GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Synechococcus elongatus PCC 7942

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__SynE:Synpcc7942_0943
          Length = 422

 Score =  226 bits (576), Expect = 1e-63
 Identities = 137/380 (36%), Positives = 209/380 (55%), Gaps = 13/380 (3%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           DTQG+ ++D + G     +GH +P +V A+ +Q+ K    S     P +  LA  L A +
Sbjct: 48  DTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVSNLYYIPEQGQLAAWLTANS 107

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSP--RGKFTFIATSGA-FHGKSLGALSATAKS 194
                  FFCNSG E+ EAA+KLA+ + +     +   I T+ A FHG++L A++AT + 
Sbjct: 108 CADRV--FFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQASFHGRTLAAVTATGQP 165

Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYL 254
            + K F PL+ GFR+VP+ ++ A+   L E    G+ VAA++LEP+QGEGGV      Y 
Sbjct: 166 KYHKGFQPLVQGFRYVPYNDLAALEATLAELDAAGETVAAILLEPLQGEGGVNPGDRAYF 225

Query: 255 TAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIA 314
            AVR+LCD+   L+ILDEVQ GMGR+G+++  E+  ++PD   +AK LGGGV PIGA + 
Sbjct: 226 QAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGGGV-PIGALLV 284

Query: 315 TEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLA 374
                 +       H +TFGGNPLAC A LA   V+    L A  + +G+ L  G ++L 
Sbjct: 285 KASCNILQAGE---HASTFGGNPLACRAGLAIAQVMERDQLLANVQARGEQLRAGLQELV 341

Query: 375 REYPDLVQEARGKGML--MAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432
             YP+L+   RG G++  + +    N            Q +L+      A+ +R  PPL 
Sbjct: 342 DRYPNLLAGVRGWGLINGLVLRNDPNVTPIALVKAAIEQGLLLVPA--GAEVVRFVPPLI 399

Query: 433 LTIEQCELVIKAARKALAAM 452
           ++  + +  +    +AL A+
Sbjct: 400 VSAAEIDEALAMTERALLAI 419


Lambda     K      H
   0.320    0.135    0.393 

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: 433
Number of extensions: 22
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: 459
Length of database: 422
Length adjustment: 32
Effective length of query: 427
Effective length of database: 390
Effective search space:   166530
Effective search space used:   166530
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 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