GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Dinoroseobacter shibae DFL-12

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate 3608881 Dshi_2273 Homoserine dehydrogenase (RefSeq)

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>FitnessBrowser__Dino:3608881
          Length = 428

 Score =  408 bits (1048), Expect = e-118
 Identities = 217/427 (50%), Positives = 287/427 (67%), Gaps = 2/427 (0%)

Query: 1   MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60
           M+ PLR+ +AGLGTVGAGV+++I    EL+A RAGRPIE+ AVSAR R KDRGVD++ + 
Sbjct: 1   MSSPLRLGIAGLGTVGAGVVKIISRKQELLAARAGRPIEVTAVSARSRDKDRGVDMSTYG 60

Query: 61  WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120
           W +D   LAR    DV VEL+GG DGPA     A LAAGK +VTANKAM+AHHG  LA  
Sbjct: 61  WENDPVALARRDDVDVFVELMGGEDGPARNATEAALAAGKDVVTANKAMLAHHGQALAMA 120

Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180
           AE +   ++FEAAVAGG+PVIK L EG A N+I RV G++NGTCN+IL++MEAEG  +  
Sbjct: 121 AEDAGRVIRFEAAVAGGIPVIKALTEGLAGNEITRVMGVMNGTCNYILTRMEAEGLGYNI 180

Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240
           +  EA   G+ EADP+ D+ G+DAAHKL++LASIAFGT+  F  V + GI  +   DI  
Sbjct: 181 LFEEAGKLGYLEADPTLDVGGIDAAHKLALLASIAFGTKVDFDGVELEGIEQVTLEDIRH 240

Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300
           AA +G+RI+LLG+A  SG GL QR+ P LVP S PL  + G TN VV EG+ VG+++ +G
Sbjct: 241 AADMGFRIKLLGVAQRSGRGLEQRMRPCLVPASSPLGQLEGGTNMVVIEGDQVGQVVLRG 300

Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360
           AGAG+GPTASAV++D++DIAR +    +  PA+ L   P+          YLR  + DK 
Sbjct: 301 AGAGEGPTASAVLSDIMDIARGDRISTFGQPASGLVT-PIRAQSAVAAPYYLRMELEDKP 359

Query: 361 GVLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAG 420
           G LA++A  + D+GVSI+ + Q G     S  V IVTH+    ++  ALE L  +  + G
Sbjct: 360 GALAKVATVLGDSGVSIDRMRQYG-HESSSAPVLIVTHKAARNAVDAALEALPKTGVVLG 418

Query: 421 EPMWMHI 427
            P+ + I
Sbjct: 419 TPVALRI 425


Lambda     K      H
   0.319    0.136    0.388 

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: 476
Number of extensions: 19
Number of successful extensions: 3
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: 430
Length of database: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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