Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate GFF2664 Psest_2717 Succinylglutamate desuccinylase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977 (336 letters) >FitnessBrowser__psRCH2:GFF2664 Length = 332 Score = 322 bits (826), Expect = 6e-93 Identities = 178/329 (54%), Positives = 223/329 (67%), Gaps = 5/329 (1%) Query: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 MLALGKLLELTLAGREP EK QLT GV++ WL++GAL V PP +D GLDLLLSAGIHG Sbjct: 1 MLALGKLLELTLAGREPCEKVQLTPRGVKLHWLADGALLVSPPPGQDQGLDLLLSAGIHG 60 Query: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 NE PI +LDRL+ +AR D++PRA +L LF NP A+R+ R VE D+NRLF G H Sbjct: 61 NELIPIHVLDRLVRALARDDVRPRAPLLLLFANPAAMRRMVRQVEHDLNRLFRGEHADVW 120 Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 G EA+RA ELE L FFS RQR HYDLH+A+R S++ QFA+ PW+E Q S + L R Sbjct: 121 GGEAIRAAELEALVGGFFSGAGRQRRHYDLHSALRPSRLAQFAICPWRECEQVSAESLTR 180 Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 L +E VLLQ + + FS+ T + GAEAFTLEL A G++ V V E+ L + Sbjct: 181 LDRLAIEGVLLQRQATSTFSAMTSTRYGAEAFTLEL--AEGAGESLPVAVVQFERGLYGM 238 Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 IEG E + AL QL ++RE+IK S FRL +P+DIENF+ L +G +LAED R Sbjct: 239 IEGREAPVAAHALP--QLLQISREVIKRSPRFRLCVPSDIENFAPLPLGSVLAED-DGAR 295 Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVP 329 W+I+E GARI+FP V G RA ++VVP Sbjct: 296 WVIDEPGARILFPMADVAEGQRAALIVVP 324 Lambda K H 0.319 0.138 0.394 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: 299 Number of extensions: 16 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: 336 Length of database: 332 Length adjustment: 28 Effective length of query: 308 Effective length of database: 304 Effective search space: 93632 Effective search space used: 93632 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