GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:208026
          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:

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