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_086508063.1 BZY95_RS00585 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_002151265.1:WP_086508063.1 Length = 456 Score = 378 bits (971), Expect = e-109 Identities = 206/448 (45%), Positives = 292/448 (65%), Gaps = 13/448 (2%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVF---DPIF-----LTAMPQ 57 ++L MFA + LL G+PVA+SL GV F ++G L + D F + + + Sbjct: 5 QFLVLAMFASFMSLLLLGFPVAWSLAGVGFAFAVVGHVLVEYMAADLWFSWGGTIGVLDR 64 Query: 58 RIFGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLA 117 RI+GI+AN ++A+P FIFMG ML++SGIAERL+ ++ +LG LRGG A+ VV+VG LLA Sbjct: 65 RIYGIVANELMVALPLFIFMGIMLDRSGIAERLMNSLVRVLGGLRGGYAVTVVIVGVLLA 124 Query: 118 ATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGI 177 A+TG+V A+VV +G++SL M+R YNK LA G + GTLG ++PPS++LV++ D++G Sbjct: 125 ASTGIVGASVVLLGMLSLGPMMRAQYNKSLAVGTACSVGTLGILVPPSIMLVLMADRMGT 184 Query: 178 S---VGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQV 234 S VG LF+ +++PG+M+ + +LI A+++ D+APA P + +A +V Sbjct: 185 SDASVGRLFMAALVPGVMLGVMYIAFILIAAYLKKDLAPA-PKDREPLNARAF-MQVFIA 242 Query: 235 MIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITS 294 ++PPL LIL VLGSIF GFAT TEA AVG GA+ LA N + L +LR T R T+ Sbjct: 243 VLPPLGLILAVLGSIFTGFATTTEASAVGALGAMLLALLNRRLNLATLRHALYQTSRTTA 302 Query: 295 MVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIA 354 + I IG+T F+ V RGL GD + L LP + G + + VFLLGFF+D+ EI Sbjct: 303 FIFAIFIGATVFAAVLRGLGGDDVVRMALTGLPFSETGIVLTILLVVFLLGFFLDWVEIT 362 Query: 355 FIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYR 414 I++PL PV LG+D +W+ ++ LQTSFLTPP GFALFY++GV PP +TT DIY Sbjct: 363 LIILPLVAPVVFSLGVDPLWFAMLFAICLQTSFLTPPVGFALFYIKGVCPPGITTRDIYL 422 Query: 415 GVIPFILLQLLVLLLIIIFPGIVSFLPS 442 GV PF+ +QL LLL+ F + ++LPS Sbjct: 423 GVAPFVAIQLTGLLLVFFFAPLATWLPS 450 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: 601 Number of extensions: 24 Number of successful extensions: 4 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: 456 Length adjustment: 33 Effective length of query: 412 Effective length of database: 423 Effective search space: 174276 Effective search space used: 174276 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