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 202250 SO3136 C4-dicarboxylate transport protein (NCBI ptt file)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__MR1:202250 Length = 465 Score = 198 bits (504), Expect = 3e-55 Identities = 143/468 (30%), Positives = 231/468 (49%), Gaps = 51/468 (10%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMA-NYTLLA 70 +F + + G P+A +LG ++L L F L ++ +++ + +YTLLA Sbjct: 6 LFCVLFICMFLGMPIAIALGFSSMLTILF------FSNDSLASVALKLYESSSEHYTLLA 59 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 IP+FI A L G+A R+++ +G +RGGLA+A V+ L AA +G ATV A+ Sbjct: 60 IPFFILSSAFLSTGGVARRIIDFAMDCVGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 G I + M++ GY ++ A+GVI SGTLG +IPPS+V++V +SV +F+ ++PG Sbjct: 120 GSIVIVGMVKAGYPEKFASGVITTSGTLGILIPPSIVMLVYAAATEVSVAKIFMAGLVPG 179 Query: 191 LMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIF 250 L++ + + IVA I+ P++P G K LG + I L LI +VLGSI+ Sbjct: 180 LLLGFLIMVVIYIVARIKN--LPSIPFP----GFKKLGVSSAKA-IGGLALIFIVLGSIY 232 Query: 251 FGFATPTEAGAVGCAGAI---------------------------ALAAANGQFTL---- 279 G A+PTEA AV C A A+A G L Sbjct: 233 GGVASPTEASAVACVYAYFIAVFGYRDIGPLKNVAWRNPNEAIPSAIARNLGHMVLGLIK 292 Query: 280 ----ESLRQVCDTTLRITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLF 335 + +R V +++ M++FI+ + F+ V + + + + GFL Sbjct: 293 TPIDKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEYIVGMGLPAWGFLI 352 Query: 336 VSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFA 395 + + G F++ I I+ P+ P+A +LGID + G+I+ N++ LTPP G Sbjct: 353 IVNLLLLAAGNFMEPSAIVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412 Query: 396 LFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 LF G+ + + + V+P+++ L L+LI P I FLP L Sbjct: 413 LFVTSGITGRNI--GWVIQSVLPWLVFMLAFLMLITYVPQISLFLPEL 458 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: 480 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 465 Length adjustment: 33 Effective length of query: 412 Effective length of database: 432 Effective search space: 177984 Effective search space used: 177984 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