Alignments for a candidate for fba in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Caulobacter crescentus NA1000

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate CCNA_03360 CCNA_03360 tagatose-1,6-bisphosphate aldolase

Query= SwissProt::Q8YNK2
         (359 letters)



>FitnessBrowser__Caulo:CCNA_03360
          Length = 363

 Score =  491 bits (1264), Expect = e-143
 Identities = 241/357 (67%), Positives = 294/357 (82%)

Query: 1   MALVPLRLLLDHAAENGYGIPAFNVNNLEQIQAILKAAAETDSPVILQASRGARNYAGEN 60
           MA + LR LLDHAAE+ YG+PAFN+NN+EQ  AI++AA   +SPVI+QASRGARNYA + 
Sbjct: 1   MARITLRQLLDHAAEHEYGLPAFNINNMEQGLAIMEAADAVNSPVIIQASRGARNYANDI 60

Query: 61  FLRHLILAAVETYPEIPIVMHQDHGNAPSTCYSAIKNNFTSVMMDGSLEADAKTPASFEY 120
            L  +I A V+ YP IP+ MHQDHGN P+TC +AI+  FTSVMMDGSL  DAKTPAS+EY
Sbjct: 61  MLAKMIDALVDIYPHIPVCMHQDHGNGPATCATAIQYGFTSVMMDGSLMEDAKTPASYEY 120

Query: 121 NVNVTREVVNVAHALGVSVEGELGCLGSLETGAGEAEDGHGFEGTLDHSQLLTDPDEAVN 180
           NV VTR+VV +AH+ GVSVEGELG LGSLETG GEAEDGHGFEG L H +LLTDPD+AV+
Sbjct: 121 NVEVTRKVVQMAHSCGVSVEGELGVLGSLETGMGEAEDGHGFEGKLSHDELLTDPDQAVD 180

Query: 181 FVEATQVDALAVAIGTSHGAYKFTRKPTGEILAISRIEEIHRRLPNTHLVMHGSSSVPED 240
           FV  T VDALA+A+GTSHGAYKFTRKP G++LA++ IEEIHRRLPNTHLVMHGSSSVP+D
Sbjct: 181 FVAQTGVDALAIAMGTSHGAYKFTRKPDGDVLAMNVIEEIHRRLPNTHLVMHGSSSVPQD 240

Query: 241 LIALINEYGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAVREALAKNPKEFD 300
           L  +IN+YGG +P+T+GVPVEEIQ+GIK GVRK+N+DTDNR+AIT A+R+ L + P EFD
Sbjct: 241 LQDIINQYGGEMPQTWGVPVEEIQRGIKHGVRKINVDTDNRMAITGAIRKLLVEKPGEFD 300

Query: 301 PRHFLKPSITYMQKVCAERYVQFGTAGNASKIKQVSLETFAAKYAKGELNAISKAAA 357
           PR +LKP+   M+KVC  R+V+FG+AG+A KIK +S  T A +YA GEL+A   A+A
Sbjct: 301 PRAYLKPAKEAMRKVCQARFVEFGSAGHADKIKPMSTATMAKRYASGELHAKFGASA 357


Lambda     K      H
   0.315    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: 488
Number of extensions: 12
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: 363
Length adjustment: 29
Effective length of query: 330
Effective length of database: 334
Effective search space:   110220
Effective search space used:   110220
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 CCNA_03360 CCNA_03360 (tagatose-1,6-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.23344.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-192  625.7   0.9   1.2e-192  625.5   0.9    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03360  CCNA_03360 tagatose-1,6-bisphosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03360  CCNA_03360 tagatose-1,6-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.5   0.9  1.2e-192  1.2e-192       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 625.5 bits;  conditional E-value: 1.2e-192
                             TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 
                                           +i+lrqlldhaae+ yg+pafn+nn+eq laimeaad+ +spvi+qasrgar+ya++ +l+k++ a+v+ yp+
  lcl|FitnessBrowser__Caulo:CCNA_03360   3 RITLRQLLDHAAEHEYGLPAFNINNMEQGLAIMEAADAVNSPVIIQASRGARNYANDIMLAKMIDALVDIYPH 75 
                                           69*********************************************************************** PP

                             TIGR01521  74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146
                                           ipv++hqdhgn patc +aiq gftsvmmdgsl edaktpa+y+ynv+vt +vv++ah++g+svegelg lgs
  lcl|FitnessBrowser__Caulo:CCNA_03360  76 IPVCMHQDHGNGPATCATAIQYGFTSVMMDGSLMEDAKTPASYEYNVEVTRKVVQMAHSCGVSVEGELGVLGS 148
                                           ************************************************************************* PP

                             TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219
                                           letg+geaedghgfeg+l + +lltdp++a++fv++t+vdala+a+gtshgaykftrkp g+vla+++ieeih
  lcl|FitnessBrowser__Caulo:CCNA_03360 149 LETGMGEAEDGHGFEGKLSHDELLTDPDQAVDFVAQTGVDALAIAMGTSHGAYKFTRKPDGDVLAMNVIEEIH 221
                                           ************************************************************************* PP

                             TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292
                                           +rlp+thlvmhgsssvpq+ +d+in+ygge+++t+gvpveei++gik+gvrk+n+dtd+r+a+t+a+r+++ +
  lcl|FitnessBrowser__Caulo:CCNA_03360 222 RRLPNTHLVMHGSSSVPQDLQDIINQYGGEMPQTWGVPVEEIQRGIKHGVRKINVDTDNRMAITGAIRKLLVE 294
                                           ************************************************************************* PP

                             TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                           +p efdpr +lk+a eam++vc+ar+ +fg+ag a kik++s   ma+rya+gel
  lcl|FitnessBrowser__Caulo:CCNA_03360 295 KPGEFDPRAYLKPAKEAMRKVCQARFVEFGSAGHADKIKPMSTATMAKRYASGEL 349
                                           *****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (363 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.74
//
[ok]

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

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

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