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 Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 199 bits (505), Expect = 2e-55 Identities = 140/435 (32%), Positives = 212/435 (48%), Gaps = 16/435 (3%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70 ++ + L+ G PVA+SLG LL + + V +T + QR+ + +++LLA Sbjct: 8 ILVLSFITLMGLGVPVAWSLG----FSSLLTLMVTVAAVPSMTTIAQRMGAGLNSFSLLA 63 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 IP+FI G ++ K GIA RL+ L G+L GGL V+ L A G A A+ Sbjct: 64 IPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASAL 123 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLG-DQLGISVGDLFIGSVIP 189 G I M GY KEL V S T G +IPPS VL+V G+S+ LF+ IP Sbjct: 124 GGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYIP 183 Query: 190 GLMMASAFALHVLIVAFIRPDVAPA-LPAQVREIGGKALGKRVIQVMIPPLILILLVLGS 248 GL M L + FI+ PA P +E+G +V P L L+++V+G Sbjct: 184 GLFMG--LLLMLTAAYFIKKKKLPAGEPTSFKELG------KVFFSAAPSLTLLVIVIGG 235 Query: 249 IFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSL 308 I G T TEA A+ + L+ G+ L + + T++V ++ S A S Sbjct: 236 IVMGVFTATEASAIAVLYCLGLSFFYGELKPRDLPAILLKSSATTAVVAMLIATSMAMSW 295 Query: 309 VFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKL 368 V + Q + VL +L K L + + +G F+D I P+F+PV +L Sbjct: 296 VMSSEDIPQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVTEL 355 Query: 369 GIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLL 428 GID V +G+I+ NL TPP G LF GV + + S++ + ++PF + ++ L Sbjct: 356 GIDPVHFGIIMVLNLCIGLCTPPVGSVLFI--GVGVAKTSISNVVKPLLPFFIAMIIGLA 413 Query: 429 LIIIFPGIVSFLPSL 443 +I I+P + +LPSL Sbjct: 414 VITIWPQLTLWLPSL 428 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: 475 Number of extensions: 27 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: 445 Length of database: 431 Length adjustment: 32 Effective length of query: 413 Effective length of database: 399 Effective search space: 164787 Effective search space used: 164787 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 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