Alignments for a candidate for fbp in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Desulfovibrio vulgaris Hildenborough

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 207620 DVU2143 fructose-1,6-bisphosphate aldolase, class II

Query= BRENDA::Q9RHA2
         (305 letters)



>MicrobesOnline__882:207620
          Length = 307

 Score =  285 bits (729), Expect = 9e-82
 Identities = 148/292 (50%), Positives = 204/292 (69%), Gaps = 4/292 (1%)

Query: 7   EILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRALTLMAVE 66
           E+  +A  EG+ VGAFNVNNME +Q +++A  E+R+P+IL +S GA KY G+   +  +E
Sbjct: 8   EMFARAYREGHAVGAFNVNNMEIIQGIMQAGAEERAPLILQVSAGARKYAGQNYIIKLIE 67

Query: 67  LAK-EARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVEAAHAV 125
            A  +  +PV +HLDHG  ++     +  GFTSVMID SH  +E N+  TRRVVE AH  
Sbjct: 68  AALLDTDLPVVLHLDHGQDFDICKSCIDGGFTSVMIDGSHLSYEENIAVTRRVVEYAHDK 127

Query: 126 GVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKG 185
           GV VEAELG+LAG+E+ V+ +   ++ T+P++A  F++RTG D LA+AIGTSHGAYK  G
Sbjct: 128 GVWVEAELGQLAGVEDEVSAEH--SVYTDPDQAVEFVQRTGCDSLAIAIGTSHGAYKFTG 185

Query: 186 RPFIDHARLERIARLVPA-PLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIKKAIS 244
              +D ARLE I +++P  PLVLHGAS+VP E VE   A GG++G A G+  + ++KA +
Sbjct: 186 DAKLDFARLETITKMLPDYPLVLHGASSVPQEFVEMANAYGGKVGGARGVPEDLLRKAAT 245

Query: 245 LGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRM 296
            G+ KIN DTD+RLA TA IR+   +NP +FDPR YL PAREAVK +V+ ++
Sbjct: 246 FGVCKINIDTDIRLAMTATIRKHFIENPGDFDPRAYLKPAREAVKNMVQHKI 297


Lambda     K      H
   0.317    0.134    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: 257
Number of extensions: 10
Number of successful extensions: 4
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: 305
Length of database: 307
Length adjustment: 27
Effective length of query: 278
Effective length of database: 280
Effective search space:    77840
Effective search space used:    77840
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 207620 DVU2143 (fructose-1,6-bisphosphate aldolase, class II)
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.aa/TIGR01859.hmm
# target sequence database:        /tmp/gapView.29715.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.8e-113  364.3   0.1   8.5e-113  362.7   0.1    1.6  1  lcl|MicrobesOnline__882:207620  DVU2143 fructose-1,6-bisphosphat


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207620  DVU2143 fructose-1,6-bisphosphate aldolase, class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.7   0.1  8.5e-113  8.5e-113       5     282 .]       7     307 .]       3     307 .] 0.98

  Alignments for each domain:
  == domain 1  score: 362.7 bits;  conditional E-value: 8.5e-113
                       TIGR01859   5 kellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkalieklsivPvalhLDh 83 
                                     +e++++a++e++avgafn+nn+e++q i++a+ ee++P+i+qvs ga+kY+g  + +++l++a++ ++  +Pv+lhLDh
  lcl|MicrobesOnline__882:207620   7 REMFARAYREGHAVGAFNVNNMEIIQGIMQAGAEERAPLILQVSAGARKYAG-QNYIIKLIEAALLDTD-LPVVLHLDH 83 
                                     69*************************************************9.999*****99998888.********* PP

                       TIGR01859  84 GssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvvekeaeladideakklv 162
                                     G++++ c ++i+ Gf+svmiD+shl++een++ t++vve+ah kgv veaelG+l+G+ed+v +++++++d+d+a ++v
  lcl|MicrobesOnline__882:207620  84 GQDFDICKSCIDGGFTSVMIDGSHLSYEENIAVTRRVVEYAHDKGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVEFV 162
                                     ******************************************************************************* PP

                       TIGR01859 163 ketgvDaLaiaiGtshG..kykgepkldferlkeikklln.lPlvlhGas.....................Gipeeqlk 217
                                     ++tg D+LaiaiGtshG  k++g++kldf+rl++i+k+l+  PlvlhGas                     G+pe+ l+
  lcl|MicrobesOnline__882:207620 163 QRTGCDSLAIAIGTSHGayKFTGDAKLDFARLETITKMLPdYPLVLHGASsvpqefvemanayggkvggarGVPEDLLR 241
                                     *****************8888999***************99************************************** PP

                       TIGR01859 218 kaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekik.vlgsagka 282
                                     ka++ g++k+nidtd+rla+ta+irk++ e+   +dpR +l+parea+k++v++ki+ vlg ++k+
  lcl|MicrobesOnline__882:207620 242 KAATFGVCKINIDTDIRLAMTATIRKHFIENPGDFDPRAYLKPAREAVKNMVQHKIRnVLGCSNKI 307
                                     ********************************************************9899*99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (307 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 1.88
//
[ok]

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