GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Rhodanobacter denitrificans 2APBS1

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_015446808.1 R2APBS1_RS02860 amidase

Query= SwissProt::Q38M35
         (462 letters)



>NCBI__GCF_000230695.2:WP_015446808.1
          Length = 465

 Score =  149 bits (377), Expect = 1e-40
 Identities = 133/435 (30%), Positives = 195/435 (44%), Gaps = 35/435 (8%)

Query: 24  ALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYG 83
           AL D   Q   R++P+L+AY        +  AA  +     G  +G L G+P+++KD + 
Sbjct: 33  ALADVYQQAIERIDPQLHAYVDQRSGLVQDQAALAERRRRDGV-IGRLDGIPIALKDNFD 91

Query: 84  VPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRN 143
           + G P   G         + A  +VARL+    +++GKT+  E A G +  N H G   N
Sbjct: 92  IAGWPTRVGLPGRGKPVREDAH-VVARLRASGAVLLGKTNMDEGALGAVTDNPHSGATHN 150

Query: 144 PWSPHEHR-VPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPV 202
           P   H H    GGSS GA  ++  G A+ A+G+D+ GS+R+PAS  G   LK T G    
Sbjct: 151 P---HRHGYTAGGSSGGAAAAVAAGLAVAAVGSDSLGSIRIPASYCGVYALKPTHGEISA 207

Query: 203 EGIVPLSSSLDTAGVLTRTVEDLAYAFAAL------DTESQ------GLPAPAPVRVQGL 250
            G+VP +  LD  G+L R+ +DL      L      D  S+       LP   P     L
Sbjct: 208 RGLVPAARRLDAVGLLARSADDLTVLLQVLAGYDADDARSRRRRVAFALPDWEP---GNL 264

Query: 251 RVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGGLAASEL 310
           R G+  +     + P +    EAA+ +L  A     R  +   +  F   RR GL   E 
Sbjct: 265 RAGLLPDLAAVGVQPEVIEVFEAAMAKLPHALGD--RRTVDFADWDFARTRRAGLLLME- 321

Query: 311 AAYLDQHFPHKVERLDPV---VRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDDVDV 367
           A  L        +   PV    R  + +A   S+ +Y     VL        RLF  VDV
Sbjct: 322 AEMLGTFAADLADSRRPVSERFRRLLGYAAGKSAADYAVADRVLDAATLKMRRLFAQVDV 381

Query: 368 LLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQ 427
           L+ PT P         G      P        T+ ++L G  A+++P+G+  N MPVGLQ
Sbjct: 382 LVLPTTPQ--------GAFPLDGPVPDSQADLTSFASLAGCPAVSLPMGMLPNGMPVGLQ 433

Query: 428 LMGPPRAEARLIGIA 442
           L+G   ++ RL+ +A
Sbjct: 434 LVGARGSDLRLLELA 448


Lambda     K      H
   0.320    0.135    0.411 

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: 501
Number of extensions: 32
Number of successful extensions: 6
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: 462
Length of database: 465
Length adjustment: 33
Effective length of query: 429
Effective length of database: 432
Effective search space:   185328
Effective search space used:   185328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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