GapMind for Amino acid biosynthesis

 

Alignments 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)



>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.

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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 (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:

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. 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