GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Desulfovibrio vulgaris Miyazaki F

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__Miya:8499593
          Length = 389

 Score =  278 bits (710), Expect = 3e-79
 Identities = 142/391 (36%), Positives = 233/391 (59%), Gaps = 6/391 (1%)

Query: 1   MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60
           M++  +  ++  LP Y+FA ++++K ++   G DI+ LG+G+PD+P    II+ + +   
Sbjct: 1   MADFKLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVE 60

Query: 61  RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120
           RP  H Y +  G+   R+ + ++Y RR+GV LDP+   I  IG+KEG +H  LA + PGD
Sbjct: 61  RPANHQYPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGD 120

Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180
            V+V  P YP+++ A    GG+   +P++ E D    +L  L  +   ++ + K + +++
Sbjct: 121 LVLVCTPNYPVYHIATGFVGGEVQFIPLVEEND----YLPDLDAIPAATWDRAKMIFVNY 176

Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFD-GYTPPSILQVEGALDVAVE 239
           P+NPT       F+++++ + ++  + I HD AY ++ +D    P SIL+VEGA DV +E
Sbjct: 177 PNNPTAATAPRAFYEKLIGICRKHNVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIE 236

Query: 240 LYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEK 299
            +S+SK ++M GWRV   VGN  L+  L  +K  +D G+F  +Q ASI+AL    +   +
Sbjct: 237 FHSLSKTYNMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRE 296

Query: 300 NREIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVS 359
            R IYR+RRDV+V  LN+VG   + P  + ++WAKVP   G +S +F   +L +  V ++
Sbjct: 297 LRGIYRKRRDVVVAALNKVGIACRVPTAAFYIWAKVPAGYG-SSAEFVTAVLEKTGVVLT 355

Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGI 390
           PG GFG  GEGY R +L  +  R+ +AV  I
Sbjct: 356 PGNGFGTPGEGYFRISLTVDTDRLEEAVSRI 386


Lambda     K      H
   0.322    0.141    0.425 

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: 421
Number of extensions: 17
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: 402
Length of database: 389
Length adjustment: 31
Effective length of query: 371
Effective length of database: 358
Effective search space:   132818
Effective search space used:   132818
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 (21.9 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