Align Metal-dependent hydrolase of the TIM-barrel fold protein (characterized, see rationale)
to candidate WP_010442380.1 G7G_RS0115640 amidohydrolase family protein
Query= uniprot:D8J114 (289 letters) >NCBI__GCF_000192475.1:WP_010442380.1 Length = 303 Score = 99.4 bits (246), Expect = 9e-26 Identities = 91/303 (30%), Positives = 137/303 (45%), Gaps = 36/303 (11%) Query: 6 IDAHQHFWFYQPQAYPWIGA-GMELLACDRTP-------GQLQPLLDAEGLGQSIAVQAR 57 IDAH H W + YPW+ A G+E D TP + Q G+G SI +Q Sbjct: 5 IDAHHHLWDLEAVYYPWLMARGVERFFGDPTPIQRNYQLSEFQSEAAPCGIGASIHIQVG 64 Query: 58 A--GREETGFLLELARGNRR--IAGVVGWEDLASPHLAANVERW-------GRDKLVGFR 106 A G +E ++ +A N +A VV + DL S L+A ++ + G ++VG Sbjct: 65 AENGLDEARWVQSVADANSDWPMAQVV-YCDLTSTELSAQLDTFQTLPTVRGVRQIVGRA 123 Query: 107 HQLQDEADVGGCVDAPAFNAGVAWLQRQGMVYDVLVYARQMAEVQAFCARHDRHWLVLDH 166 + +D P F G+ + +D+ + M + A + L H Sbjct: 124 PGEDAQTGTNALLDDPQFLIGLKEAGICNLSFDLQLVPELMKKTARVLALAPDIRVALCH 183 Query: 167 LGKPALTEFGRGDTAFEGWQRQLRALAALPHVACKLSGL-VTEADWQRGLRQKDFDNISL 225 G P R + W + LRAL+ LP+V+CKLSGL + + +W D+I Sbjct: 184 AGSP----HDRSPAGLKEWAQNLRALSNLPNVSCKLSGLGMFDHNWT-------LDSIRP 232 Query: 226 CLDTALEAFGPQRLMFGSDWPVCLLAASYAKVAGVVREWAATRLSAAEQELLWGATAARC 285 +D LE FGP+R+MFGS++PV L YA +A V R+ + A ++ TA R Sbjct: 233 IVDECLEQFGPKRVMFGSNFPVDKLYGDYATLAEVYRD----LVPAESHSAVFSETAIRF 288 Query: 286 YGL 288 Y L Sbjct: 289 YDL 291 Lambda K H 0.324 0.137 0.450 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: 257 Number of extensions: 18 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: 289 Length of database: 303 Length adjustment: 26 Effective length of query: 263 Effective length of database: 277 Effective search space: 72851 Effective search space used: 72851 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 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