GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Sphingomonas indica Dd16

Align homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate WP_085217441.1 B9N75_RS02885 homoserine dehydrogenase

Query= uniprot:A0A168MV81
         (583 letters)



>NCBI__GCF_900177405.1:WP_085217441.1
          Length = 573

 Score =  313 bits (802), Expect = 1e-89
 Identities = 219/565 (38%), Positives = 303/565 (53%), Gaps = 20/565 (3%)

Query: 28  EVVVLKFGSSILRSPAEAPLVASAVYGHVRAGRKVVAVVSAFGGATDRLLGEA-RALGLA 86
           +V VLKFGSS+L S A+   +A   Y H+RAG KVV V+SA  G TD L  +A R  G A
Sbjct: 7   DVCVLKFGSSVLESEADYRCLADEAYRHIRAGEKVVLVLSAIAGETDALFAQAERVGGDA 66

Query: 87  HSNDLLPGYVALGEEKSAALVAIACDRIGLDACALSVRELGIVAEGEPEHSRPCGLRPDH 146
            +  L+     +GE +SAAL+A+A  RIG+ A AL   E+ +VAEG P  S    L    
Sbjct: 67  AAPALVARLARIGELRSAALMALALGRIGVRAAALDPHEMALVAEGAPLDSNLVALDAAA 126

Query: 147 LKQALDRHEVVVVPGFGAVRPDGKVALLGRGGSDLTAVFLAAELGLKKVRLVKDVDGLYD 206
           +   L  HE +VVPGF A   +  V  LGRGG+DL+AVF AA LG K+VRL+KDVDG+Y 
Sbjct: 127 VAAKLADHEAIVVPGFIAGHAEHGVVTLGRGGTDLSAVFFAAALGAKRVRLLKDVDGVYA 186

Query: 207 HDPNDKTAPALRYRRASWDVARKLGGALVQHDAIDLGESRGVEIEVAALDRADGTVIGDR 266
            DP      A RY    +D A +    L+Q  AI   ++ G+ IE+AAL   + TVI   
Sbjct: 187 EDP-AVNPRAERYGAIDYDTAAEASAGLIQPKAIAAAKAAGIAIEIAALGEHEATVIAAG 245

Query: 267 SAPPGPAPALPPLKVAVAGCGVVGGGVLGKL-LNDPRYEVVGVLVRNPKKARDVDCPASL 325
            A         PL+VA+ G G VG GV   +  +  R+ +  VLVR+    RD   PA  
Sbjct: 246 PAIRRLPLLTAPLRVALLGHGAVGAGVAECIDRHSDRFALGKVLVRH-LDGRD---PAR- 300

Query: 326 FTSNPADLWAKKPDVVLEALSEGEAGHAVIRAALEAGCDVASANKQAVSRDPGGLQELAK 385
           FT +  +  A  PDVV+E +   +A   ++  AL  G  V +ANK  V+         A 
Sbjct: 301 FTDDLDEALAGDPDVVIELIGGSDAAD-ILSRALRRGAHVVTANKAVVAAHYDAFHAAAT 359

Query: 386 ANGRRMFWSASVGGGSPMIETVRAARAAGEVVGFEAVLNGTVNFMLERLGDGAAFNEALA 445
           A G ++ +S +VGGG+P++E      A   +V  E V+NGT N +  RL  G   + AL 
Sbjct: 360 AGGSQLVFSGAVGGGAPVLEAAARLHAGPGLVAVEGVMNGTANHLFGRLAAGWPLDRALI 419

Query: 446 DARAAGFAEEDPSSDLEGLDAAAKVRLLCHEAFGRSPDGD-VPRDHL-------TEATSA 497
           +ARA GFAE DPS+D++G DAAAK+ +L    FG +   + +PR  L        +A  A
Sbjct: 420 EARALGFAEADPSADVDGYDAAAKLAILARACFGAALAPERIPRQSLRATTPETAQAALA 479

Query: 498 AGGV-RQIGAAH-LKDGVIRPSVSLNADHGDPLFSTLRGEGNALKVYGADGRVWRCRGRG 555
            G V +Q+G    L +G +   V++ +       +   G  N  ++    GRV    G+G
Sbjct: 480 RGEVLKQVGRCRVLPNGTLAAGVTIESLPLAHPLAGANGAENRFRLTDRAGRVHTIFGQG 539

Query: 556 AGRWATTESIMADLAEIVRARRADA 580
           AGRW T  ++ ADL + VR R  +A
Sbjct: 540 AGRWPTAAAVFADLMD-VRRRHIEA 563


Lambda     K      H
   0.317    0.135    0.396 

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: 845
Number of extensions: 43
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: 583
Length of database: 573
Length adjustment: 36
Effective length of query: 547
Effective length of database: 537
Effective search space:   293739
Effective search space used:   293739
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: 41 (21.6 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