Alignments for a candidate for fbp in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Malonomonas rubra DSM 5091

Align Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_072906149.1 BUB13_RS04920 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::A8B2U2
         (323 letters)



>NCBI__GCF_900142125.1:WP_072906149.1
          Length = 326

 Score =  265 bits (677), Expect = 1e-75
 Identities = 147/313 (46%), Positives = 198/313 (63%), Gaps = 10/313 (3%)

Query: 3   LCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYL 62
           L   R++  +A    Y + A+N NN+EQ+Q I+ A  +  SPVI+Q S+GA  Y++   L
Sbjct: 12  LVNSRELFKKAVDGGYAIPAYNFNNLEQLQAIITACAETNSPVIIQVSKGARNYANETML 71

Query: 63  KKLCEAAL----EKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRIT 118
           + +   A+    E   +IPI +HLDHGD+ E  K  ID GFSSVMID SH P+DENV +T
Sbjct: 72  RYMATGAVQMAREMGSNIPIVLHLDHGDSFEICKSCIDSGFSSVMIDGSHLPYDENVALT 131

Query: 119 KEVVAYAHARGVSVEAELGTLGGIEED-VQNTVQLTEPQDAKKFVELTGVDALAVAIGTS 177
           K+VV YAH   V+VE ELG L GIE+D V      T+P + + FV+ TGVD+LA++IGTS
Sbjct: 132 KKVVEYAHQFDVTVEGELGVLAGIEDDVVAEKSTYTQPDEVEDFVKKTGVDSLAISIGTS 191

Query: 178 HGAYKFK---SESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDA 233
           HGAYKFK    ES   L  D ++     + G P+V+HG+SSV     D+IN+YGGKM  A
Sbjct: 192 HGAYKFKLKEGESVPPLRFDILEECEKRIPGFPIVLHGASSVVPAYVDLINQYGGKMDGA 251

Query: 234 VGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEM 293
           VGVP + +  A    VCKIN+DSD R+A+T  +R+     P +FDPR YLG  R  + E+
Sbjct: 252 VGVPEDQLRKAAASAVCKINIDSDGRLAVTAKVREYLANDPGEFDPRKYLGAARKELIEL 311

Query: 294 LIPKIKA-FGSAG 305
           +  K +A  GSAG
Sbjct: 312 IKHKNEAVLGSAG 324


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: 13
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: 326
Length adjustment: 28
Effective length of query: 295
Effective length of database: 298
Effective search space:    87910
Effective search space used:    87910
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_072906149.1 BUB13_RS04920 (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.2837720.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-118  380.0   0.1   5.1e-118  379.8   0.1    1.0  1  NCBI__GCF_900142125.1:WP_072906149.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072906149.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.8   0.1  5.1e-118  5.1e-118       1     281 [.      12     325 ..      12     326 .] 0.97

  Alignments for each domain:
  == domain 1  score: 379.8 bits;  conditional E-value: 5.1e-118
                             TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg...gikvvvalvkalie 70 
                                           lv+ +el++ka +++Ya++a+n+nnle+lqai++a+ e++sPvi+qvs+ga++Y++   ++ +++++v+ + e
  NCBI__GCF_900142125.1:WP_072906149.1  12 LVNSRELFKKAVDGGYAIPAYNFNNLEQLQAIITACAETNSPVIIQVSKGARNYANetmLRYMATGAVQMARE 84 
                                           79******************************************************87777899999999999 PP

                             TIGR01859  71 klsivPvalhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGied 143
                                             s++P++lhLDhG+s+e c ++i++GfssvmiD+shlp++en+++tkkvve+ah+  v+ve elG+l+Gied
  NCBI__GCF_900142125.1:WP_072906149.1  85 MGSNIPIVLHLDHGDSFEICKSCIDSGFSSVMIDGSHLPYDENVALTKKVVEYAHQFDVTVEGELGVLAGIED 157
                                           9999********************************************************************* PP

                             TIGR01859 144 dvvekeaeladideakklvketgvDaLaiaiGtshGkykge.......pkldferlkeikklln.lPlvlhGa 208
                                           dvv+++++++++de++++vk+tgvD+Lai+iGtshG yk +       p l+f+ l+e +k+++ +P+vlhGa
  NCBI__GCF_900142125.1:WP_072906149.1 158 DVVAEKSTYTQPDEVEDFVKKTGVDSLAISIGTSHGAYKFKlkegesvPPLRFDILEECEKRIPgFPIVLHGA 230
                                           ************************************7776666899*****************99******** PP

                             TIGR01859 209 s.....................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilap 260
                                           s                     G+pe+ql+ka+ ++++k+nid+d rla+ta++r++l+++  e+dpRk+l+ 
  NCBI__GCF_900142125.1:WP_072906149.1 231 SsvvpayvdlinqyggkmdgavGVPEDQLRKAAASAVCKINIDSDGRLAVTAKVREYLANDPGEFDPRKYLGA 303
                                           ************************************************************************* PP

                             TIGR01859 261 arealkevvkekik.vlgsagk 281
                                           ar++l e++k+k++ vlgsagk
  NCBI__GCF_900142125.1:WP_072906149.1 304 ARKELIELIKHKNEaVLGSAGK 325
                                           *************989***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (326 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: 20.02
//
[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