Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02119 (397 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 90.1 bits (222), Expect = 6e-23 Identities = 66/211 (31%), Positives = 103/211 (48%), Gaps = 16/211 (7%) Query: 190 TLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLG-----LIIGLPLVTFLVTGAPI 244 TL AF A+ + A + R L +W L +I G+P++ L+ A Sbjct: 51 TLFAFAGALVLGLVLAVASLSRHL--------IWRQLARFYTEVIRGVPIIVMLLYVAFA 102 Query: 245 TFDIPVAG--KFNLTGGSVVG-PEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAH 301 VAG L SV P LAL AAF+AE+ RAG+ V +GQ EAA Sbjct: 103 LVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQIEAAK 162 Query: 302 ALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTG 361 ALG+ L RL++ PQA R ++PPL + ++ + K+SSL +G AD+ +G Sbjct: 163 ALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTAAGNF 222 Query: 362 QSIEIVSIWLIVYLSLSLATSLFMNWYNARM 392 + E ++ ++YL++++ SL + A + Sbjct: 223 RYFETYNVVALIYLAMTVTLSLALRKLEAHL 253 Score = 35.8 bits (81), Expect = 1e-06 Identities = 17/71 (23%), Positives = 37/71 (52%) Query: 96 TLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSI 155 T+ V + A ++G ++ + LS + I +L+ Y EV R +P ++++ + ++ Sbjct: 47 TVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFALVPA 106 Query: 156 LPQARDALALP 166 + +AL LP Sbjct: 107 VVAGWNALGLP 117 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: 248 Number of extensions: 10 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: 262 Length adjustment: 28 Effective length of query: 369 Effective length of database: 234 Effective search space: 86346 Effective search space used: 86346 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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