GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Dechlorosoma suillum PS

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate Dsui_0050 Dsui_0050 fructose-bisphosphate aldolase, class II, Calvin cycle subtype

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__PS:Dsui_0050
          Length = 354

 Score =  516 bits (1328), Expect = e-151
 Identities = 257/353 (72%), Positives = 296/353 (83%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           M +VSMRQLLDHAA++ YGLPAFNVNNMEQV AIM+AA   ++PVI+Q SAGARKYAGE 
Sbjct: 1   MPIVSMRQLLDHAAENGYGLPAFNVNNMEQVWAIMEAANELNAPVIMQASAGARKYAGEA 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           FLRH I AA+EAYP IPVVMHQDHG SPAVCM AIKSGFSSVMMDGSL+EDGK+ A YDY
Sbjct: 61  FLRHQILAALEAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLQEDGKSVASYDY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV+VT +VV+ +HA+GVSVE ELG LGSLET K + EDGHGAE  +    LLTDPD+AA 
Sbjct: 121 NVAVTQEVVKFSHAIGVSVEAELGVLGSLETMKADKEDGHGAEGHMTREDLLTDPDQAAD 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FV  T CDALAIAIGTSHGAYKFT+KPTGDILAIDRIK IH RIP THLVMHGSSSVPQ+
Sbjct: 181 FVARTNCDALAIAIGTSHGAYKFTKKPTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQD 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           LL EIR +GGD+KETYGVPVEEI  GI++GVRKVNIDTDIRLAMT A+RR   +N S+FD
Sbjct: 241 LLAEIREFGGDMKETYGVPVEEIVNGIKHGVRKVNIDTDIRLAMTGAVRRYLFENPSKFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353
           PR F+  A E AKK+C+AR++AFG  G+A +I+ I L++MA+RY  GEL Q+V
Sbjct: 301 PRDFLKPAREAAKKICVARYQAFGCEGRAGQIKPISLEKMAERYKKGELNQIV 353


Lambda     K      H
   0.316    0.132    0.369 

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: 446
Number of extensions: 12
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 Dsui_0050 Dsui_0050 (fructose-bisphosphate aldolase, class II, Calvin cycle subtype)
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.10132.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-186  605.5   1.0   1.7e-186  605.3   1.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0050  Dsui_0050 fructose-bisphosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0050  Dsui_0050 fructose-bisphosphate aldolase, class II, Calvin cycle subtype
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.3   1.0  1.7e-186  1.7e-186       2     347 .]       4     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 605.3 bits;  conditional E-value: 1.7e-186
                         TIGR01521   2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvvl 78 
                                       +s+rqlldhaae+gyg+pafnvnn+eq+ aimeaa++ ++pvi+qas+gar+yage++lr+ +laa e yp+ipvv+
  lcl|FitnessBrowser__PS:Dsui_0050   4 VSMRQLLDHAAENGYGLPAFNVNNMEQVWAIMEAANELNAPVIMQASAGARKYAGEAFLRHQILAALEAYPHIPVVM 80 
                                       89*************************************************************************** PP

                         TIGR01521  79 hqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgeae 155
                                       hqdhg+spa+c++ai+ gf+svmmdgsl+ed+k+ a+ydynv vt+evvk++ha+g+sve elg lgslet k+++e
  lcl|FitnessBrowser__PS:Dsui_0050  81 HQDHGQSPAVCMAAIKSGFSSVMMDGSLQEDGKSVASYDYNVAVTQEVVKFSHAIGVSVEAELGVLGSLETMKADKE 157
                                       ***************************************************************************** PP

                         TIGR01521 156 dghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhgs 232
                                       dghg+eg + r +lltdp++aa+fv++t+ dala+aigtshgaykft+kptg++laidri+eih+r+p+thlvmhgs
  lcl|FitnessBrowser__PS:Dsui_0050 158 DGHGAEGHMTREDLLTDPDQAADFVARTNCDALAIAIGTSHGAYKFTKKPTGDILAIDRIKEIHARIPNTHLVMHGS 234
                                       ***************************************************************************** PP

                         TIGR01521 233 ssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkavea 309
                                       ssvpq+ l+ i e+gg++ketygvpveeiv+gik+gvrkvnidtd rla+t+a+rr + ++ps+fdpr flk+a ea
  lcl|FitnessBrowser__PS:Dsui_0050 235 SSVPQDLLAEIREFGGDMKETYGVPVEEIVNGIKHGVRKVNIDTDIRLAMTGAVRRYLFENPSKFDPRDFLKPAREA 311
                                       ***************************************************************************** PP

                         TIGR01521 310 mkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                        k++c+ary+afg  g a +ik++sle+ma+ry kgel
  lcl|FitnessBrowser__PS:Dsui_0050 312 AKKICVARYQAFGCEGRAGQIKPISLEKMAERYKKGEL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.56
//
[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