GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Pseudomonas fluorescens GW456-L13

Align MazG family protein (characterized, see rationale)
to candidate PfGW456L13_2036 Nucleoside triphosphate pyrophosphohydrolase MazG (EC 3.6.1.8)

Query= uniprot:Q72CU7_DESVH
         (267 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2036
          Length = 277

 Score =  167 bits (424), Expect = 2e-46
 Identities = 92/268 (34%), Positives = 150/268 (55%), Gaps = 11/268 (4%)

Query: 7   SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65
           SL  L  +++RL  P+ GCPWD +QT  ++  + +EE +E+ +AI  G+ D ++ E+GD+
Sbjct: 3   SLEDLLHLMNRLRDPQYGCPWDIKQTYATIVPHTLEEAYEVADAIERGDFDHLQGELGDL 62

Query: 66  MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFS--------DTTYADRDEFLRN 117
           +F + +  +L  ++G F  +  + +   K+IRRHPHVF         D      ++  + 
Sbjct: 63  LFQVVYYSQLAREEGRFEFEGVVDSITRKLIRRHPHVFPTGDLYAPLDVPRLSEEQVKQR 122

Query: 118 WESIKRAEKADAEGEPQ--GVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVE 175
           WE IK  E+A+    P+   + D +PA+LP L ++ ++  +A +VGF WP+   V  +V 
Sbjct: 123 WEEIKTEERAEKSCAPEQLSLLDDVPAALPALSRSAKLQKRAGQVGFDWPDALPVLDKVR 182

Query: 176 AEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEA 235
            E  E+L+ ++ +D  A   E+GDL+FS+V L R   +   TAL   N KF RRFR +E 
Sbjct: 183 EELDEVLEAMSENDPEAVAEEIGDLLFSVVNLARHLKVDPETALRSANGKFERRFRFIEQ 242

Query: 236 LARERGLDFPALSLDDKDELWNEAKAAE 263
             R+        +L++ D LW EAK  E
Sbjct: 243 ALRDTRRPMEDCTLEELDALWGEAKRQE 270



 Score = 34.3 bits (77), Expect = 3e-06
 Identities = 28/96 (29%), Positives = 42/96 (43%), Gaps = 5/96 (5%)

Query: 177 EWLELLDVLAGDDKAAQENELGDLIFSLV---ELGRRKG-IKANTALDMTNLKFLRRFRR 232
           E  E+ D +   D    + ELGDL+F +V   +L R +G  +    +D    K +RR   
Sbjct: 39  EAYEVADAIERGDFDHLQGELGDLLFQVVYYSQLAREEGRFEFEGVVDSITRKLIRRHPH 98

Query: 233 MEALARERG-LDFPALSLDDKDELWNEAKAAEAAAR 267
           +         LD P LS +   + W E K  E A +
Sbjct: 99  VFPTGDLYAPLDVPRLSEEQVKQRWEEIKTEERAEK 134


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: 204
Number of extensions: 12
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 267
Length of database: 277
Length adjustment: 25
Effective length of query: 242
Effective length of database: 252
Effective search space:    60984
Effective search space used:    60984
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