Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 265 bits (678), Expect = 2e-75 Identities = 162/477 (33%), Positives = 257/477 (53%), Gaps = 26/477 (5%) Query: 1 MNPSSSPSQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV 60 +N +S P+ T FV +++ +A LGG LFG+DT VI+GA+ + TGL Sbjct: 9 LNKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVT 68 Query: 61 SLALLGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIG 120 S L G+A GA +G +A+ GR K ++ AVLF + +IG+ + + IF+R++ G+ Sbjct: 69 SSLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVA 128 Query: 121 VGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLF 180 VG A+ P YIAE++PA+ RG+L +LQ+L IVSG +A +SN + GG Sbjct: 129 VGGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGE------- 181 Query: 181 GAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEE 240 + WRWM +PA+L +P+SPR+ +G+ +A +L + D E Sbjct: 182 --STWRWMLAVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKD-DVEWEL 238 Query: 241 IQATVSLDH-----KPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRS 295 ++ T +LD KPRFS++++ L + IG+G++ +QQ G+N I YY+ + S Sbjct: 239 LEITETLDEQRNLGKPRFSEIMT--PWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTS 296 Query: 296 VGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVV-FGG 354 VG T+ +L T+ G +++L T V I + K GR+P+ ++G G T L + V + Sbjct: 297 VGMTDNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLL 356 Query: 355 ATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWG---PIVWVLLGEMFNNKIRAAALSVA 411 VNGQP A +V A + +F F G P+ W+L+ E+F ++R + A Sbjct: 357 PETVNGQPDALRA----YMVLAGMLLF-LSFQQGALSPVTWLLMSEIFPTRLRGIFMGGA 411 Query: 412 AGVQWIANFIISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 WIANF+IS FP LL +GL + ++A F+ V ET+ ++LEQ+ Sbjct: 412 VFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQI 468 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: 638 Number of extensions: 41 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: 468 Length of database: 499 Length adjustment: 34 Effective length of query: 434 Effective length of database: 465 Effective search space: 201810 Effective search space used: 201810 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: 52 (24.6 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