GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fba in Pseudomonas putida KT2440

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate PP_4960 PP_4960 Fructose-bisphosphate aldolase

Query= BRENDA::Q602L6
         (354 letters)



>lcl|FitnessBrowser__Putida:PP_4960 PP_4960 Fructose-bisphosphate
           aldolase
          Length = 354

 Score =  523 bits (1346), Expect = e-153
 Identities = 257/349 (73%), Positives = 290/349 (83%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALIS+RQ+LDHAAE GYG+PAFNVNN+EQ++AIMEAA   D+PVI+Q SAGAR YAG P
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE +PHIPVCMHQDHG SP VC RSIQ GFSSVMMDGSL ED KTP  Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++ V MAHACGVSVEGELGCLGSLETG AG+EDG GAEG LDHS +LTDP+EAAD
Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV++TQVDALAIAIGTSHGAYKFT+ PTG VL IDR+K IH+RIP  HLVMHGSSSVP+E
Sbjct: 181 FVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W  +IN YGGDI +TYGVPVEEIVEGI+HGVRKVNIDTDLR+AS GAMRR M ++   FD
Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKL 349
           PRK +     AM  +C ARYEAFG AG A+KIKP+ LE M   Y +G+L
Sbjct: 301 PRKFFGETIKAMRDVCIARYEAFGTAGNASKIKPISLEGMYQRYLKGEL 349


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: 494
Number of extensions: 17
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 PP_4960 PP_4960 (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.5129.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.4e-215  699.3   0.2   4.9e-215  699.1   0.2    1.0  1  lcl|FitnessBrowser__Putida:PP_4960  PP_4960 Fructose-bisphosphate al


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4960  PP_4960 Fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.1   0.2  4.9e-215  4.9e-215       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 699.1 bits;  conditional E-value: 4.9e-215
                           TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdip 75 
                                         lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+laa+ee+p+ip
  lcl|FitnessBrowser__Putida:PP_4960   3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIP 77 
                                         69************************************************************************* PP

                           TIGR01521  76 vvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletg 150
                                         v++hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt+++v++aha+g+svegelgclgsletg
  lcl|FitnessBrowser__Putida:PP_4960  78 VCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVRVTQQTVAMAHACGVSVEGELGCLGSLETG 152
                                         *************************************************************************** PP

                           TIGR01521 151 kgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdt 225
                                         ++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykft++ptg+vlaidri+eih+r+p+t
  lcl|FitnessBrowser__Putida:PP_4960 153 MAGEEDGIGAEGVLDHSQMLTDPEEAADFVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNT 227
                                         *************************************************************************** PP

                           TIGR01521 226 hlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdpr 300
                                         hlvmhgsssvpqewl++in+ygg+iketygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++psefdpr
  lcl|FitnessBrowser__Putida:PP_4960 228 HLVMHGSSSVPQEWLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNPSEFDPR 302
                                         *************************************************************************** PP

                           TIGR01521 301 kflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347
                                         kf+ ++++am+dvc+aryeafgtagnaskik++sle+m++ry kgel
  lcl|FitnessBrowser__Putida:PP_4960 303 KFFGETIKAMRDVCIARYEAFGTAGNASKIKPISLEGMYQRYLKGEL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.41
//
[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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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