GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Ruegeria conchae TW15

Align acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_010441737.1 G7G_RS0112345 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Marino:GFF3099
         (404 letters)



>NCBI__GCF_000192475.1:WP_010441737.1
          Length = 424

 Score =  165 bits (417), Expect = 3e-45
 Identities = 128/417 (30%), Positives = 206/417 (49%), Gaps = 47/417 (11%)

Query: 18  NYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSN 77
           N+ PG +I  RGEGSR+WD++G E++D   G     LGH HP ++GA+ +Q  K   ++ 
Sbjct: 25  NFDPGIVI-ARGEGSRVWDEDGNEYVDYLIGSGPMLLGHGHPEIIGAVLEQLPK--GMTF 81

Query: 78  VMTNEPALRLAKTLCD-LTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFK 136
              N   + LA+ + + +   E+V F  SG EA+  A +LAR Y     G++K  ++ F+
Sbjct: 82  FANNAKGIELAEAIVEAVPCCEQVRFVASGGEADMYAIRLARAYT----GRDK--VLKFE 135

Query: 137 NSFHGRTL-FTVSVGGQ-----PKYLEGFEPAPGGIHH----AEFNDLESVKKLISKEK- 185
             +HG +    +S+  +     P+ +      P G+      A FNDL +V+ L+ + K 
Sbjct: 136 GGYHGMSAEAQMSLAPEVRINFPQAIPDSAGIPQGVADQMLIAPFNDLTAVEALLDENKD 195

Query: 186 TCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGV 245
             AI+VEP+Q    ++P    +LQGLRDLCD+   LL+FDE+ +G  R  +  A + YGV
Sbjct: 196 VAAIIVEPLQ---RIIPALPGYLQGLRDLCDKYSVLLIFDEIVTGF-RLAYGGAQERYGV 251

Query: 246 VPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGS--------TYGGNALACAVAQRV 297
            PDI +  K +GGGFP+AA+    ++       T G+        T  GN +A A   + 
Sbjct: 252 TPDICTLGKIIGGGFPLAAIGANTEIMQHFDKSTVGANKWLMQLGTLSGNPIAAAAGLKT 311

Query: 298 VDTVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLT----------E 347
           +D + +    + ++A   KL+    +   +  +  ++ G   L     T          +
Sbjct: 312 MDILRREGSYERLRAIGKKLQDMQSEELSKADIPHQICGDETLFDIFFTASVCRDYRTAK 371

Query: 348 KWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404
               K  +  NA L    +   AG    +L PSL I E D+EL     +AAV+ + A
Sbjct: 372 HDDPKRNEAYNATLRHHGIFKSAG----KLYPSLAISEMDLELTKNAVQAAVRSIHA 424


Lambda     K      H
   0.318    0.137    0.406 

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: 467
Number of extensions: 32
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: 404
Length of database: 424
Length adjustment: 31
Effective length of query: 373
Effective length of database: 393
Effective search space:   146589
Effective search space used:   146589
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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