Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::Smeli:SMc02119 (397 letters) >MicrobesOnline__882:206399 Length = 337 Score = 91.7 bits (226), Expect = 3e-23 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 13/213 (6%) Query: 185 EGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLW-TVLGLIIGLPLVT-----FL 238 EG TL ++A+ + +++ L L T + +I G PL+ + Sbjct: 129 EGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFLWYF 188 Query: 239 VTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTE 298 V G + F G S + P + + +AL+ +T A++AEIVRAGI+ V +GQ E Sbjct: 189 VVGTLLN------ALFEKVGLSAIPPLWYGV-MALAIFTGAYVAEIVRAGIQSVHRGQME 241 Query: 299 AAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILN 358 AA +LG+ A + R V++PQA R I+PPL Q+++L K+SSL I +L ++ Sbjct: 242 AARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVT 301 Query: 359 QTGQSIEIVSIWLIVYLSLSLATSLFMNWYNAR 391 + Q E+ + ++YL L+ SL + + R Sbjct: 302 TSLQPFELWIVCALLYLVLTFTLSLCVQYLERR 334 Score = 49.7 bits (117), Expect = 1e-10 Identities = 32/100 (32%), Positives = 53/100 (53%), Gaps = 8/100 (8%) Query: 57 IASGYDFVRSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGI 116 + SG D++ S G VG+ +S LL G TL V++ II ++G + G+ Sbjct: 103 LISGGDYIYS--GDPVGRYEVSKPG------ILLEGLWITLEVSMLAIIIGIVLGVVTGL 154 Query: 117 GRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSIL 156 R+S N + L++ Y+E+ R P L+ +F WY V ++L Sbjct: 155 ARISVNPALRWLAITYIEIIRGSPLLVQVFLWYFVVGTLL 194 Score = 23.9 bits (50), Expect = 0.007 Identities = 32/150 (21%), Positives = 57/150 (38%), Gaps = 39/150 (26%) Query: 245 TFDIPVAGKFNLTGGSVV--------------GPEFMSLFLALSFYTAAFIAEIVRAGIR 290 T+ +P AGK ++GG + G L++ L A I IV + Sbjct: 93 TYTVPPAGKVLISGGDYIYSGDPVGRYEVSKPGILLEGLWITLEVSMLAIIIGIVLGVVT 152 Query: 291 GVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLV 350 G+++ + + PAL L Y+ + + S L V + V Sbjct: 153 GLAR--------ISVNPALRW---------------LAITYIEIIRGSPLLVQVFLWYFV 189 Query: 351 AVGGTILNQTGQSIEIVSIWLIVYLSLSLA 380 GT+LN + + + +I + Y ++LA Sbjct: 190 V--GTLLNALFEKVGLSAIPPLWYGVMALA 217 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: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 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