GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Burkholderia phytofirmans PsJN

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate BPHYT_RS14615 BPHYT_RS14615 fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>FitnessBrowser__BFirm:BPHYT_RS14615
          Length = 466

 Score =  387 bits (994), Expect = e-112
 Identities = 192/460 (41%), Positives = 289/460 (62%), Gaps = 1/460 (0%)

Query: 1   MNTDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALAN 60
           M  DVR+E+D  GE  +P    +G QT R+ +NF I+  +  PELI +L ++K++AA  N
Sbjct: 1   MTEDVRMERDTFGEIAVPNARLWGAQTQRSLQNFRISTEKQSPELIVALAVIKRAAAEVN 60

Query: 61  MEVGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMG 120
           + +G+LD+   + I++AADE+I+GK  D+F +   Q G+GT  NMN NEVIANRA EL+G
Sbjct: 61  LGLGVLDESKAKAIMQAADEIIDGKHPDEFPLAVWQTGSGTQTNMNLNEVIANRASELLG 120

Query: 121 EEKGNYSKISPNSHVNMSQSTNDAFPTATHIAVL-SLLNQLIETTKYMQQEFMKKADEFA 179
             +G   K+ PN  VN  QS+ND FPTA H+A   +++  L    K ++     KA  FA
Sbjct: 121 GVRGEERKVHPNDDVNRGQSSNDVFPTAMHVAAAYAIVKHLQPALKTLRDTLDGKAKAFA 180

Query: 180 GVIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNAD 239
            ++K+GRTHLQDA P+ LGQEF  Y   +   I  +     +LY++  G TAVGTGLNA 
Sbjct: 181 DIVKIGRTHLQDATPLTLGQEFSGYVAQLDHGIRHVETALPHLYELAQGGTAVGTGLNAH 240

Query: 240 PEYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMA 299
           P++   V   + K +G P  SA +  +     D       ALK    +++KIAND+R +A
Sbjct: 241 PQFADKVAAAIGKLTGLPFVSAPNKFEVMAAADALVFAHGALKTVAASLNKIANDVRWLA 300

Query: 300 SGPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELN 359
           SGPR GL E+ +P  +PGSSIMPGKVNP   E +  +  QVFGND+ +     +G FELN
Sbjct: 301 SGPRCGLGELSIPENEPGSSIMPGKVNPTQSEALTMLCAQVFGNDVAVNIGGASGNFELN 360

Query: 360 VMEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYE 419
           V  P++  N++QS+ ++ +  +SF +NC  GI+ N ER++  + +S+ ++TA+NPH+GY+
Sbjct: 361 VFRPMIAHNVLQSVRLLADGARSFNDNCAVGIEPNRERIETLLNESLMLVTALNPHIGYD 420

Query: 420 TAAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459
            AAK+A++A+  G +++   +  G +TE+Q +E + P +M
Sbjct: 421 KAAKIAKKAHKEGTTLKAAALALGFVTEQQFDEWVRPKDM 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: 546
Number of extensions: 19
Number of successful extensions: 3
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: 466
Length adjustment: 33
Effective length of query: 435
Effective length of database: 433
Effective search space:   188355
Effective search space used:   188355
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