Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BPHYT_RS13545 BPHYT_RS13545 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__BFirm:BPHYT_RS13545 Length = 706 Score = 648 bits (1672), Expect = 0.0 Identities = 349/706 (49%), Positives = 468/706 (66%), Gaps = 22/706 (3%) Query: 2 SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61 ++VV+R + +V +VT+D PVNALSA VRRG+L + AA AD AV+A+++V AGR FIA Sbjct: 7 ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66 Query: 62 GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121 GADI EFGKPP PP+L DV +E KP +AAIHG ALGGGLEVAL H+R+AV AKL Sbjct: 67 GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126 Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEV--VENLVA 179 GLPEV+LGLLPGAGGTQR PR +G + A+ +I+ G A EAL GL++ + ++++A Sbjct: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186 Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAM----TKKARGLEAPFAC 235 +A+ ++LA P+RR RD AAA +DR+ AVA KK+RGL +P Sbjct: 187 EGLAYVHELLAAHAPVRRTRD-----AAALSDRAASLAAVATARAETAKKSRGLFSPLKI 241 Query: 236 ADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPV 295 DA+ AAI+ PF+EGL+ ER+ F++ + S Q +AFFAERE K KPR + Sbjct: 242 VDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETR-AAKPRTL 300 Query: 296 SRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA 355 + + ++G GTMG GIA++ +AG+PVT+IE + L RG ++K ++ A+G L + Sbjct: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360 Query: 356 PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSI 415 A M+ +G + + ADL+IEAVFE +AVK+ VF +D K GAVLA+NTSYL I Sbjct: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420 Query: 416 DEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGV 475 D +A++ RP DV+G+HFFSPAN+MKL E+V + + D + TA +AKK+ K PV GV Sbjct: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480 Query: 476 CDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRK 535 CDGF+GNR+LA ++ ++ +GA P Q+DA V FG PMGPF + DLAG DIGW +RK Sbjct: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540 Query: 536 DRGIKS-------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKL 588 R +IAD LCE G FGQK+G+G+Y Y +GSR+ PDPEVE +I+ A+ Sbjct: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600 Query: 589 GLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYA 648 G+ R TDEEI+ R + MINEGA ++ E+IA RP D+DV +LYGYG+P YRGGPM YA Sbjct: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660 Query: 649 DSVGLKHIAERLSAYAKATNDPSL-EPAPLLARLAAEGKTFASLTQ 693 D VGL I + +AK DP +P+PLL L G FASL Q Sbjct: 661 DMVGLPKILADIREFAK--EDPLFWKPSPLLIELVERGADFASLNQ 704 Lambda K H 0.317 0.134 0.383 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: 1187 Number of extensions: 55 Number of successful extensions: 4 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: 699 Length of database: 706 Length adjustment: 39 Effective length of query: 660 Effective length of database: 667 Effective search space: 440220 Effective search space used: 440220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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