Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_013723214.1 ALIDE2_RS22385 type 1 glutamine amidotransferase
Query= reanno::Koxy:BWI76_RS10705 (254 letters) >NCBI__GCF_000204645.1:WP_013723214.1 Length = 293 Score = 99.8 bits (247), Expect = 6e-26 Identities = 77/233 (33%), Positives = 117/233 (50%), Gaps = 19/233 (8%) Query: 25 QTLQEKYLNAIVNAGGVPIALPHALAEPELLSALLPK----LDGIYLPGSPSNVQPHLYG 80 Q +++ + I++AG + + +P E L LDG+ + G S+V P YG Sbjct: 35 QYVEQSIAHWIMSAGALVVMVPCPTGETARGDVTLKHYAEWLDGVVMHGG-SDVWPGSYG 93 Query: 81 ENG--DEPDADPGRDLLSMALIDAALERRIPIFAICRGLQELVVATGGTLYRRLFEQ-PE 137 E D D RDL +A+++A ++ PIF +CRGLQ + VA GGTLY+ + Q P Sbjct: 94 EVPLKDAWLGDRVRDLYDLAVVEAFEQQGKPIFGVCRGLQLINVAFGGTLYQDIETQHPG 153 Query: 138 LLEHREDPELPVEQQYAPSHEVQVQEGGLLSQLIPGCNTFWVNSLHGQGAKTTGPRLRVE 197 ++HR +Q + HEV + G L++L PG VNS+H QG K P +E Sbjct: 154 AMQHRN--ATAYDQHF---HEVDIVPGTRLARLYPGQPRVTVNSIHHQGIKNLAPGFDIE 208 Query: 198 ARS-PDGLAEAV---SVNDHPFALGVQWHPEWNSSEYAL--SRMLFEGFITAC 244 A S PD + EA+ + + QWHPE+ ++ A+ L F+ AC Sbjct: 209 AWSYPDAVPEAIRRRHGHGRGYIAATQWHPEFRAASGAMLDDTPLLHDFLAAC 261 Lambda K H 0.318 0.137 0.415 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: 202 Number of extensions: 14 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: 254 Length of database: 293 Length adjustment: 25 Effective length of query: 229 Effective length of database: 268 Effective search space: 61372 Effective search space used: 61372 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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