GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Acidovorax sp. GW101-3H11

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          Length = 398

 Score =  267 bits (683), Expect = 3e-76
 Identities = 158/398 (39%), Positives = 226/398 (56%), Gaps = 16/398 (4%)

Query: 11  ALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAV 70
           A +EA        Y +  + + RGQG RVWD  G EYID +GG  V  LGH + ++V A+
Sbjct: 3   AFIEAASPHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPAL 62

Query: 71  KRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAH--- 127
           + Q   L+        P++ +    L  +    +  VF  NSG EANEAALK AR     
Sbjct: 63  QDQIAKLIHTSNYYHVPLQEKLATKLVEL--SGMQNVFFCNSGLEANEAALKIARKFGVD 120

Query: 128 --TGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD-- 183
               + + V   + F GR++ ++S T  PK    F PLVE    +P ND+EA+K+A +  
Sbjct: 121 KGIAKPEIVVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQATEGN 180

Query: 184 EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF 243
               AV  E +QGEGG+     E+L+  R++  E+G L+++DE+Q GMGRTGK FA +  
Sbjct: 181 PNVVAVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWA 240

Query: 244 GIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLER 303
           GIVPD++ LAK LG GVP+GA V   + A  +  G HGTTFGGNPLAM AGV  IR +E 
Sbjct: 241 GIVPDVMPLAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEE 300

Query: 304 TRLWERAAELGPWFMEKL-RAIPS-PKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVL 361
             L   AA++G      L R + S P ++E+RG GLM+G+EL +     I R  +   +L
Sbjct: 301 DGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIELNKPCGALIGRAAEAGLLL 360

Query: 362 ALQAGPTVIRFLPPLVIEKEDLERVV----EAVRAVLA 395
           ++ A  +VIR +PPL++   + + +V      V+A+LA
Sbjct: 361 SVTA-DSVIRLVPPLILTTAEADAIVAILTPLVKAILA 397


Lambda     K      H
   0.319    0.137    0.402 

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: 418
Number of extensions: 22
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: 395
Length of database: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
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 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