Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate GFF4142 PS417_21215 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__WCS417:GFF4142 Length = 715 Score = 388 bits (996), Expect = e-112 Identities = 266/725 (36%), Positives = 376/725 (51%), Gaps = 33/725 (4%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 MT A D I V+T+D+PG+ NT+ + + A++++L K+ L GVV SAK Sbjct: 1 MTQAIRYEKGQDGIVVLTLDMPGQSANTMNGAYREAMAAMVERLEAQKDDLAGVVITSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQEAEAL--ARQGQQLMAEIHALPIQVIAAIHGACLGGGLEL 119 F AG D+N + A + R+ + + + L V+AAI+GA LGGG E+ Sbjct: 61 K-TFFAGGDLNELIKVDKAHAKDFYDSVRELKAQLRRLETLGKPVVAAINGAALGGGWEI 119 Query: 120 ALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQA 179 LACH RV DD LGLPEV LGLLPG GG R+ R++G+ AL +L GK++R +QA Sbjct: 120 CLACHYRVALDDKSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPQQA 179 Query: 180 LKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGR------ALLFKMVG 233 L+ GLV+++ L A P ++ P + P G A + + Sbjct: 180 LQAGLVNELAADRDELLAKSRAWILANPDAKQ-PWDNKGYQIPGGTPSSPKVAQMLAIAP 238 Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293 KTQG +PA E+IL G + + E R F EL ++ + F+ Sbjct: 239 SILRSKTQGCFPAPEKILCAAVEGAQVDFDTAHLIETRYFTELVTGQVAKNMIGTFWFQL 298 Query: 294 DVKKDPGSDAP----PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL 349 + + + GS P P VG+LG G+MG GIAYV+A AGI V +KDIN Sbjct: 299 N-EINAGSSRPQGFAPYVTRKVGVLGAGMMGAGIAYVSA-SAGIEVVLKDINLAAAEKGK 356 Query: 350 KYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAE 409 +S L+ KV R L A +R+ LA I T A DLIIEAVFE+ ELK ++ A Sbjct: 357 AHSAALLDKKVSRGQLTAEQRETFLARIHPTATDEDLAGCDLIIEAVFEDRELKAKVSAA 416 Query: 410 VEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQT 469 + A + ASNTS+LPI +A + IGLHFFSPV+KMPLVEII A TS +T Sbjct: 417 AQSVVGADAVIASNTSTLPISGLATAVPDQTRFIGLHFFSPVDKMPLVEIIKGARTSDET 476 Query: 470 IATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFP 529 +A + KTPIVV D GF+ +R+ + NE I ML +G I+ K G P Sbjct: 477 LARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVAAPMIETEARKAGMP 536 Query: 530 VGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPANVVSSILNDD--RKGRKNGRGF 583 VGP+ + DEV + I L+A + PA V +L ++ R G+ G GF Sbjct: 537 VGPLAVSDEVSLSLMNHIRQQTAKDLQAEGKAVPTHPATAVIDLLVNEYQRMGKAAGGGF 596 Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQ---GRISAPQVAERCVMLMLNEAVRCVDEQVIR 640 Y Y G K ++P + ++ + RIS V +R + + E VRCV+E V+ Sbjct: 597 YDYPSGGHK-------YLWPELKSRFERPDQRISPQDVRDRLLFIQAIETVRCVEEGVLM 649 Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700 S D ++G++FGIGF P+ GG ++I+ G + +A + LA QYG RF P L+E A Sbjct: 650 STADANVGSIFGIGFAPWSGGALQFINQYGLNDFIARARYLAEQYGERFMPPALLLEKAA 709 Query: 701 RGESF 705 +G+ F Sbjct: 710 QGDVF 714 Lambda K H 0.319 0.137 0.393 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: 1005 Number of extensions: 40 Number of successful extensions: 7 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: 714 Length of database: 715 Length adjustment: 39 Effective length of query: 675 Effective length of database: 676 Effective search space: 456300 Effective search space used: 456300 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: 55 (25.8 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