Alignments for a candidate for fba in Desulfuromonas acetexigens DSM 1397

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Desulfuromonas acetexigens DSM 1397

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_092058754.1 BQ4888_RS16670 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::Q8YNK2
         (359 letters)



>NCBI__GCF_900111775.1:WP_092058754.1
          Length = 326

 Score =  266 bits (680), Expect = 6e-76
 Identities = 158/339 (46%), Positives = 210/339 (61%), Gaps = 32/339 (9%)

Query: 1   MALVPLRLLLDHAAENGYGIPAFNVNNLEQIQAILKAAAETDSPVILQASRGARNYAGEN 60
           + LV  R L   A + GY IPA+N NNLEQ+QAI+ A AET SPVI+Q S+GAR+YA + 
Sbjct: 10  LGLVNTRELFQKAVKGGYAIPAYNFNNLEQLQAIVLACAETSSPVIVQVSKGARDYANQT 69

Query: 61  FLRHLILAAVETYPE----IPIVMHQDHGNAPSTCYSAIKNNFTSVMMDGSLEADAKTPA 116
            LR++ L AV+   E    IPI +H DHG++   C S + + F+SVM+DGS  A      
Sbjct: 70  MLRYMALGAVQMARELGSNIPICLHLDHGDSFELCKSCVDSGFSSVMIDGSHLA------ 123

Query: 117 SFEYNVNVTREVVNVAHALGVSVEGELGCLGSLETGAGEAEDGHGFEGTLDHSQLLTDPD 176
            +E NV +TR+VV  AH   VSVEGELG L  +E            E   DHS   T P+
Sbjct: 124 -YEENVALTRQVVEYAHKYDVSVEGELGVLAGIED-----------EVQADHSTY-TKPE 170

Query: 177 EAVNFVEATQVDALAVAIGTSHGAYKFTRKPTGEI--LAISRIEEIHRRLPNTHLVMHGS 234
           E  +FV+ T VD+LA++IGTSHGAYKF  K   E+  L    +EE+ RR+P   +V+HG+
Sbjct: 171 EVEDFVKKTGVDSLAISIGTSHGAYKFKLKDGEEVPPLRFDILEEVERRIPGFPIVLHGA 230

Query: 235 SSVPEDLIALINEYGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAVREALAK 294
           SSV ++ + LIN+YGG +    GVP  +++K   S V K+NID+D RLA+TA VRE LAK
Sbjct: 231 SSVVQEYVQLINQYGGKMDGAVGVPEGQLRKAAASAVCKINIDSDGRLAVTAKVREFLAK 290

Query: 295 NPKEFDPRHFL----KPSITYMQKVCAERYVQFGTAGNA 329
           NP EFDPR +L    K  IT ++    +  V  G+AG A
Sbjct: 291 NPGEFDPRKYLGAARKELITLIKH---KNQVVLGSAGKA 326


Lambda     K      H
   0.315    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: 376
Number of extensions: 23
Number of successful extensions: 5
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: 359
Length of database: 326
Length adjustment: 29
Effective length of query: 330
Effective length of database: 297
Effective search space:    98010
Effective search space used:    98010
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_092058754.1 BQ4888_RS16670 (class II fructose-1,6-bisphosphate aldolase)
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (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.carbon/TIGR01859.hmm
# target sequence database:        /tmp/gapView.2932228.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01859  [M=282]
Accession:   TIGR01859
Description: fruc_bis_ald_: fructose-1,6-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-115  372.2   0.1   1.5e-115  371.8   0.1    1.1  1  NCBI__GCF_900111775.1:WP_092058754.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900111775.1:WP_092058754.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.8   0.1  1.5e-115  1.5e-115       1     282 []      12     326 .]      12     326 .] 0.98

  Alignments for each domain:
  == domain 1  score: 371.8 bits;  conditional E-value: 1.5e-115
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg...gikvvvalvkalie 70 
                                           lv+++el++ka k++Ya++a+n+nnle+lqai+ a+ e+ sPvivqvs+ga++Y++   ++ ++ ++v+ + e
  NCBI__GCF_900111775.1:WP_092058754.1  12 LVNTRELFQKAVKGGYAIPAYNFNNLEQLQAIVLACAETSSPVIVQVSKGARDYANqtmLRYMALGAVQMARE 84 
                                           79******************************************************77777899999*99999 PP

                             TIGR01859  71 klsivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGied 143
                                             s++P++lhLDhG+s+e c +++++GfssvmiD+shl++een+++t++vve+ah+  vsve elG+l+Gied
  NCBI__GCF_900111775.1:WP_092058754.1  85 LGSNIPICLHLDHGDSFELCKSCVDSGFSSVMIDGSHLAYEENVALTRQVVEYAHKYDVSVEGELGVLAGIED 157
                                           9999********************************************************************* PP

                             TIGR01859 144 dvvekeaeladideakklvketgvDaLaiaiGtshGkykge.......pkldferlkeikklln.lPlvlhGa 208
                                           +v ++++++++++e++++vk+tgvD+Lai+iGtshG yk +       p l+f+ l+e++++++ +P+vlhGa
  NCBI__GCF_900111775.1:WP_092058754.1 158 EVQADHSTYTKPEEVEDFVKKTGVDSLAISIGTSHGAYKFKlkdgeevPPLRFDILEEVERRIPgFPIVLHGA 230
                                           ************************************77766669999****************99******** PP

                             TIGR01859 209 s.....................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilap 260
                                           s                     G+pe ql+ka+ ++++k+nid+d rla+ta++r++l+++  e+dpRk+l+ 
  NCBI__GCF_900111775.1:WP_092058754.1 231 SsvvqeyvqlinqyggkmdgavGVPEGQLRKAAASAVCKINIDSDGRLAVTAKVREFLAKNPGEFDPRKYLGA 303
                                           ************************************************************************* PP

                             TIGR01859 261 arealkevvkekik.vlgsagka 282
                                           ar++l  ++k+k++ vlgsagka
  NCBI__GCF_900111775.1:WP_092058754.1 304 ARKELITLIKHKNQvVLGSAGKA 326
                                           *************9889****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (326 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: 21.76
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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

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 catabolism of small carbon sources