Alignments for a candidate for fbp in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Prosthecochloris aestuarii DSM 271

Align Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_012505621.1 PAES_RS05255 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::A8B2U2
         (323 letters)



>NCBI__GCF_000020625.1:WP_012505621.1
          Length = 324

 Score =  285 bits (729), Expect = 1e-81
 Identities = 148/304 (48%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 7   RQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYLKKLC 66
           +++  +A K  Y + A+N NN+EQ+Q I+ A V+  SPVILQ S+GA  Y++   L+ L 
Sbjct: 17  KELFAKAVKGGYAIPAYNFNNLEQLQAIIMACVETNSPVILQVSKGARNYANQTLLRNLA 76

Query: 67  EAALEKHPD----IPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKEVV 122
             A+E   +    +PI +HLDHGD+ E  K  I  GFSSVMID SH  +++NV +T++VV
Sbjct: 77  RGAVEYAAELGNPVPIVLHLDHGDSFELCKDCIQTGFSSVMIDGSHLSYEDNVTLTRQVV 136

Query: 123 AYAHARGVSVEAELGTLGGIEEDVQN-TVQLTEPQDAKKFVELTGVDALAVAIGTSHGAY 181
            YAH   V+VE ELG L G+E++V + T   T+P++ + FV  TGVD+LA+AIGTSHGA+
Sbjct: 137 DYAHQYDVTVEGELGVLAGVEDEVASETHTYTQPEEVEDFVTRTGVDSLAIAIGTSHGAF 196

Query: 182 KFKSESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPIES 240
           KFK   D ++ +D +  I   + G P+V+HGSSSVP+D+   IN++GGK+ DA+G+  E 
Sbjct: 197 KFKPGEDHKIRLDILSEIEKRIPGFPIVLHGSSSVPQDLVKTINEHGGKLKDAIGISEEQ 256

Query: 241 IVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPK-IK 299
           +  A    VCKIN+DSD R+AMT AIRKV  E PE+FDPR YLGP RDA+ E+   K I 
Sbjct: 257 LRKAAQSAVCKINIDSDGRLAMTAAIRKVLDEKPEEFDPRKYLGPARDALKELYKHKNIN 316

Query: 300 AFGS 303
             GS
Sbjct: 317 VLGS 320


Lambda     K      H
   0.318    0.135    0.391 

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: 292
Number of extensions: 11
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_012505621.1 PAES_RS05255 (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.aa/TIGR01859.hmm
# target sequence database:        /tmp/gapView.2689906.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-117  375.8   0.1   1.2e-116  375.4   0.1    1.2  1  NCBI__GCF_000020625.1:WP_012505621.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020625.1:WP_012505621.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.4   0.1  1.2e-116  1.2e-116       3     282 .]      15     324 .]      13     324 .] 0.97

  Alignments for each domain:
  == domain 1  score: 375.4 bits;  conditional E-value: 1.2e-116
                             TIGR01859   3 kakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg...gikvvvalvkaliekl 72 
                                           + kel++ka k++Ya++a+n+nnle+lqai+ a+ e++sPvi+qvs+ga++Y++   +++ ++++v++++e  
  NCBI__GCF_000020625.1:WP_012505621.1  15 NSKELFAKAVKGGYAIPAYNFNNLEQLQAIIMACVETNSPVILQVSKGARNYANqtlLRNLARGAVEYAAELG 87 
                                           789***************************************************8888999************ PP

                             TIGR01859  73 sivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddv 145
                                           + vP++lhLDhG+s+e c ++i++GfssvmiD+shl++e+n+++t++vv++ah+  v+ve elG+l+G+ed+v
  NCBI__GCF_000020625.1:WP_012505621.1  88 NPVPIVLHLDHGDSFELCKDCIQTGFSSVMIDGSHLSYEDNVTLTRQVVDYAHQYDVTVEGELGVLAGVEDEV 160
                                           ************************************************************************* PP

                             TIGR01859 146 vekeaeladideakklvketgvDaLaiaiGtshGkykge....pkldferlkeikklln.lPlvlhGas.... 209
                                            ++  ++++++e++++v +tgvD+LaiaiGtshG +k +    +k++++ l ei+k+++ +P+vlhG+s    
  NCBI__GCF_000020625.1:WP_012505621.1 161 ASETHTYTQPEEVEDFVTRTGVDSLAIAIGTSHGAFKFKpgedHKIRLDILSEIEKRIPgFPIVLHGSSsvpq 233
                                           **********************************66655446799*************99************* PP

                             TIGR01859 210 .................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilapareal 265
                                                            Gi+eeql+ka++++++k+nid+d rla+taairkvl+ek +e+dpRk+l+par+al
  NCBI__GCF_000020625.1:WP_012505621.1 234 dlvktinehggklkdaiGISEEQLRKAAQSAVCKINIDSDGRLAMTAAIRKVLDEKPEEFDPRKYLGPARDAL 306
                                           ************************************************************************* PP

                             TIGR01859 266 kevvkekik.vlgsagka 282
                                           ke++k+k+  vlgs++ka
  NCBI__GCF_000020625.1:WP_012505621.1 307 KELYKHKNInVLGSNDKA 324
                                           ******97559***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (324 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.23
//
[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