Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 164 bits (415), Expect = 2e-45 Identities = 93/289 (32%), Positives = 155/289 (53%), Gaps = 30/289 (10%) Query: 27 LVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQ------------- 73 L+ LP LWI L+S + + +A PPV + + S++ Y +F+ + Sbjct: 30 LIAILPILWICLTSFKTQEDAIAYPPVVLFQP-SMEGYVNLFTIRSRQTPEFIASLPPAQ 88 Query: 74 ---------------GGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAI 118 G V F NSL++ ST +A+ +G YAF+R++ + Sbjct: 89 TWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDL 148 Query: 119 FLGFMLTRAVPGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPK 178 + TR +P IA+++P++++Y G+ D++ +I+ Y A+NV +WL+ GF ++P+ Sbjct: 149 LFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDEIPR 208 Query: 179 DLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLP 238 + EAA +DG T QAF +V P A GIA+ IF + +WNEYA AS +T S +++T+P Sbjct: 209 EYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLT-SGDAQTMP 267 Query: 239 VGLLDYTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVK 287 + E DW + A + +VP L T +++KHL+ G+TFGAV+ Sbjct: 268 PFIPFIIGEGGQDWPAVAAATTLFVVPILIFTVVLRKHLLRGITFGAVR 316 Lambda K H 0.328 0.141 0.442 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: 246 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 288 Length of database: 317 Length adjustment: 27 Effective length of query: 261 Effective length of database: 290 Effective search space: 75690 Effective search space used: 75690 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 (21.8 bits) S2: 48 (23.1 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