GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Rhodobacter viridis JA737

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_110806310.1 C8J30_RS13165 class II fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_003217355.1:WP_110806310.1
          Length = 464

 Score =  372 bits (954), Expect = e-107
 Identities = 190/461 (41%), Positives = 285/461 (61%), Gaps = 1/461 (0%)

Query: 3   TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANME 62
           T  R E D  G  E+P D Y+G QT R+  NFPI   +    +I++LG++KK+AAL N  
Sbjct: 2   TATRTETDSFGPLEVPADKYWGAQTQRSILNFPIGWEKQPKPIIRALGVIKKAAALVNKA 61

Query: 63  VGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEE 122
            G ++  + + I  AA EVIEGK++D F +   Q G+GT  NMNANEVI+NRA+E++G  
Sbjct: 62  QGDMEPAIAEAIAAAATEVIEGKFDDNFPLVVWQTGSGTQSNMNANEVISNRAIEMLGGV 121

Query: 123 KGNYSKISPNSHVNMSQSTNDAFPTATHIAV-LSLLNQLIETTKYMQQEFMKKADEFAGV 181
            G+   + PN HVNM QS+ND FPTA H+A+ +   + LI   + + +    K++EF  +
Sbjct: 122 MGSKKPVHPNDHVNMGQSSNDTFPTAMHVAIAMQARDVLIPGLEKLSKALWAKSEEFKDI 181

Query: 182 IKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPE 241
           IK+GRTH QDA P+ LGQEF  YA  + R IER+     ++Y++  G TAVGTGLN    
Sbjct: 182 IKIGRTHTQDATPLTLGQEFSGYATQVDRGIERVKLALPHIYELAQGGTAVGTGLNTRVG 241

Query: 242 YISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301
           + + +   +A+ +G P  +A +  +A    D     S ALK    ++ KIAND+RL+ SG
Sbjct: 242 WDTRIAAQIAEITGLPFVTAPNKFEALAAHDAMVFFSGALKTVAASLFKIANDMRLLGSG 301

Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361
           PR+GL E++LP  +PGSSIMPGKVNP   E +  V   V GND  I  A   G FELNV 
Sbjct: 302 PRSGLGELILPENEPGSSIMPGKVNPTQAEALTMVCAHVMGNDAAIGFAGSQGHFELNVY 361

Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421
            P++ +N++QS+ ++ +   +FT+N + G +AN  R+ + +++S+ ++TA+ P +GY+ A
Sbjct: 362 NPMMSYNVLQSMQLLGDSASAFTDNMVVGTQANTARIDKLMKESLMLVTALAPTIGYDAA 421

Query: 422 AKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462
            K+A+ A+  G ++RE  I  G +  E  + ++ P +M  P
Sbjct: 422 TKVAKTAHKNGTTLREEAIALGYVDGETFDRVVRPEDMISP 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: 523
Number of extensions: 19
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: 464
Length adjustment: 33
Effective length of query: 435
Effective length of database: 431
Effective search space:   187485
Effective search space used:   187485
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