Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate WP_073036165.1 BUB04_RS01155 TRAP transporter large permease
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_900129305.1:WP_073036165.1 Length = 427 Score = 222 bits (565), Expect = 2e-62 Identities = 140/433 (32%), Positives = 230/433 (53%), Gaps = 27/433 (6%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFL-TAMPQRIFGIMANYTLL 69 ++F L+LLS PVA +L + +L G +F P L AM + + ++ L Sbjct: 6 LVFLLGLLLLS--IPVAAALAALGLLVGQ------IFSPFPLYRAMGEIAWTASTDFILF 57 Query: 70 AIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVA 129 AIP F+ +G +L ++GIA R + + L L GGL A + A+ AAT+G AT Sbjct: 58 AIPLFVLLGEILLQAGIAARTYRALDLWLSWLPGGLMHANIGTSAMFAATSGSSVATAAT 117 Query: 130 MGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIP 189 + ++LP RYGY + L G IAA GTLG +IPPS+ L+V G S+ LFI ++P Sbjct: 118 ITTVALPQARRYGYPEGLFAGSIAAGGTLGILIPPSINLIVYGFLTNTSIPQLFIAGIVP 177 Query: 190 GLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKR------VIQVMIPPLILIL 243 GL++A F + +LI I P +GG R ++ ++P L + L Sbjct: 178 GLILALLFMICILIACSINP-----------RLGGSRRSARWSDRIESLKDLLPVLFIFL 226 Query: 244 LVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGS 303 +V+GSI+ G+ATPTE+ A+G A+ LA +L ++V + T+R T+M++ ILI + Sbjct: 227 VVIGSIYAGWATPTESAALGVIAALLLAFRYRAVSLGFFKRVFEGTMRTTAMIMLILIAA 286 Query: 304 TAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVP 363 + + + + + + NL L V + +LG F++ + I +P+ P Sbjct: 287 NFLNFILDSIGLAETLRQFVNNLGLSPFKTLLVIIALYLVLGLFVETLSLMVITVPIVTP 346 Query: 364 VAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQ 423 V G D VW+GV+L ++ + +TPP G L+ ++GV + SD+ G PF+L+ Sbjct: 347 VITGAGYDPVWFGVLLILLIEMALITPPVGLNLYVVQGVR-RSGSISDVMIGAFPFVLMI 405 Query: 424 LLVLLLIIIFPGI 436 L+++ +++ FPG+ Sbjct: 406 LVMIGVLVAFPGL 418 Lambda K H 0.331 0.149 0.437 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: 510 Number of extensions: 27 Number of successful extensions: 2 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: 445 Length of database: 427 Length adjustment: 32 Effective length of query: 413 Effective length of database: 395 Effective search space: 163135 Effective search space used: 163135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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