Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 173 bits (438), Expect = 5e-48 Identities = 91/278 (32%), Positives = 159/278 (57%), Gaps = 2/278 (0%) Query: 12 LLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVTT 71 L M P ++++ + +PL + L FTD K +G EG F+G N+ + G S Q +L T Sbjct: 15 LFMAPAVILLVVFLTYPLGLGIWLGFTDTK-IGGEGSFIGLDNFTYLAGDSLAQLSLFNT 73 Query: 72 TWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEYG 131 ++ V + + +LG+ A+LLN+ +T RA+++LPW +PT ++A + +Y+ ++ Sbjct: 74 VFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALSALAFWWLYDAQFS 133 Query: 132 ALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAAS 191 ++ AL ++GL+D Y +LG+P A + + A+ W+ P VA+ LA LQ + + A+ Sbjct: 134 VISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPSLYEAA 193 Query: 192 LVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSILV 251 +DGA P+ +FR V +P L + V + + F F +I+V+TRGGP N+T ++ L Sbjct: 194 AIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGGPLNATHLMATLS 253 Query: 252 YQEAFSFQRAGSGASLA-LIVTLLVTILAAAYAALLRK 288 +Q A G GA+LA ++ L+ + +Y L R+ Sbjct: 254 FQRAIPGGALGEGAALATYMIPFLLAAIMFSYFGLQRR 291 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: 288 Number of extensions: 11 Number of successful extensions: 2 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: 299 Length adjustment: 26 Effective length of query: 267 Effective length of database: 273 Effective search space: 72891 Effective search space used: 72891 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