GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Shewanella oneidensis MR-1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 200116 SO0932 phosphoglycerate kinase (NCBI ptt file)

Query= BRENDA::P36204
         (654 letters)



>lcl|FitnessBrowser__MR1:200116 SO0932 phosphoglycerate kinase (NCBI
           ptt file)
          Length = 391

 Score =  332 bits (850), Expect = 2e-95
 Identities = 182/396 (45%), Positives = 260/396 (65%), Gaps = 12/396 (3%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DL+GKRV++R D NVPV +GVV  D R+RA+LPTI+ AL +GA V+++SHL
Sbjct: 1   MAIINMSDLDLQGKRVLIREDLNVPVSNGVVTSDARLRASLPTIELALAKGAAVMVMSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +GE + EFS+ PV   L++ L   V+     + D V+ AV     GEV++ EN RF
Sbjct: 61  GRPTEGEYNSEFSMQPVVDYLAKALSCPVRLATDYL-DGVEVAV-----GEVVVFENVRF 114

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
           + GE KND  L+K  A+L D++V DAFGTAHRA AS  G+  + P + AG L+ +E+  L
Sbjct: 115 NKGEKKNDEALSKKMAALCDVYVMDAFGTAHRAEASTNGVGLYAPIACAGPLLAQELDAL 174

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K   NP +P V ++GG+KVS K+ V+ +L    D++++GG +  TF+ A G  VG S  
Sbjct: 175 GKALDNPARPLVAIVGGSKVSTKLTVLESLSGIVDQLVVGGGIANTFIAAAGHNVGKSLY 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E D ID AK L+  A+ +G +I +P D V+A +  P     +  + D + +  M  DIGP
Sbjct: 235 EADLIDEAKRLVANAQSRGGDIPVPTDVVVAGEFSPTAAATLKAVSD-VGDSDMIFDIGP 293

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           ++ E   + +  A T+VWNGP+GVFE D F EGTK++A AIA   +  A ++ GGGD+ A
Sbjct: 294 DSAEALAKIIESAGTIVWNGPVGVFEFDQFGEGTKRIAHAIA---DSKAFSIAGGGDTLA 350

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           AV+K+G+ DK S++STGGGA LEFLEGKELP +A +
Sbjct: 351 AVDKYGIADKVSYISTGGGAFLEFLEGKELPAVAML 386


Lambda     K      H
   0.317    0.137    0.386 

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: 605
Number of extensions: 42
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: 654
Length of database: 391
Length adjustment: 34
Effective length of query: 620
Effective length of database: 357
Effective search space:   221340
Effective search space used:   221340
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: 52 (24.6 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