Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_010626095.1 BZY95_RS06825 3-hydroxyacyl-CoA dehydrogenase PaaH
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_002151265.1:WP_010626095.1 Length = 513 Score = 567 bits (1462), Expect = e-166 Identities = 292/512 (57%), Positives = 375/512 (73%), Gaps = 7/512 (1%) Query: 1 MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDK 60 MPAL VAV+GAGAMG+GIAQVAAQAGH V L+D R+G A+A DG +QL++RV K Sbjct: 1 MPALAASDIVAVIGAGAMGAGIAQVAAQAGHPVRLYDNRDGTAQAAIDGARRQLEQRVAK 60 Query: 61 GKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILAT 120 GKM Q+E+D +I R+ P A L ++AD+ LV+EAI+E+L++KR + A LE LC+ DA+L + Sbjct: 61 GKMAQEEVDAIIARMSPAATLAELADSRLVVEAIVENLEVKRGVFAELETLCSPDALLTS 120 Query: 121 NTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGK 180 NTSS+S+T++ + + PER+ G+HFFNPAP+M LVEV+ GLATS +A+T++ATA AWGK Sbjct: 121 NTSSLSITSIASGLEHPERVAGLHFFNPAPVMKLVEVISGLATSAEIAETLYATAAAWGK 180 Query: 181 KPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIG 240 PV+A+STPGFIVNRVARPFYAE LRL QE A ATLDA++R+AG FRMG FEL DLIG Sbjct: 181 VPVHASSTPGFIVNRVARPFYAEGLRLRQEGAAAPATLDALLRQAGGFRMGPFELMDLIG 240 Query: 241 HDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPY----GESAEKPQP 296 HDVNYAVT SVF++YY D RF PSL+Q+ LVEAGRLGRKSG GFY Y E+A P Sbjct: 241 HDVNYAVTRSVFDAYYGDTRFQPSLVQQALVEAGRLGRKSGHGFYDYREEQREAAGPAAP 300 Query: 297 KTEPAHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERD---GPGQIRFGDAVLALTDG 353 P+ ++ ++AEG GV PL+ R +AAGL + R+ G ++R G LAL+DG Sbjct: 301 DFAPSVVAELPPLVAEGQLGVITPLVIRAEAAGLETLRRESMSGQARLRLGGLTLALSDG 360 Query: 354 RMATERAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLI 413 R ATERA EG+ LVLFDL DY +A +ALA + DAA + A Q G +V+ + Sbjct: 361 RCATERARDEGLEALVLFDLCLDYGEAGAIALAASPGVDDAARTLVTAFFQHLGFDVAWL 420 Query: 414 ADRPGLVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVF 473 D PGL ++RTVAMLANEAADA L GV + D DLAM+AGLNYP GPL+W+D LG V Sbjct: 421 TDTPGLAVLRTVAMLANEAADAVLQGVCSARDGDLAMQAGLNYPRGPLAWADSLGLAFVH 480 Query: 474 KVLTNIQTSYAEDRYRPALLLRKNAFAQKGFY 505 + LT++Q SY E+RYRP+ LLR+ A A++ F+ Sbjct: 481 RTLTHLQQSYGEERYRPSFLLRRKALAEETFH 512 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: 692 Number of extensions: 31 Number of successful extensions: 3 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: 513 Length adjustment: 34 Effective length of query: 472 Effective length of database: 479 Effective search space: 226088 Effective search space used: 226088 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 Apr 09 2024. 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