GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fba in Bacteroides thetaiotaomicron VPI-5482

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 351219 BT1691 fructose-bisphosphate aldolase (NCBI ptt file)

Query= BRENDA::O97447
         (323 letters)



>lcl|FitnessBrowser__Btheta:351219 BT1691 fructose-bisphosphate
           aldolase (NCBI ptt file)
          Length = 334

 Score =  280 bits (716), Expect = 3e-80
 Identities = 152/316 (48%), Positives = 203/316 (64%), Gaps = 22/316 (6%)

Query: 3   LCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYL 62
           L   R M  +A K  Y + AFN NNMEQ+Q I+KA V+ KSPVILQ S+GA +Y++   L
Sbjct: 9   LVNTRDMFAKAIKGGYAIPAFNFNNMEQMQAIIKAAVETKSPVILQVSKGARQYANATLL 68

Query: 63  KKLCEAALE-------KHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENV 115
           + + + A+E        HP+I   +HLDHGDT E+ K  ID GFSSVMID SH P++ENV
Sbjct: 69  RYMAQGAVEYAKELGCAHPEI--VLHLDHGDTFETCKSCIDSGFSSVMIDGSHLPYEENV 126

Query: 116 RITKEVVAYAHARSVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAI 174
            +TK+VV YAH   V+VE ELG L G+E++V +     T+P++   F   TG D+LA++I
Sbjct: 127 ALTKKVVEYAHQFDVTVEGELGVLAGVEDEVSSDHHTYTDPEEVIDFATRTGCDSLAISI 186

Query: 175 GTSHGAYKFKSES-----------DIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDM 222
           GTSHGAYKF  E               LA + +  + + L G P+V+HGSSSVP++  + 
Sbjct: 187 GTSHGAYKFTPEQCHIDPATGRMVPPPLAFEVLDAVMEKLPGFPIVLHGSSSVPEEEVET 246

Query: 223 INKYGGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDY 282
           INK+GG +  A+G+P E +  A    VCKIN+DSDSR+AMT AIRK F E P +FDPR Y
Sbjct: 247 INKFGGALKAAIGIPEEELRKAAKSAVCKINIDSDSRLAMTAAIRKTFAEKPAEFDPRKY 306

Query: 283 LGPGRDAITEMLIPKI 298
           LGP RD + ++   KI
Sbjct: 307 LGPARDNMEKLYKHKI 322


Lambda     K      H
   0.318    0.135    0.389 

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: 317
Number of extensions: 11
Number of successful extensions: 5
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: 323
Length of database: 334
Length adjustment: 28
Effective length of query: 295
Effective length of database: 306
Effective search space:    90270
Effective search space used:    90270
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 351219 BT1691 (fructose-bisphosphate aldolase (NCBI ptt file))
to HMM TIGR01859 (fba: fructose-1,6-bisphosphate aldolase, class II (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/TIGR01859.hmm
# target sequence database:        /tmp/gapView.22607.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01859  [M=282]
Accession:   TIGR01859
Description: fruc_bis_ald_: fructose-1,6-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.6e-112  359.6   0.0   1.2e-111  358.9   0.0    1.3  1  lcl|FitnessBrowser__Btheta:351219  BT1691 fructose-bisphosphate ald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351219  BT1691 fructose-bisphosphate aldolase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.9   0.0  1.2e-111  1.2e-111       1     281 [.       9     331 ..       9     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 358.9 bits;  conditional E-value: 1.2e-111
                          TIGR01859   1 lvkakellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlg...gikvvvalvkaliekls 73 
                                        lv+++++++ka k++Ya++afn+nn+e++qai++aa e+ksPvi+qvs+ga++Y++   ++ +++++v+++ e   
  lcl|FitnessBrowser__Btheta:351219   9 LVNTRDMFAKAIKGGYAIPAFNFNNMEQMQAIIKAAVETKSPVILQVSKGARQYANatlLRYMAQGAVEYAKELGC 84 
                                        79******************************************************87777899999999999888 PP

                          TIGR01859  74 ivP.valhLDhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvvek 148
                                          P ++lhLDhG+++e+c ++i++GfssvmiD+shlp+een+++tkkvve+ah+  v+ve elG+l+G+ed+v ++
  lcl|FitnessBrowser__Btheta:351219  85 AHPeIVLHLDHGDTFETCKSCIDSGFSSVMIDGSHLPYEENVALTKKVVEYAHQFDVTVEGELGVLAGVEDEVSSD 160
                                        8555************************************************************************ PP

                          TIGR01859 149 eaeladideakklvketgvDaLaiaiGtshG..kykge.............pkldferlkeikklln.lPlvlhGa 208
                                        + +++d++e+ +++ +tg D+Lai+iGtshG  k++ e             p l fe l+++ ++l+ +P+vlhG+
  lcl|FitnessBrowser__Btheta:351219 161 HHTYTDPEEVIDFATRTGCDSLAISIGTSHGayKFTPEqchidpatgrmvpPPLAFEVLDAVMEKLPgFPIVLHGS 236
                                        *******************************5555566****************************99******** PP

                          TIGR01859 209 s.....................GipeeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilapare 263
                                        s                     Gipee+l+ka+k++++k+nid+d rla+taairk+++ek  e+dpRk+l+par+
  lcl|FitnessBrowser__Btheta:351219 237 SsvpeeevetinkfggalkaaiGIPEEELRKAAKSAVCKINIDSDSRLAMTAAIRKTFAEKPAEFDPRKYLGPARD 312
                                        **************************************************************************** PP

                          TIGR01859 264 alkevvkekik.vlgsagk 281
                                        ++++++k+ki  vlgs +k
  lcl|FitnessBrowser__Btheta:351219 313 NMEKLYKHKILnVLGSDNK 331
                                        *********9669***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (334 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 2.04
//
[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