GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Phaeobacter inhibens BS107

Align Serine O-acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate GFF1439 PGA1_c14560 homoserine O-succinyltransferase MetA

Query= SwissProt::A0A120HUS7
         (271 letters)



>FitnessBrowser__Phaeo:GFF1439
          Length = 305

 Score =  141 bits (356), Expect = 1e-38
 Identities = 80/260 (30%), Positives = 128/260 (49%), Gaps = 3/260 (1%)

Query: 5   PLKIGILNVMHDKADTKTRLQHVLTHTAIPVDLHFYYPMTHYAGRTVPEAVSSILDPLDI 64
           PL+IG+LN+M  K  T+ +   ++  T + +DL       H    T  E ++    P   
Sbjct: 35  PLRIGLLNLMPKKIQTENQFARLIGATPLQIDLSLIRMTEHQTRNTAAEHMAEFYRPFQE 94

Query: 65  HEVATMDGFIITGSPIETLEFDQVHYIAEVRTLLKTLSQHVPNQLYLCWGGMVALNYFFG 124
            +    DG IITG+PIE LEF+ V Y  E+  +      +V +   +CWGGM  +NYF G
Sbjct: 95  IKDQRFDGLIITGAPIEHLEFEDVTYWDELCEVFDWTQTNVHSTFGVCWGGMAMINYFHG 154

Query: 125 ISKLILPHKLFGVYPQTILEP-HPLLKGLKNDFKSPHARYAEMDVRGIHADPRLTINATT 183
           + K +L HK+FG +    L+P  P L+G  +D   P +R+ E+    I A P L     +
Sbjct: 155 VKKHLLDHKVFGCFRHQNLDPASPYLRGFSDDCVIPVSRWTEIRQSEIDARPGLRSLLGS 214

Query: 184 TKGKLFMVTEPTDTQTFVFSHIEYDRWGLDSEYKREVAAHPEIDYVRAKHYYHHKNDYDH 243
                 ++ +P+    ++F+H EYD   L  EY R+VA+   I+     +YY   +    
Sbjct: 215 QDAGPCLIEDPSHRALYIFNHFEYDSDTLKQEYDRDVASGTPINV--PMNYYPDDDPSRK 272

Query: 244 PKFNWKKTQRTIFDNWIQHV 263
           P+  W+     ++ NWI  +
Sbjct: 273 PQNRWRSHAHLLYGNWINDI 292


Lambda     K      H
   0.322    0.138    0.434 

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: 242
Number of extensions: 9
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: 271
Length of database: 305
Length adjustment: 26
Effective length of query: 245
Effective length of database: 279
Effective search space:    68355
Effective search space used:    68355
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 (21.9 bits)
S2: 47 (22.7 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