Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate 8499235 DvMF_0015 peptidase C26 (RefSeq)
Query= reanno::MR1:200445 (253 letters) >FitnessBrowser__Miya:8499235 Length = 207 Score = 63.9 bits (154), Expect = 2e-15 Identities = 64/199 (32%), Positives = 84/199 (42%), Gaps = 45/199 (22%) Query: 28 KYLLGVVNGAKGWPLVIPSLGADQPIEAILARLDGILFTGSPSNVEPHLYAGVPSEAGTH 87 ++L + GA P+ P+ G D A ++G++ TG GV SE Sbjct: 30 RFLAVALPGAAWLPM--PNAGDDAVRLADAFAVNGLVLTGGDD-------WGVFSE---- 76 Query: 88 HDPKRDATTLPLIRAAIAAGVPVLGICRGFQEMNVAFGGSLHQKLHEVGHFIEHREDKEA 147 RDAT L R A+A +PVLG+CRG Q +N GG Sbjct: 77 ----RDATEAALFRWAMARDIPVLGVCRGAQVINRMLGG--------------------- 111 Query: 148 SLEVQYGPSHSITVEPGGVIYEAWGRNSAEVNSVHTQGVER--LGIGLRPEACAPDGLVE 205 S V G H+ T P + E +VNS H ++R L GL A APDG VE Sbjct: 112 SARVTDGAVHAGTRHP---LTERQDWTPEDVNSYHRLVLDRDMLAPGLASAALAPDGTVE 168 Query: 206 AFSVIDATEFALGVQWHPE 224 AF + +GV WHPE Sbjct: 169 AFHL--PGRRVVGVLWHPE 185 Lambda K H 0.320 0.139 0.429 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: 169 Number of extensions: 9 Number of successful extensions: 2 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: 253 Length of database: 207 Length adjustment: 23 Effective length of query: 230 Effective length of database: 184 Effective search space: 42320 Effective search space used: 42320 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 (21.8 bits) S2: 46 (22.3 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