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_041416449.1 SHAL_RS13845 fatty acid oxidation complex subunit alpha FadJ
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000019185.1:WP_041416449.1 Length = 706 Score = 803 bits (2074), Expect = 0.0 Identities = 402/708 (56%), Positives = 527/708 (74%), Gaps = 7/708 (0%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKP 62 M F L R D IA++T+DVPGE MNTL++EF ++ ++ +++ + ++G+V VS K Sbjct: 1 MEKTFNLTRRDDGIAILTMDVPGETMNTLRSEFGPEISDVLAEIKADTSIKGLVLVSGKK 60 Query: 63 DNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALA 122 D+F+AGADI+M+ C+TA +A+ L++QG + E+ +LPI V+AAI+GACLGGGLELALA Sbjct: 61 DSFVAGADISMLDACETATDAKQLSQQGHVVFNELESLPIPVVAAINGACLGGGLELALA 120 Query: 123 CHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKL 182 CH RVC+ +PKT++G+PEVQLGLLPG GGTQRLPRL+GV+TAL+M+LTGKQLR KQALK+ Sbjct: 121 CHKRVCSLNPKTMMGVPEVQLGLLPGGGGTQRLPRLVGVTTALDMMLTGKQLRPKQALKM 180 Query: 183 GLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAGP-LGRALLFKMVGKKTEHK 239 GLVDD VP SILL AVE LA K + ++L G GR ++F GK+ K Sbjct: 181 GLVDDAVPESILLRTAVEMALAGKRPAKKKHQSFFNKVLEGTSAGRNIIFDQAGKQVAKK 240 Query: 240 TQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDP 299 TQGNYPA +I++ V G+ +G + G + EA F +L M+ +S A+RS+FFA+T++KK+ Sbjct: 241 TQGNYPAPAKIIDCVRQGMTKGMAKGLEVEASHFADLVMSKESGAMRSVFFATTEMKKET 300 Query: 300 GS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358 G+ D P +N V +LGGGLMGGGIA VT KA IP R+KDI+ G+++AL Y++ L+ Sbjct: 301 GAGDVEPQKVNKVMVLGGGLMGGGIASVTTTKAKIPARVKDISETGLSNALAYAYKLLDK 360 Query: 359 KVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418 V+RRH+ + RD +AL++ TT+Y+G D+++EAVFE+L LK QMV +VE+ C HT Sbjct: 361 GVKRRHMTPAVRDNLMALMTTTTEYKGIKDADIVVEAVFEDLALKHQMVKDVERECGEHT 420 Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478 IFASNTSSLPIG IA A+RPE VIGLH+FSPVEKMPLVE+I H TSA+TIATTV AK Sbjct: 421 IFASNTSSLPIGQIAEAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSAETIATTVAFAK 480 Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538 KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ VEH+D AL+KFGFPVGP+ LLDE Sbjct: 481 KQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALIKFGFPVGPMTLLDE 540 Query: 539 VGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVD 598 VGID G KI P+LE GERF AP +L DDRKGRKNG+GFYLYG G+K K+VD Sbjct: 541 VGIDVGAKISPILEKELGERFKAP-TAFDKLLADDRKGRKNGKGFYLYG--GKKKAKEVD 597 Query: 599 PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPF 658 +Y ++G + A +VA+RCV+ MLNEAVRC++E +I RDGDIGA+FGIGFPPF Sbjct: 598 QTVYSVLGLKPGVDTEATEVAQRCVVQMLNEAVRCLEESIIACPRDGDIGAIFGIGFPPF 657 Query: 659 LGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706 LGGPF YID+LGA +V I++ ++YGSRF P +L +M G F+ Sbjct: 658 LGGPFHYIDTLGAANLVKILENYQSRYGSRFEPAAKLKQMAEEGTRFF 705 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: 1163 Number of extensions: 61 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: 714 Length of database: 706 Length adjustment: 39 Effective length of query: 675 Effective length of database: 667 Effective search space: 450225 Effective search space used: 450225 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