Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_059151871.1 V474_RS12920 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_001046635.1:WP_059151871.1 Length = 255 Score = 150 bits (380), Expect = 2e-41 Identities = 93/251 (37%), Positives = 137/251 (54%), Gaps = 4/251 (1%) Query: 8 DAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSR-KAFAAGAD 66 DA E G+ +ITL RPE NAL ++ + L A A E D R +LTGS KAF AG D Sbjct: 8 DAREDGIAVITLNRPEQRNALTAEVREGLRAAWARFEADDALRIAILTGSGDKAFCAGGD 67 Query: 67 IKEMAERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDAR 126 +KEM E + D + I SKP IAAVNG GG +A D+ +A A+ Sbjct: 68 LKEMVETGMAVPPRDMYALPYDTIE-LSKPTIAAVNGVAFAGGWMIAQACDLCVASTAAK 126 Query: 127 FGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTI 186 F E+ +G G+ L+ +G+ + M++VL+G+ IDA A GLV+ + P + Sbjct: 127 FAITEVKVG--RGSPWAAPLIHMIGQRIFMEIVLTGKPIDAARAYEIGLVNRLAQPGAVL 184 Query: 187 ERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAF 246 + A+ +AR + + APL+V+ A+E ++ + + ++ L R A + D EG RAF Sbjct: 185 DAAIELAREVLEGAPLSVKAARETVMLSTEMGRSAALAAARSAHEHTYNSQDAQEGPRAF 244 Query: 247 QEKRRPEFTGR 257 EKRRP ++GR Sbjct: 245 AEKRRPVWSGR 255 Lambda K H 0.320 0.134 0.374 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: 158 Number of extensions: 12 Number of successful extensions: 4 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: 255 Length adjustment: 24 Effective length of query: 233 Effective length of database: 231 Effective search space: 53823 Effective search space used: 53823 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 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