GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Sinorhizobium meliloti 1021

Align cysteine synthase; EC 2.5.1.47 (characterized)
to candidate SMc01174 SMc01174 cysteine synthase A

Query= CharProtDB::CH_013302
         (370 letters)



>FitnessBrowser__Smeli:SMc01174
          Length = 361

 Score =  322 bits (826), Expect = 8e-93
 Identities = 176/351 (50%), Positives = 232/351 (66%), Gaps = 16/351 (4%)

Query: 10  ATAALRSAAESPYNVRVSQAQGFVNGLTEAIGNTPLIRLKRLSEETGSNILAKAEFQNPG 69
           A A +RS     +N+ V      +  + EAIGNTPLIRLK +SE TG NIL KAEF NPG
Sbjct: 2   ANAGIRSVQREVFNMPV------LPSVLEAIGNTPLIRLKAVSEATGCNILGKAEFLNPG 55

Query: 70  GSVKDRAALYVVKDAEERGLLKPGGTVVEGTAGNTGIGLAHVCRSKGYKLVIYMPNTQSQ 129
            SVKDRAAL++++ AE+ G L+PGG +VEGTAGNTGIGLA V  + GY+ VI +P TQSQ
Sbjct: 56  QSVKDRAALWIIRQAEKSGQLRPGGVIVEGTAGNTGIGLAVVGSALGYRTVIVIPETQSQ 115

Query: 130 GKIDLLRLLGAEVYPVPAVAFDNPENYNHKARRHAESL-----DNAVWTNQFDNTANRRA 184
            K D LRLLGAE+  VPAV + NP NY   + R A  L     + A+W NQFDN ANR+A
Sbjct: 116 EKKDALRLLGAELVEVPAVPYRNPNNYVKISGRLAAQLAETEPNGAIWANQFDNVANRQA 175

Query: 185 HIETTGPEIWAQTGGKLDAFTCSTGTGGTLAGITYYLKQASGGRVKSFLADPPGSVLHSY 244
           H++TT PEIW  T GK+D F C+ G+GGTLAG+   L+ A    +K  +ADP G+ L+++
Sbjct: 176 HVDTTAPEIWRDTDGKVDGFICAVGSGGTLAGVAEGLR-ARNAAIKIGIADPEGAALYNF 234

Query: 245 IQSGGKLVERSGSSITEGIGQGRITDNLQPDVGTLDGSLNISDEKTIEMIYRCLDEEGLY 304
              G   ++ SGSSITEGIGQGRIT NL+    T D +  I D + +  ++  +++EG+ 
Sbjct: 235 YAHGE--LKSSGSSITEGIGQGRITANLED--FTPDFAYQIPDAEAVPYVFDLIEKEGIC 290

Query: 305 LGASSALNVVAAKEVAEKLGKGSTVVTILADGAYRYADRLFSKSWLESKGL 355
           +G S+ +N+  A  +A  LG G T+VTIL D   RY  +LF+  +L SKGL
Sbjct: 291 VGGSTGINIAGAVRLARDLGPGHTIVTILCDYGNRYQSKLFNPDFLTSKGL 341


Lambda     K      H
   0.314    0.133    0.381 

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: 456
Number of extensions: 30
Number of successful extensions: 5
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: 370
Length of database: 361
Length adjustment: 30
Effective length of query: 340
Effective length of database: 331
Effective search space:   112540
Effective search space used:   112540
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: 42 (22.0 bits)
S2: 49 (23.5 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