GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Methylosarcina fibrata AML-C10

Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_020562319.1 A3OW_RS0104935 HAD-IB family hydrolase

Query= reanno::Marino:GFF473
         (218 letters)



>NCBI__GCF_000372865.1:WP_020562319.1
          Length = 228

 Score =  260 bits (664), Expect = 2e-74
 Identities = 119/217 (54%), Positives = 157/217 (72%)

Query: 1   MTLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGF 60
           M+LAIFDLDNTL+A DSD+ WG+FLV++GIVD  +Y  AN RFY++Y  G LDI+ +L F
Sbjct: 1   MSLAIFDLDNTLIADDSDYLWGQFLVDQGIVDKHQYEAANARFYEDYKQGRLDIVEFLRF 60

Query: 61  ALQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEP 120
           +L+PL  H   +L AWR+ F+ + + P++   A  L+  H+ +G TL++ITATNRFVTEP
Sbjct: 61  SLRPLTLHAPRQLFAWRDRFVSEIITPILLEPARELIAKHKSRGDTLLVITATNRFVTEP 120

Query: 121 IAEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDS 180
           I +  GI+HL+AT PE V+GRYTG   G P FQ+GKV  L  WL  +  T+  +WFYSDS
Sbjct: 121 IVKLYGIDHLLATPPEFVDGRYTGNFVGEPCFQEGKVRLLQQWLEDNRETMNDSWFYSDS 180

Query: 181 HNDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217
           HNDLPLL +VD+ VAVDPD  L  +AR  GW ++SLR
Sbjct: 181 HNDLPLLNRVDHAVAVDPDEKLKAHARKAGWPIISLR 217


Lambda     K      H
   0.318    0.135    0.408 

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: 226
Number of extensions: 10
Number of successful extensions: 1
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: 218
Length of database: 228
Length adjustment: 22
Effective length of query: 196
Effective length of database: 206
Effective search space:    40376
Effective search space used:    40376
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: 46 (22.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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