GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:351219
          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.12941.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: 2.24
//
[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:

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