GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Pseudomonas simiae WCS417

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate GFF5157 PS417_26415 fructose-1,6-bisphosphate aldolase

Query= BRENDA::A0Q7I9
         (354 letters)



>FitnessBrowser__WCS417:GFF5157
          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 GFF5157 PS417_26415 (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.12914.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  lcl|FitnessBrowser__WCS417:GFF5157  PS417_26415 fructose-1,6-bisphos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5157  PS417_26415 fructose-1,6-bisphosphate aldolase
   #    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 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdip 75 
                                         lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+laa+ee+p+ip
  lcl|FitnessBrowser__WCS417:GFF5157   3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIP 77 
                                         69************************************************************************* PP

                           TIGR01521  76 vvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletg 150
                                         v++hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt+++v++aha+g+svegelgclgsletg
  lcl|FitnessBrowser__WCS417:GFF5157  78 VCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVRVTQQTVAMAHACGVSVEGELGCLGSLETG 152
                                         *************************************************************************** PP

                           TIGR01521 151 kgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdt 225
                                         ++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykft++ptg+vlaidri+eih+r+p+t
  lcl|FitnessBrowser__WCS417:GFF5157 153 MAGEEDGIGAEGVLDHSQMLTDPEEAADFVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNT 227
                                         *************************************************************************** PP

                           TIGR01521 226 hlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdpr 300
                                         hlvmhgsssvpqewl++in+ygg+iketygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++psefdpr
  lcl|FitnessBrowser__WCS417:GFF5157 228 HLVMHGSSSVPQEWLAIINQYGGDIKETYGVPVEEIVEGIKYGVRKVNIDTDLRLASTGAMRRLMATNPSEFDPR 302
                                         *************************************************************************** PP

                           TIGR01521 301 kflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                         kf+  +v am+dvc+aryeafgtagnaskik++sle m++ry kgel
  lcl|FitnessBrowser__WCS417:GFF5157 303 KFFGATVTAMRDVCIARYEAFGTAGNASKIKPISLEAMYQRYLKGEL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.93
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

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