Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate H281DRAFT_05871 H281DRAFT_05871 amino acid ABC transporter membrane protein 1, PAAT family (TC 3.A.1.3.-)
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Burk376:H281DRAFT_05871 Length = 238 Score = 136 bits (342), Expect = 4e-37 Identities = 82/219 (37%), Positives = 121/219 (55%), Gaps = 6/219 (2%) Query: 1 MNYQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVY 60 MNYQ + +W L L L + L+S + +GL A A +S ++R +A Y Sbjct: 1 MNYQ--WLTLWGYVPEFLKAGWLTLQVTLLSFVLALALGLIAALASMSPSAIVRFIARAY 58 Query: 61 VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQ 120 V IRNTP+L+ I +++F LPS+GI LD + VI L + GAYL+EVFR G+ S+ +GQ Sbjct: 59 VEAIRNTPVLLQIFIVFFGLPSMGIALDAYWAGVIALGVNVGAYLSEVFRAGMQSVPRGQ 118 Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180 EA +GL Q+ + +P R V PA+ N I L TSL +AIA+PELT A I Sbjct: 119 IEAAGILGLERGQIFKEIVMPQAARAVYPAIVNYLIQLLLGTSLLSAIALPELTGTATVI 178 Query: 181 NVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLAIR 219 N + ++T+ V Y+ +++ VL + +L R Sbjct: 179 NSRTLLYVQTFAVVLVAYL----VLSNVLSWIASQLGAR 213 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: 151 Number of extensions: 9 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: 238 Length adjustment: 23 Effective length of query: 197 Effective length of database: 215 Effective search space: 42355 Effective search space used: 42355 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