Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate WP_041096190.1 SUTH_RS00300 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >NCBI__GCF_000828635.1:WP_041096190.1 Length = 220 Score = 110 bits (275), Expect = 2e-29 Identities = 67/212 (31%), Positives = 118/212 (55%), Gaps = 12/212 (5%) Query: 28 GLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFL 87 GL +T+ + +VA +++G++L + R P ++ IA YV+L R++PL++ + +W+FL Sbjct: 19 GLLFTLRLTLVAMTGGIVIGTLLALARLSPIVPLARIAGAYVDLMRSIPLVL-VILWFFL 77 Query: 88 VPDLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQESAARA 147 V L A S ++ F AA CE +R+GIQ++PRGQ +AA A Sbjct: 78 VIPFLT-----------GAPVGAETSAIITFTAFEAAFYCEIMRSGIQSVPRGQVNAAFA 126 Query: 148 MGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G Q +V+LPQA R ++P L ++ + +F+++S+ IG ++L + Sbjct: 127 LGLGQAQTMIHVILPQAVRNMLPVLLTQTIVLFQDTSLVYAIGAKDMLKAADVVGKNYNR 186 Query: 208 LFEAFTLATLIYFTLNMSLMLLMRMVEKKVAV 239 E L+ LIYF + SL L ++ ++K+VA+ Sbjct: 187 PVEMIVLSALIYFAICFSLSLAVKQLQKRVAI 218 Lambda K H 0.326 0.139 0.432 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: 138 Number of extensions: 11 Number of successful extensions: 3 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: 248 Length of database: 220 Length adjustment: 23 Effective length of query: 225 Effective length of database: 197 Effective search space: 44325 Effective search space used: 44325 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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