GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Methanoculleus horonobensis T10

Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (characterized)
to candidate WP_067074391.1 MCUHO_RS05000 fructose 1,6-bisphosphatase

Query= SwissProt::Q2RG86
         (379 letters)



>NCBI__GCF_001602375.1:WP_067074391.1
          Length = 365

 Score =  472 bits (1215), Expect = e-138
 Identities = 229/359 (63%), Positives = 279/359 (77%), Gaps = 3/359 (0%)

Query: 4   RITLSVIKADIGGFVGHSSVHPRLLETAERYL--AESKLLIDYRVAHVGDDIDLIMTHKY 61
           +IT+SVIKADIG F GHS  HP++LE A R L  AE  +LID  V H GDD++LIMTH  
Sbjct: 3   KITVSVIKADIGSFPGHSRTHPKILEVAARRLKEAEGSILIDSYVTHCGDDLELIMTHTK 62

Query: 62  GVDCPEIHHLAWNVFLQCTEVARELKLYGAGQDLLSDAFSGNVKGMGPGVAEMEFEERKS 121
           G D  EIH LAW++F++C  +A+E+KLYGAGQDLL DAFSGNVKGMGPGVAEMEFEER S
Sbjct: 63  GEDNEEIHKLAWDIFMECAGLAKEMKLYGAGQDLLGDAFSGNVKGMGPGVAEMEFEERGS 122

Query: 122 EPIIVFAADKTEPGAWNLPLYKMFADPFNTIGLVIDPKMHQGFRFEVYDLIKNERVEFSL 181
           +PI++F ADKTEPGAWN  LYK+FADPF+T GLVIDP +H GF FEV+D+IK  ++ F+ 
Sbjct: 123 DPILIFMADKTEPGAWNYFLYKIFADPFSTSGLVIDPSLHDGFTFEVHDVIKKRKILFNT 182

Query: 182 PEELYDLLVFIGAPGRYCIKSVYSKTTGEIAAVSSTQRLNLMAGRYVGKDDPVCIVRCQS 241
           PEE Y LL +IGAP RY IK V+ K  G I A +STQRLNLMAGRYVGKDDPV I+R QS
Sbjct: 183 PEESYSLLAYIGAPSRYVIKYVW-KRNGLIGASTSTQRLNLMAGRYVGKDDPVMIIRAQS 241

Query: 242 GLPAVGEALEPFANPHLVAGWMRGSHIGPLMPVGLDQSAPTRFDGPPRVVAMGFQLSGGR 301
           G PAVGE ++PF  P LVAGWMRGSH GP MPVG+  +  T+FDGPPRV+ +GFQ+  G+
Sbjct: 242 GFPAVGEVIDPFRTPILVAGWMRGSHHGPFMPVGVCDANCTQFDGPPRVICLGFQVCNGK 301

Query: 302 LVGPQDFFGDVAFDKARQTANEIASYLRSLGPFEPHRLPLEDMEYTTMPEVMAKLKNRF 360
           L+GP D F D A+++ R    E++S LR+ GPFEPHRL LE+MEYTT+P V  + K+R+
Sbjct: 302 LIGPADMFDDPAYNRVRDQCCELSSMLRAHGPFEPHRLSLEEMEYTTLPGVEKQFKDRW 360


Lambda     K      H
   0.321    0.140    0.423 

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: 535
Number of extensions: 28
Number of successful extensions: 3
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: 379
Length of database: 365
Length adjustment: 30
Effective length of query: 349
Effective length of database: 335
Effective search space:   116915
Effective search space used:   116915
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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