Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate 206098 DVU0674 ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >MicrobesOnline__882:206098 Length = 271 Score = 135 bits (341), Expect = 6e-37 Identities = 74/201 (36%), Positives = 122/201 (60%), Gaps = 3/201 (1%) Query: 17 LLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLI 76 LL GLG+ L++A S+ + ++ + LS R R++A +YV +RNTP+LV + + Sbjct: 69 LLQGLGVTLQVAAGSLVLALLLAAVAVALRLSCLRTGRLVARLYVESVRNTPLLVQLFVT 128 Query: 77 YFAL-PSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVK 135 YFA+ P G L ++ S ++ L ++ GAY+ E+ R G+ ++P+G EA ++G+ E Sbjct: 129 YFAIAPVFG--LGRMASAVMALGVFEGAYMAEILRAGIAAVPQGQWEASRSLGMDEPGTY 186 Query: 136 AYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTT 195 V +P LR LP L+ +SL KD+SLA+AIA+ ELT A+ I E++ E WL+T Sbjct: 187 VQVILPQALRRALPPLTGQAVSLVKDSSLASAIAIHELTMQAQTIIAETFLTFEVWLLTA 246 Query: 196 ALYVAACYLIAMLLRYLEQRL 216 A+Y+ ++ + R LE+R+ Sbjct: 247 AIYLCVTLSLSAVARLLERRM 267 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: 175 Number of extensions: 6 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: 271 Length adjustment: 24 Effective length of query: 196 Effective length of database: 247 Effective search space: 48412 Effective search space used: 48412 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