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 408289 DVU0030 transcriptional regulator, GntR family

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>MicrobesOnline__882:408289
          Length = 500

 Score =  156 bits (395), Expect = 1e-42
 Identities = 109/378 (28%), Positives = 179/378 (47%), Gaps = 13/378 (3%)

Query: 21  IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80
           I  +L+ +   E++ F    PD    P  A+ R   +  +S      A  Y   +G   L
Sbjct: 106 ISTVLEAVGNHELVPFGVLCPDTSLLPLKALVRIMGETMRSAPQV--ATGYETVQGNAEL 163

Query: 81  REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140
           R  I   +G  G+    + +++T+G+ +AL    + L  PG+ +++  PTY   LQ    
Sbjct: 164 RRRIAWRMGECGMDVSAEGLVITTGAVEALYIALRALTRPGDIVVIQSPTYYCFLQLLET 223

Query: 141 YEPQYLSVPGDAE-GPDLAAVEAALEQ-KPKFFYLVPDFQNPNGTTISLARREALLDLCA 198
              + +  P   E G D  AV   +++ +       P+F NP+G+      +  +LD+ A
Sbjct: 224 LGLRAIEAPSSPEKGIDPEAVRHIVDRHRVACCIFSPNFNNPDGSLTPDDAKREILDILA 283

Query: 199 KHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWIN 258
             G+ ++ED    +L Y   P+         R+G     V  C SFSKT+ P  RVGW+ 
Sbjct: 284 PRGIHVIEDDVAADLHYG--PVRPSTFSQYDRHG----LVTLCSSFSKTVAPGFRVGWM- 336

Query: 259 GPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNF-DSHIRRLRAGYKERRDAMLTALS 317
            P  + ++ + +K   ++   T  Q+ L   + Q     H+RRLR     + +AM   ++
Sbjct: 337 APGRIFDKAMEVKATTNVCCPTPTQMALARYLEQGLLQRHLRRLRTALVRQMEAMRQTIA 396

Query: 318 EFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLR 377
              P G + T+P GG  +W+ LPEGTDG +L  RA +DA +A  PGS F    S  N +R
Sbjct: 397 CSFPEGTSATRPLGGGVLWVRLPEGTDGTELFYRA-RDAGIAIAPGSIFSTQDSYTNYVR 455

Query: 378 LSFSNNNPERIREGIRRL 395
           L  +    +R+ +G+R L
Sbjct: 456 LGCNGVWDDRMAQGLRTL 473


Lambda     K      H
   0.320    0.138    0.410 

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: 542
Number of extensions: 28
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: 404
Length of database: 500
Length adjustment: 33
Effective length of query: 371
Effective length of database: 467
Effective search space:   173257
Effective search space used:   173257
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 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