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_106713095.1 CU102_RS21190 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_003010955.1:WP_106713095.1
          Length = 432

 Score =  217 bits (552), Expect = 1e-60
 Identities = 139/407 (34%), Positives = 211/407 (51%), Gaps = 17/407 (4%)

Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENV 447
           V  II NVR +G++A+ +Y+  +D   +    +      E    L  + ++  + +IE V
Sbjct: 33  VKDIIANVRAQGDAAVRKYSRTYDRADIEAFEVGLEDRLEAVANLDPQTRKDTEFAIERV 92

Query: 448 RKFHAAQLPTET-LEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQ 506
           ++F  AQL T   LE +  PG+       PIE VG Y+PGG   + S  +M  VPA+VA 
Sbjct: 93  KEFAEAQLRTILPLEFDALPGLHLGHRIIPIEVVGAYVPGGRYPILSAPVMTIVPAKVAG 152

Query: 507 CKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILG 566
           C +++   PP        P ++      GA +I   GGAQA+AAMA+GTETIP VDKI+G
Sbjct: 153 CDQVIACLPPN-----AHPAMIAGCHLSGADRIFKVGGAQAIAAMAFGTETIPAVDKIVG 207

Query: 567 PGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQ 626
           PGN +V  AK  V         ID  AGPSE+ V+ADE  D + +A+DLL+QAEH + ++
Sbjct: 208 PGNAYVNEAKRQVFGQV----GIDQLAGPSEIFVVADESGDAEMIATDLLAQAEHDVRTR 263

Query: 627 VILVGVN--LSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQ 683
           V L+  +  L+E  ++E++     Q   LP  D+       +  I +C      ++ S+ 
Sbjct: 264 VGLITTDQKLAEATLKEVE----RQLETLPTADVAGVAWRDYGEIAVCADESAMIQYSDH 319

Query: 684 YAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGAN 743
            A EHL +   + +     + N GS+F+G        D   GTNHTLPT   AR   G  
Sbjct: 320 IAAEHLEVHTRDPHSTAGKLRNYGSLFIGKLASVVYSDKCCGTNHTLPTMAAARYTGGLW 379

Query: 744 TATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790
             ++ K  T Q +   G+  +    +  ++ EG++GHR A   R+S+
Sbjct: 380 VGSYVKVCTHQWLDERGVAAVAPPSVRQSRTEGMEGHRRAAAFRLSQ 426


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: 642
Number of extensions: 31
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: 432
Length adjustment: 37
Effective length of query: 762
Effective length of database: 395
Effective search space:   300990
Effective search space used:   300990
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