Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_037453109.1 N825_RS14315 ATP-binding cassette domain-containing protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >NCBI__GCF_000576635.1:WP_037453109.1 Length = 250 Score = 229 bits (584), Expect = 4e-65 Identities = 126/252 (50%), Positives = 166/252 (65%), Gaps = 12/252 (4%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 M+ V K +G +VL+ + EV+ + GPSGSGKSTL++C+N LE G ++V Sbjct: 1 MVEAIGVRKSFGAVEVLSGIDMTILPREVVCLLGPSGSGKSTLLRCINHLEKLSGGRILV 60 Query: 61 DGTSIADPK----------TNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSK 110 DG I + L + R +GMVFQ F LFPHL ++ N+T A + + G S+ Sbjct: 61 DGELIGYRERGDRLHELGSAELARQRRDIGMVFQRFNLFPHLDVVGNITQAPMLIKGESR 120 Query: 111 EEASKKALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPE 170 EA+++A +LLE V L+ A +P QLSGGQQQRVAIARALAM P +MLFDEPTSALDPE Sbjct: 121 AEATRRAHELLEIVDLAGKANAYPHQLSGGQQQRVAIARALAMRPKLMLFDEPTSALDPE 180 Query: 171 MVNEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITAR 230 +V EVL VM +LA EGMTM+ VTHEMGFAR+VADRVIFMD+G ++E + R Sbjct: 181 LVGEVLAVMKRLALEGMTMLVVTHEMGFAREVADRVIFMDRGVVVEQGTAADVIA--RPR 238 Query: 231 SDRAQHFLEKIL 242 DR + FL+++L Sbjct: 239 HDRTKAFLKRVL 250 Lambda K H 0.321 0.135 0.390 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: 196 Number of extensions: 9 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: 244 Length of database: 250 Length adjustment: 24 Effective length of query: 220 Effective length of database: 226 Effective search space: 49720 Effective search space used: 49720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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