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

GapMind for catabolism of small carbon sources

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

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate H281DRAFT_03815 H281DRAFT_03815 D-glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__Burk376:H281DRAFT_03815
          Length = 468

 Score =  734 bits (1894), Expect = 0.0
 Identities = 352/438 (80%), Positives = 392/438 (89%)

Query: 14  PVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLED 73
           P +T+L+VVPVAG DSMLLNLSGAHGP FTRNI+IL DS+GHVGVGEVPGGE IRKT++D
Sbjct: 31  PTVTELRVVPVAGRDSMLLNLSGAHGPYFTRNIVILRDSAGHVGVGEVPGGENIRKTIDD 90

Query: 74  ARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQH 133
           AR  ++ QSIGN Q++LNKVR  FADRD GGRGLQTFDLR  +HAVTA+E+ALLDLLGQH
Sbjct: 91  ARSFVVGQSIGNLQAILNKVRTQFADRDAGGRGLQTFDLRTTIHAVTALEAALLDLLGQH 150

Query: 134 LQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPES 193
           L VPVAALLGEGQQRDAVEMLGYLFY+GDRNKTDL Y S  +A ++W R+R +EALTPE+
Sbjct: 151 LGVPVAALLGEGQQRDAVEMLGYLFYIGDRNKTDLPYASGADARDDWDRVRTEEALTPEA 210

Query: 194 VVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAVA 253
           VV LAEAA  RYGF DFKLKGGVL G+ EI AVTAL+ERFP+AR+TLDPNGAWSL EA+ 
Sbjct: 211 VVRLAEAAQARYGFNDFKLKGGVLPGDAEIEAVTALAERFPNARVTLDPNGAWSLAEAIR 270

Query: 254 LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQSV 313
           LCRD+H VLAYAEDPCGAENGYSGREVMAEFRR+TGL TATNMIATDWRQMGHAIQLQSV
Sbjct: 271 LCRDKHDVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMGHAIQLQSV 330

Query: 314 DIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAIDT 373
           DIPLADPHFWTMQGSVRVAQMCN+WGLTWGSHSNNHFDISLAMFTHVAAAAPG ITAIDT
Sbjct: 331 DIPLADPHFWTMQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTHVAAAAPGKITAIDT 390

Query: 374 HWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATAM 433
           HWIWQDGQRLT+EPLQI GG V+VP+KPGLGVELD D + KAH +Y+  GLGARDD  AM
Sbjct: 391 HWIWQDGQRLTREPLQIVGGKVKVPQKPGLGVELDMDEIEKAHALYQQHGLGARDDGVAM 450

Query: 434 RYLVSGWEFNNKRPCMVR 451
           +YL+  W+F+NKRPC+VR
Sbjct: 451 QYLIPNWKFDNKRPCLVR 468


Lambda     K      H
   0.319    0.135    0.410 

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: 708
Number of extensions: 15
Number of successful extensions: 1
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: 451
Length of database: 468
Length adjustment: 33
Effective length of query: 418
Effective length of database: 435
Effective search space:   181830
Effective search space used:   181830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_03815 H281DRAFT_03815 (D-glucarate dehydratase)
to HMM TIGR03247 (gudD: glucarate dehydratase (EC 4.2.1.40))

# 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/TIGR03247.hmm
# target sequence database:        /tmp/gapView.9016.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03247  [M=441]
Accession:   TIGR03247
Description: glucar-dehydr: glucarate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.1e-272  887.3   0.6   9.4e-272  887.1   0.6    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03815  H281DRAFT_03815 D-glucarate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03815  H281DRAFT_03815 D-glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.1   0.6  9.4e-272  9.4e-272       2     441 .]      29     468 .]      28     468 .] 1.00

  Alignments for each domain:
  == domain 1  score: 887.1 bits;  conditional E-value: 9.4e-272
                                    TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakal 67 
                                                   tp+vtelrvvpvagrdsmllnlsgah+p+ftrnivil+ds+g++gvgevpgge+irkt++da+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815  29 DTPTVTELRVVPVAGRDSMLLNLSGAHGPYFTRNIVILRDSAGHVGVGEVPGGENIRKTIDDARSF 94 
                                                  589*************************************************************** PP

                                    TIGR03247  68 vvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallg 133
                                                  vvg+++g+ +++l+kvr++fadrdaggrg+qtfdlr+t+havtale+alldllgqhl+vpvaallg
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815  95 VVGQSIGNLQAILNKVRTQFADRDAGGRGLQTFDLRTTIHAVTALEAALLDLLGQHLGVPVAALLG 160
                                                  ****************************************************************** PP

                                    TIGR03247 134 egqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkd 199
                                                  egqqrd+ve+lgylf++gdr+kt+l+y+s+ +a+ddw r+r eealtpeavvrlaeaa++rygf+d
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815 161 EGQQRDAVEMLGYLFYIGDRNKTDLPYASGADARDDWDRVRTEEALTPEAVVRLAEAAQARYGFND 226
                                                  ****************************************************************** PP

                                    TIGR03247 200 fklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegy 265
                                                  fklkggvl g+ eieavtala+rfp+ar+tldpngawsl eai+lc+d++dvlayaedp+gae+gy
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815 227 FKLKGGVLPGDAEIEAVTALAERFPNARVTLDPNGAWSLAEAIRLCRDKHDVLAYAEDPCGAENGY 292
                                                  ****************************************************************** PP

                                    TIGR03247 266 sgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeyglt 331
                                                  sgrevmaefrratglptatnmiatdwr++gha++lq+vdipladphfwt+qgsvrvaq+c+++glt
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815 293 SGREVMAEFRRATGLPTATNMIATDWRQMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCNDWGLT 358
                                                  ****************************************************************** PP

                                    TIGR03247 332 wgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgvel 397
                                                  wgshsnnhfdislamfthvaaaapgk+taidthwiwqdgqrlt+epl+i +gk+kvp+kpglgvel
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815 359 WGSHSNNHFDISLAMFTHVAAAAPGKITAIDTHWIWQDGQRLTREPLQIVGGKVKVPQKPGLGVEL 424
                                                  ****************************************************************** PP

                                    TIGR03247 398 dedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                  d+d++ekah ly+++glgardd vamq+lipnwkfd+krpclvr
  lcl|FitnessBrowser__Burk376:H281DRAFT_03815 425 DMDEIEKAHALYQQHGLGARDDGVAMQYLIPNWKFDNKRPCLVR 468
                                                  *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (468 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.78
//
[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:

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