Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate WP_019864278.1 METMI_RS0100930 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_088342 (421 letters) >NCBI__GCF_000384075.1:WP_019864278.1 Length = 421 Score = 296 bits (757), Expect = 1e-84 Identities = 151/403 (37%), Positives = 254/403 (63%), Gaps = 10/403 (2%) Query: 4 IGLAWQIFIGLILGIIVGAIFYGNP---KVAAYLQPIGDIFLRLIKMIVIPIVISSLVVG 60 I L + +G L + +G + +P ++ A L + D+FLRL+KMI+ P+V ++LVVG Sbjct: 21 IALVLGVALGEALNLTLGGVGQHDPLLAQIVAVLNMLTDVFLRLVKMIIAPLVFATLVVG 80 Query: 61 VASVGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVD 120 +A +GD+ +G++G K +++F + ++++G+L N+F+PG +++ L TD S + Sbjct: 81 MAKMGDIHTVGRIGLKAMLWFFSASIASLLLGMLLVNVFEPGNSLHIP-LPPTDAASGLP 139 Query: 121 TTNEVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQ 180 + + F PK+IFE++S ++L I+ FS+ FG+ A++GE P ++ Sbjct: 140 NVKPTLSNFVAHIF----PKSIFEAMSANEILQIVVFSMFFGIACASLGELAHPFVKLLD 195 Query: 181 GTAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLG 240 A M VT+ +M +AP VF+ + +++ G+ L+ K + Y +L + ++LG Sbjct: 196 SLAHIMLKVTSYVMHYAPVAVFSAMASVIAQQGIGVLLSYGKFIGEFYFGLLL-LCSLLG 254 Query: 241 GVAKLF-GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGY 299 G A LF G + +I+ +++ ++LA+ TASSE+ P+++ ++E+FGC + + V+P GY Sbjct: 255 GFACLFLGRRMLSLIRHIREPMLLAFGTASSESAYPKLLQQLERFGCDEKVCGLVLPLGY 314 Query: 300 SFNLDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATL 359 SFNLDGS +Y A +FIAQ YGIDM ++ Q+ +LLVL+ TSKG+AGVP S +V+ ATL Sbjct: 315 SFNLDGSMMYMTFAVLFIAQAYGIDMPLADQLLMLLVLLFTSKGVAGVPRASLIVISATL 374 Query: 360 GTVGIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWE 402 IP GL + GID++LDM R+A NV GNS+A+ ++S+WE Sbjct: 375 SMFKIPEAGLLLLLGIDQVLDMGRSATNVYGNSIASALVSRWE 417 Lambda K H 0.326 0.143 0.402 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: 421 Number of extensions: 20 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: 421 Length of database: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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 (21.6 bits) S2: 50 (23.9 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