Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_084199858.1 C0029_RS05645 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::P21177 (729 letters) >NCBI__GCF_002869505.1:WP_084199858.1 Length = 715 Score = 348 bits (893), Expect = e-100 Identities = 233/712 (32%), Positives = 368/712 (51%), Gaps = 25/712 (3%) Query: 15 DGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEFL 74 DGI + D G VN ++ +G+ I L+++ L G++L S K F G ++ + L Sbjct: 11 DGIVTVTMDMNGPVNSMNEEYRQLMGDTITRLQEEEGLTGVVLASAKKVFFAGGNLYDLL 70 Query: 75 SLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPD-- 132 + Q Q L LE LPVP +AA+NG ALGGG E LA ++R+A + Sbjct: 71 AAREEDIPQFMQELDLTKGQLRALEKLPVPVVAAINGAALGGGFEICLACNHRIAWDNRA 130 Query: 133 LRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLV-DGVVKAE 191 +++GLPE LG++PG GG VRM +LG +AL + G V ++AL G++ + V + Sbjct: 131 VQLGLPEVSLGLLPGGGGVVRMVNLLGLQAALPYLLEGTRVSPEKALAAGMIHETVASVD 190 Query: 192 KLVEGAKAVLRQAINGDL----DWKAKRQPKLEPLKLSKIEATMSFTIAKGMVAQTAGKH 247 +LV AKA + + + + W K K+ + T A M+ Q Sbjct: 191 ELVPRAKAWILENKDNEAAAVQPWDVKGH-KIPGGNAAHPANAQMITAAPAMLFQKTRGL 249 Query: 248 YPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVG-IFLNDQYVKGKAKKL 306 PAPI + AAR + AL +E++ LA T EA+ + F V G A + Sbjct: 250 LPAPIKILDCAVEAARLNLDTALVVESRGLAELAITPEAKNQISTFFFGMNKVNGGASR- 308 Query: 307 TKDVETPK--QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQL 364 +D+E K + VLGAG+MG GIAY SA G+ VV+KDI+ ++ G + LL K++ Sbjct: 309 PQDIEPQKTTKVGVLGAGMMGQGIAYVSAMAGIEVVLKDISQEAADQGKAYSETLLAKRV 368 Query: 365 ERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVL 424 +G++D K +++ I PT + A D+V+EAV EN ++K + + + + +D + Sbjct: 369 AKGRMDQAKADAILALIKPTAEDADLQGCDLVIEAVFENMELKHTITKDLQGYMAEDGIW 428 Query: 425 ASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKM 484 SNTST+PI++LA +PENF G+HFF+PV +MPLVEII GE++ D T+AK + ++ Sbjct: 429 GSNTSTLPITQLAEVATKPENFIGIHFFSPVDKMPLVEIICGEQTGDVTLAKAFDYCKQI 488 Query: 485 GKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDVV 544 KTPIVVND GFF +R Y QLL DG ++D + K G P+GP + D V Sbjct: 489 RKTPIVVNDSLGFFTSRTFGTYLDEGMQLLVDGVHPIQVDN-LGKAIGMPVGPLQVHDEV 547 Query: 545 GIDTAHHAQAVMA--AGFPQRMQKDYRDAIDALF--DANRFGQKNGLGFWRYKEDSKGKP 600 ++ A A Q A+ A D R G+ +G GF+ Y D Sbjct: 548 SLELTKKAGQTHADLGVLDQWGDGSVGRAVIATMVDDHGRGGRHHGGGFYEYAADG---- 603 Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660 + LL +P+ D ++I R++ V E ++CLE G++ + A+ ++ + Sbjct: 604 ---SRSLWPTLLDLYHKPETDLPAQDIKDRLLFRQVIESLKCLEGGVLRSVADGNIGSIM 660 Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQ-HLGPLYEVPEGLRNKARHNE 711 G+G P + GG ++++T G +++D + + G ++ P + +K E Sbjct: 661 GIGAPVWTGGFIQFVNTYGLQRFIDRCAELEAAYGERFKAPAIVADKLAAGE 712 Lambda K H 0.318 0.136 0.399 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: 1194 Number of extensions: 76 Number of successful extensions: 5 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: 729 Length of database: 715 Length adjustment: 40 Effective length of query: 689 Effective length of database: 675 Effective search space: 465075 Effective search space used: 465075 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 (21.7 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