GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Methanobacterium arcticum M2

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_048080252.1 EI99_RS01985 fructose 1,6-bisphosphatase

Query= SwissProt::D9PUH5
         (365 letters)



>NCBI__GCF_000746075.1:WP_048080252.1
          Length = 365

 Score =  630 bits (1625), Expect = 0.0
 Identities = 294/365 (80%), Positives = 337/365 (92%)

Query: 1   MKTTISVIKADVGSVAGHAVAHEALKKKCDEILAEARDTGILEDYYITNCGDDIDLIMTH 60
           MKTTISVIKADVGSVAGH +AH AL  KC+EILA+A++  +L DYY+TNCGDD +LIMTH
Sbjct: 1   MKTTISVIKADVGSVAGHGIAHPALLAKCEEILAKAKEEELLTDYYVTNCGDDTELIMTH 60

Query: 61  RNGEENEEVHQTAWNAFREATEVARGLKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKER 120
           + GEEN+E+H+ A+NAF EAT +A+ LKLYGAGQDLLSDTFSGNIKGMGPG AEMEFKER
Sbjct: 61  KQGEENKEIHELAFNAFMEATAIAKDLKLYGAGQDLLSDTFSGNIKGMGPGVAEMEFKER 120

Query: 121 PSDPVIIFCCDKTEPGAFNLPLFRMFADPFNTAGLVIDPTLHNGYEFEVFDVVEHKKVTM 180
           PSDPV++FCCDKTEPGAFNLP+FRMFADPFNTAGLVIDP+LHNGY+FE+FDV+EHKKVTM
Sbjct: 121 PSDPVVVFCCDKTEPGAFNLPIFRMFADPFNTAGLVIDPSLHNGYKFEIFDVMEHKKVTM 180

Query: 181 ACPDEMYDLLALLGSISRYVIKKIHRRDDGEIAASVSTERLNLMAGKYIGKDDPVAIVRA 240
            CP+EMYD LALLGSISRYVIK++ R+DD EIAA++STERLNLMAG Y+GKDDPVAIVR+
Sbjct: 181 NCPEEMYDALALLGSISRYVIKRVIRKDDNEIAAAISTERLNLMAGSYVGKDDPVAIVRS 240

Query: 241 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPVAQRDATPVRFDGPPRVIGLGFQIAD 300
           QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPV Q++A PVRFDGPPRV+ LGFQIAD
Sbjct: 241 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPVGQKNAYPVRFDGPPRVMALGFQIAD 300

Query: 301 CKLVGPIDMFDDPSFDRSRQLASEIAEYMRRHGPFEPHRLPSDEMEYTSLPGVLEKLGDR 360
            +LVGP DMFDDP++D +R+ A+EIA+YMRRHGPFEPHRLP+DEMEYTSLPGV+EKL  R
Sbjct: 301 GELVGPADMFDDPAYDPARKQAAEIADYMRRHGPFEPHRLPADEMEYTSLPGVMEKLEGR 360

Query: 361 FEDMD 365
           FED+D
Sbjct: 361 FEDID 365


Lambda     K      H
   0.320    0.139    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: 618
Number of extensions: 19
Number of successful extensions: 1
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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