GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Synechococcus elongatus PCC 7942

Align Serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate Synpcc7942_B2663 Synpcc7942_B2663 putative serine acetyltransferase

Query= uniprot:B8DIT5_DESVM
         (317 letters)



>FitnessBrowser__SynE:Synpcc7942_B2663
          Length = 319

 Score =  273 bits (698), Expect = 4e-78
 Identities = 147/289 (50%), Positives = 188/289 (65%), Gaps = 6/289 (2%)

Query: 18  LERIVDEMCAPESYEAVYHRSLHDA--PMPSLEALAEMVSRLRAALLPGFFGAATVHMES 75
           L+ IV  + +  S + + H  L D   P+PS E+L  ++  LR+ L P  FG   + +E+
Sbjct: 18  LDSIVSAL-SQASTDPLPHHLLSDQFYPLPSRESLGLILHGLRSVLFPRHFGDPELSVET 76

Query: 76  MRYHLAANLDSIYRILSEQIRRGACFT-CADFARECGSCEL--HSRDKAIQFLQRLPEIR 132
             Y +   LD    +L+EQIRR            E     L  H+ +    F Q LPEI+
Sbjct: 77  THYFIGNTLDKTLNLLNEQIRRELWLQHVTQGTPEATPAVLSQHASELTQAFAQALPEIK 136

Query: 133 RMLASDVKAAYEGDPAAKSPGETVFCYPSIAAMINHRIAHELYRMEVPLIPRIISEMAHS 192
           R+L SDV AAY GDPAA+S  E +FCYP I A+  HR+AH LY++ +PL+ RI +E++HS
Sbjct: 137 RLLDSDVNAAYLGDPAAQSISEILFCYPGITAITFHRLAHRLYQLGLPLLARITAEVSHS 196

Query: 193 RTGIDIHPGARIDEEFFIDHGTGVVIGETCIIGRGCRIYQGVTLGALSFPKDGDGVLIKG 252
            TGIDIHPGA I   FFIDHGTGVVIGETC+IG   RIYQ VTLGA SFP+D  G LIKG
Sbjct: 197 ETGIDIHPGAAIGGSFFIDHGTGVVIGETCVIGDRVRIYQAVTLGAKSFPRDETGALIKG 256

Query: 253 NPRHPILEDNVTVYAGATILGRVTIGAGSMIGGNVWVTHDVPPGSKIVQ 301
             RHP++ED+V +YAGAT+LGR+T+G GS IGGNVW+T  VP GS I Q
Sbjct: 257 QARHPVIEDDVVIYAGATLLGRITVGRGSTIGGNVWLTRSVPAGSFISQ 305


Lambda     K      H
   0.322    0.138    0.417 

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: 317
Number of extensions: 20
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: 317
Length of database: 319
Length adjustment: 27
Effective length of query: 290
Effective length of database: 292
Effective search space:    84680
Effective search space used:    84680
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: 48 (23.1 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