GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Thermophagus xiamenensis HS1

Align prephenate dehydrogenase (EC 1.3.1.13) (characterized)
to candidate WP_010528793.1 GQW_RS0115585 prephenate dehydrogenase

Query= reanno::Btheta:353459
         (257 letters)



>NCBI__GCF_000220155.1:WP_010528793.1
          Length = 258

 Score =  339 bits (869), Expect = 4e-98
 Identities = 167/257 (64%), Positives = 204/257 (79%)

Query: 1   MRILILGAGKMGSFFTDILSFQHETAVFDVNPHQLRFVYNTYRFTTLEEIKEFEPELVIN 60
           M+I ILGAGKMG++ TD L  QHE A+FD +  +LRFV+NT R T  EEI +F PEL+IN
Sbjct: 1   MKICILGAGKMGTWLTDALCLQHEVAIFDPDLERLRFVFNTQRLTKREEITQFAPELLIN 60

Query: 61  AVTVKYTLDAFRKVLPVLPKDCIISDIASVKTGLKKFYEESGFRYVSSHPMFGPTFASLS 120
           A  +KYT+ AF  VL  LP+ CIISDIASVKTGLK+FYE++G R+VS+HPMFGPTFA+L 
Sbjct: 61  AANLKYTIPAFESVLDYLPETCIISDIASVKTGLKEFYEKTGRRFVSTHPMFGPTFANLK 120

Query: 121 NLSSENAIIISEGDHLGKIFFKDLYQTLRLNIFEYTFDEHDETVAYSLSIPFVSTFVFAA 180
            L   +AIIISE DH+GK FFKD + +L LN+ EY+F+EHD+T+AYSLSIPF ST VFAA
Sbjct: 121 ELKQHHAIIISESDHMGKAFFKDFFGSLGLNLHEYSFEEHDQTIAYSLSIPFSSTLVFAA 180

Query: 181 VMKHQEAPGTTFKKHMAIAKGLLSEDDYLLQEILFNPRTPGQVANIRTELKNLLEIIEKK 240
            MK Q+APGTTF+KH  IAKGLLSEDDYLL EIL NP T  QV NIR ELK+L+ +I+ K
Sbjct: 181 CMKKQDAPGTTFRKHHDIAKGLLSEDDYLLTEILMNPYTIEQVENIRQELKHLINLIKNK 240

Query: 241 DAEGMKAYLTKIREKIK 257
           D EG++A+L K+RE IK
Sbjct: 241 DTEGLQAFLKKVRENIK 257


Lambda     K      H
   0.322    0.138    0.391 

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: 266
Number of extensions: 9
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: 257
Length of database: 258
Length adjustment: 24
Effective length of query: 233
Effective length of database: 234
Effective search space:    54522
Effective search space used:    54522
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 26 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