Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate RR42_RS18255 RR42_RS18255 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS18255 Length = 256 Score = 285 bits (728), Expect = 9e-82 Identities = 148/250 (59%), Positives = 181/250 (72%), Gaps = 2/250 (0%) Query: 13 VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVD 72 V +TLNRP++LNSF EMHA L + L VE R LLLTGAGRGFCAGQDL D + Sbjct: 9 VAVITLNRPDKLNSFTREMHAVLQQALDHVEAGGA-RALLLTGAGRGFCAGQDLADLDFT 67 Query: 73 PTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKF 132 P G DLG ++ ++N L+RRL KLP PVI AVNG AAGAGA LAL D+V+AARSA F Sbjct: 68 P-GAMTDLGELIDVWFNRLIRRLQKLPLPVIAAVNGTAAGAGANLALACDMVLAARSASF 126 Query: 133 VMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLAD 192 + AF K+GL+PD GGTWLLP+ G ARAMGLA+ G++LSA++A +WG+IW+ +DD L + Sbjct: 127 IQAFVKIGLVPDSGGTWLLPKRIGMARAMGLAMTGDKLSADEAEKWGLIWEAMDDPLLPE 186 Query: 193 TAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAFL 252 A LA HLA QPT L IKQA+ + + LD QLDLERD QR G S DY EGV+AFL Sbjct: 187 QALALATHLAAQPTRALAAIKQAMYAGASQGLDAQLDLERDLQRELGASPDYAEGVNAFL 246 Query: 253 AKRSPQFTGK 262 KR+P+FTG+ Sbjct: 247 EKRAPRFTGR 256 Lambda K H 0.321 0.136 0.403 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: 194 Number of extensions: 9 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: 262 Length of database: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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: 47 (22.7 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