Align MazG family protein (characterized, see rationale)
to candidate 8502372 DvMF_3078 nucleoside triphosphate pyrophosphohydrolase (RefSeq)
Query= uniprot:Q72CU7_DESVH (267 letters) >FitnessBrowser__Miya:8502372 Length = 287 Score = 384 bits (987), Expect = e-112 Identities = 196/275 (71%), Positives = 215/275 (78%), Gaps = 16/275 (5%) Query: 7 SLARLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVM 66 SL +TDVIDRLLAPEGCPWD+EQTPESL DY++EECFELVEAIRSG +VREE+GDVM Sbjct: 13 SLQAITDVIDRLLAPEGCPWDREQTPESLADYVIEECFELVEAIRSGKVHDVREELGDVM 72 Query: 67 FLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEK 126 FLLAF+GRLYADKGAFTL DA+ NAAKMIRRHPHVF++ A R+E LRNWE IKR EK Sbjct: 73 FLLAFIGRLYADKGAFTLADAVEGNAAKMIRRHPHVFAEGECASREELLRNWERIKREEK 132 Query: 127 A-------DAEGEPQ---------GVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDV 170 A DAEGE Q GV+DSLP LPPL+KAYR+HSKAARV FTW DEDV Sbjct: 133 AAAMAEDADAEGEAQAAPAEGAQKGVFDSLPKGLPPLVKAYRLHSKAARVDFTWESDEDV 192 Query: 171 ERQVEAEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRF 230 E+QVEAEWLE LD A DK QE ELGD +F++VELGRRKGIKAN ALD LKFLRRF Sbjct: 193 EQQVEAEWLEWLDASASGDKERQEQELGDFLFTIVELGRRKGIKANAALDYATLKFLRRF 252 Query: 231 RRMEALARERGLDFPALSLDDKDELWNEAKAAEAA 265 MEALARERGLDFP L + KD LWNE KAAE A Sbjct: 253 EGMEALARERGLDFPNLPFEGKDALWNEVKAAEKA 287 Lambda K H 0.318 0.134 0.393 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: 328 Number of extensions: 15 Number of successful extensions: 5 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: 267 Length of database: 287 Length adjustment: 25 Effective length of query: 242 Effective length of database: 262 Effective search space: 63404 Effective search space used: 63404 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 Aug 03 2021. The underlying query database was built on Aug 03 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