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_037576905.1 BS73_RS27295 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000744815.1:WP_037576905.1
          Length = 439

 Score =  199 bits (505), Expect = 3e-55
 Identities = 133/414 (32%), Positives = 211/414 (50%), Gaps = 10/414 (2%)

Query: 377 PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEM 436
           P Q+   ++  V+ ++ ++   G  A+L Y+ + DG +  +  ++A   +   + L+ E+
Sbjct: 27  PAQRLPAVVETVSRMLSDIEKNGMDAVLRYSRELDGWQGGDVEISAAELKRTGDSLSPEL 86

Query: 437 KEALDLSIENVRKFHAAQLP-TETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTA 495
           ++AL    E  R F   Q    +  E E  PGV+  +   P+ +VG Y+P G   + ++A
Sbjct: 87  RQALAAGAERTRLFAVEQREHLQDFETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASA 146

Query: 496 LMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGT 555
            M    A+ A    ++  +PP    G   P V+Y A   G  +    GG QA+AAMA+G 
Sbjct: 147 FMTVGVAKAADVPTVLACTPPTAEQGG-HPAVLYAAYLSGVDRAFALGGVQALAAMAFGL 205

Query: 556 ETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDL 615
                 D ++G GN +VT AK  +         ID+ AGPSEV VIADE AD + VA+DL
Sbjct: 206 LGDQPADMLVGAGNAYVTEAKRQLFGRV----GIDLLAGPSEVAVIADETADPELVAADL 261

Query: 616 LSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGY 674
           L QAEHG  S   L  V  S +    + + V  Q  QLP  DI       H T+ + +  
Sbjct: 262 LGQAEHGRQSPASL--VTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDR 319

Query: 675 EEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYS-SGTNHTLPTY 733
           + A+E+ +  APEHL +  A+ + Y + + N GS+F+GA++  +  D   +GTNH LPT 
Sbjct: 320 QTAVELMDLLAPEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKGIAGTNHVLPTG 379

Query: 734 GYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787
             AR  +G + + F K +T Q ++ E   ++   V  ++  EG+  HR    +R
Sbjct: 380 RGARASAGLSVSRFLKPLTFQKVSAEATPDLAAHVEAISDFEGMAAHRATATLR 433


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: 690
Number of extensions: 36
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: 439
Length adjustment: 37
Effective length of query: 762
Effective length of database: 402
Effective search space:   306324
Effective search space used:   306324
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