GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Azorhizobium caulinodans ORS 571

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_043878940.1 AZC_RS05545 3'(2'),5'-bisphosphate nucleotidase CysQ

Query= reanno::Korea:Ga0059261_2035
         (260 letters)



>NCBI__GCF_000010525.1:WP_043878940.1
          Length = 266

 Score = 65.9 bits (159), Expect = 8e-16
 Identities = 72/234 (30%), Positives = 95/234 (40%), Gaps = 13/234 (5%)

Query: 13  RLADAAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAERPMDAIIGEEEDD 72
           R+A  AGA IR           K D+S VT AD+AAEA +   +    P   II EE   
Sbjct: 15  RIALDAGAVIRRIEANGIHAREKADASVVTDADEAAEALICPALRTLAPGTPIIAEEAVA 74

Query: 73  RPG---TSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERWLGVT 129
             G      R +++DP+DGTR F+ G   +   IAL+EDG P  GII  P     + G  
Sbjct: 75  AGGGVAPGRRFFLVDPLDGTREFVSGNGEYTVNIALVEDGTPRYGIIYAPAKGLLYAGGD 134

Query: 130 GRETLFNGKPARART--------CRELSKALLATTSPALFTDGQLHAFEHVDAAVMSTVL 181
           G        P  A          CR      +   +    +D    AF      V   V 
Sbjct: 135 GAAFKALRAPEDAVVPESWTPIHCRLRPAGPIRVCASRSHSDPSTSAFIG-GFEVEDCVN 193

Query: 182 GGDCYNYGLVASGHLDIVIEAGLKLH-DFAALVPVVEGAGGRMCDWQGDPLHAG 234
            G    +GL+A G +D+       +  D AA   +V  AGG +    G PL  G
Sbjct: 194 AGSALKFGLLAEGAVDLYPRLSPVMEWDSAAGHAIVVAAGGSVRRPDGSPLTYG 247


Lambda     K      H
   0.320    0.138    0.419 

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: 237
Number of extensions: 19
Number of successful extensions: 2
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: 260
Length of database: 266
Length adjustment: 25
Effective length of query: 235
Effective length of database: 241
Effective search space:    56635
Effective search space used:    56635
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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