GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Echinicola vietnamensis KMM 6221, DSM 17526

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Echvi_4660 Echvi_4660 cystathionine beta-synthase

Query= BRENDA::A0A0F6AQU1
         (342 letters)



>FitnessBrowser__Cola:Echvi_4660
          Length = 456

 Score =  231 bits (588), Expect = 4e-65
 Identities = 130/324 (40%), Positives = 199/324 (61%), Gaps = 9/324 (2%)

Query: 1   MFNSVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLR 60
           ++NS++DTIG+TPL++L++ ++     IY K E+ NPG SVKDR A+ +I DAEK G+L+
Sbjct: 2   IYNSIIDTIGDTPLVKLNRLNKGIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAEKAGILK 61

Query: 61  PGGVIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPA-APY 119
           PGG I+EGT+GNTG+GL +V  A GY+    + + QS+EK D L+ +GAE++  P     
Sbjct: 62  PGGTIIEGTSGNTGMGLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVCPTNVSP 121

Query: 120 RNPNNYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFV 179
            +P +Y      +A++L K  PN + + NQ+DN  N +AH ETT  EIW+DT  +I  F 
Sbjct: 122 DDPRSYY----SVAKKLNKDIPN-SFYPNQYDNLSNWKAHYETTGPEIWKDTEGKITHFA 176

Query: 180 AAVGSGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEG--DSITEGIGQG 237
           A VG+GGT++GTA  LKE+N +I     D +G+    +  TGE         +TEGIG+ 
Sbjct: 177 AGVGTGGTMSGTAKYLKEQNPSIVSVGIDTYGSVFKKYKETGEFDENEIYPYLTEGIGED 236

Query: 238 RITANLEGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKD-LGPGH 296
            + AN++    D   ++ D ++  +   L  EEGL +G S G  + GA+  A+  L    
Sbjct: 237 ILPANVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLTEQD 296

Query: 297 TIVTVLCDYGNRYQSKLFNPAFLR 320
           T+V +L D+G RY  K++N  +++
Sbjct: 297 TMVIILPDHGTRYLGKVYNDDWMK 320


Lambda     K      H
   0.316    0.137    0.398 

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: 400
Number of extensions: 19
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: 342
Length of database: 456
Length adjustment: 31
Effective length of query: 311
Effective length of database: 425
Effective search space:   132175
Effective search space used:   132175
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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