Align D-xylose-proton symporter (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 243 bits (620), Expect = 1e-68 Identities = 150/468 (32%), Positives = 240/468 (51%), Gaps = 51/468 (10%) Query: 16 VATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVAS-ALIGCIIGGAL 74 + +L G LFG+DTAVISG L ++ ++ GF + S AL G +IG L Sbjct: 11 IVSLTGFLFGFDTAVISGANLPLKALW--------QTSDWFHGFFIMSVALWGTVIGALL 62 Query: 75 GGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRI 134 GG + GR+++L V+F +S +G+A F F YR Sbjct: 63 GGIPCHHLGRKNTLFWIGVMFLVSALGTALATDPFV------------------FSFYRF 104 Query: 135 IGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWL 194 +GG+ +G +S+ +P Y++E++ A+ RG+ V Q I+ G L+ Y NY + GD + Sbjct: 105 VGGVAIGASSIAAPTYVSEISQAYQRGRRVGLYQINIVSGILVAYVSNYLLQGVGDHN-- 162 Query: 195 NTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQA-EGILRKIMGNTLATQAV 253 WR+M A+E IPA+++L + +PESPRWL+ + K E A + +L+KI + Q + Sbjct: 163 ---DWRWMLAAEIIPAIIYLAFILDIPESPRWLILKQKDESAAQKVLKKITTGKI-DQLL 218 Query: 254 QEIKHSLDHGRK-----TGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLG 308 IKH +K RL +F G+I +IF Q GIN +LYYAPE+ + G Sbjct: 219 LSIKHDSLRSKKMKLFSAKNRLPLFLAGII------AIFNQLSGINFILYYAPEIMEKAG 272 Query: 309 ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAP 368 T +LL + +G NL FT++ + +DK GRK L +IG++G I + + FY + Sbjct: 273 FVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTGRKQLMLIGSMGYIISLGLVSYGFYDSSS 332 Query: 369 GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPM 428 + L S+L ++AA + G V WV +SEIFPN +R + W ++ Sbjct: 333 PLFILTSILIFIAAHGIGQGAVIWVFISEIFPNKVRAMGQSFGAGVHWGGAAMITLF--- 389 Query: 429 MDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEA 476 + L+ + ++ + +L +F+W+++PETKG LE L + Sbjct: 390 ---GAVLIDTLMPFQIFMVFMALMILQFVFVWRYMPETKGLELENLHS 434 Lambda K H 0.326 0.140 0.433 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: 570 Number of extensions: 34 Number of successful extensions: 6 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: 491 Length of database: 450 Length adjustment: 33 Effective length of query: 458 Effective length of database: 417 Effective search space: 190986 Effective search space used: 190986 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: 51 (24.3 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