GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF2840 PGA1_c28860 citrate synthase GltA
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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