GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Dietzia timorensis ID05-A0528

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_067474702.1 BJL86_RS10470 class II fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_001659785.1:WP_067474702.1
          Length = 471

 Score =  361 bits (927), Expect = e-104
 Identities = 202/464 (43%), Positives = 283/464 (60%), Gaps = 13/464 (2%)

Query: 4   DVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEV 63
           + RIE D +GE  +P +A Y  QT RA ENFPI+   +    I++LG++K + A  N ++
Sbjct: 10  EYRIEHDTMGEVRVPVNALYRAQTQRAVENFPISFRPLERAQIRALGLLKSACASVNNDL 69

Query: 64  GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123
           GLLD E  + I  AA ++ +G+ +  F +D  Q G+GTS NMN NEVIA+ A +   E  
Sbjct: 70  GLLDDEKARAIEAAAQKIADGEVDADFPIDVFQTGSGTSSNMNTNEVIASLAGQAGTE-- 127

Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHIAVL-SLLNQLIETTKYMQQEFMKKADEFAGVI 182
                + PN HVNMSQS+ND FPTATH+A   S+   LI   +++      KA+E+  V+
Sbjct: 128 -----VHPNDHVNMSQSSNDTFPTATHVAAAESIAKDLIPALQHLHSALAGKAEEWKSVV 182

Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242
           K GRTHL DAVP+ LGQEF  YAR +   IER+      + ++ +G TAVGTGLNA   Y
Sbjct: 183 KSGRTHLMDAVPVTLGQEFSGYARQVEAGIERLEAALPRVAELPIGGTAVGTGLNAPEGY 242

Query: 243 ISIVTEHLAKFSG-HPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301
            S V E L + +G   +  A+   +A    D   E S AL+   I+++KIAND+R M SG
Sbjct: 243 GSAVVEKLRELTGVESISLAKDPFEAQAARDGLVEGSGALRTIAISLTKIANDVRWMGSG 302

Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361
           P  GL EI LP  QPGSSIMPGKVNPV+PE + QV  QV GND  I      G FELNV 
Sbjct: 303 PLTGLGEIQLPDLQPGSSIMPGKVNPVLPEAVTQVGAQVIGNDAAIAWGGGNGAFELNVY 362

Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421
            P++  N ++S+ ++ NV   F + C+ G+ ANE+R+K   E S  I+T +N  +GYE A
Sbjct: 363 IPMMARNFLESVKLLANVSTLFADRCISGLVANEDRLKTLAESSPSIVTPLNSAIGYEEA 422

Query: 422 AKLAREAYLTGESIRELCIKYGV----LTEEQLNEILNPYEMTH 461
           AK+A++A   G++IR+  +  G+    L+EE+L++ L+   M +
Sbjct: 423 AKVAKQALAEGKTIRQTVLDRGLVPDKLSEEELDKRLDTLAMAN 466


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: 564
Number of extensions: 32
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: 471
Length adjustment: 33
Effective length of query: 435
Effective length of database: 438
Effective search space:   190530
Effective search space used:   190530
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