Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_081948961.1 JH15_RS09265 hypothetical protein
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_000759345.1:WP_081948961.1 Length = 461 Score = 301 bits (772), Expect = 3e-86 Identities = 187/485 (38%), Positives = 262/485 (54%), Gaps = 39/485 (8%) Query: 10 VAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELD 69 +AV+GAG MG GIAQ++AQ G L+D + GAA A R+ +A+ L+RR+DKG+M E Sbjct: 8 IAVIGAGIMGQGIAQISAQQGVITTLYDVQPGAAAAARERVAEALKRRIDKGRMSDAEAQ 67 Query: 70 DVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTA 129 + + R+ + + DA LV+EAI+EDL +KR L LE +C A A+L +NTSS+S+ A Sbjct: 68 ETLSRVRLAETFEALGDADLVVEAIVEDLAVKRDLFRRLEAICGAHALLCSNTSSLSIGA 127 Query: 130 LGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTP 189 + ++ P+R+ G+HFFNPAP M LVEVV TS+ D + A GK PV +P Sbjct: 128 IAEGLTAPQRVAGLHFFNPAPAMRLVEVVSAPDTSEATRDALLEFARTLGKTPVAVNDSP 187 Query: 190 GFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTS 249 GFIVNR ARPFY E+L LL++ DA TLDA + G F +G F L DL+G D+N T+ Sbjct: 188 GFIVNRCARPFYGEALHLLEQGTADAETLDACLTCGGGFPLGPFALIDLVGVDINLKATT 247 Query: 250 SVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQSDESVI 309 +++ ++ + PRF PS + + V AG LG+KSGQGFY + E P P Q D + Sbjct: 248 TLWEAFGRHPRFRPSPLIEAKVAAGELGKKSGQGFYRH--DRETPPSTALPPAQVDSLDV 305 Query: 310 IAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACEGVANLV 369 + P L+ GL+ Q+ G AL+ R + V Sbjct: 306 LLAQLP---------LRLPGLS--------QVSDGHTAAALS-------RRHAQPV---T 338 Query: 370 LFDLAF-DYSKASRLALAPADQASDAA-----VSCACALLQKAGIEVSLIADRPGLVIMR 423 LFD++ + K + LA A A + A L G+ + + DRPGLV++R Sbjct: 339 LFDVSLVPWPKERAMTLAFASHGLSEAEHVELIEAAATL----GVRLVEVPDRPGLVVLR 394 Query: 424 TVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSY 483 ML EA A GVAT +D AM+ GLN+ GP +RLG+ V L + Sbjct: 395 VATMLIGEARRALAEGVATADAMDTAMRLGLNFALGPWDMLERLGSEPVETTLAGAASED 454 Query: 484 AEDRY 488 RY Sbjct: 455 DRGRY 459 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: 508 Number of extensions: 23 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: 461 Length adjustment: 34 Effective length of query: 472 Effective length of database: 427 Effective search space: 201544 Effective search space used: 201544 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 24 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