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 GFF1187 PGA1_c12020 fatty acid oxidation complex FadJ subunit alpha
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Phaeo:GFF1187 Length = 733 Score = 164 bits (416), Expect = 1e-44 Identities = 115/395 (29%), Positives = 195/395 (49%), Gaps = 22/395 (5%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61 K+ V+G+G+MG GIA ++A AG EV + D + + L K + G + + Sbjct: 328 KIGVLGAGMMGAGIALVSAQAGMEVVLIDRDQAAADKGKAYTESYLDKGIKRGKVTADKK 387 Query: 62 QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121 + + T LKG D +IEAV ED +K + + EA + A+NTS+LPI+ Sbjct: 388 EAMLSRITATPDLDHLKGCDLIIEAVFEDPGVKAEMTKKVEAIIPEDCIFASNTSTLPIT 447 Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181 ++A P++ +G+HFF+P M LVEI++G+ T D V + + + K IVV D Sbjct: 448 DLAEASVRPEQFIGIHFFSPVEKMFLVEIIKGEKTGDRAVAKALDYVRQIRKTPIVVNDA 507 Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241 F+ NR ++ + G ++ +G+A + +A +LGFP+G L D T +D+G + Sbjct: 508 RFFYCNRCIIPYVNEGARMITEGVA--PALIDNAARQLGFPVGPIQLTDETSIDLGAKIA 565 Query: 242 KAVTARGFKAFPCSSTEKLV----SQGKLGVKSGSGYYQYPSPG------KFVRPTLPST 291 +A A A+P S+ + L+ QG+LG KS +G++ Y G K ++ P Sbjct: 566 RATKAAMGDAYPESAADDLIFWMEEQGRLGRKSNAGFFDYDDKGKRQGYWKGMQEKYPLA 625 Query: 292 SK-----KLGRYLISPAVNEVSYLLREGI-VGKDDAEKGCVLGLGLPK---GILSYADEI 342 + ++ L+ V E L EG+ + + + G +L G G LS+ D I Sbjct: 626 DEQPDLIEVQERLMFAQVLEAVRALEEGVLMDIREGDVGAILAWGFAPWSGGPLSWLDII 685 Query: 343 GIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 G +++ G + ++ PLL M ++G+ Sbjct: 686 GTPYAAERCDQLTAKYG-ERFTCPPLLREMAEKGQ 719 Score = 67.0 bits (162), Expect = 3e-15 Identities = 52/176 (29%), Positives = 82/176 (46%), Gaps = 19/176 (10%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT------PVKAM 472 N +NG + +++ +D + V+ I IT + F+ G D+ + P + + Sbjct: 26 NVLNGQAMIDLDGLVDDALADDAVKGIVITSGKKDFAGGMDLNVLAKMKEDAGDEPARGL 85 Query: 473 IAS-RKFHEVFMKIQFLT---------KPVIAVINGLALGGGMELALSAD--FRVASKTA 520 K HE KI+ KPV A + G A+G G+EL LS F + A Sbjct: 86 FEGIMKMHEGLRKIERAGMDPKTNKGGKPVAAALPGTAVGIGLELPLSTHRIFAADNPKA 145 Query: 521 EMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAE 575 ++G PEI +G+ PG GGT RL R G +L G+ V ++A GI++ + E Sbjct: 146 KIGLPEIMVGIFPGAGGTTRLVRKMGAMAAAPFLLEGKLVDPKKAKGAGIIDEVVE 201 Score = 43.1 bits (100), Expect = 4e-08 Identities = 32/95 (33%), Positives = 46/95 (48%), Gaps = 10/95 (10%) Query: 300 ISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQT 357 I P VNE + ++ EG+ D+A + LG P G + DE ID+ + Sbjct: 516 IIPYVNEGARMITEGVAPALIDNAARQ----LGFPVGPIQLTDETSIDLGAKIARATKAA 571 Query: 358 SGMDHY---SPDPLLLSMVKEGKLGRKSGQGFHTY 389 G D Y + D L+ M ++G+LGRKS GF Y Sbjct: 572 MG-DAYPESAADDLIFWMEEQGRLGRKSNAGFFDY 605 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: 1039 Number of extensions: 57 Number of successful extensions: 8 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: 733 Length adjustment: 39 Effective length of query: 612 Effective length of database: 694 Effective search space: 424728 Effective search space used: 424728 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 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