GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Williamsia sterculiae CPCC 203464

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_076477790.1 BW971_RS06715 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_900156495.1:WP_076477790.1
          Length = 405

 Score =  355 bits (910), Expect = e-102
 Identities = 197/390 (50%), Positives = 259/390 (66%), Gaps = 13/390 (3%)

Query: 11  LKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69
           + G+ V++R D NVP+ D G + D  RI A++PT+   L+ GAKV++ +HLGRPKG P  
Sbjct: 15  VSGRGVLVRSDLNVPLDDHGQITDPGRILASVPTLTALLDAGAKVVVTAHLGRPKGAPEA 74

Query: 70  EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDP 128
           ++SLAPVA+RLS  LG+ V+    VVG +     E L +G++LL+EN RF P ET K++ 
Sbjct: 75  KYSLAPVAERLSAELGRNVQLAGDVVGQDALARSEGLTDGDILLVENVRFDPRETSKDEA 134

Query: 129 ELAKFWASLADI------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVT 182
           E      +L ++       V+D FG  HR  AS   +A+ +P  AG L+  E++ L+K+T
Sbjct: 135 ERTALAEALVELVGEDGAFVSDGFGVVHRKQASVYDVAKLLPHYAGELVAAEVEVLTKLT 194

Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242
              E+P+ VVLGG+KVSDKIGVI  L  K D ++IGG M FTFL A G  VG S +++D+
Sbjct: 195 DEVERPFAVVLGGSKVSDKIGVIEALAPKVDTLVIGGGMAFTFLAAEGLNVGDSLLQQDQ 254

Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302
           I++ K LLE+    G  I LPVD V+A       E KVV   + IP+GWMGLDIGPE+++
Sbjct: 255 IEVCKGLLERF---GDVIHLPVDVVVASAFAADAESKVVPAQE-IPDGWMGLDIGPESVK 310

Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362
            F   LS AKT+ WNGP GVFE   FA+GT+ VA AI   T  GA TVVGGGDSAAAV  
Sbjct: 311 RFAAVLSGAKTIFWNGPSGVFEFAKFADGTRGVAEAIIETTRHGAFTVVGGGDSAAAVRT 370

Query: 363 FGL-EDKFSHVSTGGGASLEFLEGKELPGI 391
            GL ED FSH+STGGGASLE+LEGK+LPG+
Sbjct: 371 LGLPEDGFSHISTGGGASLEYLEGKDLPGL 400


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: 641
Number of extensions: 36
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: 405
Length adjustment: 35
Effective length of query: 619
Effective length of database: 370
Effective search space:   229030
Effective search space used:   229030
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 24 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