Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011159255.1 TX73_RS18975 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::P07896 (722 letters) >NCBI__GCF_000195775.1:WP_011159255.1 Length = 699 Score = 540 bits (1390), Expect = e-157 Identities = 311/712 (43%), Positives = 438/712 (61%), Gaps = 35/712 (4%) Query: 11 LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFT 70 +A++ + +PPVNA+S V R + + A +D V+AIV+ A F AGADI F Sbjct: 13 VAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPP 72 Query: 71 PGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILP 130 AL ++ ++ KP +AAI G ALGGGLE+ALGCH+R+A +A++GLPEV LG+LP Sbjct: 73 QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLP 132 Query: 131 GARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKII-- 188 GA GTQ LPR VG +A+ +I G + A EAL+ G+++ VV++ V A+ FA+K++ Sbjct: 133 GAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN-LVAGAVAFAKKVLAE 191 Query: 189 DKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGI 248 +P+ R + + + S+F A+A + K+ G+ AP C +I A++ P+E G+ Sbjct: 192 KRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGL 251 Query: 249 KEEEKLFMYLRASGQAKALQYAFFAEKSANKWS-TPSGASWKTASAQPVSSVGVLGLGTM 307 K+E + FM L S Q+KA +YAFFAE+ A K P G +PVS V ++G GTM Sbjct: 252 KKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTK-----PRPVSRVAIIGAGTM 306 Query: 308 GRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSS- 366 G GIA+SFA GI V +E+ +QL I+ E A+R A AK + Sbjct: 307 GGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGL 366 Query: 367 -STKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQ 425 + + DL++EAVFE M +KK+VF + A KPGA L +NTS L++D+IA++T RPQ Sbjct: 367 VGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQ 426 Query: 426 LVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLA 485 V+G HFFSPA+VM+L E++ ++P + T +S++KKI K+ VVVG C GFVGNRMLA Sbjct: 427 DVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLA 486 Query: 486 PYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPP 545 Q LL EG+ P+ VD V+ +FG MGPF + DLAGLD+GW+ RK +G+ Sbjct: 487 ARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK------ 540 Query: 546 GTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREV 605 S + D LCEAGRFGQKTGKG+Y+Y++ R PDP + T ++ Sbjct: 541 ------------SEIADALCEAGRFGQKTGKGYYKYEQG-SRAPMPDPEVETLINDTLAK 587 Query: 606 HHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFY 665 +++R I+ EEILER +Y +INE RILEE +AARP IDV++L+GYGWP ++GGPM Y Sbjct: 588 LGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHY 647 Query: 666 AASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGSPPLKEWQSLAGP 717 A SVGL + E+L Y + D P LEP+ L RL A+G K + SL P Sbjct: 648 ADSVGLKHIAERLSAYAKATND-PSLEPAPLLARLAAEG----KTFASLTQP 694 Lambda K H 0.319 0.136 0.405 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: 1141 Number of extensions: 46 Number of successful extensions: 7 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: 722 Length of database: 699 Length adjustment: 39 Effective length of query: 683 Effective length of database: 660 Effective search space: 450780 Effective search space used: 450780 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 (21.7 bits) S2: 55 (25.8 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