Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_084076205.1 BUB04_RS05255 hypothetical protein
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_900129305.1:WP_084076205.1 Length = 329 Score = 184 bits (468), Expect = 2e-51 Identities = 108/309 (34%), Positives = 166/309 (53%), Gaps = 6/309 (1%) Query: 10 LAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATKASV 68 LA A+ A FI+I TGGT GVYYP G AL++ + + + + + T ASV Sbjct: 15 LALVLGLGATEKVDARKQFISIGTGGTGGVYYPYGGALAEIWTRHVKDVQAVAEVTGASV 74 Query: 69 ENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESG 128 EN+ L G + +GD +A++G+ F+ +++ A+ Y N +VA SG Sbjct: 75 ENVKLAHKGETVVGLIMGDVAYEAYHGL--GRFEGKPQKIAAMFMMYPNVYHVVALKGSG 132 Query: 129 IKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLD 188 IKTL DLKGKR+SVG+P SGTE + + A G+ Y D V L + E+ +++ +D Sbjct: 133 IKTLQDLKGKRVSVGSPGSGTEYMSNLVLHAVGVPY-DSFEVRRLSFVENANALRDHTID 191 Query: 189 ATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDA--YLAGVIPAGTYDGQDADVP 246 + G ++I DLA+T + V E ++K+ Y V+PAG Y G D DVP Sbjct: 192 VGIWCVGPPTSSIMDLATTHDIMIVPFSDEDIKKVTEKVKYYAPSVVPAGMYKGVDEDVP 251 Query: 247 TVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGA 306 TV++ N+ + + +++ Y + K F++ L + AK ENA K PIP HPGA Sbjct: 252 TVSVWNVAICTRDLPEDMVYNLVKATFEHQDYLLKVYPGAKYTTAENAVKYSPIPFHPGA 311 Query: 307 ERFYKEAGV 315 +++KE G+ Sbjct: 312 VKYFKEIGL 320 Lambda K H 0.314 0.131 0.359 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: 253 Number of extensions: 13 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: 317 Length of database: 329 Length adjustment: 28 Effective length of query: 289 Effective length of database: 301 Effective search space: 86989 Effective search space used: 86989 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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