Alignments for a candidate for fbp in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Clostridium kluyveri DSM 555

Align Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_012103922.1 CKL_RS17525 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::A8B2U2
         (323 letters)



>NCBI__GCF_000016505.1:WP_012103922.1
          Length = 313

 Score =  278 bits (710), Expect = 2e-79
 Identities = 146/300 (48%), Positives = 200/300 (66%), Gaps = 3/300 (1%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           M L T ++M  +A K  Y +GAFN+NNME IQG++       S VILQCS  A+KY+   
Sbjct: 1   MALVTTKKMFEKAYKGHYSIGAFNINNMEIIQGVVNGAKAKNSAVILQCSASAMKYAGPK 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           YLK + +AA+E    I I +HLDHG   E+VK+ I+ GF+SVM D SH  +++NV  TK+
Sbjct: 61  YLKAMVDAAVED-TGIDIALHLDHGPDFEAVKLCIETGFTSVMFDGSHLDYEDNVSQTKQ 119

Query: 121 VVAYAHARGVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAIGTSHG 179
           VV Y+H+ GV VEAELG L GIE++V  +  + T+P+ A  FV  TGVD+LA+AIGTSHG
Sbjct: 120 VVEYSHSHGVVVEAELGVLAGIEDEVSASDHIYTDPEQAVDFVNRTGVDSLAIAIGTSHG 179

Query: 180 AYKFKSESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPI 238
           A+KF      +L  D ++ I + L   P+V+HG+S+V     +  NKYGG + DA G+PI
Sbjct: 180 AFKFPPNFKPKLRFDILEKIQENLPNFPIVLHGASAVDPKAVETCNKYGGNIADAKGIPI 239

Query: 239 ESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKI 298
           + +  A    VCKIN+D+D R++MT AIRK F + P+ FDPR YLG GRDAI +++  KI
Sbjct: 240 DMLRKASSMAVCKINMDTDLRLSMTAAIRKTFGDSPKVFDPRKYLGAGRDAIQKVVEDKI 299


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: 297
Number of extensions: 17
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: 313
Length adjustment: 27
Effective length of query: 296
Effective length of database: 286
Effective search space:    84656
Effective search space used:    84656
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_012103922.1 CKL_RS17525 (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.519660.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-108  347.4   0.5   4.4e-108  347.2   0.5    1.0  1  NCBI__GCF_000016505.1:WP_012103922.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016505.1:WP_012103922.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.2   0.5  4.4e-108  4.4e-108       1     280 [.       3     307 ..       3     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 347.2 bits;  conditional E-value: 4.4e-108
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv++k+++eka+k++Y++gafninn+e++q +++ a++++s vi+q s  a+kY+g  k ++a+v a++e++ 
  NCBI__GCF_000016505.1:WP_012103922.1   3 LVTTKKMFEKAYKGHYSIGAFNINNMEIIQGVVNGAKAKNSAVILQCSASAMKYAG-PKYLKAMVDAAVEDTG 74 
                                           79*****************************************************9.9*************99 PP

                             TIGR01859  74 ivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvv 146
                                            + +alhLDhG ++e++  +i++Gf+svm+D+shl +e+n+++tk+vve++h++gv veaelG+l+Gied+v 
  NCBI__GCF_000016505.1:WP_012103922.1  75 -IDIALHLDHGPDFEAVKLCIETGFTSVMFDGSHLDYEDNVSQTKQVVEYSHSHGVVVEAELGVLAGIEDEVS 146
                                           .************************************************************************ PP

                             TIGR01859 147 ekeaeladideakklvketgvDaLaiaiGtshG..kykge..pkldferlkeikklln.lPlvlhGas..... 209
                                           + +  ++d+++a ++v++tgvD+LaiaiGtshG  k++ +  pkl+f+ l++i++ l+ +P+vlhGas     
  NCBI__GCF_000016505.1:WP_012103922.1 147 ASDHIYTDPEQAVDFVNRTGVDSLAIAIGTSHGafKFPPNfkPKLRFDILEKIQENLPnFPIVLHGASavdpk 219
                                           *********************************777777799*************9988************** PP

                             TIGR01859 210 ................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealk 266
                                                           Gip ++l+ka +++++k+n+dtdlrl++taairk++ +  + +dpRk+l+ +r+a++
  NCBI__GCF_000016505.1:WP_012103922.1 220 avetcnkyggniadakGIPIDMLRKASSMAVCKINMDTDLRLSMTAAIRKTFGDSPKVFDPRKYLGAGRDAIQ 292
                                           ************************************************************************* PP

                             TIGR01859 267 evvkekik.vlgsag 280
                                           +vv++ki+ vlgs++
  NCBI__GCF_000016505.1:WP_012103922.1 293 KVVEDKIDnVLGSSN 307
                                           *******9899*998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (313 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: 14.90
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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