GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Acidovorax sp. GW101-3H11

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate Ac3H11_4146 Cystathionine beta-lyase (EC 4.4.1.8)

Query= SwissProt::P9WGB7
         (388 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4146
          Length = 412

 Score =  168 bits (426), Expect = 2e-46
 Identities = 126/398 (31%), Positives = 182/398 (45%), Gaps = 29/398 (7%)

Query: 15  ATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAAL 67
           ATR +H GY P     A    +Y +ST     V  +R        G+ Y   G PT   L
Sbjct: 12  ATRIVHHGYLPPAGFEAPQPGVYKASTVIFPNVAAMRSREWKDKSGYTYGLHGTPTTFIL 71

Query: 68  EASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDV 127
           E  L  +E G       SG+AA      A+L+PGD V+IPD+AYG      +    R+ +
Sbjct: 72  EERLCTLEGGLQCVLVPSGLAAIANVGLALLKPGDEVLIPDNAYGPGKDFANGELARFGI 131

Query: 128 Q---YTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDN 184
               Y P+  ADL    A ITP TRL+W+E P +  +   D+     +   R     +DN
Sbjct: 132 THVFYDPLDPADL---AARITPATRLVWLEAPGSVSMEFPDLCEQVRICRARGVTTALDN 188

Query: 185 TFASPALQQPL------RLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNG 238
           T+ +     P        LG D+  H+ TKY  G  DV+ G+++T D  L  +       
Sbjct: 189 TWGAGLAFAPFDLTGDGSLGVDISAHALTKYPSGGGDVLMGSVITRDLGLHMKIKLTHMR 248

Query: 239 AGAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGH-- 296
            G   G  D    +R L ++ LR + H E A  +A +L   P+++ VL+P L   PGH  
Sbjct: 249 LGLGVGVNDVEAVLRALPSIGLRYRAHDEAARVLARWLQQQPAIAQVLHPALEGAPGHAH 308

Query: 297 --EIAARQMRGFG---GMVSVRM--RAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSA 349
              +      G G   G+ SV +  R  ++     C   R+F L  S GG  SL+   + 
Sbjct: 309 WKALCGAAQGGQGAAAGLFSVMIDARYTQQQVDAFCDGLRLFKLGYSWGGPMSLVVPYTI 368

Query: 350 MTHASTAGSQLEVPDDLVRLSVGIEDIADLLGDLEQAL 387
            +  S    QL+ P  LVR S+G+E + DL  DL+QA+
Sbjct: 369 GSMRSRPSPQLQ-PGTLVRFSIGLEAVEDLQRDLQQAM 405


Lambda     K      H
   0.319    0.135    0.393 

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: 444
Number of extensions: 20
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: 388
Length of database: 412
Length adjustment: 31
Effective length of query: 357
Effective length of database: 381
Effective search space:   136017
Effective search space used:   136017
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 (21.7 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