Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate GFF4195 Psest_4268 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= reanno::SB2B:6938088 (339 letters) >FitnessBrowser__psRCH2:GFF4195 Length = 331 Score = 358 bits (920), Expect = e-104 Identities = 183/324 (56%), Positives = 231/324 (71%), Gaps = 3/324 (0%) Query: 18 ASLLATVLGFSFGAVA---EPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVF 74 A LA L S +A +P+ IKFSHVVAENTPKGQ AL FK+LVE RL G+ +V V+ Sbjct: 6 AKALACALSLSIAGLAHAADPITIKFSHVVAENTPKGQGALMFKKLVEERLAGKVEVQVY 65 Query: 75 PNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEA 134 PNS LFGD E+ ALLL DVQL+APSL+KFE Y+K +QV+DLPFLF+D+ AVDRFQ+ EA Sbjct: 66 PNSSLFGDGKEMEALLLGDVQLIAPSLAKFEHYSKGVQVYDLPFLFDDIAAVDRFQKGEA 125 Query: 135 GQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGA 194 GQ LL SM K + GLGY HNGMKQ SAN L P DA G KFR+ S V+ QF+AV A Sbjct: 126 GQSLLRSMEDKNITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASAVLDEQFKAVRA 185 Query: 195 IPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFW 254 P K F+EV+ LQT ++G EN +SNIYS+K +EVQ +ITESNHG+LDYM++T+ FW Sbjct: 186 NPRKMSFAEVYQGLQTGVVNGAENPYSNIYSQKMHEVQKYITESNHGLLDYMVITNTKFW 245 Query: 255 KSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAM 314 LP D R ++ ++E NK A E D+Q I+D+ E++ LTPEQR+ W AM Sbjct: 246 NGLPADVRSELESILNEVTVAVNKQADELNQADKQRIVDAGTTEIINLTPEQREMWREAM 305 Query: 315 RPVWSQFEDKIGKDLIEAAESANK 338 +PVW +FE +IG DLI+AAE+AN+ Sbjct: 306 KPVWKKFEGEIGADLIKAAEAANQ 329 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: 316 Number of extensions: 6 Number of successful extensions: 1 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 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