GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Cupriavidus basilensis 4G11

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate RR42_RS07975 RR42_RS07975 amidase

Query= SwissProt::Q38M35
         (462 letters)



>FitnessBrowser__Cup4G11:RR42_RS07975
          Length = 444

 Score =  244 bits (624), Expect = 3e-69
 Identities = 164/447 (36%), Positives = 240/447 (53%), Gaps = 14/447 (3%)

Query: 7   SLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTW----DGARARSAAAAVDTLL 62
           ++A  AA L     T+VAL +   Q  AR++   NA  T     DGA A +AA A D   
Sbjct: 7   TIAALAADLAAGRTTSVALTE---QALARIDGHRNAGGTAFLEVDGAGALAAARAADQAR 63

Query: 63  DQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKT 122
             G    PL GLPVS+KDL+ V G    AGS     E   A  P+VARL+    +++G+T
Sbjct: 64  AAGLVASPLAGLPVSIKDLFDVKGQVTRAGSKALAGEPASADAPVVARLRAAGAVLIGRT 123

Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182
           +  EFAF GLG+N H+GTPR P+   + R+ GGS++G  +S+    A+ ALGTDT GS+R
Sbjct: 124 NMSEFAFSGLGLNPHYGTPRTPFD--DARIAGGSTSGGALSVALDLAVAALGTDTGGSIR 181

Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP 242
           +P++  G  G K T  R P+ G VPLS+SLD+AG L R+V   A AF A+ +       P
Sbjct: 182 IPSAFCGLTGFKPTASRVPLAGAVPLSTSLDSAGPLARSVACCA-AFDAIVSGETLDSRP 240

Query: 243 APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRR 302
           AP  + GLR+ V  +   D +D  +A A +  +  L++ GAQ++ F  P  +    I   
Sbjct: 241 AP--LGGLRLLVTRDFVCDGLDAEVAQAFDVTLATLSRLGAQIIPFDFPELKRLPQINAA 298

Query: 303 GGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLF 362
           GGL A+E   +       + +  DP V  R+R  EQ+ + +Y+   A  +   A AA L 
Sbjct: 299 GGLTAAEAWHWHKPLLAERGDAYDPRVAMRIRRGEQLGAADYIELLAERRAMQARAAGLL 358

Query: 363 DDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRM 422
            + D  L PTV   PPRL  + + E +   N   +RN ++ N    CA+++P  + A   
Sbjct: 359 READAWLMPTVAVRPPRLDALQSDEAFFATNGLVLRNPSVLNFLDGCAVSLP--MPAAEQ 416

Query: 423 PVGLQLMGPPRAEARLIGIALGIEALI 449
            +GL + G    +AR++ +A  IEA +
Sbjct: 417 GMGLSVGGLNGRDARVLQVAGAIEAAL 443


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: 488
Number of extensions: 24
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: 462
Length of database: 444
Length adjustment: 33
Effective length of query: 429
Effective length of database: 411
Effective search space:   176319
Effective search space used:   176319
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 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