Alignments for a candidate for fba in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Synechococcus elongatus PCC 7942

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate Synpcc7942_1443 Synpcc7942_1443 fructose-1,6-bisphosphate aldolase

Query= BRENDA::Q55664
         (359 letters)



>FitnessBrowser__SynE:Synpcc7942_1443
          Length = 357

 Score =  614 bits (1584), Expect = 0.0
 Identities = 302/354 (85%), Positives = 327/354 (92%)

Query: 1   MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60
           MALVP+RL+LDHAAEN YGIPAFNVNN+EQ+ SI+QAADETDSPVILQASRGARSYAGEN
Sbjct: 1   MALVPLRLMLDHAAENEYGIPAFNVNNLEQVQSILQAADETDSPVILQASRGARSYAGEN 60

Query: 61  FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120
           FLRHL+L AVETYPHIPIAMHQDHGNSPATCYSAI+NGFTSVMMDGSLEADAKTPAS+EY
Sbjct: 61  FLRHLILAAVETYPHIPIAMHQDHGNSPATCYSAIKNGFTSVMMDGSLEADAKTPASYEY 120

Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180
           NV VT +VV VAHS+G SVEGELGCLGSLETG+GEAEDGHGFEG LDHSQLLTDP++AV+
Sbjct: 121 NVEVTRQVVDVAHSIGVSVEGELGCLGSLETGKGEAEDGHGFEGTLDHSQLLTDPDQAVD 180

Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240
           FV KTQVDALAVAIGTSHGAYKFTRKPTGE+LAISRIEEIHR LPNTHLVMHGSSSVPQE
Sbjct: 181 FVEKTQVDALAVAIGTSHGAYKFTRKPTGEILAISRIEEIHRRLPNTHLVMHGSSSVPQE 240

Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300
            +++INE+GG IPETYGVPVEEIQK IK GVRK+NIDTDNRLA TAA REAAAKDP NFD
Sbjct: 241 LLELINEYGGQIPETYGVPVEEIQKAIKLGVRKINIDTDNRLAFTAAVREAAAKDPSNFD 300

Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYAKGELTATSR 354
           PRHF KP+IKYMKQVC DRY  F TAG ASKIKQ  LD++AAKYAKGEL A ++
Sbjct: 301 PRHFNKPAIKYMKQVCVDRYVAFNTAGQASKIKQEGLDEFAAKYAKGELRAQTK 354


Lambda     K      H
   0.315    0.131    0.377 

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: 539
Number of extensions: 14
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: 357
Length adjustment: 29
Effective length of query: 330
Effective length of database: 328
Effective search space:   108240
Effective search space used:   108240
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 Synpcc7942_1443 Synpcc7942_1443 (fructose-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.28344.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-208  676.7   0.2   3.7e-208  676.5   0.2    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1443  Synpcc7942_1443 fructose-1,6-bis


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1443  Synpcc7942_1443 fructose-1,6-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  676.5   0.2  3.7e-208  3.7e-208       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 676.5 bits;  conditional E-value: 3.7e-208
                                 TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaave 69 
                                               l++lr++ldhaae+ yg+pafnvnnleq+ +i++aad+tdspvilqasrgarsyage++lr+l+laave
  lcl|FitnessBrowser__SynE:Synpcc7942_1443   3 LVPLRLMLDHAAENEYGIPAFNVNNLEQVQSILQAADETDSPVILQASRGARSYAGENFLRHLILAAVE 71 
                                               689****************************************************************** PP

                                 TIGR01521  70 eypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasve 138
                                               +yp+ip+++hqdhgnspatc+sai++gftsvmmdgsl++daktpa+y+ynv+vt +vv +ah++g+sve
  lcl|FitnessBrowser__SynE:Synpcc7942_1443  72 TYPHIPIAMHQDHGNSPATCYSAIKNGFTSVMMDGSLEADAKTPASYEYNVEVTRQVVDVAHSIGVSVE 140
                                               ********************************************************************* PP

                                 TIGR01521 139 gelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptg 207
                                               gelgclgsletgkgeaedghgfeg+ld+sqlltdp++a++fv+kt+vdalavaigtshgaykftrkptg
  lcl|FitnessBrowser__SynE:Synpcc7942_1443 141 GELGCLGSLETGKGEAEDGHGFEGTLDHSQLLTDPDQAVDFVEKTQVDALAVAIGTSHGAYKFTRKPTG 209
                                               ********************************************************************* PP

                                 TIGR01521 208 evlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidt 276
                                               e+lai+rieeih+rlp+thlvmhgsssvpqe l++ineygg+i+etygvpveei+k ik gvrk+nidt
  lcl|FitnessBrowser__SynE:Synpcc7942_1443 210 EILAISRIEEIHRRLPNTHLVMHGSSSVPQELLELINEYGGQIPETYGVPVEEIQKAIKLGVRKINIDT 278
                                               ********************************************************************* PP

                                 TIGR01521 277 dlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakg 345
                                               d+rla taa+r++aakdps+fdpr+f k+a+++mk+vc++ry af tag+askik+  l+e+a++yakg
  lcl|FitnessBrowser__SynE:Synpcc7942_1443 279 DNRLAFTAAVREAAAKDPSNFDPRHFNKPAIKYMKQVCVDRYVAFNTAGQASKIKQEGLDEFAAKYAKG 347
                                               ********************************************************************* PP

                                 TIGR01521 346 el 347
                                               el
  lcl|FitnessBrowser__SynE:Synpcc7942_1443 348 EL 349
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (357 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.85
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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