Align ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized)
to candidate WP_017220928.1 A923_RS0106860 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_773 (223 letters) >NCBI__GCF_000276805.1:WP_017220928.1 Length = 359 Score = 117 bits (294), Expect = 2e-31 Identities = 64/210 (30%), Positives = 114/210 (54%), Gaps = 8/210 (3%) Query: 16 WNGMIMTLKLMALGVIGGIILGTILALMRLSHNK-LLSNIAGAYVNYFRSIPLLLVITWF 74 W G+++T+ + A+G+I +G +LAL R S N ++ + ++ + R +PL+ ++ Sbjct: 150 WGGLMLTILVAAVGIIASFPIGILLALGRQSDNMPIVKTLCVGFIEFIRGVPLITILFMA 209 Query: 75 YLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134 + +P + ++ +F+AAY E++R G+Q+IPKGQ A+++LG+ Sbjct: 210 SVVLPLFF----SDGIEFDKLLRALIGITLFQAAYIAEVIRGGLQAIPKGQYEASESLGL 265 Query: 135 EYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFL---NASRASGDIIGR 191 Y Q M LIILPQA + P L+ I LF+DT+LV +GL D L + + +G Sbjct: 266 SYWQGMILIILPQALKISIPNLVGSFISLFKDTTLVLIIGLFDILAMVTLTNSDTSWLGF 325 Query: 192 SNEFLIFAGLTYFTISFAASLLVKRLQKRF 221 E +F L Y+ F+ S + +++R+ Sbjct: 326 EIEGYVFVTLIYWVFCFSMSQYSRVIERRY 355 Lambda K H 0.331 0.144 0.429 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: 205 Number of extensions: 11 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: 223 Length of database: 359 Length adjustment: 26 Effective length of query: 197 Effective length of database: 333 Effective search space: 65601 Effective search space used: 65601 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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