GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Dinoroseobacter shibae DFL-12

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__Dino:3608039
          Length = 444

 Score =  192 bits (489), Expect = 1e-53
 Identities = 139/409 (33%), Positives = 202/409 (49%), Gaps = 49/409 (11%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANR--FWHIGNGYTNEPA 83
           V G G  + D  GK Y+D +GG AV+ LGH HPA+R AL+ Q ++  F H G  +T+EPA
Sbjct: 17  VAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGF-FTSEPA 75

Query: 84  LRLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGR 141
             L   LI A     E+V+  + G+E+ EAALKLAR++  +     +  ++A + ++HG 
Sbjct: 76  EVLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGN 135

Query: 142 TLFTVSAGGQPTYSQDFAPLPPDI---------RHAAYNDLNSA-------------SAL 179
           TL  ++AGG     + +APL  +          RH A  + ++A               L
Sbjct: 136 TLGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERL 195

Query: 180 IDDNTCAVIVEPVQGE-GGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAY 238
             +   A I EPV G   G +P    + + +RE+CD +  LLI DEV  G+GRTG L+A 
Sbjct: 196 GPETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFAC 255

Query: 239 MHYGVTPDILTTAKALGGGF-PIGAMLTTQDYASVMTPGT----HGTTYGGNPLATAVAG 293
              G++PDI+T AK LG G+ PIGAML +      +  G+    HG TY G+PLA A AG
Sbjct: 256 EQDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAG 315

Query: 294 KVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVL--------QT 345
            V++ +  P     VR +      RL     +     +IRG GL  G  L          
Sbjct: 316 AVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPL 375

Query: 346 EFAGKAKLIAQEAAKAGVMVLIAG--------GDVVRFAPALNVSDEEI 386
           + A K     + AA A  ++   G        GD +  AP   + D++I
Sbjct: 376 DPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQI 424


Lambda     K      H
   0.320    0.137    0.413 

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: 484
Number of extensions: 18
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: 408
Length of database: 444
Length adjustment: 32
Effective length of query: 376
Effective length of database: 412
Effective search space:   154912
Effective search space used:   154912
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