GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Sphingomonas koreensis DSMZ 15582

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Ga0059261_1281 Ga0059261_1281 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Korea:Ga0059261_1281
          Length = 428

 Score =  233 bits (593), Expect = 2e-65
 Identities = 151/412 (36%), Positives = 227/412 (55%), Gaps = 16/412 (3%)

Query: 382 SEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE--EYFEGLTEEMKEA 439
           +++   V  I+ +VRD+G++AL  +T KFD   L+         +    F+ L  ++++A
Sbjct: 27  ADVARDVRTIVASVRDEGDAALHAFTRKFDRHDLNETGWRIEKADCAAAFDALEPKLRDA 86

Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499
           L L+ + +  +H  Q P ++ +     GV      + +E  G+Y+PGG A  PS+ LM  
Sbjct: 87  LQLAADRITAYHEKQKPADS-DTTDAAGVRTGARWQAVEAAGVYVPGGRAAYPSSVLMNA 145

Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559
           +PA+VA    +V  +P    DG+V+P V+  A   G  +I   GGAQA+AA+AYGT  I 
Sbjct: 146 IPAKVAGVDRLVMVTPT--PDGEVNPLVLAAAHIAGVDEIWRVGGAQAIAALAYGTGRIA 203

Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619
            VD I GPGN +V  AK  +      +  IDM AGPSE++VIAD   D +++A+DLLSQ+
Sbjct: 204 AVDVITGPGNAWVAEAKRQLYG----VVGIDMVAGPSEIVVIADGKNDPEWIAADLLSQS 259

Query: 620 EHGIDSQVILVGVNLSEKKI--QEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEE 676
           EH   SQ IL    L++  I   ++ +AV  Q   L    + R+   A+  I+L    +E
Sbjct: 260 EHDPTSQSIL----LTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDANGAIILTGSLDE 315

Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736
           A+ + N+ APEHL L   + +     V +AGSVF+G  TPE+ GDY +G NH LPT   A
Sbjct: 316 AIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVAGPNHVLPTGRRA 375

Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788
           R  SG +   F K  +   +   GL  IG A + +A+ EGL  H  +V +R+
Sbjct: 376 RFASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSVSLRL 427


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: 630
Number of extensions: 26
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: 428
Length adjustment: 36
Effective length of query: 763
Effective length of database: 392
Effective search space:   299096
Effective search space used:   299096
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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