Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate RR42_RS21785 RR42_RS21785 MFS transporter
Query= SwissProt::P11178 (455 letters) >FitnessBrowser__Cup4G11:RR42_RS21785 Length = 729 Score = 124 bits (311), Expect = 1e-32 Identities = 98/314 (31%), Positives = 142/314 (45%), Gaps = 35/314 (11%) Query: 143 TNYGEEGTHVGSAAALDDTDLVFGQYR--------------EAGVLMYRDYP------LE 182 ++ G+EG GS L D + G +R G+ P L+ Sbjct: 63 SSIGQEGGAAGSIVPLTGADQINGSHRGHHQFISKALGYLAPNGIDPRAPLPADVQTLLQ 122 Query: 183 LFMAQCYGNVSDLGKGRQMPVHYGCRERHFVTISSPLATQIPQAVGAAYAAKRANANRVV 242 +A+ G KGR +H E + ++ + +P A GAA++ + A + V Sbjct: 123 RTLAEILGLAQGYCKGRGGSMHLQWAEAGALGTNAIVGGGVPMAAGAAWSHRHAGTDAVA 182 Query: 243 ICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYG 302 I YFG+GA + G N AA + P+ FF NN YA+ST E ++ARG G+ Sbjct: 183 ITYFGDGAVNIGSVLETMNLAAAWKLPLCFFIENNRYAVSTTVEESTAEPRLSARGMGFN 242 Query: 303 ILSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSA--YRSVDE 360 I S +VDG D AVY AT+EA A P +IEA YR H + SA YRS DE Sbjct: 243 IPSWKVDGMDPLAVYLATREALAHMRAGKGPTIIEADLYRFFHQNGPFPGSAFGYRSKDE 302 Query: 361 VNYWDKQDHPISRLRHHLQSRGWWDDEQEKAWR---KQSRKKVMEAFEQAE-------RK 410 W +D P+ + +Q+RG + A R KQ+ + M A +A+ R+ Sbjct: 303 EQQWRARD-PLELMARRMQARGLISADDVAALRERIKQAMRDAMAALTEADPSGKPGKRR 361 Query: 411 LKPN--PSLIFSDV 422 ++P PS F DV Sbjct: 362 IRPELWPSPDFRDV 375 Lambda K H 0.320 0.135 0.411 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: 648 Number of extensions: 30 Number of successful extensions: 1 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: 455 Length of database: 729 Length adjustment: 36 Effective length of query: 419 Effective length of database: 693 Effective search space: 290367 Effective search space used: 290367 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 (21.8 bits) S2: 53 (25.0 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