GapMind for Amino acid biosynthesis

 

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

Align Acetylornithine aminotransferase (characterized, see rationale)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)

Query= uniprot:Q8A1A8
         (373 letters)



>FitnessBrowser__Dino:3609962
          Length = 413

 Score =  163 bits (413), Expect = 7e-45
 Identities = 125/398 (31%), Positives = 197/398 (49%), Gaps = 53/398 (13%)

Query: 5   DVYPLYD--INIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGF 62
           +V   YD  ++IV+G+G  +WD  G  YLD Y    V  +GH HP  V+ I+ Q   L  
Sbjct: 15  NVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNN--VPHVGHCHPRVVDAIARQARVL-- 70

Query: 63  YSNSVINKLQQQVAERLGKISGYEDYSL---FLINSGAEANENALKLASFYNGRTKVISF 119
             N+    L + V + + +++G  D  L    L+ +G+EA + AL++A    G+T +I+ 
Sbjct: 71  --NTHTRYLHEGVLDYIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIAT 128

Query: 120 SKAFHGRTSLAVE-ATNNPTIIAPINN-NGHVTYLPLNDI-------------EAMKQEL 164
              +HG T+   + +T  P    PI   + HV  +P  +               A + E 
Sbjct: 129 DNTYHGNTTAVAQLSTRRP----PIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELET 184

Query: 165 AKGDVCAVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGK-FFAH 223
           A   V A+I+  I    G+      F++         G +LI DE+Q G+GR G  F+ +
Sbjct: 185 AGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGY 244

Query: 224 QYNHIQPDIITVAKGIGNGFPMAGVL----ISPMFKPVYGQLGTTFGGNHLACSAALAVM 279
           Q   I PD++T+ K +GNG+P+AGV+    I   F+  +G   T FGG+ +A +AA+AV+
Sbjct: 245 QALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNT-FGGSPVAAAAAMAVL 303

Query: 280 DVIEQDNLVENAKAVGDYLLEELK--KFPQIKEVRGRGLMIGLEFEEP------------ 325
           DV+E + LVENAK VG Y LE L+  + P I  VRG GL   L+  +             
Sbjct: 304 DVLEDEGLVENAKRVGRYTLERLQALRHPAIDGVRGYGLAFALDLVDTDGAPNTALAAAV 363

Query: 326 IKELRSRLIYDEHVFTGASGTNVLRLLPPLCLSMEEAD 363
            +E + R +    +       ++L++ PPL  + E  D
Sbjct: 364 TEEAKRRSVLINRI---GRDMHILKIRPPLPFAPEHGD 398


Lambda     K      H
   0.320    0.139    0.403 

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: 335
Number of extensions: 20
Number of successful extensions: 7
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: 373
Length of database: 413
Length adjustment: 31
Effective length of query: 342
Effective length of database: 382
Effective search space:   130644
Effective search space used:   130644
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