GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Dechlorosoma suillum PS

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= CharProtDB::CH_002469
         (406 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  293 bits (750), Expect = 6e-84
 Identities = 165/362 (45%), Positives = 220/362 (60%), Gaps = 9/362 (2%)

Query: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87
           G GS L DQQGK Y+DF  G AVN LGH HP + EAL  QA K  +    + NEP L+LA
Sbjct: 28  GRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEPSLKLA 87

Query: 88  KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG---IVAFKNAFHGRTLF 144
             L   +  DRVFF ++GAEANE A+KLARK+       HK G   I+ F   FHGRTL 
Sbjct: 88  AGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQ----KHKGGAHEIITFAGGFHGRTLA 143

Query: 145 TVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNA 204
           T+SA G+P +   FAP       A  ND++S +ALI++ T A+++EPIQGEGGVVPAS  
Sbjct: 144 TMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVPASAE 203

Query: 205 FLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALL 264
           FLQ LR++C+    LLI DEVQTG+GRTG+L+A+ H G+ PD++T  K +GGG P+ ALL
Sbjct: 204 FLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGVPLSALL 263

Query: 265 ATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINH 324
           A E        G  G TY GNPL +AV   VLE++  P  L  V  + ++    L  ++ 
Sbjct: 264 AKESVC-CFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGLQRLSD 322

Query: 325 RYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEE 384
           R GL  E RG GLL   +L  +      + ++E    G+++     +++RF P+L VS E
Sbjct: 323 RLGLRGE-RGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLTVSRE 381

Query: 385 EV 386
           E+
Sbjct: 382 EI 383


Lambda     K      H
   0.319    0.136    0.407 

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: 469
Number of extensions: 23
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: 406
Length of database: 396
Length adjustment: 31
Effective length of query: 375
Effective length of database: 365
Effective search space:   136875
Effective search space used:   136875
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: 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