Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 92.8 bits (229), Expect = 1e-23 Identities = 48/121 (39%), Positives = 75/121 (61%) Query: 271 LALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQ 330 +AL+ +T A++AEIVRAGI+ V +GQ EAA +LG+ A R V++PQA R I+PPL Q Sbjct: 214 MALALFTGAYVAEIVRAGIQSVHRGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQ 273 Query: 331 YLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNA 390 +++L K+SSL I +L ++ + Q E+ + ++YL L+ SLF+ + Sbjct: 274 FISLIKDSSLLGVIAIRELTKATREVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLER 333 Query: 391 R 391 R Sbjct: 334 R 334 Score = 48.9 bits (115), Expect = 2e-10 Identities = 48/181 (26%), Positives = 82/181 (45%), Gaps = 50/181 (27%) Query: 19 INDPQVRG--IFYQAITIIILAALI--YWIVDNTVDNLRRANIASGYDFV------RSRA 68 ++ P+ RG +F++A+ + + AL+ +W+ ++V+ + R N Y +V R+ A Sbjct: 7 LDKPKGRGFFLFWKAMFVAAMLALVAFFWVASSSVEYIWRWNRVPQYFWVNEAADVRAEA 66 Query: 69 GFDV---------------------------GQSLISFTS-DSTY-----GR-------A 88 DV G+S + +S D TY GR Sbjct: 67 EGDVTIIDRQGNEQRVVVRDASGEEHTHLLPGESKVLVSSGDFTYRGDVLGRYQLNRPGI 126 Query: 89 LLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFW 148 LL G TL V++ II +IG + G+ R+S N ++ ++ Y+E+ R P L+ IF W Sbjct: 127 LLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLW 186 Query: 149 Y 149 Y Sbjct: 187 Y 187 Lambda K H 0.327 0.141 0.412 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: 324 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 397 Length of database: 337 Length adjustment: 30 Effective length of query: 367 Effective length of database: 307 Effective search space: 112669 Effective search space used: 112669 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: 49 (23.5 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