GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Klebsiella michiganensis M5al

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein

Query= BRENDA::Q88RB9
         (425 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14020 BWI76_RS14020 aspartate
           aminotransferase family protein
          Length = 461

 Score =  237 bits (604), Expect = 6e-67
 Identities = 152/404 (37%), Positives = 222/404 (54%), Gaps = 19/404 (4%)

Query: 25  PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84
           P+ +  A+   + D + ++ +D   G   L  GH HP V+ ++Q  +T         L  
Sbjct: 42  PLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTT 101

Query: 85  EPYVELCEKINKLVPGDFDKKTLLVT--TGSEAVENAVKIARAATGRAGVIAFTGGYHGR 142
                  E +  L+PG+  +  L  T  +G++AVE A+K+A+  TGR+ VI+F+GGYHG 
Sbjct: 102 PLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFSGGYHGM 161

Query: 143 TMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELH---GISVDDAIASVERIFKN----- 194
           T   L +TG + P +A  G+MP   F   +P +     GI  +  + ++   F+N     
Sbjct: 162 THGALSVTGNLSPKAAVNGMMPEVQFMP-YPHQYRCPLGIGGEAGVKALTYYFENLINDV 220

Query: 195 DAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFA 254
           ++  R  AA+ILE VQGEGG  PAP E ++R+R +  +HGILLI DEVQ G  RTG FFA
Sbjct: 221 ESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFARTGKFFA 280

Query: 255 MEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIE 314
            E  G+ PD+   +K++ GG PLA V G  +  DA  PG   GT+ G+ +A A  L  + 
Sbjct: 281 FEHAGIEPDIIVMSKAVGGGLPLA-VLGIKKQFDAWEPGHHTGTFRGNQLAMATGLTTLR 339

Query: 315 VFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVF---EKGTHTPNAA 371
             ++ K+ D++ A GE L   L E+QK+YP+IG VRGLG MI +E+    E   H     
Sbjct: 340 HLKDNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGLMIGIEIVKPNEAPDHMGCYP 399

Query: 372 AVGQVVA----KAREKGLILLSCGTYGNVLRILVPLTAEDALLD 411
           A G++ A    K  E GLIL   G +G VLR+L  L   +A L+
Sbjct: 400 ADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELE 443


Lambda     K      H
   0.320    0.138    0.395 

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: 545
Number of extensions: 23
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: 425
Length of database: 461
Length adjustment: 32
Effective length of query: 393
Effective length of database: 429
Effective search space:   168597
Effective search space used:   168597
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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