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_073041930.1 BUB04_RS17585 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_900129305.1:WP_073041930.1 Length = 441 Score = 301 bits (771), Expect = 3e-86 Identities = 158/438 (36%), Positives = 264/438 (60%), Gaps = 6/438 (1%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65 E LG + G L+ SG+P++F++ + + FG LGIG VF M + + +M++ Sbjct: 7 EMLGMLSLVGLLLAFVSGFPISFTMMFIGLAFGYLGIGKLVFH-----LMNIQFYQVMSD 61 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 L AIP+F+FMG +LE +G+ + L ++ LL + G L LA++L + AA TG+V + Sbjct: 62 PVLGAIPFFLFMGYILESAGLMDNLFHSIQKLLAPVPGSLYLAIILTATIFAAATGIVGS 121 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185 ++ + +++ P M R Y+ + G IAA GTLG +IPPS++LVV+G +G+ V DLF G Sbjct: 122 SITLLCMMAGPAMARSNYDIRMGAGAIAAGGTLGILIPPSIMLVVMGPLMGVPVTDLFAG 181 Query: 186 SVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLV 245 +VIPGL+++ + + LI F +P P L ++R AL +I+ ++P ++LI Sbjct: 182 AVIPGLLLSGIYIAYSLIRCFFQPQYGPPLAKELRAESMGALVVDLIKGVVPLILLIGAT 241 Query: 246 LGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTA 305 LGSI G ATPTEA A G GA L G+F E+L+ +T ++++M++ ++ S Sbjct: 242 LGSILAGLATPTEASACGALGAFLLVVCYGKFKWENLKGAMYSTAKLSAMILIMIAASNF 301 Query: 306 FSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVA 365 + VF L G ++ + L ++ +G + + M VFLLG+ +++ I I++P+ +P Sbjct: 302 YGSVFSRLGGAGWLSNQLVSMSLPPMGMVILIMGLVFLLGWAMEWVPIVLIILPIMMPTV 361 Query: 366 QKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLL 425 + LGID +W+ ++ LQTS+LTPP + ++++G P SDIYRG+ +I Q + Sbjct: 362 RALGIDPLWFAIVYAVTLQTSWLTPPVALSCYFIKGCL-PHWQLSDIYRGMFQYIACQAV 420 Query: 426 VLLLIIIFPGIVSFLPSL 443 + LI++FP IV++LPS+ Sbjct: 421 GIALILLFPSIVTWLPSI 438 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: 556 Number of extensions: 23 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: 441 Length adjustment: 32 Effective length of query: 413 Effective length of database: 409 Effective search space: 168917 Effective search space used: 168917 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