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_084198499.1 C0029_RS14200 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_002869505.1:WP_084198499.1 Length = 718 Score = 361 bits (927), Expect = e-104 Identities = 239/714 (33%), Positives = 363/714 (50%), Gaps = 29/714 (4%) Query: 14 DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRE-NKELRGVVFVSAKPDNFIAGADIN 72 D I + D G+ +N + E+A + + +L EL+G+ S KP F AG DI Sbjct: 11 DGIVDLIFDQEGKSVNVMGEEYAEAMPKALDELEAMGDELKGLYIRSGKPGQFFAGGDIT 70 Query: 73 MIGNCK---TAQEAEALAR---QGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGR 126 M+ + +E E + R ++ +A I L + V I+G LGGG E+ALACH R Sbjct: 71 MMLEMDLNPSQEEREEMHRGLLDAKEPLARIERLGVPVAVGINGPALGGGYEIALACHYR 130 Query: 127 VCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVD 186 + D PK +GLPE LGLLPG+GG R+ R++G+ AL +I GKQL A +AL+ GL+ Sbjct: 131 IAMDSPKVKVGLPEAMLGLLPGAGGIVRMTRMLGMQEALGLISQGKQLVAAKALEKGLIH 190 Query: 187 DVVPHSILLEAAVELAKKERPSSRP---LPVRERILAGPLGRAL--LFKMVGKKTEHKTQ 241 ++ + A + K P +R P GP A L ++T+ Sbjct: 191 ELAADEEAMAAQAKAWIKANPDARQPWEQPGYSIPGGGPQDEATQGLTYFGPVNVMNQTK 250 Query: 242 GNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGS 301 GN A + I+ V ++ + EAR F L + S+ + + FF + D G+ Sbjct: 251 GNMTAPQVIIAAVIDTARVDYATAHKIEARYFQRLLLDQVSRNMMTTFFIQMNAL-DAGA 309 Query: 302 DAPPA----PLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357 P + +GILG G+MG GIA+ A K G+ V +KD+ + + Y+ E Sbjct: 310 SRPEGIAKTEVKKLGILGAGVMGAGIAF-NAAKVGMNVVLKDLTQENADKGKAYAASACE 368 Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAH 417 + R + + ++ L I T D A DL+IEAVFEN ++K + E E Sbjct: 369 ---KSRRIDEQQAEEILGRIQPTADVADLADCDLVIEAVFENRDVKAAVTRETEAVLGEQ 425 Query: 418 TIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLA 477 +FASNTS+LPI ++A + RP+ IG+HFFSP E+MPLVEII TS + +A LA Sbjct: 426 AVFASNTSALPITELAQASVRPQNFIGMHFFSPAERMPLVEIITGEQTSDECLAWAFDLA 485 Query: 478 KKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLD 537 +K GK PIVV+D GF+ R++ I + RML +G I+ G P+GP++ LD Sbjct: 486 QKMGKKPIVVKDAPGFFTTRVIGQTITQGQRMLAEGVNPALIENGAAFNGSPMGPLETLD 545 Query: 538 EVGIDTGTKII---PVLEAAYGERF--SAPANVVSSILND-DRKGRKNGRGFYLYGQKGR 591 + ++T V A GE+ SA + V+ ++ + +R G+ G GFY Y G+ Sbjct: 546 TISLETAYHAANQQRVDAEARGEQVEPSAESEVIRIMVEEAERVGQAKGAGFYDYDDNGK 605 Query: 592 KSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVF 651 K + L G + V +R + + EA+R ++E V+ SV DG+IG++ Sbjct: 606 KVATWA--GLKALFAKDGYKDVPYQDVKDRLLFSQVLEAIRIMEEGVLTSVGDGNIGSIM 663 Query: 652 GIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESF 705 GIGFPP GG ++ +++ G + LA YG F P + L++M A G +F Sbjct: 664 GIGFPPHTGGVYQCVNAYGVQAFADRAKELAAAYGEAFEPPQLLLDMAADGRTF 717 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: 1070 Number of extensions: 50 Number of successful extensions: 6 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: 718 Length adjustment: 40 Effective length of query: 674 Effective length of database: 678 Effective search space: 456972 Effective search space used: 456972 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 24 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