GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisI in Desulfovibrio vulgaris Miyazaki F

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 8502101 DvMF_2814 histidinol dehydrogenase (RefSeq)

Query= SwissProt::P00815
         (799 letters)



>lcl|FitnessBrowser__Miya:8502101 DvMF_2814 histidinol dehydrogenase
           (RefSeq)
          Length = 434

 Score =  216 bits (551), Expect = 2e-60
 Identities = 144/407 (35%), Positives = 219/407 (53%), Gaps = 16/407 (3%)

Query: 388 VNPIIENVRDKGNSALLEYTEKFD--GVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIE 445
           V  I++ VR  G++AL +YT +FD  G   +   +         E +  + +  +  +  
Sbjct: 35  VREILDTVRAGGDAALADYTSRFDCPGFDAARIRVGEDEIAAALEEVGPDDRAIIAEAAA 94

Query: 446 NVRKFHAAQLPTETLEVETQP-GVLCSRFPRPIEKVGLYIPGG---TAILPSTALMLGVP 501
           N+R FH AQ   E     T+P G +  +   P+++ GLY+PGG      L S+ LM  +P
Sbjct: 95  NIRAFHEAQ--KEQSWFTTRPDGSVLGQMVTPVDRAGLYVPGGQGGNTPLISSLLMNAIP 152

Query: 502 AQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKV 561
           AQVA   EI   SPPRK DG ++P ++  A  +G +++  AG A A+AA+A+GTET+  V
Sbjct: 153 AQVAGVPEIAVISPPRK-DGTLNPFILAAAHHLGITEVHRAGSAWAIAALAFGTETVRPV 211

Query: 562 DKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEH 621
           D I GPGN +VT AK  +         IDM AGPSE+L++AD  A  D+VA+D+LSQAEH
Sbjct: 212 DVIAGPGNIWVTTAKRLLIGRV----GIDMIAGPSEILILADHTARADWVAADMLSQAEH 267

Query: 622 GIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEALEM 680
             D     + +  S   +  ++  +  Q   LPR DI RK +A    IV+       + +
Sbjct: 268 --DPLASSICITDSPALVDALKLELAAQCDTLPRADIARKALADWGAIVVVPDMATGIGI 325

Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740
           +N+ APEHL +   +    +  + +AG+VF+G ++PE  GDY +G NH LPT G AR  S
Sbjct: 326 TNKVAPEHLEVLTKDPWALLGTIRHAGAVFLGGWSPEPVGDYYAGPNHVLPTMGTARFSS 385

Query: 741 GANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787
             +  TF K  +  + T         ++  +A+ EGL+ H  + + R
Sbjct: 386 ALSVQTFCKRTSVISATAAFTRGHAASIARLARLEGLEAHARSAESR 432


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: 631
Number of extensions: 31
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: 434
Length adjustment: 37
Effective length of query: 762
Effective length of database: 397
Effective search space:   302514
Effective search space used:   302514
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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