Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate GFF400 PGA1_c04110 putative fatty acid oxidation complex subunit alpha
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Phaeo:GFF400 Length = 697 Score = 729 bits (1883), Expect = 0.0 Identities = 389/701 (55%), Positives = 491/701 (70%), Gaps = 13/701 (1%) Query: 8 DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67 + + E G + ++ + PVNAL DVRRGLLA IE A+ + A AVLI G GR + AG Sbjct: 3 EAIVYERIGDIAVLAAQNPPVNALGIDVRRGLLAGIERAEKEGA-RAVLIYGEGRTYFAG 61 Query: 68 ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127 ADIREFGKP P LPD+CNRIEA VV+A+HG ALGGGLEVAL++HYRIAV GAK+G Sbjct: 62 ADIREFGKPMEEPGLPDLCNRIEAAKLIVVSALHGTALGGGLEVALSSHYRIAVPGAKMG 121 Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187 LPEV LG++PGAGGTQR PR+ G +AAL++I +GRH +A EA G+IDR+ + Sbjct: 122 LPEVHLGIIPGAGGTQRLPRVAGTEAALEMITTGRHVAAAEAFDKGVIDRIAEGNP-REV 180 Query: 188 GLAYVHELLAAHAPVRRTRDAAALS--DRAASLAAVATARAETAKKSRGLFSPLKIVDAV 245 GLAY ELL +AP R D A D A+ V + RG SP V AV Sbjct: 181 GLAYTRELLEQNAPRRPVCDMPAPEPVDFDATYERVLV-------RGRGQLSPAIAVRAV 233 Query: 246 EAAIEQP-FDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIG 304 +AA E P F +G+R ER+LF++ ++S QR GLIHAFF+ER V K PE PR + +G Sbjct: 234 QAACEAPSFLDGVRQERELFMKLMESDQRQGLIHAFFSERAVSKLPELVDVFPRDVAAMG 293 Query: 305 VVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAAL 364 V+GGGTMGAGIA A L AGL V +IERD+A+ R IE G + +G++S + A+ Sbjct: 294 VIGGGTMGAGIATAALLAGLSVVLIERDEAASVAARERIEGNLRGALKRGKISQSQFDAI 353 Query: 365 MSRWSG-STSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDAL 423 ++ +T Y AL+ DLV+EAVFED+ VK+ VFA LD CK GA+LA+NTSYLDI+ + Sbjct: 354 LNETLKLATDYAALSQVDLVVEAVFEDMDVKRDVFAALDEHCKPGAILASNTSYLDINDI 413 Query: 424 ASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDG 483 A++ SRP+DVIGLHFFSPA++MKLLEVVV Q + DVVAT F L K+L+KT VR+GVCDG Sbjct: 414 AAATSRPSDVIGLHFFSPAHVMKLLEVVVADQTAPDVVATGFALGKRLKKTSVRSGVCDG 473 Query: 484 FIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRA 543 FIGNR++ YR AAD M+ DGASPYQID + FGF MGPF V DLAG DIGWAARKRRA Sbjct: 474 FIGNRIMNSYRKAADYMVLDGASPYQIDKVMTGFGFAMGPFAVADLAGLDIGWAARKRRA 533 Query: 544 ATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGIT 603 T +P R V +D LCE G FGQK+GRGFY+Y EG R GTP+P+V I+ ++ G+T Sbjct: 534 PTLDPRERVVHFSDMLCEGGDFGQKTGRGFYVYEEGKRGGTPNPQVAEYIERDQRDQGVT 593 Query: 604 PRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMV 663 P+ F ++E++RRYM AM+NE A VV E IA RPLDVD+ L+GYGFPR+ GGP+K+AD+ Sbjct: 594 PQIFANDEVLRRYMCAMVNEAAKVVGEGIARRPLDVDMVLLFGYGFPRFWGGPLKWADLQ 653 Query: 664 GLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQ 704 G IL DIR +AKED FW+P+PLL ++V G F LN+ Sbjct: 654 GPDSILKDIRRYAKEDAFFWQPAPLLEQMVAEGRSFDDLNK 694 Lambda K H 0.320 0.136 0.392 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: 1251 Number of extensions: 45 Number of successful extensions: 6 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: 706 Length of database: 697 Length adjustment: 39 Effective length of query: 667 Effective length of database: 658 Effective search space: 438886 Effective search space used: 438886 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: 54 (25.4 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