GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:207852
          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 (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