Alignments for a candidate for fba in Desulfovibrio vulgaris Miyazaki F

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.21770.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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 1.94
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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