GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisI in Desulfovibrio vulgaris Miyazaki F

Align MazG family protein (characterized, see rationale)
to candidate 8502372 DvMF_3078 nucleoside triphosphate pyrophosphohydrolase (RefSeq)

Query= uniprot:Q72CU7_DESVH
         (267 letters)



>lcl|FitnessBrowser__Miya:8502372 DvMF_3078 nucleoside triphosphate
           pyrophosphohydrolase (RefSeq)
          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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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