Alignments for a candidate for fbp in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Thauera aminoaromatica S2

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_004299846.1 C665_RS03075 class II fructose-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>NCBI__GCF_000310185.1:WP_004299846.1
          Length = 354

 Score =  535 bits (1379), Expect = e-157
 Identities = 265/353 (75%), Positives = 304/353 (86%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           M LVSMRQLLDHAA+ SYGLPAFNVNN+EQV+AIM+AA    +PVI+Q SAGARKYAGE 
Sbjct: 1   MPLVSMRQLLDHAAEHSYGLPAFNVNNLEQVQAIMEAAAECDAPVIMQASAGARKYAGEA 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           FLRHLI AA+EAYP IPVVMHQDHG SPA+CMGAI+SGFSSVMMDGSL EDGKTP+ Y+Y
Sbjct: 61  FLRHLIDAAIEAYPHIPVVMHQDHGQSPAICMGAIRSGFSSVMMDGSLLEDGKTPSSYEY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV+VT +VV+ +HA+GVSVE ELGCLGSLETG+   EDG GAE  LDHS++LTDPD+AA 
Sbjct: 121 NVAVTREVVKFSHAIGVSVEAELGCLGSLETGQAGEEDGVGAEGTLDHSQMLTDPDQAAD 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FVK T CDALAIAIGTSHGAYKFTRKPTGDILAI+R+KAIH RIP THLVMHGSSSVPQE
Sbjct: 181 FVKQTDCDALAIAIGTSHGAYKFTRKPTGDILAIERVKAIHARIPNTHLVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           LLE IR YGGD+KETYGVPVEEI +GI+YGVRK+NIDTDIRLAMT AIR+   +N S+FD
Sbjct: 241 LLEIIRQYGGDMKETYGVPVEEIVQGIKYGVRKINIDTDIRLAMTGAIRKFMFENPSKFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353
           PR++   A E AK VC AR+EAFG AG A KI+ + LD++A RY +GEL+Q+V
Sbjct: 301 PREYNKPAREAAKLVCKARYEAFGCAGMASKIKPVALDKIAARYKAGELSQIV 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: 473
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 WP_004299846.1 C665_RS03075 (class II fructose-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.78428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-193  628.3   0.9   1.9e-193  628.2   0.9    1.0  1  NCBI__GCF_000310185.1:WP_004299846.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000310185.1:WP_004299846.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.2   0.9  1.9e-193  1.9e-193       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 628.2 bits;  conditional E-value: 1.9e-193
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           l+s+rqlldhaae++yg+pafnvnnleq+ aimeaa ++d+pvi+qas+gar+yage++lr+l+ aa+e yp+
  NCBI__GCF_000310185.1:WP_004299846.1   3 LVSMRQLLDHAAEHSYGLPAFNVNNLEQVQAIMEAAAECDAPVIMQASAGARKYAGEAFLRHLIDAAIEAYPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipvv+hqdhg+spa+c+ ai+ gf+svmmdgsl ed+ktp++y+ynv vt evvk++ha+g+sve elgclgs
  NCBI__GCF_000310185.1:WP_004299846.1  76 IPVVMHQDHGQSPAICMGAIRSGFSSVMMDGSLLEDGKTPSSYEYNVAVTREVVKFSHAIGVSVEAELGCLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg++++edg+g+eg+ld+sq+ltdp++aa+fvk+t+ dala+aigtshgaykftrkptg++lai+r++ ih
  NCBI__GCF_000310185.1:WP_004299846.1 149 LETGQAGEEDGVGAEGTLDHSQMLTDPDQAADFVKQTDCDALAIAIGTSHGAYKFTRKPTGDILAIERVKAIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           +r+p+thlvmhgsssvpqe l++i +ygg++ketygvpveeiv+gik+gvrk+nidtd rla+t+a+r+++ +
  NCBI__GCF_000310185.1:WP_004299846.1 222 ARIPNTHLVMHGSSSVPQELLEIIRQYGGDMKETYGVPVEEIVQGIKYGVRKINIDTDIRLAMTGAIRKFMFE 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           +ps+fdpr++ k+a ea k vckaryeafg ag askik+v+l+++a+ry  gel
  NCBI__GCF_000310185.1:WP_004299846.1 295 NPSKFDPREYNKPAREAAKLVCKARYEAFGCAGMASKIKPVALDKIAARYKAGEL 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.06
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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