Alignments for a candidate for fba in Alicycliphilus denitrificans K601

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Alicycliphilus denitrificans K601

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate WP_013723211.1 ALIDE2_RS22315 class II fructose-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>NCBI__GCF_000204645.1:WP_013723211.1
          Length = 354

 Score =  490 bits (1261), Expect = e-143
 Identities = 241/354 (68%), Positives = 288/354 (81%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           M LVSMR+LLDHAAD  YG+PAFNVNN+EQV+A+M AA    +PVILQ SAGARKYAGE 
Sbjct: 1   MPLVSMRELLDHAADSGYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGES 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           F+++LI AA EAY  IP+VMHQDHG SPAVC GA+K GF SVMMDGSLKEDGKTPAD+DY
Sbjct: 61  FIKYLILAAAEAYSHIPLVMHQDHGTSPAVCEGALKLGFGSVMMDGSLKEDGKTPADFDY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV VT +VVE+AH VG +VEGELGCLGSLETG+   EDG GA   L H+++LTDP+EAAQ
Sbjct: 121 NVRVTRQVVEMAHKVGATVEGELGCLGSLETGEAGEEDGIGAAGKLSHAQMLTDPEEAAQ 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FVK TQ DALAIAIGTSHGAYKFTR PTGD+LAI R+K IH RIP THLVMHGSSSVPQ+
Sbjct: 181 FVKTTQLDALAIAIGTSHGAYKFTRPPTGDVLAISRVKEIHARIPNTHLVMHGSSSVPQD 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           LL+ I  YGG +K+TYGVPV+EIQE I++GVRK+NIDTDIR+AMT A+R+  A+N  +FD
Sbjct: 241 LLDIINQYGGKMKQTYGVPVKEIQEAIKHGVRKINIDTDIRMAMTGAVRKFQAENPDKFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVVH 354
            R++M  A E AK +C  R+  FG  G+  KI+   L++MA++YA+G L QVV+
Sbjct: 301 MREWMKPAREAAKAICKQRYLEFGCEGQGAKIKGHTLEQMAQKYAAGALGQVVN 354


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: 467
Number of extensions: 15
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: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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_013723211.1 ALIDE2_RS22315 (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.carbon/TIGR01521.hmm
# target sequence database:        /tmp/gapView.1994102.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-182  592.3   1.5   1.7e-182  592.1   1.5    1.0  1  NCBI__GCF_000204645.1:WP_013723211.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204645.1:WP_013723211.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.1   1.5  1.7e-182  1.7e-182       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 592.1 bits;  conditional E-value: 1.7e-182
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           l+s+r lldhaa+ gyg+pafnvnnleq+ a+m aad+  +pvilqas+gar+yage++++ l+laa e y +
  NCBI__GCF_000204645.1:WP_013723211.1   3 LVSMRELLDHAADSGYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGESFIKYLILAAAEAYSH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ip+v+hqdhg+spa+c  a++lgf svmmdgslked+ktpad+dynv+vt +vv++ah vga+vegelgclgs
  NCBI__GCF_000204645.1:WP_013723211.1  76 IPLVMHQDHGTSPAVCEGALKLGFGSVMMDGSLKEDGKTPADFDYNVRVTRQVVEMAHKVGATVEGELGCLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg++++edg g+ g+l ++q+ltdpeeaa+fvk t++dala+aigtshgaykftr+ptg+vlai+r++eih
  NCBI__GCF_000204645.1:WP_013723211.1 149 LETGEAGEEDGIGAAGKLSHAQMLTDPEEAAQFVKTTQLDALAIAIGTSHGAYKFTRPPTGDVLAISRVKEIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           +r+p+thlvmhgsssvpq+ ld+in+ygg++k+tygvpv+ei++ ik+gvrk+nidtd r+a+t+a+r++ a+
  NCBI__GCF_000204645.1:WP_013723211.1 222 ARIPNTHLVMHGSSSVPQDLLDIINQYGGKMKQTYGVPVKEIQEAIKHGVRKINIDTDIRMAMTGAVRKFQAE 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           +p++fd r+++k+a ea k++ck+ry +fg  g+ +kik  +le+ma++ya g l
  NCBI__GCF_000204645.1:WP_013723211.1 295 NPDKFDMREWMKPAREAAKAICKQRYLEFGCEGQGAKIKGHTLEQMAQKYAAGAL 349
                                           ****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 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: 15.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 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

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 catabolism of small carbon sources