Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_011385366.1 AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_000009985.1:WP_011385366.1 Length = 703 Score = 568 bits (1463), Expect = e-166 Identities = 317/701 (45%), Positives = 430/701 (61%), Gaps = 4/701 (0%) Query: 7 ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66 +DVV+ + ++ VTID PVNA VR GL A +AVL++ AGR F+A Sbjct: 2 SDVVTLSVSDRIATVTIDSPPVNAADHPVRAGLQKVFTDLAARSDYDAVLVLCAGRTFMA 61 Query: 67 GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126 GADI EF P D+ N +E C KPVVAA+HG ALG G E+A+A HYRIA GA++ Sbjct: 62 GADIGEFDTGIKAPHHQDLFNLVENCAKPVVAALHGTALGAGTELAMACHYRIADKGARI 121 Query: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186 GLPE+ LG++PGAGGTQR PRLIG AA+DL+LSG+ A +A GL+D + S D + A Sbjct: 122 GLPELSLGIIPGAGGTQRAPRLIGLDAAMDLVLSGKPLPAPKAAELGLVDEIASGD-LNA 180 Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246 LA+ +L+A VRRT D A D A +A +A+ AK + SPLK ++A+ Sbjct: 181 AALAFAKKLVAEGKGVRRTCDMAP-KDAAKDAEIIAARQAQVAKTMKNRTSPLKALEAMA 239 Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPE-TRAAKPRTLNTIGV 305 A F EGLR+E + + + + + H FFA+REV K P T+ K R + +G+ Sbjct: 240 ATTTLSFAEGLRLEADISKQLEHAVEARAMRHLFFADREVRKIPGITKDIKARPIRKVGI 299 Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365 +G GTMG GIA+ + G+PVT+I+ D +L RG I K Y+ +++G L+ E+ + M Sbjct: 300 IGAGTMGGGIAMCFANIGIPVTIIDVSDENLQRGLGVIRKNYERSVSRGSLTQEQLESRM 359 Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425 S ST Y AL ADL IEAVFE + +K+ +FA+LD V AGA+L TNTS LDID +A+ Sbjct: 360 GLLSASTDYAALKDADLAIEAVFEKMELKKDIFAKLDAVLPAGAILGTNTSTLDIDEIAN 419 Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485 + RPADVIGLHFFSPAN+M LLE+V KQ + DV+ TA ++AK ++KT V + VC GFI Sbjct: 420 TTKRPADVIGLHFFSPANVMPLLEIVQGKQTAMDVLLTALDMAKLIKKTGVVSKVCYGFI 479 Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545 GNR++ Y A+ M+ +GA+P +ID A+ +G MG V D+AG ++G R Sbjct: 480 GNRMMDPYGREAERMVLEGATPAEIDGALEGWGMAMGILAVYDMAGVEVGDNTRIANPHM 539 Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605 + + + L W GQK GRG+Y Y R DPEV ++ AE R + R Sbjct: 540 VPDDPSFYRCSTLLVANKWLGQKVGRGYYRYDSPDRKRASDPEVIEMMHAEGKRLNVPAR 599 Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665 +EI+ R + +MINEGA ++ E IALR D+DV + GYGFPRYRGGPM YAD +GL Sbjct: 600 KPGKDEILERCLYSMINEGAKLLEEGIALRASDIDVVYTAGYGFPRYRGGPMFYADTIGL 659 Query: 666 PKILADIREFAKE-DPLFWKPSPLLIELVERGADFASLNQS 705 I I EF K DP +W P+PLL +L + G+ FA + S Sbjct: 660 KVIYDKIVEFQKTLDPRYWTPAPLLEKLAKAGSTFAQWDAS 700 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: 1141 Number of extensions: 46 Number of successful extensions: 5 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: 703 Length adjustment: 39 Effective length of query: 667 Effective length of database: 664 Effective search space: 442888 Effective search space used: 442888 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