Alignments for a candidate for fbp in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Pseudomonas fluorescens FW300-N2C3

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate AO356_13705 AO356_13705 fructose-1,6-bisphosphate aldolase

Query= BRENDA::A0Q7I9
         (354 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13705
          Length = 354

 Score =  574 bits (1480), Expect = e-168
 Identities = 277/350 (79%), Positives = 311/350 (88%)

Query: 1   MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60
           MAL+S+RQ+LDHAAE GYG+PAFNVNNLEQ+RA+MEAADK +SPVI+Q SAGARKYAGA 
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120
           F+RHL+LAAIEE+PHIPVCMHQDHGTSP VCQRSIQLGFSSVMMDGSL  DGKTP DYEY
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120

Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180
           NV VT+    MAHACGVSVEGELGCLGSLETG AGEEDGIGAEG L   Q+LTDPEEAAD
Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180

Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240
           FV++T+VDALAIAIGTSHGAYKFTKPPTGDVL+I R+KEIH RIP+THLVMHGSSSVPQ+
Sbjct: 181 FVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240

Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300
           WL +IN YGG + ETYGVPVEEIVE IKYGVRK+NIDTDLR+A+TGA+RR +A NP+EFD
Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAMRRLMATNPSEFD 300

Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGELD 350
           PRK+      AM ++C ARYEAFG+AG ASKIKPISLE M+QRY  GEL+
Sbjct: 301 PRKFFGATVTAMRDVCIARYEAFGTAGNASKIKPISLEAMYQRYLKGELN 350


Lambda     K      H
   0.316    0.132    0.380 

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: 520
Number of extensions: 14
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: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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: 49 (23.5 bits)

Align candidate AO356_13705 AO356_13705 (fructose-1,6-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (EC 4.1.2.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01521.hmm
# target sequence database:        /tmp/gapView.3973480.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01521  [M=347]
Accession:   TIGR01521
Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                   Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                   -----------
   1.2e-214  697.9   0.2   1.3e-214  697.7   0.2    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_13705  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_13705  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.7   0.2  1.3e-214  1.3e-214       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 697.7 bits;  conditional E-value: 1.3e-214
                                   TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaa 67 
                                                 lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+laa
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705   3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLILAA 69 
                                                 69***************************************************************** PP

                                   TIGR01521  68 veeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavg 134
                                                 +ee+p+ipv++hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt+++v++aha+g
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705  70 IEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVRVTQQTVAMAHACG 136
                                                 ******************************************************************* PP

                                   TIGR01521 135 asvegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykf 201
                                                 +svegelgclgsletg++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykf
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705 137 VSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAADFVKKTQVDALAIAIGTSHGAYKF 203
                                                 ******************************************************************* PP

                                   TIGR01521 202 trkptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfg 268
                                                 t++ptg+vlaidri+eih+r+p+thlvmhgsssvpqewl++in+ygg+iketygvpveeiv+gik+g
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705 204 TKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQEWLAIINQYGGDIKETYGVPVEEIVEGIKYG 270
                                                 ******************************************************************* PP

                                   TIGR01521 269 vrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsl 335
                                                 vrkvnidtdlrla+t+a+rr++a++psefdprkf+  +v am+dvc+aryeafgtagnaskik++sl
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705 271 VRKVNIDTDLRLASTGAMRRLMATNPSEFDPRKFFGATVTAMRDVCIARYEAFGTAGNASKIKPISL 337
                                                 ******************************************************************* PP

                                   TIGR01521 336 eemarryakgel 347
                                                 e m++ry kgel
  FitnessBrowser__pseudo5_N2C3_1:AO356_13705 338 EAMYQRYLKGEL 349
                                                 **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 19.94
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis