GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Pseudomonas simiae WCS417

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase

Query= SwissProt::P9WGB7
         (388 letters)



>FitnessBrowser__WCS417:GFF2301
          Length = 411

 Score =  305 bits (780), Expect = 2e-87
 Identities = 175/387 (45%), Positives = 231/387 (59%), Gaps = 12/387 (3%)

Query: 13  GPATRAIHAGYRPDPATGAVNVPIYASSTFAQDGV-------GGLRGGFEYARTGNPTRA 65
           G +TRAIH GY P    GA+  PIY S+TFA            G   G  Y R  NPT A
Sbjct: 9   GFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNPTLA 68

Query: 66  ALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRW 125
            LE+ +A +E G  A AFSSGM A       +LRPGD V++    YG TF L+      +
Sbjct: 69  LLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGIGEF 128

Query: 126 DVQYTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDR-SAKVLVDN 184
            ++   V L DL A+ AA+TP TR+I+ ETP NP L + DI A+A L   + +  ++VDN
Sbjct: 129 GIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLVVDN 188

Query: 185 TFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDE-EFAFLQNGAGAVP 243
           T+ +P LQ+PL LGADVV+HS TKY+ GH D+  G  V+N           L++  GAV 
Sbjct: 189 TYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAVSNQALAQRIRLQGLKDLTGAVM 248

Query: 244 GPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQM 303
            P DA L MRGLKTL LRM RH  NA AVAE L  HP+V SV YPGL S P +E+A +QM
Sbjct: 249 SPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYELATQQM 308

Query: 304 RGFGGMVSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLE-- 361
           +  GGM++  ++ G    +      ++F  A SLG  ESL +HP++MTH++    +    
Sbjct: 309 KMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQERAAH 368

Query: 362 -VPDDLVRLSVGIEDIADLLGDLEQAL 387
            + + LVRLSVG+ED+ADLL D++QAL
Sbjct: 369 GISEGLVRLSVGLEDVADLLADVQQAL 395


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: 454
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: 411
Length adjustment: 31
Effective length of query: 357
Effective length of database: 380
Effective search space:   135660
Effective search space used:   135660
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