Align Amidohydrolase 2 (characterized, see rationale)
to candidate BPHYT_RS27205 BPHYT_RS27205 amidohydrolase
Query= uniprot:B2T9V4 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS27205 Length = 290 Score = 268 bits (684), Expect = 1e-76 Identities = 140/282 (49%), Positives = 180/282 (63%), Gaps = 10/282 (3%) Query: 1 MHIDAHQHYWDPARGDYEWLTPELKILYRTFGPEDLKPLRERAGIERTVVVQAAPTIDET 60 + IDAHQH+W A + W L +YR FG +DL+P+ R+ ++RTV+VQ+ PT ++T Sbjct: 3 LRIDAHQHFWQIADREGYWPPHTLDAIYRDFGAQDLEPILARSNVQRTVLVQSLPTPEDT 62 Query: 61 RYLLDLARHEPSIAGVVGWVPLLLPTAPQVIEALAHEPKFKGVRPMLQDLPDDTWIANPD 120 RYLLD+A +A VVGWV L AP + LA +PKF+GVRPMLQDL DD WI +P Sbjct: 63 RYLLDIACASSVVAAVVGWVDLKSAGAPASLAMLARQPKFRGVRPMLQDLDDDGWIDDPM 122 Query: 121 LTPAIEALIAHDLAFDALIYARHVEPFETFATRFPALRIVVDHGAKPPIRYGRAGYQSWA 180 L PA+EA+ HDL+FDAL+ RH+ FA R+P LRIV+DH AKPPI GR+ + W Sbjct: 123 LEPAVEAMFEHDLSFDALVTPRHLHALLAFARRYPRLRIVIDHAAKPPIASGRS--EPWH 180 Query: 181 DAITRLAQLPHVHCKLSGLVTEASPGWTEETLHPYVEHLLKSFGPARLMWGSDWPVLDL- 239 A++RLA+LP+VHCKLSGL TEA P + PYV + + FG +RLMWGSDWPV L Sbjct: 181 VAMSRLAELPNVHCKLSGLWTEAGPHPDLTLVEPYVRAVCEWFGASRLMWGSDWPVSRLA 240 Query: 240 -----NGDYLLWHSVANTLLTSLSDAERDAVFGGNAAAFYRL 276 GD+L W L +VFGGNA FYR+ Sbjct: 241 GHFGDYGDWLAW--CEQCCDRFLGPDAHASVFGGNACHFYRI 280 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: 358 Number of extensions: 19 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: 276 Length of database: 290 Length adjustment: 26 Effective length of query: 250 Effective length of database: 264 Effective search space: 66000 Effective search space used: 66000 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