Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate SM_b21632 SM_b21632 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Smeli:SM_b21632 Length = 438 Score = 322 bits (825), Expect = 2e-92 Identities = 184/421 (43%), Positives = 253/421 (60%), Gaps = 12/421 (2%) Query: 271 RYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQ 330 RY F AER AA+ G +PRP+ A+IG GTMG GIA + +AG+P+ L+E E Sbjct: 21 RYVFHAER-AARHPPALAGIEPRPIRSAAVIGGGTMGTGIAAALLHAGLPLVLVERDEAA 79 Query: 331 LKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKK 390 ++R L ++ ++ RG + A+R+A +TG + +ADLIIEAVFE + VK+ Sbjct: 80 VERALARLRTIFDGAVKRGRISAGLAAERLAGVTGSTDYTAIAEADLIIEAVFEDLDVKR 139 Query: 391 EVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAK 450 +VF + A + A+LA+NTSYL + IAA + LG+HFFSPA VMKL EIV Sbjct: 140 DVFRRLAAVCRADAILATNTSYLDPERIAADIGSRERFLGLHFFSPAQVMKLLEIVPTQA 199 Query: 451 TAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVT 510 TAPD L T ++A+ + K+PV G+ DGF+GNR+L Q+E+LL GA P VDA + Sbjct: 200 TAPDVLATGFALARMLNKIPVRAGISDGFIGNRILKVTRAQAERLLLSGATPAAVDAAMR 259 Query: 511 KFGMPMGPFAMGDLAGLDIGWRSRKDRGIKSE-----IADALCEAGRFGQKTGKGYYKYE 565 FG+PMGPF DL GLDI R+ + E +AD L RFGQK+G G+Y Y Sbjct: 260 AFGLPMGPFEAQDLGGLDIAAFQRRAARARGETTFAPVADRLSAIERFGQKSGGGWYDYA 319 Query: 566 QGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPS 625 G R P P V +I + G RRD + I+ +++PM+NE ARILE+ A R S Sbjct: 320 PGDRTPRPSATVARIIAEEAR--GWPRRDWDEASIVGCILWPMVNEAARILEDGTALRAS 377 Query: 626 DIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKA-TNDPSLEPAPLLARLAAE 684 DID+V ++GYG+P +RGG MH+A++ GL +A LS A+A DP +P L R A+ Sbjct: 378 DIDLVEIHGYGFPRWRGGLMHHAEAHGLHKVAGALSGLAEAGLADPPCDP---LLRAASR 434 Query: 685 G 685 G Sbjct: 435 G 435 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: 696 Number of extensions: 36 Number of successful extensions: 3 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: 438 Length adjustment: 36 Effective length of query: 663 Effective length of database: 402 Effective search space: 266526 Effective search space used: 266526 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: 53 (25.0 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