Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_002115805.1:WP_085640004.1 Length = 695 Score = 722 bits (1863), Expect = 0.0 Identities = 388/692 (56%), Positives = 484/692 (69%), Gaps = 14/692 (2%) Query: 16 GKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGK 75 G + ++ ID+ PVNAL VR+GL+ A+E A+AD A A LI G GR+F AGADIREFGK Sbjct: 11 GDIAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGA-RAALIYGEGRSFPAGADIREFGK 69 Query: 76 PPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135 PP+ P LPDVCNR+E VV+A+HG ALGGGLE+ALA+ YRIA AK+GLPEV +G+ Sbjct: 70 PPLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVGLPEVLIGV 129 Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRL--GSSDDILAEGLAYVH 193 +PGAGGTQR PRL+G + ++D+I SGR SA EA G+IDR+ G+ DI GL+Y Sbjct: 130 MPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRDI---GLSYTR 186 Query: 194 ELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPF 253 LLA +AP R R+ A A + R K+RG SP V ++AA E PF Sbjct: 187 ALLAENAPRRPIREMPAPQPIDFDAAYDSALR-----KARGQISPAYAVRGIQAACELPF 241 Query: 254 DEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGA 313 +EGL ER+LF +++ QR GLIHAFFAER V E + R +N++ V+GGGTMGA Sbjct: 242 EEGLTRERELFRALLETDQRQGLIHAFFAERAVGVLAELKDTNARDVNSVAVIGGGTMGA 301 Query: 314 GIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS-RWSGST 372 GIA + L AG PVT++E + + R I G + +G++ + L + +T Sbjct: 302 GIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYDRLTGPALALTT 361 Query: 373 SYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPAD 432 SYD L ADLVIEAVFED+ VK+ VF+ LD +CK GAVLATNTSYLDI+ +A + RP D Sbjct: 362 SYDDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLDINKIADATQRPED 421 Query: 433 VIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAV 492 VIGLHFFSPA++MKLLEVVV + + D VAT F LAK+L+KT VRAGVCDGFIGNR+LA Sbjct: 422 VIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAGVCDGFIGNRILAA 481 Query: 493 YRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARY 552 YR+AAD M+ DGA+PY IDAA+R FGF MGPFQV DLAG DI WAARKRRAATR+P R Sbjct: 482 YRAAADHMVLDGATPYDIDAAIREFGFAMGPFQVSDLAGLDIAWAARKRRAATRDPRERV 541 Query: 553 VQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEI 612 +ADRLCE G FGQK+G+G+YLY E P+PEV II++ R GI PR+F+ EI Sbjct: 542 PLVADRLCEAGLFGQKTGQGYYLYNE--TPPKPNPEVAGIIESARETLGIKPRAFSRPEI 599 Query: 613 IRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADI 672 RRY+ AM+NE A VV + IA RPLDVDV L GYGFPRYRGGP+K+ADM GLPKIL+DI Sbjct: 600 QRRYLCAMVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKWADMDGLPKILSDI 659 Query: 673 REFAKEDPLFWKPSPLLIELVERGADFASLNQ 704 +A++D FW P+PLL +LV G F LN+ Sbjct: 660 TAYAQDDRYFWSPAPLLEQLVAEGRTFDDLNK 691 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: 1300 Number of extensions: 59 Number of successful extensions: 8 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: 695 Length adjustment: 39 Effective length of query: 667 Effective length of database: 656 Effective search space: 437552 Effective search space used: 437552 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 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