Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate 3607229 Dshi_0645 TRAP transporter solute receptor, TAXI family (RefSeq)
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__Dino:3607229 Length = 335 Score = 140 bits (354), Expect = 3e-38 Identities = 103/325 (31%), Positives = 159/325 (48%), Gaps = 14/325 (4%) Query: 5 KRLGLLAAAAAFTASTAAVAAPTFINIL--TGGTSGVYYPIGVALSQQYN-KIDGAKT-- 59 K L AAAAA + S A A N + T T G YYP+GVALS K++ ++ Sbjct: 2 KHLVCAAAAAAISLSVATGAKAEGANYILATASTGGTYYPVGVALSTLVKVKLEPSQKIG 61 Query: 60 -SVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNY 118 S ++ S EN+ L++ G + G A G + LR++ + N Sbjct: 62 MSAISSAGSGENVRLIREGEAQFGIMQGLFGYYAATGTGPLEESGKQENLRSVTMLWQNV 121 Query: 119 IQIVASAESG----IKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLP 174 V +A++ I+ L LKG+ +++G SGT + I + G+D + + F Sbjct: 122 EHFVVAADAAPTGTIEDLVALKGEAMALGRQNSGTIGSNATILSSFGVDIESDYELVFGG 181 Query: 175 YAESVELIKNRQLDATLQSSGLGMAAIRDL--ASTMPVTFVEIPAEVVEKIES--DAYLA 230 Y S E ++N Q+ +G+ + AI L A+ VT + E + + + + Sbjct: 182 YGPSAEALQNGQVKGIGTPAGVPVGAISQLMAAAGDSVTLLNFTPEQAAQADGGRELWTP 241 Query: 231 GVIPAGTYDGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIK 290 I AGTY GQ DV T+A N L T + DE YQ+TK +++NL L H A K + Sbjct: 242 YTIAAGTYPGQAEDVQTIAQPNFLATSADLPDEHVYQITKTIYENLPFLNAIHPATKAMA 301 Query: 291 LENATKNLPIPLHPGAERFYKEAGV 315 +E+A LP+PLHPGA+R+Y+E G+ Sbjct: 302 IESAIAGLPLPLHPGAQRYYEEVGI 326 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: 244 Number of extensions: 13 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: 317 Length of database: 335 Length adjustment: 28 Effective length of query: 289 Effective length of database: 307 Effective search space: 88723 Effective search space used: 88723 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 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