Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 298 bits (762), Expect = 3e-85 Identities = 169/444 (38%), Positives = 257/444 (57%), Gaps = 6/444 (1%) Query: 18 HSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGV 77 +S +VI +S A LGG L+G+DTAVISGA F+++ + LS + G+ ++ + G V+G Sbjct: 2 NSKKYVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSDWTHGMAVAIALYGTVIGA 61 Query: 78 GISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTY 137 G +D++GR+ L+ +L+ ISA+ SAL+ DV + + R IGGLG+G S ++ Y Sbjct: 62 LFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPMY 121 Query: 138 ITEAAPPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPS 197 I+E AP RG L +LYQ + GI YF N ++ + E WRWM+ +P+ Sbjct: 122 ISEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNE-----SWRWMMGMEAIPA 176 Query: 198 VIFFLVLLVVPESPRWL-AKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLS 256 +I+ L+ + VP+SPRWL A K EA +IL + + E V + IE + + + Sbjct: 177 LIYTLLSIRVPKSPRWLIAHHNKVEEATQILRKTDPEGVDEAIHLAIEERNREKIKVGFA 236 Query: 257 QLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVI 316 LFK K ++ I++ALFNQ+ G+NAI Y+ P +F+M G Q + ++T +GVV +I Sbjct: 237 VLFKHSHLKTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMI 296 Query: 317 FTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVS 376 T+I + LID++GRKKLM IGS I ++L+ SF + + + + + F+A+ V Sbjct: 297 ATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMAYSFSGGVINSGYLPLFVFVFIASHAVG 356 Query: 377 VGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVIN 436 G + W+ ISE+FPN RA I W I P +SFG A F FAV+ Sbjct: 357 QGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMM 416 Query: 437 ILCFLFVVTICPETKNKSLEEIEK 460 L L+V+T PETK +SLEEI++ Sbjct: 417 GLQLLWVLTKMPETKGRSLEEIQQ 440 Lambda K H 0.327 0.142 0.425 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: 545 Number of extensions: 25 Number of successful extensions: 4 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: 464 Length of database: 448 Length adjustment: 33 Effective length of query: 431 Effective length of database: 415 Effective search space: 178865 Effective search space used: 178865 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