GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Paraburkholderia bryophila 376MFSha3.1

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate H281DRAFT_00859 H281DRAFT_00859 cystathionine beta-lyase

Query= SwissProt::P9WGB7
         (388 letters)



>FitnessBrowser__Burk376:H281DRAFT_00859
          Length = 394

 Score =  165 bits (418), Expect = 2e-45
 Identities = 117/384 (30%), Positives = 181/384 (47%), Gaps = 17/384 (4%)

Query: 16  TRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAALE 68
           TR +HA  +  P   + ++P+  +ST     +  +R         + Y     PT  AL 
Sbjct: 12  TRIVHAEDKLTPGFESFSMPVTRASTVVFPDLATMRALDWKNDAQWRYGLHATPTSLALA 71

Query: 69  ASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQ 128
             LA +E G  A    SG+++       +++ GD V+IPD+ Y       D +   + V 
Sbjct: 72  QRLATIEGGNHALLQPSGLSSISNVYFGLVKAGDDVLIPDNVYSPNRDHGDWLARDFGVT 131

Query: 129 ---YTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNT 185
              Y P+  A    +   I P TRLIW+E P +  + +AD+ AI      R+    +DNT
Sbjct: 132 VRYYDPMIGA---GIAELIQPNTRLIWLEAPGSVTMEVADVPAITAAARARNVVTAIDNT 188

Query: 186 FASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAGAVPGP 245
           +++    +P   G D+ + + TKY  G  DV+ GA +T D EL  +    +   G     
Sbjct: 189 WSAGLGFRPFDHGVDISVQALTKYQSGGGDVLMGATITVDRELHLKLKAARMRMGIGVSS 248

Query: 246 FDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMRG 305
            D  L +R L T+ +R Q+H  +A A+A++L   P +++VL+P +   PGHE   R   G
Sbjct: 249 DDCSLILRSLPTMQVRFQQHDRSALALAQWLKTRPEIAAVLHPAIEDCPGHEFFKRDFTG 308

Query: 306 FGGMVSVRMRAGRRAAQ--DLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVP 363
            GG+ SV       AAQ    C    +F +  S GG  SL+  P  +    T G +    
Sbjct: 309 AGGLFSVVFDGRYSAAQIDTFCESLELFAIGWSWGGAHSLV-MPYDIASMRTEG-EWPHR 366

Query: 364 DDLVRLSVGIEDIADLLGDLEQAL 387
             LVR  +G+E+ ADL  D+EQ L
Sbjct: 367 GTLVRFYIGLEEEADLRADIEQCL 390


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: 383
Number of extensions: 24
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: 388
Length of database: 394
Length adjustment: 31
Effective length of query: 357
Effective length of database: 363
Effective search space:   129591
Effective search space used:   129591
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