GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Lentibacillus jeotgali Grbi

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_010529189.1 ON01_RS01235 homoserine dehydrogenase

Query= BRENDA::D8WXQ1
         (432 letters)



>NCBI__GCF_000224785.1:WP_010529189.1
          Length = 435

 Score =  522 bits (1344), Expect = e-153
 Identities = 263/431 (61%), Positives = 329/431 (76%), Gaps = 2/431 (0%)

Query: 2   EAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDV--DPAQ 59
           +++ VGLLG+G VGSGV+ +IE HQ KL HQ+GC V VK  LV++ NK RDV+   +   
Sbjct: 3   DSVSVGLLGVGVVGSGVISLIEQHQAKLAHQLGCSVHVKSALVRNPNKVRDVNAKTNGTL 62

Query: 60  LTTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAA 119
           LTTN DD+L DP+IDV++EVMGGIEE R  +LKA   KKHVVTANKDL+A+YG+EL  +A
Sbjct: 63  LTTNPDDVLNDPEIDVIVEVMGGIEEARESILKAFEAKKHVVTANKDLVALYGAELHDSA 122

Query: 120 SANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEV 179
             N CD +YEASVAGGIPILR + DG ASD I ++MGIVNGTTNYILTKM   G +YE+ 
Sbjct: 123 GKNKCDFYYEASVAGGIPILRGITDGFASDHIEQLMGIVNGTTNYILTKMHNEGVSYEDA 182

Query: 180 LKEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYG 239
           LKEAQELG+AEADPA+DVEGLDAARKMAIL  L FS  IDLDDV+V GI  I  +D+QYG
Sbjct: 183 LKEAQELGFAEADPAADVEGLDAARKMAILGRLAFSTHIDLDDVEVTGINGIELDDLQYG 242

Query: 240 KQLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGP 299
             LG+ MKLIG A  +G++VEV+VQP L+S  HPLA V +EYNAVYVYGEAVGE MFYG 
Sbjct: 243 DSLGFNMKLIGFAKFDGKQVEVNVQPALISKEHPLADVKNEYNAVYVYGEAVGEAMFYGA 302

Query: 300 GAGSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEV 359
           GAGS+PTA AV+SD+V V+KNM  GV G+  V P+++K+LK  D+ + +++ R H KDE 
Sbjct: 303 GAGSMPTAAAVISDVVTVIKNMHRGVTGSQFVEPRFKKELKTEDQRFGQYYARFHAKDEA 362

Query: 360 GVFANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHE 419
           GVF+ I+S+F+E  +SF++ILQ PLKE   AEIV++TH++SL+     L  L  L+ V E
Sbjct: 363 GVFSRISSLFNEFDISFKQILQNPLKEADAAEIVVITHRSSLEKMHQALDALSKLDEVLE 422

Query: 420 IKSSYRVEGSA 430
            KS Y+VEG A
Sbjct: 423 TKSFYKVEGDA 433


Lambda     K      H
   0.316    0.134    0.368 

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: 600
Number of extensions: 21
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: 432
Length of database: 435
Length adjustment: 32
Effective length of query: 400
Effective length of database: 403
Effective search space:   161200
Effective search space used:   161200
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 (21.6 bits)
S2: 51 (24.3 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