Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate 17718 b3657 putative permease (VIMSS)
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Keio:17718 Length = 460 Score = 379 bits (972), Expect = e-109 Identities = 190/441 (43%), Positives = 276/441 (62%), Gaps = 3/441 (0%) Query: 1 MLSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPL 60 +LSV+EKI YG+GD AS+I+F VML++ FFYTDIFGI A +VGTMFL R +DA++DP Sbjct: 5 VLSVKEKIGYGMGDAASHIIFDNVMLYMMFFYTDIFGIPAGFVGTMFLVARALDAISDPC 64 Query: 61 MGYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYT 120 MG LADRT +RWG++RP++L+ A PF + VLA++TPDLS +GK YA TY LL L YT Sbjct: 65 MGLLADRTRSRWGKFRPWVLFGALPFGIVCVLAYSTPDLSMNGKMIYAAITYTLLTLLYT 124 Query: 121 AINIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQL 180 +NIPYCALG +T +P +R+S+QS+RFV A GG++ + L +PLV+ G +K G+Q Sbjct: 125 VVNIPYCALGGVITNDPTQRISLQSWRFVLATAGGMLSTVLMMPLVNLIGGDNKPLGFQG 184 Query: 181 TILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQWRVLSAAAIFLLTG 240 I +S+V +M CF TKER + + + + + +W NDQWR++ IF + Sbjct: 185 GIAVLSVVAFMMLAFCFFTTKER-VEAPPTTTSMREDLRDIWQNDQWRIVGLLTIFNILA 243 Query: 241 LVLKSTLAIYYVKYFLGREDMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLIA 300 + ++ +YYV + LG ++ F+T+ VGN+ G ALAK L D CKV + + Sbjct: 244 VCVRGGAMMYYVTWILGTPEVFVAFLTTYCVGNLIGSALAKPLTDWKCKVTIFWWTNALL 303 Query: 301 AALCMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTGLVY 360 A + +A +FVP + VF + TP+ W M+DTVDYG++ G R TG+ + Sbjct: 304 AVISLAMFFVPMQASITMFVFIFVIGVLHQLVTPIQWVMMSDTVDYGEWCNGKRLTGISF 363 Query: 361 SSVIFFIKLGLAIGGALGGWLLAAYGYQ-PDVAQTEETRAGILLCFTLYPALASIAVAFV 419 + +F +KLGLA GGAL GW+LA GY + AQ T + I+ FT+ PA+ + A + Sbjct: 364 AGTLFVLKLGLAFGGALIGWMLAYGGYDAAEKAQNSATISIIIALFTIVPAICYLLSAII 423 Query: 420 -MRHYTLDSQRVAEISVSLQQ 439 R+Y+L + + + L Q Sbjct: 424 AKRYYSLTTHNLKTVMEQLAQ 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: 571 Number of extensions: 24 Number of successful extensions: 3 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