GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE 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)



>FitnessBrowser__Miya:8502101
          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 (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