Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate AZOBR_RS18175 AZOBR_RS18175 sugar ABC transporter
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__azobra:AZOBR_RS18175 Length = 295 Score = 178 bits (452), Expect = 1e-49 Identities = 101/293 (34%), Positives = 163/293 (55%), Gaps = 7/293 (2%) Query: 3 GTWISTRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGT-EGGFVGTANYIKMLGG 61 G W+ L + P+ + + G+PLV LS T L+ + +VG NY +++ Sbjct: 4 GRWVPA---LFVAPVALYLLVFQGYPLVQEFLLSVTSTSLLSPGQQTYVGLDNYRELVFD 60 Query: 62 SNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATL 121 F + L T + ++ V A + LG+LAALLL+ FRGR RAL+ +PWA P V A + Sbjct: 61 PEFHQVLRVTAVYTLVCVVASIGLGLLAALLLDGTFRGRGIARALVTIPWAAPPVAAALI 120 Query: 122 WRLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQ 181 + ++N +YG + LG + +WL EP AL A+++ W+ FP +++ LAALQ Sbjct: 121 FVWMFNAQYGLFSHLAQFLGFAEGGVNWLDEPSFALPAILITTIWQIFPFSSVVILAALQ 180 Query: 182 AVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPA 241 VP ++ A+++DGA + FR V P + + + +L T+ + + FD+IW+MT+GGP Sbjct: 181 GVPSELREAAVIDGADRLSIFRAVTWPTIRPSVALLTLLITVWSLRRFDVIWLMTQGGPL 240 Query: 242 NSTRTLSILVYQEAFSFQRAGSGAS---LALIVTLLVTILAAAYAALLRKAAG 291 T TL I +Y+ AF + G A+ + L+V +LVT++ + KAAG Sbjct: 241 GETNTLVIDLYRRAFVYLDLGRAAAVGIIGLVVAILVTLVYFWLSTRAEKAAG 293 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: 251 Number of extensions: 12 Number of successful extensions: 1 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: 295 Length adjustment: 26 Effective length of query: 267 Effective length of database: 269 Effective search space: 71823 Effective search space used: 71823 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