Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate HSERO_RS19245 HSERO_RS19245 glutamate/aspartate transporter permease GltK
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772 (223 letters) >FitnessBrowser__HerbieS:HSERO_RS19245 Length = 231 Score = 224 bits (570), Expect = 1e-63 Identities = 121/225 (53%), Positives = 156/225 (69%), Gaps = 4/225 (1%) Query: 3 FDFSGIIPSLPGLWN-GMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNY 61 FDF I S L+ G+ TL L + GGIILGT+LA+MRLS NK LS IA YVN Sbjct: 5 FDFDVIQRSWFYLFTTGLKFTLILTFSAMAGGIILGTLLAMMRLSSNKPLSFIATTYVNL 64 Query: 62 FRSIPLLLVITWFYLAVPFVLRWITGEDTPI--GAFASCIVAFMMFEAAYFCEIVRAGVQ 119 RSIPL+LVI WFY VPF+ W+ G PI GAF S ++ F++FEAAY+CEI+R+G+Q Sbjct: 65 IRSIPLVLVIFWFYFLVPFIGAWMIGASEPIQVGAFQSALITFILFEAAYYCEIMRSGIQ 124 Query: 120 SIPKGQMGAAQALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLV-DF 178 SIP+GQ+ A A+GM+Y QMM ++LPQAFR MTP+LL Q+I+LFQD SLVY +G V DF Sbjct: 125 SIPRGQVFAGYAIGMNYWQMMGNVVLPQAFRNMTPILLTQTIVLFQDVSLVYVLGSVPDF 184 Query: 179 LNASRASGDIIGRSNEFLIFAGLVYFIISFAASQLVKRLQKRFAV 223 + ++ GR E +F +VYF++SF S LVKR QK+ A+ Sbjct: 185 VTSASKIAQRDGRLVEMYLFVAVVYFVLSFGLSTLVKRFQKKIAI 229 Lambda K H 0.332 0.144 0.428 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: 176 Number of extensions: 4 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: 223 Length of database: 231 Length adjustment: 22 Effective length of query: 201 Effective length of database: 209 Effective search space: 42009 Effective search space used: 42009 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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