GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Phaeobacter inhibens BS107

Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate GFF1378 PGA1_c13950 cysteine synthase CysK

Query= SwissProt::P32232
         (561 letters)



>FitnessBrowser__Phaeo:GFF1378
          Length = 344

 Score =  208 bits (529), Expect = 3e-58
 Identities = 130/326 (39%), Positives = 188/326 (57%), Gaps = 11/326 (3%)

Query: 72  KILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERAG 131
           +I  D+   IG+TP++R+NR+S   G  CE+L K EF N G SVKDR +L +I+DA   G
Sbjct: 2   RIAHDLADAIGHTPLIRLNRVSDETG--CEILGKAEFMNPGQSVKDRAALYIIKDAIARG 59

Query: 132 TLKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTN 191
            LKPG TI+E T+GNTGIGLAL  A  G++ +IV+PE  S EK D+LR  GA++V+ P  
Sbjct: 60  DLKPGGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGAQLVQVPA- 118

Query: 192 ARFDSPESHVGVAWRLKNEI----PNSHI-LDQYRNASNPLAHYDDTAEEILQQCDGKVD 246
           A + +P + V  + RL  E+    PN  I  +Q+ N +N  AH + TA EI +Q  GKVD
Sbjct: 119 APYRNPNNFVRYSERLAKELAKTEPNGAIWANQFDNVANRQAHVETTAPEIWEQTGGKVD 178

Query: 247 MLVASAGTGGTITGIARKLKEKCPGCKIIGVDPEGSILAEPEELNQTEQTAYEV-EGIGY 305
             V + G+GGT+ G+A  L+ K  G KI   DP G+ L       +       + EGIG 
Sbjct: 179 GFVCAVGSGGTLAGVADALQPK--GVKIGLADPMGAALYSYYTTGEIATEGGSIAEGIGQ 236

Query: 306 DFIPTVLDRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSAMAVAVKAAQELKEGQ 365
             I   L+    D  ++  D D+  +   L+ +EGL+ GGSS   +A AV+ A+++  G+
Sbjct: 237 VRITKNLEGFKPDFCYQIEDRDALPYVFDLLHEEGLVLGGSSAINIAGAVRMAKDMGPGK 296

Query: 366 RCVVILPDSVRNYMSKFLSDKWMLQK 391
             V +L D    Y SK  +  ++ +K
Sbjct: 297 TIVTVLCDYGTRYQSKLFNPDFLREK 322


Lambda     K      H
   0.317    0.134    0.401 

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: 474
Number of extensions: 25
Number of successful extensions: 4
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: 561
Length of database: 344
Length adjustment: 32
Effective length of query: 529
Effective length of database: 312
Effective search space:   165048
Effective search space used:   165048
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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