Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 3607946 Dshi_1354 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Dino:3607946 Length = 416 Score = 145 bits (367), Expect = 1e-39 Identities = 76/238 (31%), Positives = 133/238 (55%), Gaps = 2/238 (0%) Query: 54 NYIKMLGGSNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWAL 113 N+ ++ F L T ++ V ++ G+ AALLLN+ FRG+ LR L + P+ Sbjct: 180 NFARIFDADEFWGVLGVTMFYTVFGTLGALLFGLFAALLLNKSFRGQGILRGLYLFPYVA 239 Query: 114 PTVVNATLWRLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVA 173 P + A W +++P G+ NA L Q+G+ + ++ G+ AL + V + W+ FPL Sbjct: 240 PVIAVAFTWVTLFDPFSGSANALLIQMGVTNEAINFFGQRPLALIMVTVFEIWRYFPLSF 299 Query: 174 LIALAALQAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIW 233 L LA +Q++ D+ A+ +DGA PF +F ++ +P L G L V +LR I F FD I+ Sbjct: 300 LFILARMQSIDTDMYEAADMDGASPFQKFWYLSLPMLVGILSVLFLLRFIWTFNKFDDIF 359 Query: 234 VMTRGGPANSTRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRKAAG 291 ++T G TRTL++ VY++AF+ G+GA++A+++ + + + + + + G Sbjct: 360 LLTGGNA--GTRTLTVNVYEQAFAVSNIGAGAAVAVVIFGCLLLFSVLFFRFISREEG 415 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: 283 Number of extensions: 15 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: 293 Length of database: 416 Length adjustment: 29 Effective length of query: 264 Effective length of database: 387 Effective search space: 102168 Effective search space used: 102168 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: 49 (23.5 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