Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate RR42_RS33050 RR42_RS33050 2-oxoisovalerate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS33050 Length = 325 Score = 290 bits (741), Expect = 4e-83 Identities = 160/322 (49%), Positives = 198/322 (61%), Gaps = 9/322 (2%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M+EI + +A+N AL AL DPR +L GEDIG GGVFR T GL A FG ER DTPLAE Sbjct: 1 MAEINLVEAVNQALGHALAHDPRVVLLGEDIGVNGGVFRATAGLQARFGAERVIDTPLAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 S I G A+GMA G PV E+QF F YPA + +++H +LR+RTRG + P+ +R PYG Sbjct: 61 SGIAGAAIGMAAMGLAPVAEIQFTGFIYPAIDHIINHAGRLRHRTRGRLSCPMVLRSPYG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY--W 178 GI EHHS+S E + PG+ VV P+T A AY LL ++ PDPVVFLEP RLY + Sbjct: 121 AGIHAPEHHSESPEAMFAHIPGIRVVIPSTPARAYGLLLAAMRDPDPVVFLEPTRLYRLF 180 Query: 179 RKEALGLPVDTG---PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDL 235 R+E D G PL + R G TL+++G + AA+ + G VID+ Sbjct: 181 REEV----PDNGEALPLDTCFTLRDGDDITLVSWGAMLQETQAAADLLLDEGIAAAVIDV 236 Query: 236 RTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFD 295 TL PLD T+ SV RTGR V+VHEA AG GAEIAA + + Y L APV+RVTG+D Sbjct: 237 ATLKPLDMDTILESVARTGRCVIVHEAPRSAGFGAEIAANLADAGLYSLAAPVQRVTGYD 296 Query: 296 VPYPPPLLERHYLPGVDRILDA 317 P LE YLP V RI DA Sbjct: 297 TVVPMARLEYTYLPSVARIADA 318 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: 316 Number of extensions: 17 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: 325 Length adjustment: 28 Effective length of query: 300 Effective length of database: 297 Effective search space: 89100 Effective search space used: 89100 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