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 WP_011840656.1 RSPH17029_RS04435 enoyl-CoA hydratase/isomerase family protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000015985.1:WP_011840656.1 Length = 733 Score = 418 bits (1075), Expect = e-121 Identities = 267/731 (36%), Positives = 394/731 (53%), Gaps = 42/731 (5%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 FT D + IT DVPG+ MN + +++ +I ++ ++GV+ S K D F Sbjct: 4 FTSRTDADGVCTITWDVPGKSMNVMSMAGFAELDGLIAAALDDPSVKGVILTSGKKD-FA 62 Query: 67 AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQV----------------IAAIHG 110 AG D+N+I K + + AR + + E+HA+ ++ +AA+ G Sbjct: 63 AGMDLNVIARMKE-EGGDDPARAVFEGVMEMHAVLRRIERAGMDPKTLKGGKPIVAALPG 121 Query: 111 ACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILT 170 LG GLEL LACH + D+PK +GLPE+ +G+ PG GGT RL R +G A ++L Sbjct: 122 TALGLGLELPLACHRIIAADNPKAKIGLPEIMVGIFPGGGGTTRLVRRLGAMMAAPLLLE 181 Query: 171 GKQLRAKQALKLGLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAG--PLGRA 226 GK K A +G+VD+VVP LL A E L K+ +P + + G P A Sbjct: 182 GKLNDPKGAKAMGVVDEVVPADQLLARAKEWVLGAKDADLVKPWDAKGYKMPGGAPYHPA 241 Query: 227 LLFKMVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284 VG KT G YPA + +L V G + EAR F + M P S A Sbjct: 242 GFMTFVGASAMVTGKTMGVYPAAKGLLAAVYEGALVPFDTALKIEARWFTHVLMNPSSSA 301 Query: 285 L-RSIFFASTDVKKDPGSDAPPAPLNSV---GILGGGLMGGGIAYVTACKAGIPVRIKDI 340 + RS+F ++K G+ P P SV G++G G+MG GIA+V A AGI V + D Sbjct: 302 MIRSLFINKEALEK--GAVRPALPDQSVRKLGVIGAGMMGAGIAHVAA-NAGIEVVLIDA 358 Query: 341 NPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENL 400 + + +S L+ ++R + A ++ + L I+ TTDY + DLI+EAVFE+ Sbjct: 359 TQEAADRGKAHSEGLLDKGMKRGKVSAEKKAEVLGRIAATTDYAALSGCDLIVEAVFEDP 418 Query: 401 ELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEII 460 +K ++ +VE IFA+NTS+LPI +A + P Q IG+HFFSPV+KM LVEII Sbjct: 419 AVKAEVTQKVEAAVGPDCIFATNTSTLPISGLAKASRDPAQFIGIHFFSPVDKMMLVEII 478 Query: 461 PHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHID 520 T + +A + ++ KTPIVV D FY NR + PY+NE IRM+ +G I+ Sbjct: 479 RGKATGDRAVAKALDFVRQIRKTPIVVHDARFFYANRCIIPYLNEGIRMVAEGVAPALIE 538 Query: 521 AALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGRK 578 A G P+GP+QL+DE ID G KI +AA GE + +A V+ + ++ R GRK Sbjct: 539 NAAKLVGMPLGPLQLVDETSIDLGVKIAKATKAALGEAYPDAAVDAVIFPLADEGRLGRK 598 Query: 579 NGRGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAE---RCVMLMLNEAVRCVD 635 G GFY Y G++ ++P + + + P++AE R + + EAVR ++ Sbjct: 599 AGAGFYAYDAAGKRD------GLWPGLADRWPLAETQPELAEVQHRLLFAQVLEAVRALE 652 Query: 636 EQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERL 695 E V+ +R+GD+GA+ G GF P+ GGPF ++D +GA V I + LA ++G+RF P + L Sbjct: 653 EGVLTDIREGDVGAILGWGFAPWSGGPFSWLDMIGAPRAVEICEGLAERHGTRFAPPKLL 712 Query: 696 VEMGARGESFW 706 VEM +GESF+ Sbjct: 713 VEMAGKGESFY 723 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: 1127 Number of extensions: 52 Number of successful extensions: 9 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: 733 Length adjustment: 40 Effective length of query: 674 Effective length of database: 693 Effective search space: 467082 Effective search space used: 467082 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 Apr 10 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