GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_018232211.1 THITHI_RS0106230 HAD family hydrolase

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



>NCBI__GCF_000378965.1:WP_018232211.1
          Length = 219

 Score =  268 bits (684), Expect = 8e-77
 Identities = 124/217 (57%), Positives = 158/217 (72%)

Query: 1   MTLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGF 60
           MTLAIFDLDNTL+AGDSD+ WG FL + G+VDA+ Y+  N  FY++Y  G LDI  +  F
Sbjct: 1   MTLAIFDLDNTLIAGDSDYEWGRFLTDIGVVDADTYQATNRVFYEQYKAGTLDIHEFCRF 60

Query: 61  ALQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEP 120
           A +PLA H++E L  WR  F+ +++ P++   A  LL  HR+ G TL+IITATN F+TEP
Sbjct: 61  AFRPLAEHDVETLHGWRNRFLTERIEPLILPAAEALLARHRQAGDTLLIITATNLFITEP 120

Query: 121 IAEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDS 180
           IAE LG+  L+ATEP   +GRYTGE+ G P FQ GKVTRL+ WL  H   L+G+WFYSDS
Sbjct: 121 IAERLGVNDLLATEPAFRDGRYTGELQGVPCFQGGKVTRLEAWLREHGENLDGSWFYSDS 180

Query: 181 HNDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217
           HND+PLL++VDNPVAVDPD  LA +A    W ++SLR
Sbjct: 181 HNDIPLLERVDNPVAVDPDEALADHAAARDWPIISLR 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: 231
Number of extensions: 11
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: 219
Length adjustment: 22
Effective length of query: 196
Effective length of database: 197
Effective search space:    38612
Effective search space used:    38612
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: 45 (21.9 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