GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Desulfovibrio vulgaris Hildenborough

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 207852 DVU2364 aminotransferase, classes I and II

Query= BRENDA::A0A060PQX5
         (417 letters)



>lcl|MicrobesOnline__882:207852 DVU2364 aminotransferase, classes I
           and II
          Length = 388

 Score =  305 bits (781), Expect = 2e-87
 Identities = 162/398 (40%), Positives = 245/398 (61%), Gaps = 16/398 (4%)

Query: 23  SKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQY 82
           +K+   ++ S +RE+LK+    D+IS AGGLP P++FPV+ +AE    VL +  ++ALQY
Sbjct: 4   AKRMDNVQRSYIREILKVTARPDIISFAGGLPHPDSFPVQGVAEAAAAVLAESGSEALQY 63

Query: 83  GTTKGFTPLRLALAEWMRKRY---DIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVE 139
            TT+G+ PLR    EW+  RY    I +S  +I+IT+GSQQALDL+ +  I+ G  VV+E
Sbjct: 64  STTEGYLPLR----EWISARYARQGIEVSPDEILITTGSQQALDLVAKTTIDRGAPVVIE 119

Query: 140 APTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPA 199
            P YL A+Q F +Y  +F  + L   G+ V+ L        +E K  +L Y +P+FQNP+
Sbjct: 120 RPGYLGAIQCFSFYGAQFRTVDLTPLGVDVEALR-------REAKGARLFYAVPSFQNPS 172

Query: 200 GVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKI 259
           G+T  E  R+ +  + +E   ++VEDNPYGELR+ G PV PI+ W +   V+ LG+FSK+
Sbjct: 173 GITYDEPTRREVAAIMAETGCMLVEDNPYGELRFMGTPVAPIRKWAESPSVL-LGSFSKV 231

Query: 260 LAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYK 319
           ++PG RIGW  A   L+R +  AKQ+ DL T  F+Q +  +++    +D HI +I + Y 
Sbjct: 232 VSPGLRIGWACAPAELMRHMVTAKQASDLHTPMFTQRLLHRFLVDNDVDEHIASIRKRYG 291

Query: 320 PRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFF 379
            +R  M+ A+ +  PE V  T+PEGGMF+W  LPEG+ ++ +  KA+ + VA+VPG  F+
Sbjct: 292 AQRQCMMDAIRKHFPECVTVTEPEGGMFLWCGLPEGVTSEHLFHKAIERKVAFVPGCPFY 351

Query: 380 AHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417
                    RLNF+   ++ I EGI RL   + EE+ +
Sbjct: 352 VD-GTDTGFRLNFSNASQDDIVEGIARLGACLTEELAR 388


Lambda     K      H
   0.318    0.137    0.398 

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: 453
Number of extensions: 19
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: 417
Length of database: 388
Length adjustment: 31
Effective length of query: 386
Effective length of database: 357
Effective search space:   137802
Effective search space used:   137802
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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, or see changes to Amino acid biosynthesis since the publication.

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