GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Dinoroseobacter shibae DFL-12

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 3610038 Dshi_3419 Amidase (RefSeq)

Query= curated2:A7NKM0
         (490 letters)



>FitnessBrowser__Dino:3610038
          Length = 441

 Score =  191 bits (485), Expect = 4e-53
 Identities = 160/465 (34%), Positives = 216/465 (46%), Gaps = 46/465 (9%)

Query: 4   LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63
           L  L++ Q    L  GE+++L L DA L RIAA +P V+A+  +D   ARAQA A DA +
Sbjct: 7   LPDLSLQQMSAALRTGEVTALALLDAHLDRIAARDPSVKAWAWLDPDQARAQAIALDAAQ 66

Query: 64  AAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKL 122
           A G A  PL GIP+G+KDVI T  + T   +       P  DA   ARL+A GAVI+GK 
Sbjct: 67  AEGKALGPLHGIPVGLKDVIDTADMPTENGTPPDAGRQPDQDAWITARLRAVGAVIVGKT 126

Query: 123 NCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQP 182
              E A  + TE      T NP N    PGGSS GSAA+VAAG  P A+GT TGGS+ +P
Sbjct: 127 TTTELAFLNPTE------TLNPHNPNHTPGGSSAGSAASVAAGMVPLAVGTQTGGSVIRP 180

Query: 183 AALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTD 242
           AA CG+ G+KPT+G + R G+   + +LD +G   R   D A  L  +   D  D+    
Sbjct: 181 AAFCGVVGVKPTFGAIPRQGVTMQSHTLDTLGVFTRDAEDAAFALTCM--MDTEDSDPAT 238

Query: 243 YPAPDYEAALTGDIRGLRIGVPREYFVAGMQPD-VEAAVRTAIEVLREQGAEVCEISLPH 301
            P  D   A+ G  R    G     FV   + D   A  + A+E L  Q      +SLP 
Sbjct: 239 LPPQDAHPAIAGATRPPVFG-----FVRPPEWDRASAETKAALEKL-AQALGAIPLSLPE 292

Query: 302 TPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLG 361
           +      +  +A   A  N A         R  G   +D L            R  +  G
Sbjct: 293 S------FEQVADLRARINFAEMAWHYSRYRTAG---WDALSAA--------TRDAMEAG 335

Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLAMY 421
               +  Y  A  +R     +L        F QVD +  P+    A +  + T D +   
Sbjct: 336 AACAAVDYLAALMQREPLYASL-----DPLFSQVDCLLCPSALGAAPEGLSSTGDAIFNG 390

Query: 422 LEDVCTLPLNLAGLPGLVVPCGFAE-GLPIGLQLIGRAFDEESLL 465
           L           G P + +P    E GLPIG+QL+GR  ++ +LL
Sbjct: 391 L-------WTFMGTPCVTLPLPETEKGLPIGVQLVGRRGEDRALL 428


Lambda     K      H
   0.320    0.136    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: 489
Number of extensions: 30
Number of successful extensions: 4
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: 490
Length of database: 441
Length adjustment: 33
Effective length of query: 457
Effective length of database: 408
Effective search space:   186456
Effective search space used:   186456
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