Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_084198637.1 C0029_RS18685 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-17591 (715 letters) >NCBI__GCF_002869505.1:WP_084198637.1 Length = 715 Score = 835 bits (2158), Expect = 0.0 Identities = 422/715 (59%), Positives = 529/715 (73%), Gaps = 1/715 (0%) Query: 1 MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60 MIYQ +T+K LEG I ELNFDL+GESVNKF++ T++ L A +DA++A++ +KG++VTS Sbjct: 1 MIYQSDQLTIKRLEGDIAELNFDLQGESVNKFDQATVASLTAGLDALEAESGIKGLLVTS 60 Query: 61 GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120 GK VFIVGADITEFV F EE+ N F+ L P+ AING A+GGGLE Sbjct: 61 GKPVFIVGADITEFVQLFGSSKEEIKPFTGINNANFNRLAALPYPSAVAINGFAMGGGLE 120 Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180 +CLA DFR+MS AKVGLPE KLGI PG+GGTVRLPR+IG D AV W+A+G + + + AL Sbjct: 121 ICLACDFRIMSTAAKVGLPETKLGILPGWGGTVRLPRIIGVDEAVMWMATGADKRPDAAL 180 Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240 K GAVDAV APEQL+ AL A+ G LD+K RR K L LN IE MM+F T K Sbjct: 181 KAGAVDAVAAPEQLREVALTTLNNAIEGGLDYKGRRAQKHGPLPLNDIEAMMSFFTIKSM 240 Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300 V QAG NYPAP++ + I++A + + AL+VEA GF +LA T VA +L+G+FLNDQ L Sbjct: 241 VGQQAGKNYPAPLKVVDVIEQARSMSLEDALDVEAEGFAELATTPVAAALVGVFLNDQLL 300 Query: 301 KKKAKKYDEVA-KDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAK 359 K AK +++ A K ++ AAVLGAGIMGGGIAYQSALKGTPI MKDI ++G+ +GL+EA K Sbjct: 301 GKVAKGWEKQADKKIENAAVLGAGIMGGGIAYQSALKGTPIKMKDINQDGLDLGLSEANK 360 Query: 360 LLGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAV 419 LL KRV KGR+T M + LN I PT++Y F VDIVVEAVVEN KVK VLAE E + Sbjct: 361 LLAKRVAKGRMTADTMGDILNSIDPTLTYAGFDGVDIVVEAVVENEKVKGIVLAETEKEI 420 Query: 420 KEDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTV 479 +DA++ASNTSTISI+ LA+ L+RPENFCGMHFFNPVH MPLVEVIRGEKT + AIA TV Sbjct: 421 DKDAVLASNTSTISITRLAENLERPENFCGMHFFNPVHAMPLVEVIRGEKTSDNAIARTV 480 Query: 480 AYAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAY 539 AYA KMGK +VVNDCPGFLVNRVLFPYFGGF LL G DF IDKVME++GWPMGPAY Sbjct: 481 AYANKMGKKAVVVNDCPGFLVNRVLFPYFGGFNALLRDGADFQAIDKVMERWGWPMGPAY 540 Query: 540 LSDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGK 599 L DVVGIDTG H +VMAEGFPDRM + K+A +V++E +R GQKNGKG Y Y TDKRGK Sbjct: 541 LMDVVGIDTGVHAANVMAEGFPDRMQPDFKSATEVLFENDRYGQKNGKGMYEYVTDKRGK 600 Query: 600 PKKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLI 659 PKKV + + Y+++ P+ E+ E +DI+ MM+P+ +E RC+E+GIV T +EAD+ L+ Sbjct: 601 PKKVVNEEVYDLIAPVCGERAEFDKDDIIMRMMLPMAIEMARCVEEGIVGTPSEADLALL 660 Query: 660 YGIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFF 714 YG+GFPPFRGG R++D++G+ + K+A LG Y T +++M NG+ ++ Sbjct: 661 YGVGFPPFRGGIFRWMDTVGMQAIADASAKFAHLGKAYELTDNMKDMLANGKTYY 715 Lambda K H 0.318 0.137 0.388 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: 1367 Number of extensions: 71 Number of successful extensions: 2 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: 715 Length adjustment: 39 Effective length of query: 676 Effective length of database: 676 Effective search space: 456976 Effective search space used: 456976 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