GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Phaeobacter inhibens BS107

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF2840 PGA1_c28860 citrate synthase GltA

Query= BRENDA::Q8NSL1
         (383 letters)



>FitnessBrowser__Phaeo:GFF2840
          Length = 377

 Score =  259 bits (662), Expect = 9e-74
 Identities = 150/377 (39%), Positives = 212/377 (56%), Gaps = 8/377 (2%)

Query: 9   VRKGLYGVIADYTAVSKVMPETNSLTYRGYAVEDLVENCSFEEVFYLLWHGELPTAQQLA 68
           + +GL G+  + + VS +      L+YRGY++ +L  + +FEEV YLL HGELPTA QLA
Sbjct: 7   INRGLKGIYFERSGVSDIDGAKGELSYRGYSIHNLATHSTFEEVCYLLIHGELPTADQLA 66

Query: 69  EFNERGRSYRSLDAGLISLIHSLPKEAHPMDVMRTAVSYMGTKDSEYFTTDSEHIRKVGH 128
            F+   +S R L A ++ +I +  K+ HPMDV+RTAVS +   D +      +     G 
Sbjct: 67  GFDAALKSARVLPAPVLDIIRAT-KDGHPMDVLRTAVSALAALDPDSQQVGEDAFIANGI 125

Query: 129 TLLAQLPMVLAMDIRRRKGLDIIAPDSSKSVAENLLSMVFGTGPESPASNPADVRDFEKS 188
            L++Q+P+++A     R G  ++ PD   S A N L M+ G  P   A+  ADV DF   
Sbjct: 126 RLISQVPIIIAAHDAIRNGRAVVTPDMDLSHAGNWLWMLKGEKPTPEATRLADV-DF--- 181

Query: 189 LILYAEHSFNASTFTARVITSTKSDVYSAITGAIGALKGPLHGGANEFVMHTMLAIDDPN 248
            IL+AEH  NAS+F ARV   T+++++  I  A+  L GP HGGA E VM  +  I  P+
Sbjct: 182 -ILHAEHGANASSFAARVTIGTETNLHGGIVTALSTLAGPAHGGAAEDVMKMVHEIGTPD 240

Query: 249 KAAAWINNALDNKNVVMGFGHRVYKRGDSRVPSMEKSFRELAARHDGEKWVAMYENMRDA 308
           KAAA++      K  V GFGHRVY++ D R   M    R+L A     +W  + + + +A
Sbjct: 241 KAAAYVKAKRAAKEAVTGFGHRVYRKEDPRARHMRDGVRQLGAEMGAPEWYEILQAVVEA 300

Query: 309 MD--ARTGIKPNLDFPAGPAYHLLGFPVDFFTPLFVIARVAGWTAHIVEQYENNSLIRPL 366
           M   AR G+  N+DF +G  Y L G  +D + P+F I R+ GW    +EQ   N LIRPL
Sbjct: 301 MQPYARHGLNVNVDFYSGVIYQLHGIAMDLYVPIFAIGRMPGWIIQCIEQQRGNILIRPL 360

Query: 367 SEYNGEEQREVAPIEKR 383
           + YNG E R   PI  R
Sbjct: 361 TLYNGPEPRAYTPINTR 377


Lambda     K      H
   0.318    0.133    0.388 

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: 404
Number of extensions: 13
Number of successful extensions: 4
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: 383
Length of database: 377
Length adjustment: 30
Effective length of query: 353
Effective length of database: 347
Effective search space:   122491
Effective search space used:   122491
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 (21.7 bits)
S2: 50 (23.9 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