Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_110804310.1 C8J30_RS03235 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >NCBI__GCF_003217355.1:WP_110804310.1 Length = 290 Score = 126 bits (317), Expect = 5e-34 Identities = 93/286 (32%), Positives = 148/286 (51%), Gaps = 12/286 (4%) Query: 8 TRAWLLMLPLLVVMTAVIGW---PLVDTVRLSFTDAKLVGTE-GGFVGTANYIKMLGGSN 63 T A L++ P ++++ +GW PL T+ S L+ GGF G NY L Sbjct: 8 TAARLMISPAVILL---LGWMIVPLAMTLWFSMQRYNLLMPGMGGFTGFDNYSYFLTDPA 64 Query: 64 FQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWR 123 F A+ T + +A V G+L ALLL+Q F G+ +R L+I P+ + V+A +W+ Sbjct: 65 FFDAIKNTLVLVLGVLAITTVGGLLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWK 124 Query: 124 LIY-NPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQA 182 ++ NP G +GL +L + A LIVA W+ P LI L ALQ+ Sbjct: 125 NMFMNPVNGVFAHLAKSIGLQPY--DFLAQSPLASIVLIVA--WQWLPFATLILLTALQS 180 Query: 183 VPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPAN 242 + + A+ +DGAGP +RF +V++P+LA + V ++++TI F I V T GGP Sbjct: 181 LDSEQLEAAEMDGAGPISRFFYVMLPHLARAITVVILIQTIFLLSTFAEILVTTNGGPGT 240 Query: 243 STRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288 ++ TL+ LVY ++ GSGA+ ++ +L I+A ++ K Sbjct: 241 ASTTLTYLVYVQSLLQFDVGSGAAGGIVAVVLANIVAIFLMRMIGK 286 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: 218 Number of extensions: 16 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: 290 Length adjustment: 26 Effective length of query: 267 Effective length of database: 264 Effective search space: 70488 Effective search space used: 70488 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