GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Caulobacter crescentus NA1000

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate CCNA_02194 CCNA_02194 fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>FitnessBrowser__Caulo:CCNA_02194
          Length = 463

 Score =  387 bits (993), Expect = e-112
 Identities = 203/462 (43%), Positives = 287/462 (62%), Gaps = 1/462 (0%)

Query: 3   TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANME 62
           T  RIE D  G  E+  D Y+G Q  R+  NF I   +    ++++LGIVK++AA AN+ 
Sbjct: 2   TATRIETDTFGPIEVAADRYWGAQAQRSLGNFKIGWEKQPLPVVRALGIVKRAAAEANLA 61

Query: 63  VGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEE 122
           +G LD ++ + I+ AA+EVIEGK ND F +   Q G+GT  NMNANEVI+NRA+E++G E
Sbjct: 62  LGKLDPKIAETIIAAANEVIEGKLNDHFPLVVWQTGSGTQSNMNANEVISNRAIEMLGGE 121

Query: 123 KGNYSKISPNSHVNMSQSTNDAFPTATHIAVLS-LLNQLIETTKYMQQEFMKKADEFAGV 181
            G+   + PN HVNMSQS+ND FPTA HIA    +++ L+   K++ +    KA E+  +
Sbjct: 122 MGSKKPVHPNDHVNMSQSSNDTFPTAMHIACAEQVVHDLLPALKHLHKALAAKAAEWKDI 181

Query: 182 IKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPE 241
           IK+GRTH QDA P+ LGQEF  YA+ I   I RI  T   L  +  G TAVGTGLNA   
Sbjct: 182 IKIGRTHTQDATPLTLGQEFGGYAQQIENGIARIEMTLPMLMQLAQGGTAVGTGLNAPVG 241

Query: 242 YISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301
           +  +V E +A  +G    +A +  +A    D       A+     ++ KIAND+R + SG
Sbjct: 242 FAELVAEQIAGITGLGFTTAPNKFEALAAHDAMVFTHGAINTVAASLFKIANDIRFLGSG 301

Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361
           PRAGL E+ LP  +PGSSIMPGKVNP   E + QV  QVFGN  T+T A   G FELNV 
Sbjct: 302 PRAGLGELSLPENEPGSSIMPGKVNPTQSEALTQVCAQVFGNHSTLTFAGSQGHFELNVF 361

Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421
            PV+ +N +QS+ ++ +   SFT+NC+ GI+   + +K+ VE S+ ++TA+N  +GY+  
Sbjct: 362 NPVMAYNFLQSVRLVADAAISFTDNCVVGIEPRVDNIKKGVENSLMLVTALNGKLGYDAC 421

Query: 422 AKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPG 463
           AK+A+ A+  G ++RE  +  G LT E+  + + P +M  PG
Sbjct: 422 AKIAKTAHKNGTTLREEAVGGGYLTNEEFEQYVRPEKMISPG 463


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: 539
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: 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:

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