Alignments for a candidate for fbp in Paraburkholderia atlantica CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for fbp in Paraburkholderia atlantica CCGE1002

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_013091061.1 BC1002_RS16105 class II fructose-bisphosphate aldolase

Query= BRENDA::Q602L6
         (354 letters)



>NCBI__GCF_000092885.1:WP_013091061.1
          Length = 345

 Score =  486 bits (1250), Expect = e-142
 Identities = 242/344 (70%), Positives = 279/344 (81%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MA I+LRQLLDHAAEH YG+PAFNVNNMEQI AIM AA A D+PVILQ SAGAR YAGEP
Sbjct: 1   MAFITLRQLLDHAAEHDYGVPAFNVNNMEQIHAIMRAAEATDSPVILQASAGARKYAGEP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           +LRHLV AA+E +P IP+ +HQDHGASPAVC ++I+SGF+SVMMDGSLL D KTPA+Y Y
Sbjct: 61  YLRHLVLAALEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPAAYDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NVE +R+VV+ AHA GVSVEGELGCLGSLETG AG+EDG GAEG+L    LLTDPDEA  
Sbjct: 121 NVEVSRRVVDAAHAVGVSVEGELGCLGSLETGTAGEEDGVGAEGKLTREHLLTDPDEARR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV  T VDALAIAIGTSHGAYKF+R+PTG +L IDR+ +IH RIP  HLVMHGSSSVP+E
Sbjct: 181 FVEATGVDALAIAIGTSHGAYKFSREPTGDILAIDRIASIHSRIPDTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W  +I +YGG+I  TYGVPV+EI  GI HGVRKVNIDTD+R+A  GAMR+ +   R  FD
Sbjct: 241 WLAVIREYGGEIPTTYGVPVDEIRRGIAHGVRKVNIDTDIRLAMSGAMRKSLANARSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAY 344
           PR   KAA  A +AIC  R+EAFG AGQAA+IKPL L+ M+  Y
Sbjct: 301 PRAALKAATAAASAICIERFEAFGCAGQAARIKPLPLDTMASRY 344


Lambda     K      H
   0.320    0.134    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: 488
Number of extensions: 19
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: 345
Length adjustment: 29
Effective length of query: 325
Effective length of database: 316
Effective search space:   102700
Effective search space used:   102700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_013091061.1 BC1002_RS16105 (class II fructose-bisphosphate aldolase)
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.2723045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-184  596.9   0.2   6.7e-184  596.7   0.2    1.0  1  NCBI__GCF_000092885.1:WP_013091061.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092885.1:WP_013091061.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.7   0.2  6.7e-184  6.7e-184       2     342 ..       4     344 ..       3     345 .] 1.00

  Alignments for each domain:
  == domain 1  score: 596.7 bits;  conditional E-value: 6.7e-184
                             TIGR01521   2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdi 74 
                                           i+lrqlldhaae+ ygvpafnvnn+eqi aim+aa++tdspvilqas+gar+yage++lr+lvlaa e +pdi
  NCBI__GCF_000092885.1:WP_013091061.1   4 ITLRQLLDHAAEHDYGVPAFNVNNMEQIHAIMRAAEATDSPVILQASAGARKYAGEPYLRHLVLAALEAHPDI 76 
                                           89*********************************************************************** PP

                             TIGR01521  75 pvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsl 147
                                           p+vlhqdhg+spa+c++ai+ gftsvmmdgsl  d ktpa ydynv+v+ +vv  ahavg+svegelgclgsl
  NCBI__GCF_000092885.1:WP_013091061.1  77 PLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPAAYDYNVEVSRRVVDAAHAVGVSVEGELGCLGSL 149
                                           ************************************************************************* PP

                             TIGR01521 148 etgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeihe 220
                                           etg++++edg+g+eg+l r  lltdp+ea +fv+ t+vdala+aigtshgaykf+r+ptg++laidri  ih+
  NCBI__GCF_000092885.1:WP_013091061.1 150 ETGTAGEEDGVGAEGKLTREHLLTDPDEARRFVEATGVDALAIAIGTSHGAYKFSREPTGDILAIDRIASIHS 222
                                           ************************************************************************* PP

                             TIGR01521 221 rlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakd 293
                                           r+pdthlvmhgsssvpqewl+vi eyggei+ tygvpv+ei +gi +gvrkvnidtd rla+++a+r+ +a+ 
  NCBI__GCF_000092885.1:WP_013091061.1 223 RIPDTHLVMHGSSSVPQEWLAVIREYGGEIPTTYGVPVDEIRRGIAHGVRKVNIDTDIRLAMSGAMRKSLANA 295
                                           ************************************************************************* PP

                             TIGR01521 294 psefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarry 342
                                           +sefdpr  lk a  a +++c++r+eafg ag+a++ik+++l+ ma ry
  NCBI__GCF_000092885.1:WP_013091061.1 296 RSEFDPRAALKAATAAASAICIERFEAFGCAGQAARIKPLPLDTMASRY 344
                                           ************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (345 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: 15.79
//
[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