Alignments for a candidate for garD in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Paraburkholderia bryophila 376MFSha3.1

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate H281DRAFT_05320 H281DRAFT_05320 galactarate dehydratase

Query= reanno::HerbieS:HSERO_RS15800
         (522 letters)



>FitnessBrowser__Burk376:H281DRAFT_05320
          Length = 529

 Score =  788 bits (2035), Expect = 0.0
 Identities = 388/526 (73%), Positives = 446/526 (84%), Gaps = 15/526 (2%)

Query: 12  APRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDV 71
           +P YI ++  DNVAIVVNDGGL  G VFPDGL L +RVPQGHK+AL DL +G+ ++RY+V
Sbjct: 4   SPLYIRVHPNDNVAIVVNDGGLGEGAVFPDGLVLRERVPQGHKVALADLAEGDEVIRYNV 63

Query: 72  AIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVG 131
            IGYA++ +PKG WI E +++MP    L++LPIAT K    PPLEGYTFEGYRNADGSVG
Sbjct: 64  VIGYALKALPKGSWINEHVIRMPSPPGLEDLPIATIKAPEMPPLEGYTFEGYRNADGSVG 123

Query: 132 TRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIP 191
           +RN+LAITTTVQCVA VVEHAV RI++ELLPKYPNV+DVV L HTYGCGVAIDAP+A +P
Sbjct: 124 SRNILAITTTVQCVADVVEHAVVRIKSELLPKYPNVDDVVGLGHTYGCGVAIDAPDAMVP 183

Query: 192 IRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPY------------- 238
           IRT+RNI+LNPNFGG+ M+VSLGCEKLQP RL+P   IPI     P              
Sbjct: 184 IRTVRNIALNPNFGGEVMMVSLGCEKLQPERLMPPGTIPIAAAQNPSEIADIGDLGADEN 243

Query: 239 --VVCLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGV 296
             VV LQD  HVGF SM++SIM  AE  L  LN RRRETCPA+DLVVGVQCGGSDAFSG+
Sbjct: 244 GDVVVLQDEAHVGFQSMVESIMRTAEGHLKRLNNRRRETCPAADLVVGVQCGGSDAFSGL 303

Query: 297 TANPAVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLK 356
           TANPAVGFATDLLVRAGA+VMFSEVTEVRDG+DQLT+RA N +VAQA+IREM WYD+YLK
Sbjct: 304 TANPAVGFATDLLVRAGATVMFSEVTEVRDGVDQLTARAENADVAQAIIREMQWYDDYLK 363

Query: 357 QGGVDRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPA 416
           +GG DRSANTTPGNKKGGL+NIVEKAMGSI+KSG+SPISGVLSPG+K++QKGLIYAATPA
Sbjct: 364 RGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSPISGVLSPGEKVRQKGLIYAATPA 423

Query: 417 SDFICGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIAS 476
           SDFICGTLQLAAG+NLH+FTTGRGTPY LA VPVIKVATR+DLARRWHDLMD+NAG IA+
Sbjct: 424 SDFICGTLQLAAGINLHVFTTGRGTPYSLAEVPVIKVATRSDLARRWHDLMDINAGTIAT 483

Query: 477 GEASIEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
           G A+IE+VGWELF+ MLDVASG+K+T AE+ KLHNAL LFNPAPVT
Sbjct: 484 GSATIEEVGWELFRFMLDVASGRKKTCAEKLKLHNALALFNPAPVT 529


Lambda     K      H
   0.317    0.134    0.397 

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: 926
Number of extensions: 32
Number of successful extensions: 2
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: 522
Length of database: 529
Length adjustment: 35
Effective length of query: 487
Effective length of database: 494
Effective search space:   240578
Effective search space used:   240578
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate H281DRAFT_05320 H281DRAFT_05320 (galactarate dehydratase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.7172.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.9e-284  929.7   0.4   2.2e-284  929.5   0.4    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05320  H281DRAFT_05320 galactarate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05320  H281DRAFT_05320 galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  929.5   0.4  2.2e-284  2.2e-284       1     507 []       6     529 .]       6     529 .] 0.99

  Alignments for each domain:
  == domain 1  score: 929.5 bits;  conditional E-value: 2.2e-284
                                    TIGR03248   1 lyirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkd 66 
                                                  lyirv+++dnvaivvnd Gl +g++f+dgl+l+e++pqghkval+dl++gd++iry+ viGya+k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320   6 LYIRVHPNDNVAIVVNDGGLGEGAVFPDGLVLRERVPQGHKVALADLAEGDEVIRYNVVIGYALKA 71 
                                                  79**************************************************************** PP

                                    TIGR03248  67 iarGswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcv 132
                                                  +++Gsw++e+++++ps+p le+lp+at ++++++pleGytfeGyrnadGsvG++nil+itt+vqcv
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320  72 LPKGSWINEHVIRMPSPPGLEDLPIATIKAPEMPPLEGYTFEGYRNADGSVGSRNILAITTTVQCV 137
                                                  ****************************************************************** PP

                                    TIGR03248 133 agvvdyavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvv 198
                                                  a vv++av rik+ellpkypnvddvv+l h+yGcGvaidapda+vpirt+rn+alnpn+GGe+++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 138 ADVVEHAVVRIKSELLPKYPNVDDVVGLGHTYGCGVAIDAPDAMVPIRTVRNIALNPNFGGEVMMV 203
                                                  ****************************************************************** PP

                                    TIGR03248 199 glGceklqperllpeelsa................velkdaavlrlqdekl.Gfaemveailelae 247
                                                  +lGceklqperl+p ++++                   ++  v+ lqde++ Gf++mve+i+++ae
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 204 SLGCEKLQPERLMPPGTIPiaaaqnpseiadigdlGADENGDVVVLQDEAHvGFQSMVESIMRTAE 269
                                                  ****************9999999*****99987753445678************************ PP

                                    TIGR03248 248 erlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdai 313
                                                   +lk+ln+r+ret+pa++lvvG+qcGGsdafsG+tanpavGfa+dllvraGatv+fsevtevrd++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 270 GHLKRLNNRRRETCPAADLVVGVQCGGSDAFSGLTANPAVGFATDLLVRAGATVMFSEVTEVRDGV 335
                                                  ****************************************************************** PP

                                    TIGR03248 314 hlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssai 379
                                                  ++lt+rae+a+va+a+irem+wyd+yl+rG adrsanttpGnkkGGlsniveka+Gsi+ksG s+i
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 336 DQLTARAENADVAQAIIREMQWYDDYLKRGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSPI 401
                                                  ****************************************************************** PP

                                    TIGR03248 380 vevlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtela 445
                                                  ++vlspGekv++kGliyaatpasdf+cGtlqla+g+nlhvfttGrGtpy la+vpvikv+tr++la
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 402 SGVLSPGEKVRQKGLIYAATPASDFICGTLQLAAGINLHVFTTGRGTPYSLAEVPVIKVATRSDLA 467
                                                  ****************************************************************** PP

                                    TIGR03248 446 erwadlidldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                                  +rw+dl+d++aG+iatG+atie+vGwelfr++ldvasGrkkt+aek+klhn+lalfnpapvt
  lcl|FitnessBrowser__Burk376:H281DRAFT_05320 468 RRWHDLMDINAGTIATGSATIEEVGWELFRFMLDVASGRKKTCAEKLKLHNALALFNPAPVT 529
                                                  *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (529 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: 00:00:00.03
# Mc/sec: 7.90
//
[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