Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 248 bits (633), Expect = 3e-70 Identities = 152/448 (33%), Positives = 240/448 (53%), Gaps = 28/448 (6%) Query: 23 VAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV-SLALLGSALGAFGAGPIADRH 81 + +L GFLFGFDTAVI+GA L+ +QT G + S+AL G+ +GA G Sbjct: 11 IVSLTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHL 70 Query: 82 GRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEVSPAHLR 141 GR T+ V+F +S++G+ L + F F+R +GG+ +GA+S+ AP Y++E+S A+ R Sbjct: 71 GRKNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQR 130 Query: 142 GRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGV 201 GR L Q+ IVSGI +A +SN+ L+ G N WRWM E+IPA++Y Sbjct: 131 GRRVGLYQINIVSGILVAYVSNY---LLQGVGDHND-------WRWMLAAEIIPAIIYLA 180 Query: 202 CAFLIPESPRYLVAQGQGEKAA-AILWKVEGGDVPSRIEEIQATVSLDHKPRFSDLLSRR 260 IPESPR+L+ + + E AA +L K+ G + + I+ K + +R Sbjct: 181 FILDIPESPRWLILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSKKMKLFSAKNR- 239 Query: 261 GGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGFINILTTLV 320 LP+ G+ ++ Q GIN I YY+ + GF SLL V GF N++ TL+ Sbjct: 240 ---LPLFLAGI-IAIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLI 295 Query: 321 AIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIALVTANLYV 380 ++ +DK GRK L+L+GS+G I+LG++S F ++ + L + +++ Sbjct: 296 GMSLIDKTGRKQLMLIGSMGYIISLGLVSYGF-----------YDSSSPLFILTSILIFI 344 Query: 381 FSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDTVGLGPAYG 440 + G G ++WV + E+F NK+RA S AGV W +I+ L+DT+ + Sbjct: 345 AAHGIGQGAVIWVFISEIFPNKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFM 404 Query: 441 LYATSAAISIFFIWFFVKETKGKTLEQM 468 ++ + F+W ++ ETKG LE + Sbjct: 405 VFMALMILQFVFVWRYMPETKGLELENL 432 Lambda K H 0.325 0.140 0.430 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: 580 Number of extensions: 29 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: 468 Length of database: 450 Length adjustment: 33 Effective length of query: 435 Effective length of database: 417 Effective search space: 181395 Effective search space used: 181395 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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