GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pedobacter sp. GW460-11-11-14-LB5

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate CA265_RS04375 CA265_RS04375 cystathionine beta-synthase

Query= BRENDA::P47998
         (322 letters)



>FitnessBrowser__Pedo557:CA265_RS04375
          Length = 453

 Score =  227 bits (578), Expect = 5e-64
 Identities = 128/309 (41%), Positives = 183/309 (59%), Gaps = 17/309 (5%)

Query: 8   DVTELIGNTPLVYLNNVAEGCVGRVAAKLEMMEPCSSVKDRIGFSMISDAEKKGLIKPGE 67
           ++ E IGNTPLV LN + +G  G + AK+E   P +S+KDR+   MI DAEK G +KPG 
Sbjct: 5   NILETIGNTPLVKLNTITKGVPGTILAKIETTNPGNSIKDRMAVKMIEDAEKSGKLKPGG 64

Query: 68  SVLIEPTSGNTGVGLAFTAAAKGYKLIITMPASMSTERRIILLAFGVELVLTDP---AKG 124
           ++ IE TSGNTG+GLA  A  KGYK I T     S E+   L AFG E+++       + 
Sbjct: 65  TI-IEGTSGNTGMGLAMAAIIKGYKCIFTTTDKQSKEKVDALRAFGAEVIVCPTNVEPED 123

Query: 125 MKGAIAKAEEILAKTPNGYMLQQFENPANPKIHYETTGPEIWKGTGGKIDGFVSGIGTGG 184
            +   + +  +  + PN +   Q++N AN + HYE TGPEIW  T GKI   V G+GTGG
Sbjct: 124 PRSYYSVSSRLEREVPNSWKPNQYDNLANSQAHYEQTGPEIWAQTEGKITHLVVGVGTGG 183

Query: 185 TITGAGKYLKEQNANVKLYGVEPV--------ESAILSGGKPGPHKIQGIGAGFIPSVLN 236
           TI+G GKYLKE+N N+K++G++          E+ I    +  P+  +GIG  F+P+ +N
Sbjct: 184 TISGTGKYLKEKNPNIKVWGIDTYGSVFKKYKETGIFDKDEIYPYITEGIGEDFLPANVN 243

Query: 237 VDLIDEVVQVSSDESIDMARQLALKEGLLVGISSGAAAAAAIKLAQ--RPENAGKLFVAI 294
            D+ID   +V+  ++  M R +A KEG+ VG S+GAA    I+L    +PE+   + V I
Sbjct: 244 FDVIDLFEKVTDKDAALMTRDIARKEGIFVGNSAGAAIGGLIQLKDKLKPED---VVVVI 300

Query: 295 FPSFGERYL 303
           F   G RY+
Sbjct: 301 FHDHGSRYM 309


Lambda     K      H
   0.315    0.134    0.374 

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: 391
Number of extensions: 21
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: 322
Length of database: 453
Length adjustment: 30
Effective length of query: 292
Effective length of database: 423
Effective search space:   123516
Effective search space used:   123516
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: 50 (23.9 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