Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Ga0059261_2827 Ga0059261_2827 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Korea:Ga0059261_2827 Length = 683 Score = 540 bits (1390), Expect = e-157 Identities = 309/689 (44%), Positives = 418/689 (60%), Gaps = 29/689 (4%) Query: 18 VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77 V +VT+D PVNA+S + GL A+ AA +D A +A++++ AGR FIAGAD++ GK Sbjct: 16 VAIVTLDFPPVNAMSPALMDGLYDALMAALSDDAAKAIVLICAGRTFIAGADLKSLGKVQ 75 Query: 78 VPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLP 137 + + IE KP VAA+HG ALGGG+E AL HYRIAV A++GLPEV LGLLP Sbjct: 76 PKVDFFALQDSIENSPKPTVAALHGTALGGGMETALTFHYRIAVPSARMGLPEVNLGLLP 135 Query: 138 GAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLA 197 G GGTQR PR+ GA+AALDL++SGR AKEAL GLIDRL + + + +A+ EL+ Sbjct: 136 GGGGTQRLPRITGAEAALDLLISGRQVGAKEALTIGLIDRLAAEGALREDAIAFAKELVD 195 Query: 198 AHAPVRRTRDAAA--LSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255 A P +R RD A +DR + R AK+ GL +P IV VEAA+ P+++ Sbjct: 196 AGEPPKRIRDCEAKVAADRKDA-NLFERFRTSHAKQLNGLDAPQAIVRCVEAAVAGPWEK 254 Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVVGGGTMGAG 314 GL +ER F + PQ A L H F AER K P RA P + +G+VG GTMG+G Sbjct: 255 GLAIERTEFQTLLAGPQSAALRHVFMAERAAQKIPGLRADLPLIPVTKVGIVGAGTMGSG 314 Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374 IA+A L AG VT++E A+L RG AHI + +G+L+A+K A ++ + + Sbjct: 315 IAMAFLAAGFAVTVVETQQAALDRGVAHITATLQSRVERGKLAADKAEAQIAALTPTLDL 374 Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434 ALA ADLV+EA+FE+LA KQA+F L + + +LATNTS+LD+DA+A+ + P V+ Sbjct: 375 SALADADLVVEAIFENLAAKQALFGTLSAIVRPDTILATNTSFLDVDAIAAGAAGPERVL 434 Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494 G+HFFSPAN+M+LLEVV + S V+A+ LAKKL K V +GVC GFIGNR+LA + Sbjct: 435 GMHFFSPANVMRLLEVVRAAKTSEAVLASVMALAKKLGKAAVVSGVCFGFIGNRMLAARQ 494 Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554 ADAM+ G P+ ID + FGFPMGPF ++DLAG DIGW Sbjct: 495 VHADAMVLAGVLPWNIDRILTGFGFPMGPFAMLDLAGLDIGWEGDTD------------S 542 Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFT--DEEI 612 + RL G GQKSG G+Y Y + TP P + +D A + P S T D EI Sbjct: 543 VKSRLVAAGRKGQKSGAGYYDY----ENKTPSPS-QTALDVIAGLASVAPGSVTLSDREI 597 Query: 613 IRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADI 672 + R + MINEGA ++ E IALR D+D+ ++ GYG+P GGPM +AD +GL +++ + Sbjct: 598 LDRLLLPMINEGAKILEEGIALRGSDIDLVWITGYGWPAQTGGPMFHADAIGLTRVVDGL 657 Query: 673 REFAKEDPLFWKPSPLLIELVERGADFAS 701 R E P+ LL++L G A+ Sbjct: 658 RHMGVE------PAALLLKLASEGGSLAA 680 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: 1082 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: 683 Length adjustment: 39 Effective length of query: 667 Effective length of database: 644 Effective search space: 429548 Effective search space used: 429548 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