Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 103 bits (257), Expect = 4e-27 Identities = 65/203 (32%), Positives = 106/203 (52%), Gaps = 6/203 (2%) Query: 20 GLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLIYFA 79 GL L L LA + I IG+L+A S +R + V++ V R P++ ++ + Sbjct: 154 GLMLTLILAYIGIIASLPIGILLALGRRSDMPIIRGICVVFIEVWRAVPLITVLFMASVM 213 Query: 80 LPSL---GIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVKA 136 LP G+ +KL +I ++L+ AY+ EV RGGL +IP+G EA A+GLG W+ Sbjct: 214 LPLFLPEGVNFEKLARALIGITLWQSAYMAEVIRGGLQAIPRGQYEAADALGLGYWRKMG 273 Query: 137 YVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVE---SYRVIETWLV 193 V +P L+ V+P + N FISLFKDT+L I + ++ + + IE ++ Sbjct: 274 LVILPQALKMVIPGIVNTFISLFKDTTLVLIIGLFDILGTVQSTVTDPAWQNVAIEGYVF 333 Query: 194 TTALYVAACYLIAMLLRYLEQRL 216 + C+ I+ + LE++L Sbjct: 334 VAFCFWVFCFGISRYSQNLERKL 356 Lambda K H 0.329 0.143 0.416 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: 222 Number of extensions: 16 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: 220 Length of database: 362 Length adjustment: 26 Effective length of query: 194 Effective length of database: 336 Effective search space: 65184 Effective search space used: 65184 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: 47 (22.7 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