Alignments for a candidate for fbp in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Pelobacter propionicus DSM 2379

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_041532230.1 PPRO_RS09220 class II fructose-bisphosphate aldolase

Query= BRENDA::P9WQA3
         (344 letters)



>NCBI__GCF_000015045.1:WP_041532230.1
          Length = 341

 Score =  372 bits (956), Expect = e-108
 Identities = 193/345 (55%), Positives = 244/345 (70%), Gaps = 10/345 (2%)

Query: 1   MPIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFG 60
           MP+A    Y  ML +A++N +A+PAIN +S  T NA ++G A+A  DGIIQ STGGA F 
Sbjct: 1   MPVADLTTYRRMLDRARENRFAYPAINVSSLATANAVLRGLAEARCDGIIQVSTGGAAFA 60

Query: 61  SGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKG 120
           SG  +KDM  GA+++AE  H  A +YP+ VALHTDHCP DKLDS+V PL+A + +R + G
Sbjct: 61  SGTALKDMPLGAISIAEHVHRAAQRYPIYVALHTDHCPADKLDSFVLPLVAETERRRAAG 120

Query: 121 GNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKL 180
              LF SHM+DGSA+ + +NL  A  LL+   A ++ILEIE GVVGGEEDG+  + + KL
Sbjct: 121 LPNLFNSHMFDGSALALKDNLDTATRLLERFTACELILEIETGVVGGEEDGIKADASAKL 180

Query: 181 YTSPE---DFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAK 237
           YT+PE   +  + +  LG    G YLLAATFGNVHGVYKPG VKLRP +L + Q     +
Sbjct: 181 YTTPEETLEVARRLNPLG----GHYLLAATFGNVHGVYKPGAVKLRPSVLKECQDAVVTR 236

Query: 238 LGLPADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDG 297
            G   +A  F  VFHGGSGS   EI EAL YGVVKMN+DTDTQYAFTRPIAGHMF++YDG
Sbjct: 237 YG---EAARFHLVFHGGSGSELHEIREALDYGVVKMNIDTDTQYAFTRPIAGHMFSHYDG 293

Query: 298 VLKVDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSL 342
           VLKVDG++G KK YDPR+YL  AE +M++RV +A +DL     +L
Sbjct: 294 VLKVDGDMGDKKAYDPRTYLALAETAMAERVKRAVSDLRGTNSTL 338


Lambda     K      H
   0.316    0.133    0.384 

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: 328
Number of extensions: 8
Number of successful extensions: 3
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: 344
Length of database: 341
Length adjustment: 29
Effective length of query: 315
Effective length of database: 312
Effective search space:    98280
Effective search space used:    98280
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_041532230.1 PPRO_RS09220 (class II fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-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/TIGR01520.hmm
# target sequence database:        /tmp/gapView.2192373.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-120  386.3   0.0     8e-120  386.0   0.0    1.0  1  NCBI__GCF_000015045.1:WP_041532230.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015045.1:WP_041532230.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.0   0.0    8e-120    8e-120      14     356 ..       8     336 ..       2     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 386.0 bits;  conditional E-value: 8e-120
                             TIGR01520  14 dvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaekaasiaGaia 86 
                                            ++++++ a+e++fa Painv s  t+na+l++ ++a++++i+q+s+ggaaf +G  +kd      +  Gai+
  NCBI__GCF_000015045.1:WP_041532230.1   8 TYRRMLDRARENRFAYPAINVSSLATANAVLRGLAEARCDGIIQVSTGGAAFASGTALKD------MPLGAIS 74 
                                           5789********************************************************......889**** PP

                             TIGR01520  87 aaeyvrsiaekygvpvvlhtdhCakkllp.yvdglleadekyfkkegkPlfsshmldlseepieenieiakky 158
                                            ae+v+  a++y++ v+lhtdhC+ ++l+ +v +l+++ e++ +++   lf+shm+d+s+ ++++n+++a+++
  NCBI__GCF_000015045.1:WP_041532230.1  75 IAEHVHRAAQRYPIYVALHTDHCPADKLDsFVLPLVAETERRRAAGLPNLFNSHMFDGSALALKDNLDTATRL 147
                                           *****************************9*************999999************************ PP

                             TIGR01520 159 lkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafGnvhGvykpGn 231
                                           l+r ++ +lileie G++GGeedG++ +    ++lyt+Pe+  +v + l++  +++ +aa+fGnvhGvykpG 
  NCBI__GCF_000015045.1:WP_041532230.1 148 LERFTACELILEIETGVVGGEEDGIKADAS--AKLYTTPEETLEVARRLNPLGGHYLLAATFGNVHGVYKPGA 218
                                           *************************99887..99*************************************** PP

                             TIGR01520 232 vklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaalegildyvlk 304
                                           vklrP +l++ q+ v  + g      +++vfhGGsGs  +ei+eal+yGvvk+n+dtdtqya++++i++++++
  NCBI__GCF_000015045.1:WP_041532230.1 219 VKLRPSVLKECQDAVVTRYGEA--ARFHLVFHGGSGSELHEIREALDYGVVKMNIDTDTQYAFTRPIAGHMFS 289
                                           ******************9966..78*********************************************** PP

                             TIGR01520 305 nedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                           ++d +++++G     +++ kk ydPr++l  ae++m +rv++a+ +l+ +n 
  NCBI__GCF_000015045.1:WP_041532230.1 290 HYDGVLKVDG-----DMGDKKAYDPRTYLALAETAMAERVKRAVSDLRGTNS 336
                                           **********.....99******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (341 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: 00:00:00.00
# Mc/sec: 24.64
//
[ok]

This GapMind analysis is from Jul 25 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 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