GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Synechococcus elongatus PCC 7942

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__SynE:Synpcc7942_0943
          Length = 422

 Score =  226 bits (576), Expect = 1e-63
 Identities = 144/425 (33%), Positives = 220/425 (51%), Gaps = 40/425 (9%)

Query: 27  AMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKF 86
           A   Q     P+ +ERGEG RV+D  G  + DF +G+    +GH+HP +V+AI  Q  K 
Sbjct: 25  ACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKL 84

Query: 87  THYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV-KYGTGRKQ-- 143
            H S   +  E   + A     L       +V + NSGAEANEAA+KL  K+G    +  
Sbjct: 85  HHVSNLYYIPEQGQLAAW----LTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAE 140

Query: 144 ---FLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEP 200
               L    +FHGRT A ++ T      + GF P + G  ++PY +              
Sbjct: 141 NPIILTAQASFHGRTLAAVTATGQPKYHK-GFQPLVQGFRYVPYNDLAAL---------- 189

Query: 201 DELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILL 260
            E T   LD   E V          AI  EP+QGEGG     + +F+A+++  D+  +LL
Sbjct: 190 -EATLAELDAAGETV---------AAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLL 239

Query: 261 ADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATT 320
             DEVQ+G+GR+G+ W  E+ G+EPD     K +GGG+P+  ++ +A     + G HA+T
Sbjct: 240 ILDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGGGVPIGALLVKASCNILQAGEHAST 299

Query: 321 FGGNPVAIAAGIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQA 377
           FGGNP+A  AG+ + ++++  +LL +VQ  G+ L   L+E  ++Y  ++   RG GL   
Sbjct: 300 FGGNPLACRAGLAIAQVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLING 359

Query: 378 VEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFE 437
           + +                +VK + ++GL+L+  G   +RF+PPLIV+  EID A+ + E
Sbjct: 360 LVLRNDPNVTP------IALVKAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTE 413

Query: 438 EALKA 442
            AL A
Sbjct: 414 RALLA 418


Lambda     K      H
   0.320    0.141    0.418 

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: 448
Number of extensions: 21
Number of successful extensions: 5
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: 445
Length of database: 422
Length adjustment: 32
Effective length of query: 413
Effective length of database: 390
Effective search space:   161070
Effective search space used:   161070
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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