GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Synechococcus elongatus PCC 7942

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Synpcc7942_1007 Synpcc7942_1007 fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>FitnessBrowser__SynE:Synpcc7942_1007
          Length = 463

 Score =  366 bits (940), Expect = e-106
 Identities = 185/455 (40%), Positives = 290/455 (63%), Gaps = 1/455 (0%)

Query: 6   RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65
           R E D +GE  +P D Y+G QT R+   F I   R+  E+  +L I KK++ALAN ++G+
Sbjct: 8   RRESDSMGEVLVPTDRYWGAQTQRSLHYFSIGQDRMPIEVCHALAIAKKASALANRDLGV 67

Query: 66  LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125
           L  E    I +AADE+I G+ +D F +     G+GT  NMN NEVIANRA+E+ G   G+
Sbjct: 68  LSAEKADLIAQAADEIIAGQLDDHFPLYVWMTGSGTQANMNVNEVIANRAIEMAGGVLGS 127

Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLLN-QLIETTKYMQQEFMKKADEFAGVIKM 184
            + I PN  VN SQS+ND FPTA HIA    +  QL+ + + ++Q    K DE+ G++K+
Sbjct: 128 KTPIHPNDDVNRSQSSNDVFPTAMHIAAAQAIGRQLLPSIERLEQSLQAKVDEWQGIVKI 187

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRTHLQDAVP+ LGQEF  +  ++A + +R+ N    LY + +G TAVGTGLNA   +  
Sbjct: 188 GRTHLQDAVPLTLGQEFSGFVAMLAENRQRLHNALQELYPLALGGTAVGTGLNAPTGFDV 247

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
            V +++A+ +G P  +A +        D +  +S +L+   +++ KIAND+RL+A GPR 
Sbjct: 248 AVADYIAQLTGLPFVTATNKFAQIGAHDAFVALSGSLRGLAVSLYKIANDIRLLACGPRC 307

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           G +E+ LPA +PGSSIMPGKVNP   E +  VA QV G D  +  A  +G  ELNV +P+
Sbjct: 308 GFNELSLPANEPGSSIMPGKVNPTQCEALAMVAVQVMGYDAAVAFAGASGYLELNVYKPL 367

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           + +N+++SI I+++   +F    ++G+ AN +++  Y+E+S+ ++TA+ P +GY+ AAK+
Sbjct: 368 MVYNVLESIRILSDASDNFRRFTVEGMTANTDQINTYLERSLMLVTALTPAIGYDQAAKV 427

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459
           A+ A+    S++E C++ G ++ E+ +  ++P ++
Sbjct: 428 AKYAFEKNLSLKEACLELGCISSEEFDRWVDPAQL 462


Lambda     K      H
   0.316    0.133    0.370 

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: 528
Number of extensions: 29
Number of successful extensions: 2
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: 468
Length of database: 463
Length adjustment: 33
Effective length of query: 435
Effective length of database: 430
Effective search space:   187050
Effective search space used:   187050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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