Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate WP_028312344.1 H566_RS0116815 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >NCBI__GCF_000482785.1:WP_028312344.1 Length = 222 Score = 213 bits (543), Expect = 2e-60 Identities = 115/223 (51%), Positives = 149/223 (66%), Gaps = 6/223 (2%) Query: 1 MDLDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVN 60 +D DF + G+ +LQLTV+ ++GGI GTLLALMRLS K L A YVN Sbjct: 4 LDWDFFSWQLVTDYLLKGLAFSLQLTVVAMLGGIFFGTLLALMRLSGRKWLEWPATFYVN 63 Query: 61 YFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQS 120 R+IPL++VI WF+L +P++L PIGA S ++ F+ FEAAY+ EI+RAG+QS Sbjct: 64 AMRAIPLVMVILWFFLLMPYLL------GRPIGAEASAVITFIAFEAAYYAEIMRAGIQS 117 Query: 121 IPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLN 180 IP+GQ+ A +ALG+ Y Q MRL+ILPQAFR M P+LL Q+IILFQDTSLVY +G D Sbjct: 118 IPRGQIFAGQALGLTYAQNMRLVILPQAFRNMLPVLLTQTIILFQDTSLVYAIGAYDLFK 177 Query: 181 ATRASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKRFAV 223 +G GR E ++A +VYF ISF+ S LVKRLQ R A+ Sbjct: 178 GFNVAGRNFGRPIESTLLAVVVYFLISFSLSTLVKRLQARIAI 220 Lambda K H 0.331 0.143 0.425 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: 143 Number of extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 201 Effective length of database: 200 Effective search space: 40200 Effective search space used: 40200 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: 45 (21.9 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