Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF2749 HP15_2693 3-hydroxybutyryl-CoA dehydrogenase
Query= SwissProt::P76083 (475 letters) >FitnessBrowser__Marino:GFF2749 Length = 506 Score = 385 bits (988), Expect = e-111 Identities = 224/503 (44%), Positives = 306/503 (60%), Gaps = 30/503 (5%) Query: 3 INVQT-VAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKL 61 ++ QT VAV+G+G MG+GIA+VAA GHQV L+D A DGI +L RV +GK+ Sbjct: 4 LDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKM 63 Query: 62 TAETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTS 121 + + + R+ PV + +A A LVIEA E L++K+ L A L ++C +L TNTS Sbjct: 64 QQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTS 123 Query: 122 SISITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPV 181 SIS+TA+ A++ PER+ G+HFFNPAP+M LVEVV GLAT+ V + + +WGK+PV Sbjct: 124 SISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPV 183 Query: 182 RCHSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDV 241 STPGFIVNRVARP+Y+E+ R L+EQ +DA +R+ F MG ELTDLIG DV Sbjct: 184 YATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDV 243 Query: 242 NFAVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDW--RAER---------- 289 N+AVT SVFN+++Q+ RFLPSL+Q+ELV GRLG+KSG G Y + AE+ Sbjct: 244 NYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQ 303 Query: 290 --EAVVGLEAVSDSFSPMKVEKKSDGVTEID----------DVLLIETQGE--TAQALAI 335 E+V+ E +P+ K+ G+T I+ D +L T G T +A Sbjct: 304 SDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACE 363 Query: 336 RLARPV---VVIDKMAGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWR 392 +A V + D + +A A D+A A LQ+ G V IAD PG++I R Sbjct: 364 GVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMR 423 Query: 393 TVAMIINEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHY 452 TVAM+ NEA DA GVA+ DID AM+ G+NYP GPL+W +LG + ++L N+Q Y Sbjct: 424 TVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSY 483 Query: 453 GEERYRPCSLLRQRALLESGYES 475 E+RYRP LLR+ A + G+ S Sbjct: 484 AEDRYRPALLLRKNAFAQKGFYS 506 Lambda K H 0.319 0.134 0.386 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: 550 Number of extensions: 17 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: 475 Length of database: 506 Length adjustment: 34 Effective length of query: 441 Effective length of database: 472 Effective search space: 208152 Effective search space used: 208152 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: 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