GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Snodgrassella alvi wkB2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_025329981.1 SALWKB2_RS01810 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000600005.1:WP_025329981.1
          Length = 391

 Score =  355 bits (912), Expect = e-102
 Identities = 183/391 (46%), Positives = 267/391 (68%), Gaps = 11/391 (2%)

Query: 6   IRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK- 64
           + D D+ GK V++RVD NVP+KDGV+ DDTRIRA+L +I++ L+QGA V++L+HLGRPK 
Sbjct: 6   LADQDVSGKTVVIRVDMNVPIKDGVIVDDTRIRASLASIRFCLQQGAAVVVLTHLGRPKA 65

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G P PE S+APVA+RL ELLG+ V      V ++ ++   +L+ G V++L N R + GE 
Sbjct: 66  GAPKPEDSVAPVAQRLGELLGQNVS-----VAEDWREHKPQLQAGHVIMLPNVRLNIGEK 120

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTY 183
           +ND  LA  +A+L DI+VNDAFGTAHRA AS   +A+F P + AG L+  E++ L+    
Sbjct: 121 ENDQALAAAYAALGDIYVNDAFGTAHRAEASTAAVAEFAPLACAGMLLTAELEALTHAVQ 180

Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243
           NP+ P V ++GG+KVS K+ ++ +L +K D +++GG +  TFL A G  VG S  E D +
Sbjct: 181 NPQAPVVAIVGGSKVSTKLTILESLADKVDHLIVGGGIANTFLLAKGLPVGQSLAEADLV 240

Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303
           D A++++ K   KG +I LPVD V+A++       ++  + D + E  M LDIGP++ + 
Sbjct: 241 DSARQIMAKIAAKGGDIPLPVDVVVAKRFAADAAAEIKNVAD-VAEDDMILDIGPQSAQR 299

Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKF 363
             + + +AKT+VWNGP+GVFE   FA GTK +A AIA   +  A ++ GGGD+ AA+ +F
Sbjct: 300 LAEMMKEAKTIVWNGPVGVFEFAAFAHGTKVLAKAIA---DSDAYSIAGGGDTLAAIAQF 356

Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           G+ D  S++STGGGA LEFLEGK LP +A++
Sbjct: 357 GITDDISYISTGGGAFLEFLEGKTLPAVAAL 387


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: 603
Number of extensions: 32
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 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