Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_099020024.1 CCS90_RS13100 hypothetical protein
Query= curated2:Q52995 (257 letters) >NCBI__GCF_002591915.1:WP_099020024.1 Length = 258 Score = 208 bits (530), Expect = 8e-59 Identities = 116/253 (45%), Positives = 161/253 (63%), Gaps = 3/253 (1%) Query: 6 LLVETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGS-EKAFAAG 64 +L + + + IT+NRP LNALN ++ELD ++ D V IV+ GS +KAF AG Sbjct: 4 VLSQLENNILTITINRPDKLNALNQATLKELDTIIQGAADDDNVACIVITGSGDKAFVAG 63 Query: 65 ADIKEMQGLDFVDGYLADFLGG--WEHVANARKPMIAAVSGFALGGGCELAMMCDFIIAS 122 ADI E+ D + G G + H+ N KP+IAAV+GFALGGGCELAM C IAS Sbjct: 64 ADISELATTDAMTGMKFARFGQSVFNHIENCGKPVIAAVNGFALGGGCELAMACHLRIAS 123 Query: 123 ETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERSGLVSRVVAP 182 + AKFGQPEI LGVIPG GG+QRLTR VGK+K+M++ L G M+ A +AE GL++ VV Sbjct: 124 DNAKFGQPEIKLGVIPGFGGTQRLTRLVGKSKSMEMNLLGDMVSADKAEHIGLINWVVPQ 183 Query: 183 DRLLEEALGAAEKIASFSLPAAMMAKEAVNRSLELTLAEGLRFERRLFQSLFATEDQKEG 242 L+ A+++A+ + A M +A+N+ LE L + L +E + F A+ D+ EG Sbjct: 184 GELMASVTQVAQQLAASAPIALSMTIDAINKGLECALPDALDYEVKAFGICCASADKNEG 243 Query: 243 MAAFVAKRKAEFK 255 +AF+ KRKA+F+ Sbjct: 244 TSAFLEKRKAKFQ 256 Lambda K H 0.321 0.134 0.371 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: 175 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: 257 Length of database: 258 Length adjustment: 24 Effective length of query: 233 Effective length of database: 234 Effective search space: 54522 Effective search space used: 54522 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 (21.9 bits) S2: 47 (22.7 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