Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__SynE:Synpcc7942_0597 Length = 279 Score = 130 bits (327), Expect = 3e-35 Identities = 96/271 (35%), Positives = 138/271 (50%), Gaps = 23/271 (8%) Query: 2 EFETIETKK--EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGK 59 E+E I +K EG + IT+NRP K NA K + EL A A D I VI++TG G Sbjct: 11 EYEDIRYEKCAEG-IAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGP 69 Query: 60 ------AFCAGADITQFNQLTPAEAWKFSKKGR------EIMDKIEALSKPTIAMINGYA 107 AFCAG D Q ++G ++ I + K IA++ GYA Sbjct: 70 HTDGRYAFCAGGD-----QSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALVAGYA 124 Query: 108 LGGGLELALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRI 167 +GGG L + CD+ IAA+ A G +G + G G L R++G+ +A E+ + Sbjct: 125 IGGGHVLHILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQY 184 Query: 168 PGKDAEKYGLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-A 226 K+A + GLVN VVP+ LE E + A +I +KSPI++ +K N LD ++G+ Sbjct: 185 GAKEALQMGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELDG--MAGIQE 242 Query: 227 LESVGWGVVFSTEDKKEGVSAFLEKREPTFK 257 L + + TE+ EG AFLEKR P F+ Sbjct: 243 LAGHATHLYYLTEEGSEGKQAFLEKRSPDFR 273 Lambda K H 0.315 0.135 0.382 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: 128 Number of extensions: 7 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: 259 Length of database: 279 Length adjustment: 25 Effective length of query: 234 Effective length of database: 254 Effective search space: 59436 Effective search space used: 59436 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: 42 (22.0 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