Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate 14408 b0270 CP4-6 prophage; predicted sugar transporter (NCBI)
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Keio:14408 Length = 460 Score = 324 bits (831), Expect = 3e-93 Identities = 167/437 (38%), Positives = 247/437 (56%), Gaps = 1/437 (0%) Query: 2 LSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLM 61 L++++KI YGLGDTA V+Q M L +FYTD+FG+SA +GT+FL R++DAVTDPLM Sbjct: 4 LTMKDKIGYGLGDTACGFVWQATMFLLAYFYTDVFGLSAGIMGTLFLVSRVLDAVTDPLM 63 Query: 62 GYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYTA 121 G L DRT TR G++RP+LLW A PF + VL F TPD S GK YA TY LL L YT Sbjct: 64 GLLVDRTRTRHGQFRPFLLWGAIPFGIVCVLTFYTPDFSAQGKIIYACVTYILLTLVYTF 123 Query: 122 INIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQLT 181 +N+PYCA+ +T +P ER ++QS+RF A G + +S + LPLV G+GD+ GY Sbjct: 124 VNVPYCAMPGVITADPKERHALQSWRFFLAAAGSLAISGIALPLVSIIGKGDEQVGYFGA 183 Query: 182 ILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQWRVLSAAAIFLLTGL 241 + + + G V+ +CF TKER + K L N QWR++ A + Sbjct: 184 MCVLGLSGVVLLYVCFFTTKERYTFEVQPGSSVAKDLKLLLGNSQWRIMCAFKMMATCSN 243 Query: 242 VLKSTLAIYYVKYFLGREDMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLIAA 301 V++ +Y+VKY + ++ + F+ G + +FG + +L + +V A+ + + + Sbjct: 244 VVRGGATLYFVKYVMDHPELATQFLLYGSLATMFGSLCSSRLLGRFDRVTAFKWIIVAYS 303 Query: 302 ALCMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTGLVYS 361 + + + PA+ L I + F N TPL W +D VDY + ++G R GLV+S Sbjct: 304 LISLLIFVTPAEHIALIFALNILFLFVFNTTTPLQWLMASDVVDYEESRSGRRLDGLVFS 363 Query: 362 SVIFFIKLGLAIGGALGGWLLAAYGYQPDVA-QTEETRAGILLCFTLYPALASIAVAFVM 420 + +F +K+GLAIGGA+ GW+LA Y + Q E I + F + P + + ++ Sbjct: 364 TYLFSLKIGLAIGGAVVGWILAYVNYSASSSVQPVEVLTTIKILFCVVPVVLYAGMFIML 423 Query: 421 RHYTLDSQRVAEISVSL 437 Y L RV IS L Sbjct: 424 SLYKLTDARVEAISRQL 440 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: 547 Number of extensions: 24 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: 460 Length adjustment: 33 Effective length of query: 411 Effective length of database: 427 Effective search space: 175497 Effective search space used: 175497 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