GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Streptacidiphilus oryzae TH49

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_037581586.1 BS73_RS28925 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000744815.1:WP_037581586.1
          Length = 435

 Score =  241 bits (616), Expect = 5e-68
 Identities = 150/407 (36%), Positives = 225/407 (55%), Gaps = 18/407 (4%)

Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENV 447
           V PI E+V  +G  AL+E TE+FDGV+L+   +      +    L  +++ AL++SIE  
Sbjct: 32  VRPICEDVHHRGVEALIEITERFDGVRLTTTRVPVEELHKALAELDPKVRAALEVSIERA 91

Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507
           RK H  Q  T+        G +  R+  P+E+VGLY+PGG A+ PS+ +M  VPAQ A  
Sbjct: 92  RKVHREQRRTDHTTQVVPGGTVTERWV-PVERVGLYVPGGRAVYPSSVVMNVVPAQEAGV 150

Query: 508 KEIVFASPPRKS-DGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILG 566
           + +   SPP+   DG   P ++     +G  ++   GGAQAVA  AYGTE    V+ + G
Sbjct: 151 ESLAVTSPPQPDFDGLPHPTILAACALLGVDEVYAVGGAQAVAMFAYGTEECRPVNLVTG 210

Query: 567 PGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQ 626
           PGN +V AAK  ++        ID  AGP+E+ ++AD  AD   VA+D++SQAEH   + 
Sbjct: 211 PGNIWVAAAKRLLKGRI----GIDAEAGPTEIAILADSTADPRHVAADMISQAEHDPLAA 266

Query: 627 VILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA------HSTIVLCDGYEEALEM 680
            +LV  +L+      + DAV  +     R     + IA       S IVL D  ++ L++
Sbjct: 267 AVLVTDSLA------LADAVEKELEPQVRATKHSERIATALDGRQSGIVLVDDIDQGLKV 320

Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740
            + YA EHL +Q A+A+     V NAG++F+GA+ P S GDY++G+NH LPT G A   S
Sbjct: 321 VDAYAAEHLEIQTADAHAVAARVRNAGAIFIGAWAPVSLGDYAAGSNHVLPTGGCACHSS 380

Query: 741 GANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787
           G +  +F + I   + + E L  +   V+ +A  E L GH +A++ R
Sbjct: 381 GLSVQSFLRGIHVVDYSREALAEVAGHVVNLANAEDLPGHGDAIRAR 427


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: 668
Number of extensions: 31
Number of successful extensions: 6
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: 435
Length adjustment: 37
Effective length of query: 762
Effective length of database: 398
Effective search space:   303276
Effective search space used:   303276
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