GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Thiohalospira halophila DSM 15071 HL 3

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_093427940.1 BM272_RS06415 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_900112605.1:WP_093427940.1
          Length = 437

 Score =  240 bits (613), Expect = 1e-67
 Identities = 152/432 (35%), Positives = 229/432 (53%), Gaps = 17/432 (3%)

Query: 365 SDKVGVQKALSRPIQ----KTSEIMHLVNPIIENVRDKGNSALLEYTEKFD---GVKLSN 417
           +D+ G   AL R +         +  +V  I+ +VR +G++A++E T + D      +++
Sbjct: 9   TDEDGFDAALDRLLAWEEGTDDRVEGIVRDILTDVRTRGDTAVVEQTNRLDRRDAATMAD 68

Query: 418 PVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPI 477
             L A   +   E L    ++AL+ + E +R +H  Q   E+ +     G +  +   P+
Sbjct: 69  LELPAERLQRALEALPSAQRQALETAAERIRGYHRHQCQ-ESWQYTEADGTVLGQQVTPM 127

Query: 478 EKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGAS 537
           ++ GLY+PGG A  PS+ LM  +PA+VA   E+V   P    DG+++  V+  A   G  
Sbjct: 128 DRAGLYVPGGKAAYPSSVLMNALPAKVAGVGELVMVVPA--PDGELNDLVLAAAAVAGVD 185

Query: 538 KIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSE 597
           ++   GGAQAVAA+AYGTET+P VDKI+GPGN FV  AK  V         IDM AGPSE
Sbjct: 186 RVFTLGGAQAVAALAYGTETVPAVDKIVGPGNIFVATAKRMVFGTV----GIDMIAGPSE 241

Query: 598 VLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVD 657
           +LV+ D + D ++VA DL SQAEH  D+Q ILV  + +   +  + +A+      + R  
Sbjct: 242 ILVVCDGETDPEWVAVDLFSQAEHDEDAQAILVCPDAAY--LDRVAEAMDRLLPTMGRET 299

Query: 658 IVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTP 716
           I+R  +A    ++ C   ++A  + N+ APEHL L +A        V +AG++F+G YT 
Sbjct: 300 IIRSSLAARGALIQCRDLDDAAAVINRVAPEHLELSVAEPEALAAKVRHAGAIFLGRYTS 359

Query: 717 ESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEG 776
           ES GDY +G NH LPT   AR  S      FQK  +    +  G   +G     +A  EG
Sbjct: 360 ESLGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIGCSAAGAAALGPTAAALADGEG 419

Query: 777 LDGHRNAVKIRM 788
           L  H  A + R+
Sbjct: 420 LGAHAEAARRRL 431


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: 712
Number of extensions: 28
Number of successful extensions: 4
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: 799
Length of database: 437
Length adjustment: 37
Effective length of query: 762
Effective length of database: 400
Effective search space:   304800
Effective search space used:   304800
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 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