GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Sinorhizobium meliloti 1021

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate SMa2400 SMa2400 diaminobutyrate--2-oxoglutarate aminotransferase

Query= curated2:A0QYS9
         (390 letters)



>FitnessBrowser__Smeli:SMa2400
          Length = 470

 Score =  215 bits (547), Expect = 2e-60
 Identities = 148/418 (35%), Positives = 213/418 (50%), Gaps = 56/418 (13%)

Query: 19  PLSLVSGEGAVVTDADGREYLDLLGGIAVNLLGHRHPAVIEAVTTQLDTLGHTSNLYATE 78
           P++L S  G +VTD DGR YLD L G     LGH HP VIE   T    LG    L+  +
Sbjct: 50  PVALKSASGCIVTDVDGRSYLDCLAGAGTLALGHNHPEVIE---TLQQVLGSGLPLHTLD 106

Query: 79  PGIALAEALVGQL-GT-------QARVFFCN-SGTEANEVAFKITRL-TGKTKIVAAEGA 128
               + +  V  + GT       +A++ FC+ SGT+A E A K+ +  TG+T +V+  GA
Sbjct: 107 LTTPVKDRFVSDIFGTLPAGLRDEAKIQFCSPSGTDAVEAAIKLAKTATGRTDLVSFRGA 166

Query: 129 FHGRTMGSLALTGQPSKQAPFEPLPGNVMHVPY------------GDVAAL-----EAAV 171
           +HG + GSL+L G    +A    L       PY             + A L     E A+
Sbjct: 167 YHGMSQGSLSLMGSLGPKASVGQLVPGAHFFPYPYAYRCPFGRGGNETATLAAEYFERAL 226

Query: 172 DD------QTAAVFLEPIMGEGGVVVPPAGYLVAAREITSKHGALLVLDEVQTGVGRTGA 225
            D      + AAV LE + GEGGV+  P  +L A R +T   G  L++DEVQ+GVGRTG+
Sbjct: 227 RDPEGGINRPAAVILEAVQGEGGVIPAPVEWLRAVRRVTRDLGIPLIVDEVQSGVGRTGS 286

Query: 226 FFAHQHDGIVPDVVTMAKGLGGGLPIGACLAVGATGDLLTPGLHGSTFGGNPVCTAAGLA 285
           F+A Q  GI+PDVV ++K +GGGLP+ A +      DL  PG H  TF GN +  AAG  
Sbjct: 287 FYAFQKAGIIPDVVVLSKAIGGGLPL-AVVIYREDLDLWKPGAHAGTFRGNQLAMAAGSK 345

Query: 286 VLKTLAAEDLVARAGVLGKTLSHGIEELG--HPLVDKVRGKGLLQGIVLTVPS------- 336
            L+ +  E LV RA + G+ L   +E +    P + +VRG+GL+ G+ +  P        
Sbjct: 346 TLEIIERERLVERAAIAGRRLRANLERIAAQTPYIGEVRGEGLMLGVEVVDPEGLPDALG 405

Query: 337 --------AKAVETAARDAGFLVNAAA--PEVVRLAPPLIITEGQIEAFITALPAVLD 384
                   A+ ++     AG ++        V+RL PPL+I++ +I+    AL A  +
Sbjct: 406 HPPHGQEIARMIQHEMFRAGIILETGGRFGSVLRLLPPLVISDAEIDQVSGALAAAFE 463


Lambda     K      H
   0.317    0.136    0.391 

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: 522
Number of extensions: 31
Number of successful extensions: 6
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: 390
Length of database: 470
Length adjustment: 32
Effective length of query: 358
Effective length of database: 438
Effective search space:   156804
Effective search space used:   156804
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 (21.6 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