GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Phyllobacterium brassicacearum STM 196

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106709380.1 CU102_RS02655 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_003010955.1:WP_106709380.1
          Length = 430

 Score =  249 bits (636), Expect = 2e-70
 Identities = 162/413 (39%), Positives = 227/413 (54%), Gaps = 14/413 (3%)

Query: 381 TSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMK--- 437
           + ++   V  II  VR +G+ AL++Y++ FD V L    + A  P E    +        
Sbjct: 27  SEDVDRAVADIIHRVRSEGDKALIDYSKAFDRVDLVQHGI-AITPAEIDAAVASAPAATV 85

Query: 438 EALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALM 497
           EAL L+ + +   HA Q+P +    +   GV        +E VGLY+PGGTA  PS+ LM
Sbjct: 86  EALKLARDRIHSHHARQVPQDDRYTDAL-GVELGSHWTAVESVGLYVPGGTASYPSSVLM 144

Query: 498 LGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTET 557
             VPAQVA  + IV   P    DG+++P V+  A   G S+I   GGAQA+AA+AYGTET
Sbjct: 145 NAVPAQVAGVERIVMVVP--SPDGRLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTET 202

Query: 558 IPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLS 617
           I  V KI+GPGN +V AAK  V         IDM AGPSEVL++AD D D D++A+DLL+
Sbjct: 203 IAPVAKIVGPGNAYVAAAKRRVFGTV----GIDMIAGPSEVLIVADSDNDPDWIAADLLA 258

Query: 618 QAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEE 676
           QAEH   +Q IL+  +  E     +  AV  Q   LPR          +  ++L    + 
Sbjct: 259 QAEHDSAAQSILITDD--EGFGNAVVSAVERQLQTLPRTATASASWRDYGAVILVQDLDA 316

Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736
           +L + N+ A EHL +  A+    +  V NAG++F+G YTPE  GDY  G+NH LPT   A
Sbjct: 317 SLPLVNRIAAEHLEIATADPERLLAGVRNAGAIFLGRYTPEVIGDYVGGSNHVLPTARSA 376

Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789
           R  SG +   + K  +   +  E L  +G A + +A+ EGLD H N+V IR++
Sbjct: 377 RFSSGLSVLDYVKRTSILKLGVEQLRALGPAAIELARAEGLDAHGNSVAIRLN 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: 650
Number of extensions: 25
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