Alignments for a candidate for fbp in Epibacterium ulvae U95

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Epibacterium ulvae U95

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_090219443.1 CV091_RS12880 fructose-bisphosphate aldolase class II

Query= SwissProt::Q56815
         (354 letters)



>NCBI__GCF_002796795.1:WP_090219443.1
          Length = 355

 Score =  465 bits (1197), Expect = e-136
 Identities = 232/349 (66%), Positives = 275/349 (78%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           MAL+S+RQLLDHAA+  YGLPAFNVNNMEQ+ AIM AA AT+SPVI+Q S GAR YA + 
Sbjct: 1   MALISLRQLLDHAAEQGYGLPAFNVNNMEQMLAIMKAADATNSPVIMQASRGARNYANDI 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
            L HLI AA+E YP IPV MHQDHG SP  C+ A+ +GFSSVMMDGSL  DGKTPAD+DY
Sbjct: 61  VLGHLIKAAIELYPHIPVCMHQDHGNSPQTCLSALTNGFSSVMMDGSLMADGKTPADFDY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           N  VT +VV++AH VG SVEGE+G LGSLETGKGEAEDGHG +  +    L+TD DEAA+
Sbjct: 121 NAGVTKQVVDMAHMVGASVEGEIGHLGSLETGKGEAEDGHGFDGEMSMDMLVTDADEAAE 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FVKAT  DALA+AIGTSHGAYKF+R+P GDILA+D +K IH ++P THLVMHGSSSVPQE
Sbjct: 181 FVKATNVDALAVAIGTSHGAYKFSREPDGDILAMDALKKIHAKLPDTHLVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           L E +  +GG+I  T+GVPVEEI+ GI++GVRKVNIDTD+RLAMT AIR++    + EFD
Sbjct: 241 LQEIVNEFGGEIAPTWGVPVEEIEVGIKHGVRKVNIDTDLRLAMTGAIRKLLWSKREEFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGEL 349
           PRK++A  +E    VC  RFE FGSAG+A  I  I L +MAKRY SG L
Sbjct: 301 PRKYLAPGIEAMSAVCKDRFERFGSAGQAANITPIPLADMAKRYDSGAL 349


Lambda     K      H
   0.316    0.132    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: 440
Number of extensions: 9
Number of successful extensions: 1
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: 354
Length of database: 355
Length adjustment: 29
Effective length of query: 325
Effective length of database: 326
Effective search space:   105950
Effective search space used:   105950
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: 49 (23.5 bits)

Align candidate WP_090219443.1 CV091_RS12880 (fructose-bisphosphate aldolase class II)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (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/TIGR01521.hmm
# target sequence database:        /tmp/gapView.2787476.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01521  [M=347]
Accession:   TIGR01521
Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-185  600.8   0.5   4.5e-185  600.6   0.5    1.0  1  NCBI__GCF_002796795.1:WP_090219443.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090219443.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.6   0.5  4.5e-185  4.5e-185       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 600.6 bits;  conditional E-value: 4.5e-185
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           lislrqlldhaae+gyg+pafnvnn+eq+laim+aad+t+spvi+qasrgar+ya++ +l +l++aa+e yp+
  NCBI__GCF_002796795.1:WP_090219443.1   3 LISLRQLLDHAAEQGYGLPAFNVNNMEQMLAIMKAADATNSPVIMQASRGARNYANDIVLGHLIKAAIELYPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipv++hqdhgnsp+tclsa+ +gf+svmmdgsl +d+ktpad+dyn  vt++vv +ah+vgasvege+g lgs
  NCBI__GCF_002796795.1:WP_090219443.1  76 IPVCMHQDHGNSPQTCLSALTNGFSSVMMDGSLMADGKTPADFDYNAGVTKQVVDMAHMVGASVEGEIGHLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letgkgeaedghgf+g +    l+td +eaaefvk t+vdalavaigtshgaykf+r+p g++la+d +++ih
  NCBI__GCF_002796795.1:WP_090219443.1 149 LETGKGEAEDGHGFDGEMSMDMLVTDADEAAEFVKATNVDALAVAIGTSHGAYKFSREPDGDILAMDALKKIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           ++lpdthlvmhgsssvpqe ++++ne+ggei  t+gvpveei  gik+gvrkvnidtdlrla+t+a+r+++  
  NCBI__GCF_002796795.1:WP_090219443.1 222 AKLPDTHLVMHGSSSVPQELQEIVNEFGGEIAPTWGVPVEEIEVGIKHGVRKVNIDTDLRLAMTGAIRKLLWS 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           +++efdprk+l + +eam++vck+r+e fg+ag+a++i +++l +ma+ry +g l
  NCBI__GCF_002796795.1:WP_090219443.1 295 KREEFDPRKYLAPGIEAMSAVCKDRFERFGSAGQAANITPIPLADMAKRYDSGAL 349
                                           ***************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (355 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: 14.50
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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