Alignments for a candidate for fba in Vagococcus penaei CD276

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Vagococcus penaei CD276

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_077276429.1 BW732_RS08955 fructose-bisphosphate aldolase

Query= SwissProt::P0A4S2
         (293 letters)



>NCBI__GCF_001998885.1:WP_077276429.1
          Length = 288

 Score =  367 bits (941), Expect = e-106
 Identities = 183/293 (62%), Positives = 224/293 (76%), Gaps = 5/293 (1%)

Query: 1   MAIVSAEKFVQAARDNGYAVGGFNTNNLEWTQAILRAAEAKKAPVLIQTSMGAAKYMGGY 60
           MA+VSA + ++ AR+  YAVG FNTNNLEWT+AIL+ A+   APV+IQTSMGAAKYMGGY
Sbjct: 1   MALVSATEMLKKAREGKYAVGAFNTNNLEWTKAILQGAQESNAPVMIQTSMGAAKYMGGY 60

Query: 61  KVARNLIANLVESMGITVPVAIHLDHGHYEDALECIEVGYTSIMFDGSHLPVEENLKLAK 120
           +V  +L+ +L++SMGITVPVA+HLDHG Y+DA+ECI+VGYTS+MFDGSHLP +ENL  AK
Sbjct: 61  QVCYDLVKDLIDSMGITVPVALHLDHGEYKDAIECIKVGYTSVMFDGSHLPFDENLAKAK 120

Query: 121 EVVEKAHAKGISVEAEVGTIGGEEDGIIGKGELAPIEDAKAMVETGIDFLAAGIGNIHGP 180
           EVV  AH  G+SVE EVG+IGGEEDGIIG GELA   + K M +TGIDFLAAGIGNIHG 
Sbjct: 121 EVVSFAHINGVSVECEVGSIGGEEDGIIGAGELADPNECKLMSDTGIDFLAAGIGNIHGA 180

Query: 181 YPVNWEGLDLDHLQKLTEALPGFPIVLHGGSGIPDEQIQAAIKLGVAKVNVNTECQIAFA 240
           YP NW GL  + L+ +     G P+VLHGGSGIP +QIQ AI  GV+K+NVNTECQ  FA
Sbjct: 181 YPTNWAGLSFETLEAIANVTDGKPLVLHGGSGIPLDQIQTAIAHGVSKINVNTECQEVFA 240

Query: 241 NATRKFARDYEANEAEYDKKKLFDPRKFLADGVKAIQASVEERIDVFGSEGKA 293
            ATRK+  + +  +      K FDPRK LA G +A+   V+ERI+ FGS+ KA
Sbjct: 241 AATRKYIEENKDLQG-----KGFDPRKLLAPGTQAVVDLVKERIEWFGSKDKA 288


Lambda     K      H
   0.315    0.135    0.384 

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: 319
Number of extensions: 9
Number of successful extensions: 2
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: 293
Length of database: 288
Length adjustment: 26
Effective length of query: 267
Effective length of database: 262
Effective search space:    69954
Effective search space used:    69954
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: 48 (23.1 bits)

Align candidate WP_077276429.1 BW732_RS08955 (fructose-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.858764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-120  386.5   0.1   5.3e-120  386.3   0.1    1.0  1  NCBI__GCF_001998885.1:WP_077276429.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001998885.1:WP_077276429.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.3   0.1  5.3e-120  5.3e-120       1     282 []       3     288 .]       3     288 .] 0.98

  Alignments for each domain:
  == domain 1  score: 386.3 bits;  conditional E-value: 5.3e-120
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv+a+e+l+ka+++kYavgafn+nnle+++ail+ a+e+++Pv++q+s+ga+kY+gg++v+++lvk+li+++ 
  NCBI__GCF_001998885.1:WP_077276429.1   3 LVSATEMLKKAREGKYAVGAFNTNNLEWTKAILQGAQESNAPVMIQTSMGAAKYMGGYQVCYDLVKDLIDSMG 75 
                                           799********************************************************************** PP

                             TIGR01859  74 i.vPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddv 145
                                           i vPvalhLDhG +y+++i++ik+G++svm+D+shlp++enl+++k+vv  ah +gvsve e+G++gG+ed++
  NCBI__GCF_001998885.1:WP_077276429.1  76 ItVPVALHLDHG-EYKDAIECIKVGYTSVMFDGSHLPFDENLAKAKEVVSFAHINGVSVECEVGSIGGEEDGI 147
                                           ************.9*********************************************************** PP

                             TIGR01859 146 vekeaeladideakklvketgvDaLaiaiGtshGkykge.pkldferlkeikklln.lPlvlhGasGipeeql 216
                                           ++  +elad++e+k + + tg+D+La++iG++hG y+++ ++l fe+l++i ++++  PlvlhG+sGip +q+
  NCBI__GCF_001998885.1:WP_077276429.1 148 IG-AGELADPNECKLMSD-TGIDFLAAGIGNIHGAYPTNwAGLSFETLEAIANVTDgKPLVLHGGSGIPLDQI 218
                                           **.9*********98887.********************99***************9**************** PP

                             TIGR01859 217 kkaiklgiakvnidtdlrlaftaairkvleekkde....ydpRkilaparealkevvkekikvlgsagka 282
                                           + ai  g++k+n++t+++  f+aa+rk++ee+kd     +dpRk+lap+++a+ ++vke+i+ +gs++ka
  NCBI__GCF_001998885.1:WP_077276429.1 219 QTAIAHGVSKINVNTECQEVFAAATRKYIEENKDLqgkgFDPRKLLAPGTQAVVDLVKERIEWFGSKDKA 288
                                           ******************************888644444****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (288 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: 14.42
//
[ok]

This GapMind analysis is from Sep 24 2021. 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