GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Sinorhizobium meliloti 1021

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate SMc00293 SMc00293 homoserine dehydrogenase

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>FitnessBrowser__Smeli:SMc00293
          Length = 440

 Score =  375 bits (962), Expect = e-108
 Identities = 203/434 (46%), Positives = 275/434 (63%), Gaps = 7/434 (1%)

Query: 1   MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60
           M + L++ +AGLGTVGA ++R++    E +A   GR IEI AV+ARDR+KDRGV +T   
Sbjct: 1   MADALKIGIAGLGTVGASLVRILQDRHETMATTCGRAIEITAVAARDRSKDRGVKLTGIA 60

Query: 61  WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120
           W +D   LA     DV VEL+GG+  PA +  +A L  G  +VTANKA++A HG+ELA++
Sbjct: 61  WFEDAVSLASEADVDVFVELMGGAGDPAYSCVKAALTRGVHVVTANKALLAAHGIELAEI 120

Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180
           AE+    + +EAAVAGG+PVIK LRE    N I RVYGI+NGTCN+IL+KME EG  F E
Sbjct: 121 AEQHGALLNYEAAVAGGIPVIKALRESMTGNTISRVYGIMNGTCNYILTKMEKEGLSFEE 180

Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240
            L EAQ  G+AEADP+FDI+G D AHKLSIL S+AFGT  A  D+ + GI ++   DI  
Sbjct: 181 CLKEAQRLGYAEADPAFDIEGNDTAHKLSILTSLAFGTAIAADDIYLEGITNISIEDIQA 240

Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300
           A+ LGYRI+LLG+A  + +G+ QRVHP +VP    +A V G TNAV  E + +G LL  G
Sbjct: 241 ASDLGYRIKLLGVAQRTDSGIEQRVHPTMVPHDTVIAQVDGVTNAVAIESDILGELLMVG 300

Query: 301 AGAGDGPTASAVVADLIDIARTEFG----PPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356
            GAG   TASAV+ D+ DIA++  G    P +  PA +L     A      G  ++R  V
Sbjct: 301 PGAGGDATASAVLGDIADIAKSRPGAQHVPAFGRPAKALLPYKRARMQSHEGGYFIRLKV 360

Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRGA-MADGS--VLVAIVTHEVPERSIAQALEKLR 413
            D+ GV A +A  M +  +S+ES++Q     AD +    + +VTH   E S+ +A+  ++
Sbjct: 361 VDRTGVFANVAKHMAENDISLESIMQHSKHYADPAEPKTIILVTHATSEASVRKAIVSIK 420

Query: 414 GSPSLAGEPMWMHI 427
           G   L GEP  + I
Sbjct: 421 GEGYLVGEPQVIRI 434


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: 466
Number of extensions: 11
Number of successful extensions: 2
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: 440
Length adjustment: 32
Effective length of query: 398
Effective length of database: 408
Effective search space:   162384
Effective search space used:   162384
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