Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__BFirm:BPHYT_RS09560 Length = 694 Score = 592 bits (1526), Expect = e-173 Identities = 317/687 (46%), Positives = 435/687 (63%), Gaps = 10/687 (1%) Query: 18 VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77 V ++T+++ PVN L R G++ +E A D A++A+++ GAG+ F GADI EF P Sbjct: 11 VAVITLNNPPVNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAGKAFSGGADITEFNTPK 70 Query: 78 V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135 P+L V +E KPV+AAIH A+GGGLE+AL AHYRIA GA++ LPEV+LG+ Sbjct: 71 AGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIALPEVKLGI 130 Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG-LAYVHE 194 LPGAGGTQR PR IG +AAL++I+SG +++ GL D L D LAE LA+ + Sbjct: 131 LPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGD--LAEAALAFARK 188 Query: 195 LLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFD 254 + A P + RD AA + AR A ++ +PLK +DAVEA +++ FD Sbjct: 189 VSAKEGPHPKVRDRKIEHPNAAGF--IQFARNTVATMAKNFPAPLKCIDAVEAGVQKGFD 246 Query: 255 EGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGA 313 +GL ER+ F+ + +P+ L HAFF ER K P+ + P R + + V+G GTMG Sbjct: 247 KGLAFERECFMALVQTPESHALRHAFFGERAASKIPDVPSDTPVRDIGQVAVIGAGTMGG 306 Query: 314 GIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTS 373 GIA+ ++AG+PVT++E +L RG A I K Y+ + KG+L E M+ + + S Sbjct: 307 GIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVLGQRMALITPTLS 366 Query: 374 YDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADV 433 YD L ADL++EAVFE+L VK+ F LD V K GA+LA+NTS LD+D +A+ RP DV Sbjct: 367 YDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDVDKIAAFTKRPQDV 426 Query: 434 IGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVY 493 +G+HFFSPAN+MKLLEVV K+ + DV+AT LAKK++KT V +GVCDGFIGNR++ Y Sbjct: 427 VGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGVCDGFIGNRMVEQY 486 Query: 494 RSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYV 553 A M+E+GA P Q+D A+ FGF MGPF++ DLAG DIGWA RKRR +P Y Sbjct: 487 IRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKRR-YLEHPDMHYS 545 Query: 554 QIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEII 613 +IADRLCE G FGQK+G G+Y Y G R+ P V+ +I A R +DEEI+ Sbjct: 546 KIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKETDTERRKISDEEIV 605 Query: 614 RRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIR 673 R + A++NEGA ++ E IA + D+D+ +L GYGFP YRGGPM YAD VGL + IR Sbjct: 606 ERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLYADTVGLYNVERAIR 665 Query: 674 EF-AKEDPLFWKPSPLLIELVERGADF 699 + A+ + W+ +P + EL + F Sbjct: 666 RYAARPNGDAWQLAPSIAELAAKNRGF 692 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: 1047 Number of extensions: 49 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: 694 Length adjustment: 39 Effective length of query: 667 Effective length of database: 655 Effective search space: 436885 Effective search space used: 436885 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