Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate BWI76_RS04865 BWI76_RS04865 MFS transporter
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Koxy:BWI76_RS04865 Length = 468 Score = 366 bits (940), Expect = e-106 Identities = 184/442 (41%), Positives = 278/442 (62%), Gaps = 4/442 (0%) Query: 2 LSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLM 61 LSV+EKI YG+GD NI+F +MLF+ +FYTDIFG++ A VG + L+VR++DAVTDP+M Sbjct: 6 LSVKEKIGYGMGDAGCNIIFGAIMLFVNYFYTDIFGLAPALVGVLLLSVRVIDAVTDPIM 65 Query: 62 GYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYTA 121 G +ADRT +++GR+RP+LLW AFP+A SVL FTTP+ + + K YAF TY LL L YTA Sbjct: 66 GAMADRTRSKYGRFRPWLLWIAFPYALFSVLMFTTPEWTYNSKVIYAFVTYFLLSLTYTA 125 Query: 122 INIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQLT 181 INIPYC+LG+ +T +P ERV+ QSYRFV + +++S LP+ D+FG DKAKGYQ+ Sbjct: 126 INIPYCSLGSVITNDPQERVACQSYRFVMVGIATLLLSLTLLPMADWFGGEDKAKGYQMA 185 Query: 182 ILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQW-RVLSAAAIFLLTG 240 + ++ +G MFL CF +ER + + K K +W NDQW R+L + G Sbjct: 186 MTVLAFIGMCMFLFCFATVRERVKPAVQTNDELKKDLKDVWKNDQWVRILLLTLCNVCPG 245 Query: 241 LVLKSTLAIYYVKYFLGRE-DMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLI 299 + + +YYV + + + ++F++ GVVG + G LAK L D+ CK++ + ++ Sbjct: 246 FI-RMAATMYYVTWVMQQSTHFATLFISLGVVGMMIGSMLAKVLTDRWCKLQVFFWTNIV 304 Query: 300 AAALCMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTGLV 359 A A +F ++ + Y N + +PL W+ MAD DYG++KTG R TG+ Sbjct: 305 LAVFSCAFYFFDPHATMMIMALYFLLNILHQIPSPLHWSLMADVDDYGEWKTGKRITGIS 364 Query: 360 YSSVIFFIKLGLAIGGALGGWLLAAYGYQPDVAQTEETRA-GILLCFTLYPALASIAVAF 418 +S +FF+K+GLAI GA+ G+LL+ YGY Q + GI+L F++ P + + A Sbjct: 365 FSGNLFFLKVGLAIAGAMVGFLLSWYGYDAGAKQQSASAINGIVLLFSVIPGVGYLITAG 424 Query: 419 VMRHYTLDSQRVAEISVSLQQK 440 V+R ++ + + +I L+++ Sbjct: 425 VVRMLKVNREFMRQIQSDLEKR 446 Lambda K H 0.327 0.139 0.421 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: 549 Number of extensions: 21 Number of successful extensions: 2 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: 444 Length of database: 468 Length adjustment: 33 Effective length of query: 411 Effective length of database: 435 Effective search space: 178785 Effective search space used: 178785 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