GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Azorhizobium caulinodans ORS 571

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012171673.1 AZC_RS16245 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000010525.1:WP_012171673.1
          Length = 430

 Score =  258 bits (660), Expect = 4e-73
 Identities = 166/434 (38%), Positives = 235/434 (54%), Gaps = 11/434 (2%)

Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415
           PI LD    +        L+   + ++++   V  II  VR +G++AL++Y+  FD V+L
Sbjct: 2   PIRLDAKSTAFPDAFATFLASKREASTDVAVAVADIIAGVRARGDAALIDYSRTFDRVEL 61

Query: 416 SNPV-LNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFP 474
              + +     E     + ++  EAL  +   +   HA QLP +    +     L  R+ 
Sbjct: 62  EGRIRVTEAEIEAALAEVPQDTFEALKFAKARIEAHHARQLPADERYTDAVGVELGQRWT 121

Query: 475 RPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV 534
            P++ VGLY+PGGTA  PS+ LM  VPA+VA    +    P    DG ++P V+  A   
Sbjct: 122 -PVDAVGLYVPGGTAAYPSSVLMNAVPAKVAGVPRVAMVVP--SPDGVIAPLVLAAARLA 178

Query: 535 GASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAG 594
           G  ++   GGAQAVAA+AYGTETI  VDKI+GPGN +V AAK  V         IDM AG
Sbjct: 179 GVDEVYRVGGAQAVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKV----GIDMIAG 234

Query: 595 PSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLP 654
           PSEVL++AD +A+  ++A+DLL+QAEH   +Q ILV    S      +  AV  Q   LP
Sbjct: 235 PSEVLILADGNANAAWIAADLLAQAEHDAAAQSILV--TDSPVLADAVTRAVEAQLTTLP 292

Query: 655 RVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGA 713
           R +I       H  I+L    +EAL + ++ APEHL +   +A+     + +AG++FVGA
Sbjct: 293 RREIAEASWRDHGAIILVGSMDEALPLVDRVAPEHLEIHADDADALADRIRHAGAIFVGA 352

Query: 714 YTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAK 773
           YTPE+ GDY  GTNH LPT   AR  SG     F K  +    +P  L  IG A + +A+
Sbjct: 353 YTPEAIGDYVGGTNHVLPTARSARFSSGLGVYDFLKRTSILKCSPASLNVIGPAAVRLAE 412

Query: 774 KEGLDGHRNAVKIR 787
            E LD H  ++ IR
Sbjct: 413 VERLDAHGRSILIR 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: 681
Number of extensions: 22
Number of successful extensions: 5
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 25 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