GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Enterococcus termitis LMG 8895

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_069662106.1 BCR25_RS00385 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_001730305.1:WP_069662106.1
          Length = 426

 Score =  280 bits (715), Expect = 2e-79
 Identities = 164/413 (39%), Positives = 242/413 (58%), Gaps = 12/413 (2%)

Query: 379 QKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKE 438
           ++T EI   V  II+ V   G+ AL  Y+++FD V L++  ++    E+ ++ +  E+  
Sbjct: 24  EETKEIEEQVKQIIQTVEQNGDQALKNYSKQFDQVVLTDLAVSEEEIEQGYQRVEPEVIA 83

Query: 439 ALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALML 498
           +L  + EN+  +H  Q   +  + E + GV+  +   P+E+VG+Y+PGGTA  PS+ LM 
Sbjct: 84  SLIAAKENIISYHKKQKQYDFFDTE-KAGVIRGQLVLPLERVGVYVPGGTAAYPSSVLMN 142

Query: 499 GVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV-GASKIVLAGGAQAVAAMAYGTET 557
            +PA++A  KEI+  +PP  S     P+V+  A K+ G   I   GGAQAVAA+AYGTE+
Sbjct: 143 VLPAKIAGVKEIIMVTPPTTSG---IPDVILAAAKIAGVDNIFQIGGAQAVAALAYGTES 199

Query: 558 IPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLS 617
           IPKVDKI+GPGN +V  AK  V      L  IDM AGPSE+ +IAD+ A+  +VA+DLLS
Sbjct: 200 IPKVDKIVGPGNVYVATAKKQVFG----LVGIDMIAGPSEIGIIADDTANPVYVAADLLS 255

Query: 618 QAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEE 676
           QAEH   ++ ILV    S++   +++  +  Q   LPR  I  K I+ H  I++    E 
Sbjct: 256 QAEHDTLARAILV--TNSKRFADQVEKEIEQQLKTLPRKTIAEKAISDHGRIIIVPTLEA 313

Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736
              + N+ APEHL +Q+++   Y+  + +AGS+F+GAY  E  GDY SGTNH LPT G A
Sbjct: 314 MFTVMNEIAPEHLEVQLSDPMSYLHEIKHAGSIFLGAYASEPVGDYFSGTNHVLPTSGTA 373

Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789
           + YS      F K+      T E L     A+  +A+KEGL+ H  A+  R +
Sbjct: 374 KFYSPLGVYDFVKYSQVTYYTKEALAQAKDAITTLARKEGLEAHARAIDCRFN 426


Lambda     K      H
   0.315    0.133    0.371 

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: 725
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 799
Length of database: 426
Length adjustment: 36
Effective length of query: 763
Effective length of database: 390
Effective search space:   297570
Effective search space used:   297570
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: 42 (22.0 bits)
S2: 53 (25.0 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