Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate H281DRAFT_05891 H281DRAFT_05891 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Burk376:H281DRAFT_05891 Length = 318 Score = 156 bits (394), Expect = 7e-43 Identities = 97/284 (34%), Positives = 155/284 (54%), Gaps = 5/284 (1%) Query: 1 MTGTWISTRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAK--LVGTEGGFVGTANYIKM 58 +TG T AWL +LP ++++ A+ +PL+ +RLSFT+ K + FVG NY+ + Sbjct: 24 LTGLSDRTIAWLFILPTILLLLAINIFPLIWALRLSFTNFKSNMPSVPARFVGIDNYVDI 83 Query: 59 LGGSNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVN 118 L + A+ T F SV E++LG ALL+N+QFRG + L++LP L V Sbjct: 84 LTDEDIWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLPMMLSPAVV 143 Query: 119 ATLWRLIYNPEYGALNAALTQL-GLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIAL 177 W + P+ G N + G+ +G+ A +++ D W P V LI L Sbjct: 144 GNFWTFLLQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVMLICL 203 Query: 178 AALQAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTR 237 A L+++P I A+ VD A P+ +F + +P L++A++ R IE FK+FD++ ++T Sbjct: 204 AGLRSIPDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVNLLTS 263 Query: 238 GGPANSTRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAA 281 GGP + T T+SI + + AF + G ++LA+I L VT+ AA Sbjct: 264 GGPGSVTETVSITLKRAAFEKWQTGYSSALAII--LFVTVFGAA 305 Lambda K H 0.326 0.138 0.417 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: 238 Number of extensions: 13 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: 293 Length of database: 318 Length adjustment: 27 Effective length of query: 266 Effective length of database: 291 Effective search space: 77406 Effective search space used: 77406 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: 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