Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_106711243.1 CU102_RS11575 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >NCBI__GCF_003010955.1:WP_106711243.1 Length = 309 Score = 182 bits (461), Expect = 1e-50 Identities = 92/278 (33%), Positives = 169/278 (60%), Gaps = 3/278 (1%) Query: 11 WLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVT 70 W ++P LV++ AVI +P V T+ +S + L G E FVG AN+I++ G F ++ Sbjct: 30 WPFVIPALVIVGAVIIFPWVFTLWMSVNEWHL-GGEKSFVGLANFIRLAGDQRFWESMSH 88 Query: 71 TTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEY 130 T + V+SV A + LG +AAL+ + + R LR + ++P V A +W ++++P+ Sbjct: 89 TVLYTVLSVVAPLFLGTIAALVFDSKLPMRGLLRGIFVMPMMATPVAIALVWTMMFHPQL 148 Query: 131 GALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAA 190 G LN L+ +G+ + W+ T + +L++ + W+ PLV LI L L A+PRD + Sbjct: 149 GVLNYLLSLIGI--GPQEWIFNQNTVIPSLVLVETWQWTPLVMLIVLGGLAAMPRDPFES 206 Query: 191 SLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSIL 250 + +DGA + +FR++ +P + ++VA+++R+I+A K FDII+ MT+GGP ++ T++I Sbjct: 207 AEIDGANGWQKFRYITLPMILPFMMVAVIIRSIDALKSFDIIFAMTQGGPGTASETINIY 266 Query: 251 VYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288 +Y AF++ G G++LA++ +++ ++ A L ++ Sbjct: 267 LYNVAFAYYDIGYGSALAVVFFIVIITMSLALLYLRQR 304 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: 267 Number of extensions: 14 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: 293 Length of database: 309 Length adjustment: 27 Effective length of query: 266 Effective length of database: 282 Effective search space: 75012 Effective search space used: 75012 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 24 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