Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_068174326.1 HTA01S_RS19105 FAD-dependent oxidoreductase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_001592305.1:WP_068174326.1 Length = 684 Score = 574 bits (1479), Expect = e-168 Identities = 314/672 (46%), Positives = 420/672 (62%), Gaps = 12/672 (1%) Query: 1 MTPNPSADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGA 60 MTP V E G + ++ ID+ P+NA SA VR+GL+AAIE D +E +++GA Sbjct: 1 MTPR-----VYLERDGGIAVIVIDNPPINAGSAAVRQGLMAAIETLRNDDTLEGAVLIGA 55 Query: 61 GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIA 120 G FIAG+D+REFG+P P LP V IEAC KPVVAA+HGAA GGG E+AL R+A Sbjct: 56 GNTFIAGSDLREFGQPLTEPQLPAVIAAIEACGKPVVAALHGAAQGGGFELALGCDARVA 115 Query: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGS 180 G +GLPEV LG++PGAGGTQR PR++G A+ +I SG A AL GL+D + + Sbjct: 116 APGTVVGLPEVTLGIIPGAGGTQRLPRIVGIPPAIRMICSGERVLAAAALEAGLVDLIAT 175 Query: 181 SDDILAEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLK 240 + + + +A+ +L R RD +A +A TA + K+ + + Sbjct: 176 GN-LRSAAVAHARQLKGQK---RLVRDRQVPPASSADVATATTAAPQAGKRRPAVQAA-- 229 Query: 241 IVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTL 300 +DA+ A + FD+GL ER +F S + L H FFAERE K P A R + Sbjct: 230 -IDAITATAQVGFDDGLADERAVFQRLRVSREAFALRHQFFAERESAKHPSLGEATARPV 288 Query: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360 + V+G GTMG+GIA+A LDAG V ++E+D A+L RG I Y + G+LSA Sbjct: 289 ERVAVIGAGTMGSGIAIAALDAGYRVLLLEQDAAALERGTGRIHAHYASRVQGGKLSASA 348 Query: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420 AA +R S + LA ADLVIEAVFE+L VKQ VF +D + + GAVLA+NTSYLD+ Sbjct: 349 AAACEARLQTSLDWADLASADLVIEAVFEELGVKQQVFQRIDALARPGAVLASNTSYLDL 408 Query: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480 DA+A++ SRP DVIGLHFFSPA++MKL+EVV + + D +AT + K+L+K PV G Sbjct: 409 DAIAAATSRPHDVIGLHFFSPAHVMKLMEVVRGQSSAPDALATGLAVGKRLKKMPVLTGN 468 Query: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540 GFIGNR+ A YR + M+E+GA P Q+DAA+RAFGF MGPF V DL+G DI W R+ Sbjct: 469 AFGFIGNRLYAAYRRQCECMVEEGAWPEQVDAALRAFGFAMGPFAVADLSGLDIAWRMRQ 528 Query: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600 +AATR+P ARYV I DRLCE G G+K+G G+Y YPEG + D V A+I RA Sbjct: 529 AQAATRDPQARYVHIPDRLCEAGRLGRKTGAGYYRYPEGDQGPQVDEAVHALIAQARADK 588 Query: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660 G+ PR D+EI+RR + A++NE A ++ E +A R DVDV + GYGFPR+ GGP+ +A Sbjct: 589 GLQPRELGDDEIVRRALLAIVNEAALLLAEGVAERATDVDVVLVNGYGFPRWEGGPVFWA 648 Query: 661 DMVGLPKILADI 672 G + D+ Sbjct: 649 RERGAAALQEDM 660 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: 1119 Number of extensions: 54 Number of successful extensions: 2 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: 684 Length adjustment: 39 Effective length of query: 667 Effective length of database: 645 Effective search space: 430215 Effective search space used: 430215 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 Apr 09 2024. 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