Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate GFF2242 PGA1_c22740 fatty acid oxidation complex subunit alpha
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Phaeo:GFF2242 Length = 706 Score = 175 bits (444), Expect = 5e-48 Identities = 123/398 (30%), Positives = 195/398 (48%), Gaps = 26/398 (6%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62 V VIG+G MG GIA AG V + + + L+Q +E+++ + + G L + Sbjct: 297 VAVIGAGTMGRGIAIAFLQAGYPVTLLETTQGALEQGLEKVREHFQRAAQKGRLSADRAE 356 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 ++ T L +D +IEA E + +KR IF + HA P A+LA+NTS+L + E Sbjct: 357 AISANATGTLSYAGLAKADLIIEAAFESMNVKRQIFEALDLHAKPGAILASNTSTLDLDE 416 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 IA+V P+ V+G+HFF+P +M L+E+VRG T+ +V+ T +AK + K + V Sbjct: 417 IATVTSRPEDVIGLHFFSPANVMRLLEVVRGAKTAPDVIATAITVAKKIRKLPVTVGVCY 476 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GF NR+L G L+ +G A+ ++VD +E G MG+ +AD G+D+G V + Sbjct: 477 GFVGNRMLEPYFREGSRLLLEG-ATPKQVD-DVLEGFGMAMGIHAMADLAGVDVGARVRQ 534 Query: 243 AVTAR-GFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKKLG----- 296 + + ++L G+LG K+G G Y Y + P + S +L Sbjct: 535 ERRSEIAHDPTYQAVQDRLFELGRLGQKTGRGSYVYEGRTRVEDPEMVQISSELADLHGV 594 Query: 297 -----------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GILSYADE 341 + P +NE +L EGI + D + V G G P G + YADE Sbjct: 595 KRRDIDDQEILERCLFPLINEGFLILEEGIATRPGDCDLIWVNGYGFPNWRGGPMHYADE 654 Query: 342 IGIDVVVNTLEEMRQTSGM---DHYSPDPLLLSMVKEG 376 IG+ ++ + RQ+ G ++P PLL + G Sbjct: 655 IGLSQIMERMTHYRQSLGAYGEMWFTPAPLLEQLATSG 692 Score = 110 bits (274), Expect = 3e-28 Identities = 66/173 (38%), Positives = 103/173 (59%), Gaps = 6/173 (3%) Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466 +A+I LN P+ NA+ M + ++ A+ L+ E V+ I + +F GAD+ EF + Sbjct: 10 VAFIELNAPS-VNALGLKMRQVLSSAIHELDADEQVKAIVLCSALPLFCGGADIVEFRT- 67 Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526 A+ ++ + I+ KP+IA I G A+GG +E+AL+ D+RVA+ A MG PE Sbjct: 68 ---GAVWDKPDLPDLCVMIETSKKPIIAAIAGPAMGGALEIALACDYRVATPDAVMGLPE 124 Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578 I LGL+PG GGTQRL R++G +++L+G VK E A G+V+ L E ++ Sbjct: 125 IKLGLLPGAGGTQRLPRIAGLEAATQMILSGDPVKGEYALSCGLVDALFENDQ 177 Score = 40.0 bits (92), Expect = 4e-07 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 7/116 (6%) Query: 295 LGRYLISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLE 352 +G ++ P E S LL EG K DD +G G+ GI + AD G+DV + Sbjct: 479 VGNRMLEPYFREGSRLLLEGATPKQVDDVLEG----FGMAMGIHAMADLAGVDVGARVRQ 534 Query: 353 EMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTIVVRVEPPLA 408 E R D + + + + G+LG+K+G+G + Y +V++ LA Sbjct: 535 ERRSEIAHDP-TYQAVQDRLFELGRLGQKTGRGSYVYEGRTRVEDPEMVQISSELA 589 Lambda K H 0.316 0.134 0.377 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: 971 Number of extensions: 47 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 651 Length of database: 706 Length adjustment: 39 Effective length of query: 612 Effective length of database: 667 Effective search space: 408204 Effective search space used: 408204 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 (21.6 bits) S2: 54 (25.4 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