Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate PfGW456L13_2432 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
Query= reanno::Marino:GFF2749 (506 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432 Length = 505 Score = 585 bits (1508), Expect = e-171 Identities = 295/505 (58%), Positives = 377/505 (74%), Gaps = 1/505 (0%) Query: 1 MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDK 60 M AL+T ++AV+GAGAMG+GIAQVAAQAGH V L D R GAA +GI +QL +RV+ Sbjct: 1 MTALNTSARIAVIGAGAMGAGIAQVAAQAGHPVLLLDNRPGAAAQAIEGIDRQLGKRVEN 60 Query: 61 GKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILAT 120 GK+ + + R+ V ++ +AD L+IEAI+E+L++KR L LE +C ILA+ Sbjct: 61 GKLSAESRSATVARLQAVEVIETLADCDLIIEAIVENLEVKRALFRQLEGICGEHCILAS 120 Query: 121 NTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGK 180 NTSS+S+T++ A + P+RL+G+HFFNPAP+MALVEVV GLA+ +A+ ++ TA AWGK Sbjct: 121 NTSSLSITSIAAQLDHPQRLLGLHFFNPAPVMALVEVVSGLASDPALAECLYDTARAWGK 180 Query: 181 KPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIG 240 KPV+ STPGFIVNRVARPFYAESLR+LQE A D TLDA++REAG F MGAFELTDLIG Sbjct: 181 KPVHTRSTPGFIVNRVARPFYAESLRMLQEGAADCPTLDALMREAGGFAMGAFELTDLIG 240 Query: 241 HDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEP 300 HDVNYAVT SVF++YYQD RFLPSLIQKELV+ GRLGRKSGQGFY Y + AE+PQ E Sbjct: 241 HDVNYAVTCSVFDAYYQDTRFLPSLIQKELVDGGRLGRKSGQGFYCYAQGAERPQ-AGEI 299 Query: 301 AHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERA 360 + + IAEG+ G+A LL RL G+ +I RDG G +R GDAVLAL+DGRMA +RA Sbjct: 300 SSSASVETCIAEGDLGIAQGLLARLSEQGVEVIRRDGRGLLRVGDAVLALSDGRMACQRA 359 Query: 361 ACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLV 420 +G+ NL+L DLAFDY A R+A++ A A+ ALLQ+AG+ VSL++D P L Sbjct: 360 REDGLRNLILLDLAFDYGNAKRIAISHAAGIDPLALEQGVALLQRAGLMVSLLSDSPALA 419 Query: 421 IMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQ 480 ++RTVAMLANEAADA L GVA+ ADIDLAM+AG+NYP GPL+W+D +G H+ + L N+Q Sbjct: 420 VLRTVAMLANEAADALLQGVASAADIDLAMRAGVNYPQGPLAWADAIGLSHILETLENLQ 479 Query: 481 TSYAEDRYRPALLLRKNAFAQKGFY 505 SY E+RYRP+LLLR+ + F+ Sbjct: 480 ASYGEERYRPSLLLRRRVAEGRTFH 504 Lambda K H 0.318 0.133 0.375 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: 689 Number of extensions: 27 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: 506 Length of database: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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