Alignments for a candidate for fbp in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Bradyrhizobium sp. BTAi1

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_024918864.1 BBTA_RS02170 fructose-bisphosphate aldolase class II

Query= BRENDA::Q55664
         (359 letters)



>NCBI__GCF_000015165.1:WP_024918864.1
          Length = 359

 Score =  479 bits (1234), Expect = e-140
 Identities = 233/349 (66%), Positives = 283/349 (81%)

Query: 1   MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60
           MAL+ +R LLDHAAE GYG+PAFN+NNMEQ ++I++AA E D+PVI+QASRGARSYAG+ 
Sbjct: 1   MALITLRQLLDHAAEQGYGVPAFNINNMEQGLAILEAAREMDAPVIIQASRGARSYAGDV 60

Query: 61  FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120
            L+ ++   VE +P IP+ +HQDHGN+  TC SAI+NGF+SVMMDGSL+ DAKTPA ++Y
Sbjct: 61  MLQKVIEALVEMFPDIPVCLHQDHGNNVNTCLSAIQNGFSSVMMDGSLKEDAKTPADYDY 120

Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180
           NV VT +V ++AH VG SVEGELGCLGSLETG GEAEDGHGFEGKLD S LLTDP+EA+ 
Sbjct: 121 NVKVTRQVTELAHMVGVSVEGELGCLGSLETGHGEAEDGHGFEGKLDKSMLLTDPDEAMR 180

Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240
           FV +T+VDALAVAIGTSHGAYKFTRKPTGEVLA++ IE IH+ LPNTH+VMHGSSSVP+E
Sbjct: 181 FVAETKVDALAVAIGTSHGAYKFTRKPTGEVLAMTVIEAIHQKLPNTHIVMHGSSSVPEE 240

Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300
           W ++ N  GG + ETYGVPVEEI +GIK GVRK+NIDTD RLA TA FR  A      FD
Sbjct: 241 WQEVFNAHGGQMRETYGVPVEEIVRGIKHGVRKINIDTDLRLAATAEFRRVANTKKDEFD 300

Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYAKGEL 349
           PR FLKP++  M++VCA+R++ F  AGNASKIK + L + A +Y  G L
Sbjct: 301 PRKFLKPAMDAMRKVCAERFEAFGAAGNASKIKPIPLSEMAKRYTNGAL 349


Lambda     K      H
   0.315    0.131    0.377 

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: 464
Number of extensions: 17
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: 359
Length of database: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
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_024918864.1 BBTA_RS02170 (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.29607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-208  675.9   0.5   6.6e-208  675.7   0.5    1.0  1  lcl|NCBI__GCF_000015165.1:WP_024918864.1  BBTA_RS02170 fructose-bisphospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_024918864.1  BBTA_RS02170 fructose-bisphosphate aldolase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.7   0.5  6.6e-208  6.6e-208       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 675.7 bits;  conditional E-value: 6.6e-208
                                 TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 
                                               li+lrqlldhaae+gygvpafn+nn+eq lai+eaa++ d+pvi+qasrgarsyag+v+l+k+++a+ve
  lcl|NCBI__GCF_000015165.1:WP_024918864.1   3 LITLRQLLDHAAEQGYGVPAFNINNMEQGLAILEAAREMDAPVIIQASRGARSYAGDVMLQKVIEALVE 71 
                                               69******************************************************************* PP

                                 TIGR01521  70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138
                                               ++pdipv+lhqdhgn+++tclsaiq+gf+svmmdgslkedaktpadydynv+vt +v++lah+vg+sve
  lcl|NCBI__GCF_000015165.1:WP_024918864.1  72 MFPDIPVCLHQDHGNNVNTCLSAIQNGFSSVMMDGSLKEDAKTPADYDYNVKVTRQVTELAHMVGVSVE 140
                                               ********************************************************************* PP

                                 TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207
                                               gelgclgsletg+geaedghgfeg+ld+s lltdp+ea++fv++tkvdalavaigtshgaykftrkptg
  lcl|NCBI__GCF_000015165.1:WP_024918864.1 141 GELGCLGSLETGHGEAEDGHGFEGKLDKSMLLTDPDEAMRFVAETKVDALAVAIGTSHGAYKFTRKPTG 209
                                               ********************************************************************* PP

                                 TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276
                                               evla+ +ie ih++lp+th+vmhgsssvp+ew++v+n++gg+++etygvpveeiv+gik+gvrk+nidt
  lcl|NCBI__GCF_000015165.1:WP_024918864.1 210 EVLAMTVIEAIHQKLPNTHIVMHGSSSVPEEWQEVFNAHGGQMRETYGVPVEEIVRGIKHGVRKINIDT 278
                                               ********************************************************************* PP

                                 TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345
                                               dlrlaata +rrva+++++efdprkflk+a++am++vc++r+eafg+agnaskik+++l ema+ry++g
  lcl|NCBI__GCF_000015165.1:WP_024918864.1 279 DLRLAATAEFRRVANTKKDEFDPRKFLKPAMDAMRKVCAERFEAFGAAGNASKIKPIPLSEMAKRYTNG 347
                                               ********************************************************************9 PP

                                 TIGR01521 346 el 347
                                                l
  lcl|NCBI__GCF_000015165.1:WP_024918864.1 348 AL 349
                                               86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (359 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.36
//
[ok]

This GapMind analysis is from Apr 10 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:

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