Alignments for a candidate for fba in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Shewanella loihica PV-4

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 5208243 Shew_0755 fructose-1,6-bisphosphate aldolase (RefSeq)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__PV4:5208243
          Length = 354

 Score =  509 bits (1310), Expect = e-149
 Identities = 252/353 (71%), Positives = 287/353 (81%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALISLRQLLDHAAEHGYG+PAFNVNN+EQ++AIM+AA A D+PVI+Q SAGAR YA   
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FL++L+ AA+E YP IPVC+HQDHG  P VC RSIQ G SSVMMDGSL+ D KTPASY Y
Sbjct: 61  FLKYLMAAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TRK V  AHACGVSVEGE+GCLGSLETG+AG+EDG GAEG L    LLT P+EAA 
Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGQAGEEDGVGAEGILSEDQLLTTPEEAAR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV  T VDALAIAIGTSHGAYKF+RKPTG VLRIDR+K IH RIP  HLVMHGSSSVP+E
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN YGG I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+F+ E+   FD
Sbjct: 241 WLEVINQYGGAIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIV 353
           PRK  KA+  AM  IC  RYEAFGAAG  +KIKP  L+ M  AY  G+LDP V
Sbjct: 301 PRKFLKASMDAMADICTVRYEAFGAAGMGSKIKPKSLQAMYKAYQSGELDPQV 353


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: 502
Number of extensions: 16
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 5208243 Shew_0755 (fructose-1,6-bisphosphate aldolase (RefSeq))
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.26106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.3e-195  633.2   0.2     6e-195  633.1   0.2    1.0  1  lcl|FitnessBrowser__PV4:5208243  Shew_0755 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208243  Shew_0755 fructose-1,6-bisphosphate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.1   0.2    6e-195    6e-195       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 633.1 bits;  conditional E-value: 6e-195
                        TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdipvvl 78 
                                      lislrqlldhaae+gygvpafnvnnleq++aim+aa++tdspvi+qas+gar+ya  ++l+ l+ aa e+ypdipv++
  lcl|FitnessBrowser__PV4:5208243   3 LISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQFLKYLMAAALEQYPDIPVCI 80 
                                      69**************************************************************************** PP

                        TIGR01521  79 hqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletgkgeaed 156
                                      hqdhg+ p++c+++iqlg++svmmdgsl  d+ktpa+y+ynv+vt ++v++aha+g+svege+gclgsletg++++ed
  lcl|FitnessBrowser__PV4:5208243  81 HQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYEYNVDVTRKTVAFAHACGVSVEGEIGCLGSLETGQAGEED 158
                                      ****************************************************************************** PP

                        TIGR01521 157 ghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdthlvmhgsss 234
                                      g+g+eg l + qllt peeaa+fv++t+vdala+aigtshgaykf+rkptg+vl idri+eih+r+p+thlvmhgsss
  lcl|FitnessBrowser__PV4:5208243 159 GVGAEGILSEDQLLTTPEEAARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSS 236
                                      ****************************************************************************** PP

                        TIGR01521 235 vpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkd 312
                                      vpqewl+vin+ygg+i+etygvp+eeiv+gik+gvrkvnidtdlrla+t+a+r+++a++psefdprkflk +++am d
  lcl|FitnessBrowser__PV4:5208243 237 VPQEWLEVINQYGGAIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFDPRKFLKASMDAMAD 314
                                      ****************************************************************************** PP

                        TIGR01521 313 vckaryeafgtagnaskikvvsleemarryakgel 347
                                      +c+ ryeafg+ag  skik+ sl+ m++ y +gel
  lcl|FitnessBrowser__PV4:5208243 315 ICTVRYEAFGAAGMGSKIKPKSLQAMYKAYQSGEL 349
                                      *********************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.37
//
[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