Alignments for a candidate for fbp in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Ammonifex degensii KC4

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_012818212.1 ADEG_RS00260 class II fructose-1,6-bisphosphate aldolase

Query= BRENDA::Q9RHA2
         (305 letters)



>NCBI__GCF_000024605.1:WP_012818212.1
          Length = 287

 Score =  289 bits (739), Expect = 6e-83
 Identities = 160/305 (52%), Positives = 200/305 (65%), Gaps = 24/305 (7%)

Query: 2   LVTGLEILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRA-L 60
           LVT  E+L  A   GY VGAFN NNME LQA++ AAE +RSPVI+  S+GA+KY G   +
Sbjct: 3   LVTLREVLGAAAAGGYAVGAFNCNNMEILQAIVTAAEAERSPVIVQASQGAIKYAGLDYI 62

Query: 61  TLMAVELAKEARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVE 120
             MA      A VPV +HLDHG+SYE V+R L AGF+SVMID S    E N+  T+ VV+
Sbjct: 63  AAMAKTALASATVPVVLHLDHGTSYEQVIRCLAAGFSSVMIDASRLPLEENIALTKEVVK 122

Query: 121 AAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGA 180
           AA AVG +VEAELGR+ G E+ ++V E++A  T+P+EA  F+E+TG D LAVAIGT+HG 
Sbjct: 123 AARAVGASVEAELGRIGGTEDDISVAEREAFFTDPDEAAYFVEQTGVDALAVAIGTAHGP 182

Query: 181 YKGKGRPFIDHARLERIARLVPAPLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIK 240
           Y+ +  P +D  RL RIA  V  PLVLHG+S VP                      EDIK
Sbjct: 183 YRWE--PKLDFERLSRIAAKVKVPLVLHGSSGVP---------------------AEDIK 219

Query: 241 KAISLGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRMELFG 300
           +AI  GI KIN DTD+R+AF   +RE L  NP E DPRK LGPAREA  EV++ +M +FG
Sbjct: 220 EAIRRGIRKINIDTDIRIAFVNRMREVLMANPDEIDPRKILGPAREAATEVIREKMRIFG 279

Query: 301 SVGRA 305
           S G+A
Sbjct: 280 SSGKA 284


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: 271
Number of extensions: 13
Number of successful extensions: 5
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: 287
Length adjustment: 26
Effective length of query: 279
Effective length of database: 261
Effective search space:    72819
Effective search space used:    72819
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_012818212.1 ADEG_RS00260 (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.3997199.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-122  394.4   0.1   2.1e-122  394.2   0.1    1.0  1  NCBI__GCF_000024605.1:WP_012818212.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000024605.1:WP_012818212.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.2   0.1  2.1e-122  2.1e-122       1     282 []       3     284 ..       3     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 394.2 bits;  conditional E-value: 2.1e-122
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkaliekls 73 
                                           lv+ +e+l +a +++Yavgafn nn+e+lqai++aae+e+sPvivq+s+ga+kY+g ++ ++a+ k+++ +++
  NCBI__GCF_000024605.1:WP_012818212.1   3 LVTLREVLGAAAAGGYAVGAFNCNNMEILQAIVTAAEAERSPVIVQASQGAIKYAG-LDYIAAMAKTALASAT 74 
                                           7999***************************************************9.9************999 PP

                             TIGR01859  74 ivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGiedd.. 144
                                            vPv+lhLDhG+sye++i+++ aGfssvmiDas+lpleen+++tk+vv++a+a g sveaelG++gG+edd  
  NCBI__GCF_000024605.1:WP_012818212.1  75 -VPVVLHLDHGTSYEQVIRCLAAGFSSVMIDASRLPLEENIALTKEVVKAARAVGASVEAELGRIGGTEDDis 146
                                           .**********************************************************************88 PP

                             TIGR01859 145 vvekeaeladideakklvketgvDaLaiaiGtshGkykgepkldferlkeikkllnlPlvlhGasGipeeqlk 217
                                           v e+ea ++d+dea  +v++tgvDaLa+aiGt+hG+y+ epkldferl +i  ++++PlvlhG+sG+p e++k
  NCBI__GCF_000024605.1:WP_012818212.1 147 VAEREAFFTDPDEAAYFVEQTGVDALAVAIGTAHGPYRWEPKLDFERLSRIAAKVKVPLVLHGSSGVPAEDIK 219
                                           99*********************************************************************** PP

                             TIGR01859 218 kaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekikvlgsagka 282
                                           +ai+ gi k+nidtd+r+af++++r+vl ++ de+dpRkil+parea  ev++ek++++gs+gka
  NCBI__GCF_000024605.1:WP_012818212.1 220 EAIRRGIRKINIDTDIRIAFVNRMREVLMANPDEIDPRKILGPAREAATEVIREKMRIFGSSGKA 284
                                           ***************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (287 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.62
//
[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