GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Phyllobacterium endophyticum PEPV15

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106715409.1 CU100_RS05115 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_003010935.1:WP_106715409.1
          Length = 430

 Score =  256 bits (655), Expect = 1e-72
 Identities = 162/414 (39%), Positives = 233/414 (56%), Gaps = 12/414 (2%)

Query: 379 QKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP--VLNAPFPEEYFEGLTEEM 436
           + + ++  +V  II  VR +G+SAL++Y+++FD V L      + +   +        + 
Sbjct: 25  EASEDVDRVVTDIIHRVRTEGDSALIDYSQRFDRVDLVQHGIAITSAEIDAAVASAPAKT 84

Query: 437 KEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTAL 496
            EAL L+   +   HA Q+P +    +     L SR+   +E VGLY+PGGTA  PS+ L
Sbjct: 85  VEALKLARNRIHSHHARQMPQDDRYTDALGVELGSRWTA-VESVGLYVPGGTASYPSSVL 143

Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556
           M  VPAQVA  + IV   P    DGK++P V+  A   G S+I   GGAQA+AA+AYGTE
Sbjct: 144 MNAVPAQVAGVERIVMVVP--SPDGKLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTE 201

Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616
           TI  V KI+GPGN +V AAK  V         IDM AGPSEVL++AD + D D++A+DLL
Sbjct: 202 TIAPVAKIIGPGNAYVAAAKRRVFGRV----GIDMIAGPSEVLIVADSNNDPDWIAADLL 257

Query: 617 SQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYE 675
           +QAEH   +Q IL+  +  E     +  AV  Q L LPR +  R   + +  ++L     
Sbjct: 258 AQAEHDSAAQSILITDD--ESFGDAVVAAVERQLLTLPRAEAARASWSDYGAVILVSDLL 315

Query: 676 EALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGY 735
            +L + N+ A EHL +   +    +  V NAG++F+G YTPE  GDY  G+NH LPT   
Sbjct: 316 SSLPLVNRIAAEHLEIATDDPELLMAGVRNAGAIFLGRYTPEVIGDYVGGSNHVLPTARS 375

Query: 736 ARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789
           AR  SG +   + K  +   +  E L  +G A + +A+ EGLD H N+V IR++
Sbjct: 376 ARFSSGLSVLDYVKRTSILKLGVEQLRALGPAAIELARAEGLDAHGNSVAIRLN 429


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: 634
Number of extensions: 26
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: 430
Length adjustment: 37
Effective length of query: 762
Effective length of database: 393
Effective search space:   299466
Effective search space used:   299466
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