Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_028584554.1 G494_RS0110770 C4-dicarboxylate ABC transporter
Query= reanno::SB2B:6938088 (339 letters) >NCBI__GCF_000429965.1:WP_028584554.1 Length = 331 Score = 170 bits (431), Expect = 4e-47 Identities = 101/328 (30%), Positives = 173/328 (52%), Gaps = 3/328 (0%) Query: 9 LQSLFTLGKASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGE 68 ++S+ ++ A L +G + A A P+ IK +H P GQ +KFKEL+E R G Sbjct: 1 MKSVRSIVTAVALCLCMGAA-SAFAGPIVIKLAHPNVPQHPMGQAFIKFKELMEERSNGA 59 Query: 69 YKVSVFPNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDR 128 ++V +F +S+ ++ + L LN +Q+ + S ++ + +FDLPFLF D + D+ Sbjct: 60 FRVDIFDSSKFGNFDSVVQGLQLNMLQMGSASTPNLAPFSDEFLIFDLPFLFPDYPSTDK 119 Query: 129 FQQSEAGQQLLNSMSRKGLVGLGYLHNGMKQFSANN-ALSLPGDAAGKKFRIMPSDVIAA 187 G ++ + G++GLGY+ G + NN A++ DA G K R PS A Sbjct: 120 ITDGPIGMNATKALEKSGIIGLGYIEIGFRNLWNNNRAVTTLEDAKGLKIRSTPSKAHIA 179 Query: 188 QFEAVGAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYML 247 +A+G P + EV+T LQ + +DG + + + F EV H+T N +++ Sbjct: 180 TLKALGMNPTPISWGEVYTALQQKTVDGIDIDLNLAWYNNFPEVNNHVTIVNSLFSPHLV 239 Query: 248 VTSETFWKSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQR 307 + S+ F SL + RE++ + +E V L + + ++ L K V + L+PE+R Sbjct: 240 MISKRFLDSLSPENRELLLTTFEE-VKLYERKLIRDGEKEIMAQLKDKGVTVTVLSPEER 298 Query: 308 QAWVNAMRPVWSQFEDKIGKDLIEAAES 335 + W A V++QFE++IGK+LIE A++ Sbjct: 299 KRWAEATAGVYAQFEERIGKELIERAKA 326 Lambda K H 0.316 0.132 0.368 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: 256 Number of extensions: 11 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: 339 Length of database: 331 Length adjustment: 28 Effective length of query: 311 Effective length of database: 303 Effective search space: 94233 Effective search space used: 94233 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: 41 (21.6 bits) S2: 49 (23.5 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