Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_007692967.1 C447_RS08630 sugar porter family MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >NCBI__GCF_000336675.1:WP_007692967.1 Length = 470 Score = 310 bits (795), Expect = 5e-89 Identities = 174/447 (38%), Positives = 262/447 (58%), Gaps = 6/447 (1%) Query: 9 RSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVG 68 R + + + F+ AL GLLFG D GVIAGALP+I + F +++ QE V S++ GA +G Sbjct: 12 REHPRFVYVMAFVGALNGLLFGFDTGVIAGALPYIQETFTLSTFLQEVVTVSVLVGAMIG 71 Query: 69 AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128 A G L+ + GR++ ++GA++F +L A +P+VE LI R++LG+AVG+AS PL Sbjct: 72 AATGGRLADRFGRRRLTLVGAVIFFVAALGLAVSPSVEWLIGWRIVLGVAVGIASLIGPL 131 Query: 129 YLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAF--SYTG--AWRWMLGVIIIPAILL 184 Y+SE APE IRG++ + QLMI +GIL AY+ + F S G WRWMLG +PA++L Sbjct: 132 YISETAPEDIRGTLGFLQQLMIVVGILVAYVVNAIFAPSLLGIIGWRWMLGFAAVPAVIL 191 Query: 185 LIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKE 244 + +FFLP+SPRW R +A VL R+R+ A+ + E+ + E + + G Sbjct: 192 GVTMFFLPESPRWLVEHDRHDEARDVLSRIRN-EADFESEIQRMEEISERESEGSWRDVL 250 Query: 245 NSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLAT 304 R A+ +GV L V+QQ TG+N ++YYAP I + G + ++GT+ +G+ NV T Sbjct: 251 EPWIRPALTVGVALAVLQQVTGINTVLYYAPTILQNIG-LGSAASLFGTIGIGIVNVALT 309 Query: 305 FIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAM 364 +A+ DR GR+P L + M +G LG ++ S YF + +++++ FA+ Sbjct: 310 IVAVYYADRIGRRPLLLVSVGGMTVMLGALGLGFYLPGLSGVVGYFTLGSMILYVAFFAL 369 Query: 365 SAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAAL 424 GP+ W+L SEI PL+ R +T NW AN+IV TFL+++ G +FW Sbjct: 370 GLGPVFWLLTSEIFPLRVRGTAEGITTFFNWSANLIVSLTFLSLIERFGQTASFWALGFF 429 Query: 425 NVLFILLTLWLVPETKHVSLEHIERNL 451 VL + + VPET SLE IE +L Sbjct: 430 GVLGFVYIYFRVPETMGRSLEDIEDDL 456 Lambda K H 0.327 0.140 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: 827 Number of extensions: 56 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: 464 Length of database: 470 Length adjustment: 33 Effective length of query: 431 Effective length of database: 437 Effective search space: 188347 Effective search space used: 188347 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 24 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