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.

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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