GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Shewanella sp. ANA-3

Align Serine O-acetyltransferase; SAT; Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate 7025621 Shewana3_2772 homoserine O-succinyltransferase (RefSeq)

Query= SwissProt::A0A1D3PCK2
         (262 letters)



>FitnessBrowser__ANA3:7025621
          Length = 313

 Score =  145 bits (366), Expect = 1e-39
 Identities = 85/258 (32%), Positives = 137/258 (53%), Gaps = 15/258 (5%)

Query: 5   VKIGILNLMHDKLDTQSHFIKVLPNADLTFFYPRMHYQNRPIP----PEVNMTSEPLDIN 60
           +K+ ILNLM +K++T++  +++L N  L      +   ++         +N      +  
Sbjct: 36  MKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEDV 95

Query: 61  RVSEFDGFIITGAPIDQIDFSKITYIEEIRYLLQALDNHKIQQLYFCWGAMAALNYFYGI 120
           R   +DG IITGAP+ QIDF ++TY + IR ++     H    L+ CW A A L + YG+
Sbjct: 96  RHKNYDGLIITGAPLGQIDFEEVTYWDHIREIIDWSQQHVTSVLFLCWAAHAGLYHLYGL 155

Query: 121 KKKILAEKIFGVFPHLITEPH-PLLSGLSQGFMAPHARYAEMDKKQIMQDERLAINAVDD 179
            +KIL +K  GVF H  T  H PLL G    F APH+R+AEMD +++ Q   L + A  D
Sbjct: 156 NRKILQQKRSGVFVHRRTCQHFPLLRGFDDEFFAPHSRFAEMDIEELKQHSELQVLAQSD 215

Query: 180 NSHLFMVSAKDNPERN-FIFSHIEYGKDSLRDEYNREINAH-----PERHYKKPINYSMS 233
            +  ++V +++N  RN F+  H EY K +L DEY+R++        P+ +Y+   +    
Sbjct: 216 EAGAYLVLSRNN--RNLFVMGHPEYQKSTLNDEYHRDLAQGLNPNVPQNYYRN--DDPKD 271

Query: 234 NPSFQWQDTQKIFFNNWL 251
           +   +W     +  +NWL
Sbjct: 272 DAIARWHSHGSLLVSNWL 289


Lambda     K      H
   0.322    0.138    0.420 

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: 197
Number of extensions: 11
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: 262
Length of database: 313
Length adjustment: 26
Effective length of query: 236
Effective length of database: 287
Effective search space:    67732
Effective search space used:    67732
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