Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate BWI76_RS27490 BWI76_RS27490 sodium:galactoside symporter
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Koxy:BWI76_RS27490 Length = 444 Score = 357 bits (915), Expect = e-103 Identities = 181/443 (40%), Positives = 271/443 (61%), Gaps = 3/443 (0%) Query: 2 LSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLM 61 LS+ EKI +G GD A N+V + L L +FYTDI+G+SAA VG +F+ VR++DA+ DP M Sbjct: 3 LSIVEKIGFGAGDMAINVVIIAMQLLLAYFYTDIYGLSAADVGVLFVVVRMIDAIIDPAM 62 Query: 62 GYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYTA 121 G L D+ NTRWGRYRP+LLWFA PF L F TPD+ K +A+ TY L+ L YTA Sbjct: 63 GVLTDKLNTRWGRYRPWLLWFAIPFGFAVYLMFITPDMVYMAKLAWAYGTYILMTLVYTA 122 Query: 122 INIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQLT 181 I IPY ++ +T++P ER+S YRFV + +V+ + L + GQG+KA GYQ + Sbjct: 123 ITIPYISMIGVITSDPVERLSANGYRFVMTKIAAFLVTIVVPMLAVWLGQGNKALGYQFS 182 Query: 182 ILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQWRVLSAAAIFLLTGL 241 + M +G ++F+ CF+ T+ER + S + K L NDQW +L + L+ G Sbjct: 183 MGLMGAMGALLFIFCFLTTRERS-EPEITSLSVGKQFKYLLRNDQWIILGVVILLLMCGY 241 Query: 242 VLKSTLAIYYVKYFL-GREDMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLIA 300 V++ ++A YY KY+L G + +IS F+T+GVV +I + + K+K + Q+I Sbjct: 242 VIRGSVAAYYAKYYLNGGDSLISPFLTTGVVASILAMIATTWITKFWDKIKMFRYTQIIT 301 Query: 301 AAL-CMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTGLV 359 L M +FV + +LA FY NF +M P+ W+ +A+ VDYG+ KTG+R +GL Sbjct: 302 FVLSAMMYFFVGRENLILAFTFYFLINFFCDMQMPVFWSSIAEAVDYGEKKTGLRVSGLA 361 Query: 360 YSSVIFFIKLGLAIGGALGGWLLAAYGYQPDVAQTEETRAGILLCFTLYPALASIAVAFV 419 + ++FF K G+ I G + G+LL+ +GYQ DV Q+ + GI L TL PAL +AV + Sbjct: 362 FGGILFFQKFGMGIAGGVLGFLLSHFGYQADVEQSARSLTGIALMMTLIPALFHLAVGLL 421 Query: 420 MRHYTLDSQRVAEISVSLQQKHS 442 M+ Y ++++ +I ++L QK + Sbjct: 422 MKKYLINNEYYRDIQLALAQKQA 444 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: 540 Number of extensions: 24 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: 444 Length of database: 444 Length adjustment: 32 Effective length of query: 412 Effective length of database: 412 Effective search space: 169744 Effective search space used: 169744 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