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 GFF1257 HP15_1232 fatty acid oxidation complex subunit alpha
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__Marino:GFF1257 Length = 716 Score = 381 bits (979), Expect = e-110 Identities = 258/726 (35%), Positives = 375/726 (51%), Gaps = 37/726 (5%) Query: 5 SAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAKPD 63 SA + D I +TID+PG+ NT+ A F + +++E+ + +RG++ SAK Sbjct: 2 SAIRYELGSDQILTLTIDMPGQSANTMNAAFRDALSETAAKVKEDLDNIRGIIIASAKK- 60 Query: 64 NFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQ---VIAAIHGACLGGGLELA 120 F AG D+ + T ++A L + + L V+AAI+G+ LGGGLE+A Sbjct: 61 TFFAGGDLKELHKV-TREDARTFEDMVNGLKSHMRFLETTGKPVVAAINGSALGGGLEIA 119 Query: 121 LACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQAL 180 LACH RV +D LGLPEV LGLLPG GGTQRLPR+IG+ A ++ GK++ K AL Sbjct: 120 LACHYRVAINDDSIQLGLPEVTLGLLPGGGGTQRLPRMIGLEAAFPFLMEGKKVNPKAAL 179 Query: 181 KLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRE--------RILAG-PLGRALLFKM 231 K G++++ L ++A ++ K R P + R G P A+ K+ Sbjct: 180 KAGIINE------LADSADDMITKARAFIEANPKCQQPWDQKGFRFPGGAPHHPAMAQKL 233 Query: 232 V--GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIF 289 + KT+G YPA ERIL G +G E R F EL + ++ + F Sbjct: 234 AIAPAMLKQKTKGCYPAPERILSAAVEGAQVDFDNGSLIETRYFAELVIGQVAKNMTGTF 293 Query: 290 FASTDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346 + + K GS VG+LG G+MG GIAY TA + GI V +KD++ + Sbjct: 294 WFQLNAIKAGGSRPEGVEKETFRKVGVLGAGMMGAGIAYSTATR-GIDVVLKDVSVENAE 352 Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406 YS + L KV R + ++ L+ I T DL+IEAVFE+ LK ++ Sbjct: 353 KGKSYSENLLAKKVSRGRMTEEQKADILSRIKATDSSDDLEGCDLVIEAVFEDSGLKAKV 412 Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466 E E A+ IFASNTS++PI +A + E IGLHFFSPV+KM LVEII TS Sbjct: 413 TQEAEPKLVANGIFASNTSTIPITQLAGASANAENFIGLHFFSPVDKMQLVEIIVGEKTS 472 Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526 +T+A + ++ GK P+VV D GF+ +R+ ++NE I ML +G I+ A V Sbjct: 473 DETLARSFDYVQQIGKIPVVVNDSRGFFTSRVFGTFVNEGICMLGEGIHPASIENAGVLA 532 Query: 527 GFPVGPIQLLDEVGIDTGTKIIPV----LEAAYGERFSAPAN-VVSSILND-DRKGRKNG 580 G PVGP+ + DEV + I EAA G PA V+ +++N+ RKG+ G Sbjct: 533 GMPVGPLAISDEVSMTLMQHIRDQSRKDTEAAGGTWNPHPAEAVIDAMVNEHGRKGKAAG 592 Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGR-ISAPQVAERCVMLMLNEAVRCVDEQVI 639 GFY Y G KK + P + L + R + ++ +R + + E VRC++E V+ Sbjct: 593 AGFYEYPANG---KKHLWPELETLFVNAEKARTVKLQELKDRILFIQAIETVRCLEEGVL 649 Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMG 699 R+V D +IG++FGIG+ P+ GG ++I+ G LA YG RF P + L E Sbjct: 650 RTVEDANIGSIFGIGYAPWTGGAIQFINQYGVRAFTERASALAETYGERFAPPKLLQEKA 709 Query: 700 ARGESF 705 F Sbjct: 710 ETNTPF 715 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: 953 Number of extensions: 37 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: 716 Length adjustment: 39 Effective length of query: 675 Effective length of database: 677 Effective search space: 456975 Effective search space used: 456975 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 17 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