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_084057805.1 B9A12_RS10305 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::P28793 (715 letters) >NCBI__GCF_900176285.1:WP_084057805.1 Length = 681 Score = 309 bits (792), Expect = 3e-88 Identities = 210/662 (31%), Positives = 336/662 (50%), Gaps = 38/662 (5%) Query: 30 NKFNRLTLNELRQAVDAIKADASVKGVIVSSGKDVFIVGADITE--FVENFKLPDAELIA 87 N F+ L L QA+D + A++ VKG++++ +F GAD+T+ FV F+ I Sbjct: 35 NVFSEAALMSLNQAIDQVLAESDVKGLMLTGKPHIFAAGADLTQVPFVTTFE--QGYQIG 92 Query: 88 GNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMADSAK-IGLPEVKLGIY 146 N + I DL PT+AA NG+ALGGGLE+ L ++R +A S +G PE +G+ Sbjct: 93 KN--GHTIMKRLMDLPFPTLAAYNGVALGGGLEIGLYCNYRTVAKSVPAMGFPECFIGLI 150 Query: 147 PGFGGTVRLPRLIGVDNAVEWIASGKENR-----AEDALKVSAVDAVVTADKLGAAALDL 201 PG+GG +LIG + A+E I N+ A ++ D + + +L Sbjct: 151 PGWGGCTLATKLIGPEKALELIVFNALNQNRMINGPKAYEMGLADRLFDGAEFFDESLQF 210 Query: 202 IKRAISGELDYKAKRQ-PKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYPAPVEAIKTIQ 260 + I+G+ K +RQ PK LK AK FV + PAP AI+ ++ Sbjct: 211 LVNIIAGK--EKVERQAPKTTNLKT-------VVSKAKAFVDSKVHGAAPAPYRAIELVE 261 Query: 261 KAANFGRDKALEVEAAGFAKLAKTSASNCLIGLF-LNDQELKKKAKVYDKIAKDVKQAAV 319 A + D+ E E L K+ C I F L ++ KK + D K VK+ + Sbjct: 262 GAVKWDIDQGFEEENKALGDLVKSRQCKCSIYAFDLVNRYAKKVKGIPDVKPKPVKKVGI 321 Query: 320 LGAGIMGGGIAYQSASK-GTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTPAKMAEV 378 +GAG+M +A + G P++MKDI + +++G+A V+KGRM A+ + Sbjct: 322 IGAGLMASQLAQVFIYRLGVPVVMKDIKQEFVDKGVAYVRGEFQKMVEKGRMPEARARHL 381 Query: 379 LNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVREDAILASNTSTISISLLA 438 + + TLSY DF + D V+EAV E +K+ V AEVE V + ILA+NTS++S++ + Sbjct: 382 SSLVEGTLSYDDFADCDFVIEAVFERMDIKKQVFAEVEAVVSPECILATNTSSLSVTEMG 441 Query: 439 KALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGF 498 LK P+ VG HFFNPV ++PLVEVI+ ++ D +AT AKK+ K ++V D P F Sbjct: 442 SDLKHPQRVVGFHFFNPVAVLPLVEVIKTPQTDDQTLATAFDLAKKLKKTGVLVKDAPAF 501 Query: 499 LVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAE 558 LVNR+L +V G DF+++D+ + G PM P L+ +VG +H + + Sbjct: 502 LVNRLLTKMLSDCLTMVDEGADFIQVDEALLALGMPMAPFDLLALVGFPVAYHVCETLNR 561 Query: 559 GFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQKKLVDSSVLEVLKPIVYE 618 F R ++A + K+L Y G + K V+ V ++ + Sbjct: 562 AF-----GPERFPVNANF--KKLIDAGISSIYV-----PGSKVKKVNPEVAKLWEK--KG 607 Query: 619 QRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPLFRGGALRYIDSI 678 ++ ++I + ++ L E LE+ +V+++ + D+ ++ G G+P F GG Y+D Sbjct: 608 DKEFHPDEIRDRVLHNLAREIDLILEEKVVDSSRDVDLAMIMGAGWPFFMGGITMYLDMA 667 Query: 679 GV 680 G+ Sbjct: 668 GI 669 Lambda K H 0.318 0.137 0.386 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: 1142 Number of extensions: 59 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: 715 Length of database: 681 Length adjustment: 39 Effective length of query: 676 Effective length of database: 642 Effective search space: 433992 Effective search space used: 433992 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: 54 (25.4 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