GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Desulfovibrio vulgaris Hildenborough

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 208026 DVU2529 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>lcl|MicrobesOnline__882:208026 DVU2529 phosphoglycerate kinase
          Length = 393

 Score =  318 bits (814), Expect = 4e-91
 Identities = 177/397 (44%), Positives = 256/397 (64%), Gaps = 14/397 (3%)

Query: 3   KMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62
           KMT  D+DLKGKRV++R D NVP+K+G +  D RIRAALP+I+ A+E GA+V+++SHLGR
Sbjct: 5   KMT--DLDLKGKRVLLREDLNVPLKEGRITSDKRIRAALPSIRMAMEAGARVLIVSHLGR 62

Query: 63  P-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHP 121
           P +GE    FSLAPVA  LS  LG++V+ V   + D V     ++ EG+ +L EN RF  
Sbjct: 63  PVEGEFDEAFSLAPVAAHLSRELGRDVRLVKDYI-DGV-----DVAEGDCVLCENVRFLK 116

Query: 122 GETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSK 180
           GE KN  EL +  A+L DI V DAFG AHRA AS   +A+F P + AG L+  E+  L +
Sbjct: 117 GEKKNTEELGRRLAALCDIFVMDAFGAAHRAQASTHAVARFAPVACAGPLLAAELDALER 176

Query: 181 VTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEE 240
               P+ P V ++GG+KVS K+ ++ NL  + DR+++GG +   F+KA G EVG S  E 
Sbjct: 177 ALDAPKHPLVGIIGGSKVSTKLTLLDNLSHRVDRLIVGGGIANNFIKAAGYEVGKSLYEP 236

Query: 241 DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPET 300
           + ++ A  L+  A+  G EI +P+D V+  ++  G    V ++ +  P+  M LDIGP T
Sbjct: 237 ELVEEAARLMAAARAAGGEIPVPLDVVVGPELADGAPATVRKVSEVGPDE-MILDIGPAT 295

Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360
              +++ L  A T+VWNGP+G FE + F  GT+ +  A+A   +  A ++ GGGD+ AAV
Sbjct: 296 ATRYREILLAAGTIVWNGPVGAFEWEQFGAGTRALCEAVA---DSPAFSIAGGGDTVAAV 352

Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397
            K+G+  +  ++STGGGA LEFLEGKELP +A + ++
Sbjct: 353 EKYGVASRVGYISTGGGAFLEFLEGKELPAVAILQER 389


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: 635
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 654
Length of database: 393
Length adjustment: 34
Effective length of query: 620
Effective length of database: 359
Effective search space:   222580
Effective search space used:   222580
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 paper from 2022 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