYILFFALKGYK 402 ++ M I GGAL+P + + + L N AY + +L CY YIL+FA+KG+K Sbjct: 371 AIMIMGIAGGALMPLLYAFLNEKL---HVNFQLAYLLTVLPCYLYILYFAIKGHK 422 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: 534 Number of extensions: 28 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: 428 Length adjustment: 32 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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