Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate CCNA_02178 CCNA_02178 short-chain alcohol dehydrogenase
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__Caulo:CCNA_02178 Length = 301 Score = 281 bits (718), Expect = 3e-80 Identities = 140/277 (50%), Positives = 199/277 (71%), Gaps = 6/277 (2%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62 + F KV IVTGAGGG+G+ +ALE A+RGAKVVVNDLGGS G G SS+AA KVV+EIKA Sbjct: 4 IRFDGKVAIVTGAGGGLGRQHALELARRGAKVVVNDLGGSMDGSGGSSEAAQKVVDEIKA 63 Query: 63 AGGTAVANYDSVEDGEKI---VQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119 GG A+AN SV D + ++ AMD++G +DILI NAGILRD + KM D++LV + Sbjct: 64 LGGEAIANGSSVTDDAGVALMIKQAMDTWGRIDILIANAGILRDKTLTKMELADFELVMQ 123 Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179 VH G +K +A W+ M+ +N+GRI++T+S++G+YGNFGQ+NYG+ KMA++GL NTL E Sbjct: 124 VHVFGTFKPIKAVWDIMKAQNYGRIVVTTSSSGMYGNFGQSNYGAAKMAVLGLMNTLKLE 183 Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVGA 239 G ++ N I+P+AA+R+TE +MPPE+L ++ P+Y+ P V+YLC D TG + GA Sbjct: 184 GAKNDVKINAISPVAATRMTEGLMPPEVLAKLAPEYVTPGVVYLC-SDEAPTGAILTAGA 242 Query: 240 GWVSKVRLQRSAGVYMKD--LTPEKIKDNWAQIESFD 274 G + R+ + GVY+ + L+ E+++D+W QI + D Sbjct: 243 GAFALSRIYETEGVYLGEGGLSAEEVRDSWGQITAED 279 Lambda K H 0.313 0.131 0.371 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: 394 Number of extensions: 26 Number of successful extensions: 4 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: 441 Length of database: 301 Length adjustment: 29 Effective length of query: 412 Effective length of database: 272 Effective search space: 112064 Effective search space used: 112064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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