Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate HSERO_RS23035 HSERO_RS23035 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__HerbieS:HSERO_RS23035 Length = 277 Score = 145 bits (366), Expect = 7e-40 Identities = 78/225 (34%), Positives = 130/225 (57%), Gaps = 5/225 (2%) Query: 1 MNYQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVY 60 MN+ L+F+ + + L G L L + +++ +G IG+ +AFA S HR L S Y Sbjct: 1 MNFSLDFSPLAPYWPVFLHGAWLTLKMTTLAVIVGVAIGIFVAFAKNSPHRWLARGCSAY 60 Query: 61 VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQ 120 + V+RNTP LV I L+YF L SLGIR+ + V+ + + AY E+ R GL S+ +GQ Sbjct: 61 IEVVRNTPFLVQIFLLYFGLASLGIRMPTFAAAVLAMIINIAAYAAEIIRAGLDSVPRGQ 120 Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180 EA +GL W+++ +V + + V PAL++ F+ + + +++A+ I+ ELT A + Sbjct: 121 IEAAQCLGLSVWRIRWHVMLQPAIERVYPALTSQFLLMMQASAMASQISAEELTAIANTV 180 Query: 181 NVESYRVIETWLVTTALYVAACYLIAMVL-----RYFEQRLAIRR 220 +++R +ET+LV ALY+ L+ +V F++R +RR Sbjct: 181 QSDTFRSLETYLVVAALYLVLAILVKLVAYAIGETIFKRRRTLRR 225 Lambda K H 0.329 0.142 0.414 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: 162 Number of extensions: 8 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: 220 Length of database: 277 Length adjustment: 24 Effective length of query: 196 Effective length of database: 253 Effective search space: 49588 Effective search space used: 49588 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 (21.8 bits) S2: 46 (22.3 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