GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aspA in Dechlorosoma suillum PS

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Dsui_0926 Dsui_0926 fumarate hydratase, class II

Query= BRENDA::Q9LCC6
         (468 letters)



>lcl|FitnessBrowser__PS:Dsui_0926 Dsui_0926 fumarate hydratase,
           class II
          Length = 463

 Score =  358 bits (918), Expect = e-103
 Identities = 195/458 (42%), Positives = 274/458 (59%), Gaps = 1/458 (0%)

Query: 6   RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65
           R+E D  G   +P +  +G QT R+ E+F I+   + PELI++L +VK++AA  N E+GL
Sbjct: 4   RLEHDTFGPIAVPAERLWGAQTQRSLEHFAISSETMPPELIRALALVKQAAAQVNGELGL 63

Query: 66  LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125
           L   V   I  AADEV+ G+   +F +   Q G+GT  NMN NEV+ANRA EL+G  +G 
Sbjct: 64  LPPPVAGAIAAAADEVLAGRHPAEFPLSVWQTGSGTQSNMNMNEVLANRASELLGGPRGE 123

Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAV-LSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184
              + PN  VN+ QS+ND FPTA H+A  L++  +L+     ++Q    KA+ FA +IK+
Sbjct: 124 GRLVHPNDQVNLGQSSNDIFPTAIHVAATLAVDGRLLPALAELRQALAAKAEAFADLIKI 183

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRTHLQDA PI LGQEF  Y   + +    I  +   L  +  G TAVGTGLN   E+ +
Sbjct: 184 GRTHLQDATPITLGQEFSGYVAQLEQAERGIQASLPGLRQLAAGGTAVGTGLNTHAEFGA 243

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
            V E LA     P   A +   A    +       ALK     + KIANDLR +ASGPR+
Sbjct: 244 RVAEKLAHGCSQPFVPAANPFAALAGHEALLFAHGALKTLAGALMKIANDLRWLASGPRS 303

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           GL EI LP  +PGSSIMPGKVNP   E +  V  QVFGND+ I     +G FELNV +P+
Sbjct: 304 GLGEIALPENEPGSSIMPGKVNPTQCEALTMVCAQVFGNDVAINIGGASGNFELNVFKPL 363

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           L  N +QS  ++ +  +SF+ +C+ GI  N ERM E +E+S+ ++TA+ PH+GYE AA +
Sbjct: 364 LAHNFLQSARLLGDAMESFSRHCVVGIVPNRERMDELLERSLMLVTALAPHIGYERAAAV 423

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462
           A++A+  G ++R+  +  G +T E+ +  + P  M  P
Sbjct: 424 AKQAHRDGSTLRQAALALGYVTAEEFDAWVRPEAMLGP 461


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: 512
Number of extensions: 17
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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