Align Metal-dependent hydrolase of the TIM-barrel fold protein (characterized, see rationale)
to candidate HSERO_RS22485 HSERO_RS22485 amidohydrolase
Query= uniprot:D8J114 (289 letters) >FitnessBrowser__HerbieS:HSERO_RS22485 Length = 308 Score = 387 bits (993), Expect = e-112 Identities = 178/286 (62%), Positives = 224/286 (78%) Query: 3 PPRIDAHQHFWFYQPQAYPWIGAGMELLACDRTPGQLQPLLDAEGLGQSIAVQARAGREE 62 P RIDAHQHFW Y+ + YPWIGAGM+LLA DR P Q QPLL+A+GL SI VQAR GR+E Sbjct: 21 PLRIDAHQHFWRYRSEDYPWIGAGMDLLAQDRLPYQFQPLLEAQGLHASITVQARQGRDE 80 Query: 63 TGFLLELARGNRRIAGVVGWEDLASPHLAANVERWGRDKLVGFRHQLQDEADVGGCVDAP 122 T FLLE+AR ++RIAG++GWEDL++P LA +ERWGR KL+G RHQLQ+ D + Sbjct: 81 TAFLLEMARRDKRIAGIIGWEDLSAPDLAEQMERWGRHKLLGLRHQLQEHDDANTLLTPA 140 Query: 123 AFNAGVAWLQRQGMVYDVLVYARQMAEVQAFCARHDRHWLVLDHLGKPALTEFGRGDTAF 182 + GV WLQ + DVL + R + +++ FCARHD+HW+VL+HLGKPAL EF +G AF Sbjct: 141 PLDQGVRWLQERSYTLDVLAHERHLPQLRQFCARHDQHWVVLNHLGKPALKEFRKGRAAF 200 Query: 183 EGWQRQLRALAALPHVACKLSGLVTEADWQRGLRQKDFDNISLCLDTALEAFGPQRLMFG 242 E W+++LR L A+PHVACK+SGL+TEADW RGL +DF++I CLDTAL+ FGPQRLMFG Sbjct: 201 ERWRQELRELTAMPHVACKISGLLTEADWLRGLCTRDFEHIVQCLDTALDLFGPQRLMFG 260 Query: 243 SDWPVCLLAASYAKVAGVVREWAATRLSAAEQELLWGATAARCYGL 288 SDWPVCLLAASY++V VVREW+ATRL ++Q+ LWG ++AR YGL Sbjct: 261 SDWPVCLLAASYSRVVTVVREWSATRLCPSDQDALWGESSARIYGL 306 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: 370 Number of extensions: 13 Number of successful extensions: 1 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: 308 Length adjustment: 27 Effective length of query: 262 Effective length of database: 281 Effective search space: 73622 Effective search space used: 73622 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 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