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.24477.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: 2.08
//
[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