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.
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:
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