GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Sporolactobacillus vineae SL153

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_010631085.1 RH97_RS04205 class II fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_000246965.1:WP_010631085.1
          Length = 462

 Score =  387 bits (995), Expect = e-112
 Identities = 198/458 (43%), Positives = 298/458 (65%), Gaps = 2/458 (0%)

Query: 6   RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65
           RIE D +GE ++P D  +  QT R+  NF I   R+   LI++  ++KK AALAN E+G 
Sbjct: 4   RIEHDTMGEVKVPADRLWAAQTERSRNNFQIGWERMPIGLIRAFAVLKKGAALANRELGK 63

Query: 66  LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125
           LD++    I ++ADEV+ GKW+D+F +   Q G+GT  NMN NEVIA+RA +++ +EKG+
Sbjct: 64  LDEDKASAISRSADEVLSGKWDDEFPLVVWQTGSGTQSNMNMNEVIASRANQIL-KEKGS 122

Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLL-NQLIETTKYMQQEFMKKADEFAGVIKM 184
              + PN  VN SQS+ND FPTA HIA L+ + ++++   +++QQ   +K++ F  ++K+
Sbjct: 123 DLHVHPNDDVNKSQSSNDTFPTALHIAALTAVEDEVLPALRHLQQTLEQKSEAFRDIVKI 182

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRTHLQDA P+ LGQE   +A ++ R    I ++ N L D+ +G TAVGTGLNA P++  
Sbjct: 183 GRTHLQDATPLTLGQEISGWAYMLDRSEAMIRSSSNYLRDLAIGGTAVGTGLNAHPDFGR 242

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
              E +++ +G    S+ +   A  + D    V  ALK    ++ KIAND+R +ASGPR 
Sbjct: 243 QAAEKISEITGKKFISSPNKFQALTSHDQIVTVHGALKALAADLMKIANDVRWLASGPRC 302

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           G+ E+ +PA +PGSSIMPGKVNP   E +  VA QV GND  I  A+  G FELNV +PV
Sbjct: 303 GIGELTIPANEPGSSIMPGKVNPTQCEAVTMVAVQVMGNDAAIGFAASQGNFELNVFKPV 362

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           + +N +QS  ++ +V KSF ++C  GIK   E++ E +  S+ ++TA+NP++GYE AAK+
Sbjct: 363 IGYNFLQSARLLADVMKSFDQHCAAGIKPVREKINENLHHSLMLVTALNPYIGYEQAAKI 422

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462
           ++ A+  G S++E  +K  +LT EQ ++ + P +MT P
Sbjct: 423 SKTAFKEGLSLKEAAVKLKILTAEQFDQYVRPEKMTGP 460


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: 534
Number of extensions: 19
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: 468
Length of database: 462
Length adjustment: 33
Effective length of query: 435
Effective length of database: 429
Effective search space:   186615
Effective search space used:   186615
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 24 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