GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Desulfovibrio vulgaris Miyazaki F

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 8499233 DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq)

Query= BRENDA::O97447
         (323 letters)



>FitnessBrowser__Miya:8499233
          Length = 307

 Score =  291 bits (746), Expect = 1e-83
 Identities = 158/301 (52%), Positives = 204/301 (67%), Gaps = 5/301 (1%)

Query: 1   MPLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMI 60
           MPL   +QM   A K  Y +GAFNVNNME IQGIM+A  + ++P+ILQ S GA KY+   
Sbjct: 1   MPLTGPKQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAGQN 60

Query: 61  YLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKE 120
           Y+ KL EAAL    D+P+ +HLDHG      K  ID GF+SVM D SH P++EN+ +T++
Sbjct: 61  YIVKLIEAAL-MDTDLPVVLHLDHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVTRQ 119

Query: 121 VVAYAHARSVSVEAELGTLGGIEEDVQNTVQL-TEPQDAKKFVELTGVDALAVAIGTSHG 179
           VV YAHAR V VEAELG L G+E++V     + T+P  A  FV+ TG D+LA+AIGTSHG
Sbjct: 120 VVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQAVDFVKRTGCDSLAIAIGTSHG 179

Query: 180 AYKFKSESDIRLAIDRVKTISD-LTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPI 238
           AYKF  E+ +  A  R++ I+  L G PLV+HG+SSVP++  DM N YGGK+  A GVP 
Sbjct: 180 AYKFTGEAKLDFA--RLEKITSMLPGYPLVLHGASSVPQEFVDMANTYGGKVGSAKGVPE 237

Query: 239 ESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKI 298
           + +  A   GVCKIN+D+D R+AMT  IRK F+E P  FDPR YL P RDA+  M+  KI
Sbjct: 238 DLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKI 297

Query: 299 K 299
           +
Sbjct: 298 R 298


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: 285
Number of extensions: 10
Number of successful extensions: 4
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: 307
Length adjustment: 27
Effective length of query: 296
Effective length of database: 280
Effective search space:    82880
Effective search space used:    82880
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: 48 (23.1 bits)

Align candidate 8499233 DvMF_0013 (fructose-1,6-bisphosphate aldolase, class II (RefSeq))
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.9001.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.7e-117  376.4   0.0   8.7e-117  375.8   0.0    1.3  1  lcl|FitnessBrowser__Miya:8499233  DvMF_0013 fructose-1,6-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499233  DvMF_0013 fructose-1,6-bisphosphate aldolase, class II (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.8   0.0  8.7e-117  8.7e-117       5     282 .]       7     307 .]       3     307 .] 0.98

  Alignments for each domain:
  == domain 1  score: 375.8 bits;  conditional E-value: 8.7e-117
                         TIGR01859   5 kellekakkekYavgafninnlellqaileaaeeeksPvivqvsegavkYlggikvvvalvkalieklsivPvalhL 81 
                                       k+++e+a+ke+Ya+gafn+nn+e++q i++aa ee++P+i+qvs ga+kY+g  + +v+l++a++ ++  +Pv+lhL
  lcl|FitnessBrowser__Miya:8499233   7 KQMFERAYKEGYAIGAFNVNNMEIIQGIMQAAGEEQAPLILQVSAGARKYAG-QNYIVKLIEAALMDTD-LPVVLHL 81 
                                       89*************************************************9.999******9999888.9****** PP

                         TIGR01859  82 DhGssyescikaikaGfssvmiDashlpleenlketkkvveiahakgvsveaelGklgGieddvvekeaeladidea 158
                                       DhG++++ c ++i+ Gf+svm+D+shlp+een++ t++vve+aha+gv veaelG+l+G+ed+v +++++++d+d+a
  lcl|FitnessBrowser__Miya:8499233  82 DHGQDFNICKDCIDGGFTSVMYDGSHLPYEENIAVTRQVVEYAHARGVWVEAELGQLAGVEDEVSAEHSVYTDPDQA 158
                                       ***************************************************************************** PP

                         TIGR01859 159 kklvketgvDaLaiaiGtshG..kykgepkldferlkeikklln.lPlvlhGas.....................Gi 211
                                        ++vk+tg D+LaiaiGtshG  k++ge+kldf+rl++i+ +l+  PlvlhGas                     G+
  lcl|FitnessBrowser__Miya:8499233 159 VDFVKRTGCDSLAIAIGTSHGayKFTGEAKLDFARLEKITSMLPgYPLVLHGASsvpqefvdmantyggkvgsakGV 235
                                       *********************999999*****************9******************************** PP

                         TIGR01859 212 peeqlkkaiklgiakvnidtdlrlaftaairkvleekkdeydpRkilaparealkevvkekik.vlgsagka 282
                                       pe+ l+ka+++g++k+nidtd+rla+ta+irk++ ek   +dpR +l+par+a+k++v++ki+ vlg ++k+
  lcl|FitnessBrowser__Miya:8499233 236 PEDLLRKAATYGVCKINIDTDIRLAMTATIRKHFMEKPADFDPRAYLKPARDAVKNMVQHKIRnVLGCSNKI 307
                                       **************************************************************9899*99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (282 nodes)
Target sequences:                          1  (307 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 3.12
//
[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