Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate BPHYT_RS15045 BPHYT_RS15045 peptidase C26
Query= reanno::pseudo6_N2E2:Pf6N2E2_4510 (258 letters) >FitnessBrowser__BFirm:BPHYT_RS15045 Length = 493 Score = 103 bits (256), Expect = 9e-27 Identities = 72/184 (39%), Positives = 97/184 (52%), Gaps = 13/184 (7%) Query: 54 DILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVDAGIPVLGIC 113 D LDG+LL G ++V P Y A++ D RD L L+ V++G PVLG+C Sbjct: 301 DYAKHLDGLLLQGG-ADVSPQSYAEQAASHEWPGDRVRDMYELELLHEFVESGKPVLGVC 359 Query: 114 RGFQEMNVAFGGSLHQKV-HEVGTFIDHREDDTQAVDVQYGPAHAVHIQPGGVLAGLGLP 172 RG Q +NVAFGG+L+Q + +V T H ++ H +H G LA + P Sbjct: 360 RGCQLINVAFGGTLYQDIATDVPTAATHVNENYDQ------HRHGIHFPDGSTLANM-FP 412 Query: 173 QRIE--VNSIHSQGIERLAPGLRAEAV-APDGLIEAVSVPGGKAFALGVQWHPEWEVSSN 229 R + VNSIH Q ++ L L EAV A DG+IEAV F +GVQWHPE+ + Sbjct: 413 GRRDAIVNSIHHQAVKTLGRDLNIEAVSASDGIIEAVRYRRA-PFVMGVQWHPEFHRAGG 471 Query: 230 PHYL 233 P L Sbjct: 472 PELL 475 Lambda K H 0.319 0.136 0.413 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: 402 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: 258 Length of database: 493 Length adjustment: 29 Effective length of query: 229 Effective length of database: 464 Effective search space: 106256 Effective search space used: 106256 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 (21.7 bits) S2: 49 (23.5 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