Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate PfGW456L13_2432 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
Query= SwissProt::P76083 (475 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2432 Length = 505 Score = 408 bits (1048), Expect = e-118 Identities = 239/488 (48%), Positives = 309/488 (63%), Gaps = 30/488 (6%) Query: 8 VAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTAETCE 67 +AVIG+G MGAGIA+VAA GH VLL D A +AI+GI +L RV GKL+AE+ Sbjct: 10 IAVIGAGAMGAGIAQVAAQAGHPVLLLDNRPGAAAQAIEGIDRQLGKRVENGKLSAESRS 69 Query: 68 RTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSISITA 127 T+ RL V I LA DL+IEA E LEVK+ALF QL +C +L +NTSS+SIT+ Sbjct: 70 ATVARLQAVEVIETLADCDLIIEAIVENLEVKRALFRQLEGICGEHCILASNTSSLSITS 129 Query: 128 IAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRCHSTP 187 IAA++ +P+R+ GLHFFNPAPVM LVEVVSGLA+ + E L + +WGK+PV STP Sbjct: 130 IAAQLDHPQRLLGLHFFNPAPVMALVEVVSGLASDPALAECLYDTARAWGKKPVHTRSTP 189 Query: 188 GFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDVNFAVTC 247 GFIVNRVARP+Y+E+ R L+E A +DA +R+ GF MG ELTDLIG DVN+AVTC Sbjct: 190 GFIVNRVARPFYAESLRMLQEGAADCPTLDALMREAGGFAMGAFELTDLIGHDVNYAVTC 249 Query: 248 SVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWR--AER---------------- 289 SVF+A++Q+ RFLPSL+Q+ELV GGRLG+KSG G Y + AER Sbjct: 250 SVFDAYYQDTRFLPSLIQKELVDGGRLGRKSGQGFYCYAQGAERPQAGEISSSASVETCI 309 Query: 290 -EAVVGL-EAVSDSFSPMKVE---KKSDGVTEIDDVLLIETQGETA-QALAIRLARPVVV 343 E +G+ + + S VE + G+ + D +L + G A Q R +++ Sbjct: 310 AEGDLGIAQGLLARLSEQGVEVIRRDGRGLLRVGDAVLALSDGRMACQRAREDGLRNLIL 369 Query: 344 IDKM-----AGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVAMII 398 +D A ++ AA ++P A + + LQ+ G V ++D P + + RTVAM+ Sbjct: 370 LDLAFDYGNAKRIAISHAAGIDP-LALEQGVALLQRAGLMVSLLSDSPALAVLRTVAMLA 428 Query: 399 NEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEERYR 458 NEA DAL +GVAS DID AMR GVNYP GPLAW +G IL LENLQ YGEERYR Sbjct: 429 NEAADALLQGVASAADIDLAMRAGVNYPQGPLAWADAIGLSHILETLENLQASYGEERYR 488 Query: 459 PCSLLRQR 466 P LLR+R Sbjct: 489 PSLLLRRR 496 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: 533 Number of extensions: 20 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: 475 Length of database: 505 Length adjustment: 34 Effective length of query: 441 Effective length of database: 471 Effective search space: 207711 Effective search space used: 207711 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