Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate GFF2175 Psest_2218 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__psRCH2:GFF2175 Length = 324 Score = 220 bits (561), Expect = 3e-62 Identities = 133/321 (41%), Positives = 183/321 (57%), Gaps = 2/321 (0%) Query: 2 SEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAES 61 + I+ +AL ALR+AL+ D R L GED+G GG + ++ GL EFG+ R DTPL+E Sbjct: 3 NRISYREALREALREALQRDERAFLMGEDVGRYGGTYAVSKGLLEEFGEARIRDTPLSEL 62 Query: 62 AILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGG 121 A +G +G A+ G RP+VE+ FA A + L++ A LR+ + G +PL +R+ G Sbjct: 63 AFVGAGIGAALGGMRPIVEVMTVNFALLALDPLINTAATLRHMSGGQFSVPLVLRMATGA 122 Query: 122 GIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKE 181 G HS S E ++ PGL V+ PAT DA +L ++ PDPV+ E +LY ++ Sbjct: 123 GRQLAAQHSHSLEGWFAHVPGLKVLAPATVEDARGMLWPALQDPDPVLIFEHAQLYNLED 182 Query: 182 ALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPL 241 L P + SA +RR G+ +LIAYG + AL+AA+ AE G EVIDLR L PL Sbjct: 183 ELP-PSMAVDIRSARVRRPGSDLSLIAYGGTLHKALQAADQLAEEGIAAEVIDLRVLRPL 241 Query: 242 DDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP-P 300 D+ T+ SVR+T RA+VV E AEI RI E+ F+ L+AP RV +VP P Sbjct: 242 DEVTILDSVRKTRRALVVDEGWRSGSLSAEIITRIIEQGFFELDAPPARVCSAEVPIPYA 301 Query: 301 PLLERHYLPGVDRILDAVASL 321 LE LP V I+ A L Sbjct: 302 RHLEEAALPQVPTIIAAARQL 322 Lambda K H 0.322 0.138 0.418 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: 311 Number of extensions: 15 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: 328 Length of database: 324 Length adjustment: 28 Effective length of query: 300 Effective length of database: 296 Effective search space: 88800 Effective search space used: 88800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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