Align Amidohydrolase 2 (characterized, see rationale)
to candidate Echvi_2938 Echvi_2938 Predicted metal-dependent hydrolase of the TIM-barrel fold
Query= uniprot:B2T9V4 (276 letters) >FitnessBrowser__Cola:Echvi_2938 Length = 275 Score = 193 bits (491), Expect = 3e-54 Identities = 109/275 (39%), Positives = 151/275 (54%), Gaps = 4/275 (1%) Query: 1 MHIDAHQHYWDPARGDYEWLTPELKILYRTFGPEDLKPLRERAGIERTVVVQAAPTIDET 60 M IDAHQH+W + W+ +K + R F P DLKPL ++ GI+ TVVVQA ++ E Sbjct: 1 MRIDAHQHFWQYDAEKHAWIDDGMKAIQRDFLPTDLKPLLDKEGIDGTVVVQADESLAEN 60 Query: 61 RYLLDLARHEPSIAGVVGWVPLLLPTAPQVIEALAHEPKFKGVRPMLQDLPDDTWIANPD 120 +LL LA P I VVGWV L +E A EPK G R +LQ P + +A Sbjct: 61 TFLLGLAEQHPWIKKVVGWVDLCSDEVLTTLERYAQEPKMTGFRMILQGQPPEL-MAEKS 119 Query: 121 LTPAIEALIAHDLAFDALIYARHVEPFETFATRFPALRIVVDHGAKPPIRYGRAGYQSWA 180 + L D +D LI+ H++ ++FP V+DH AKP I+ + WA Sbjct: 120 FRNGLGQLQKFDFTYDILIFPHHMDEAIELVSQFPNQPFVIDHLAKPYIKDRK--IDEWA 177 Query: 181 DAITRLAQLPHVHCKLSGLVTEAS-PGWTEETLHPYVEHLLKSFGPARLMWGSDWPVLDL 239 + +LA+ +V CK SG+VTEA WT E L PY++ + ++FGP RLM+GSDWPV + Sbjct: 178 GKMKQLAERENVCCKASGMVTEADWNRWTREDLRPYLDVVFEAFGPKRLMFGSDWPVAQV 237 Query: 240 NGDYLLWHSVANTLLTSLSDAERDAVFGGNAAAFY 274 DY + SV N + LS E+ + G AA+FY Sbjct: 238 AADYPVNVSVVNAYIHQLSQHEQADIMGNTAASFY 272 Lambda K H 0.322 0.139 0.448 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: 232 Number of extensions: 8 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: 276 Length of database: 275 Length adjustment: 25 Effective length of query: 251 Effective length of database: 250 Effective search space: 62750 Effective search space used: 62750 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 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