Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_073038071.1 BUB04_RS06485 C4-dicarboxylate ABC transporter substrate-binding protein
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_900129305.1:WP_073038071.1 Length = 328 Score = 160 bits (404), Expect = 5e-44 Identities = 108/319 (33%), Positives = 167/319 (52%), Gaps = 10/319 (3%) Query: 9 LLAAAAAFTASTAAV---AAPTFINILTGGTSGVYYPIGVALSQQYN-KID--GAKTSVQ 62 ++ A A A V A TF+ I TGG +GVYYP G A+ + N K D G + +V+ Sbjct: 10 IMVCAGALILGGAVVPVQAKTTFVTIGTGGITGVYYPTGGAICKIVNNKRDQYGIRCTVE 69 Query: 63 ATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIV 122 +T SV N+N + AG E + D A G + K P + LRA+ + I +V Sbjct: 70 STGGSVFNINAVLAGDLEFGIAQSDRQYQAIKGEAEWQDKGPQQDLRAVFSIHPEAITLV 129 Query: 123 ASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELI 182 A+ ++GIK++ DLKGKR+++G P SG N+ + +A G+D++ + E + AE+ L+ Sbjct: 130 AAEDAGIKSVQDLKGKRVNIGNPGSGQRQNSIDVLEAFGIDWEKDLQAEQVKAAEAPSLL 189 Query: 183 KNRQLDATLQSSGLGMAAIRDLAS-TMPVTFVEIPAEVVEKI--ESDAYLAGVIPAGTY- 238 ++ ++DA + G AI++ A+ V V I V+ + + Y VIP Y Sbjct: 190 QDGRIDAFFYTVGHPSGAIKEAAAGRRKVRIVPITGPEVDNLLKKYPYYAKAVIPIEFYP 249 Query: 239 DGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNL 298 D D+ TV + VT KV ++V Y + K +FDNL H A + EN + L Sbjct: 250 DTGTEDIQTVGVKATFVTSAKVPEDVVYAIVKEVFDNLEEFKKLHPAYSVLTRENMLEGL 309 Query: 299 PIPLHPGAERFYKEAGVLK 317 P HPGA ++YKE G++K Sbjct: 310 SAPFHPGALKYYKEVGLMK 328 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: 245 Number of extensions: 8 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: 328 Length adjustment: 28 Effective length of query: 289 Effective length of database: 300 Effective search space: 86700 Effective search space used: 86700 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