Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate HSERO_RS19245 HSERO_RS19245 glutamate/aspartate transporter permease GltK
Query= TCDB::Q88NY4 (223 letters) >FitnessBrowser__HerbieS:HSERO_RS19245 Length = 231 Score = 221 bits (562), Expect = 1e-62 Identities = 115/209 (55%), Positives = 149/209 (71%), Gaps = 3/209 (1%) Query: 18 GMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWFYLA 77 G+ TL L + GGI+LGT+LA+MRLSS+K LS +A YVN RSIPL+LVI WFY Sbjct: 21 GLKFTLILTFSAMAGGIILGTLLAMMRLSSNKPLSFIATTYVNLIRSIPLVLVIFWFYFL 80 Query: 78 VPFVLRWITGEDTP--VGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQALGMN 135 VPF+ W+ G P VGAF S ++ F++FEAAY+CEI+R+G+QSI +GQ+ A A+GMN Sbjct: 81 VPFIGAWMIGASEPIQVGAFQSALITFILFEAAYYCEIMRSGIQSIPRGQVFAGYAIGMN 140 Query: 136 YAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLV-DFLNSARSNGDIIGRSHE 194 Y Q M ++LPQAFR MTP+LL Q+I+LFQD SLVY +G V DF+ SA GR E Sbjct: 141 YWQMMGNVVLPQAFRNMTPILLTQTIVLFQDVSLVYVLGSVPDFVTSASKIAQRDGRLVE 200 Query: 195 FLIFAGVVYFLISFSASWLVKRLQKRISV 223 +F VVYF++SF S LVKR QK+I++ Sbjct: 201 MYLFVAVVYFVLSFGLSTLVKRFQKKIAI 229 Lambda K H 0.330 0.141 0.417 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: 165 Number of extensions: 5 Number of successful extensions: 4 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 ( 7.1 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