Alignments for a candidate for gudD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Burkholderia phytofirmans PsJN

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate BPHYT_RS20410 BPHYT_RS20410 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__BFirm:BPHYT_RS20410
          Length = 449

 Score =  721 bits (1860), Expect = 0.0
 Identities = 346/446 (77%), Positives = 388/446 (86%)

Query: 6   QSQAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGE 65
           +S      PV+T+L+VVPVAG DSMLLNLSGAHGP FTRNI+IL DS+GH GVGEVPGGE
Sbjct: 4   KSSELNATPVVTELRVVPVAGRDSMLLNLSGAHGPFFTRNIVILRDSAGHTGVGEVPGGE 63

Query: 66  GIRKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESA 125
            IRKT++DAR L++ QSIGN Q++LNK R  FADRD GGRGLQTFDLR  +HAVTA+E+A
Sbjct: 64  SIRKTIDDARPLVVGQSIGNLQAVLNKARTQFADRDAGGRGLQTFDLRTTIHAVTALEAA 123

Query: 126 LLDLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRN 185
           LLDLLGQHL VPVAALLGEGQQRD VEMLGYLFY+GDR KTDL Y S  +  ++W R+R 
Sbjct: 124 LLDLLGQHLGVPVAALLGEGQQRDEVEMLGYLFYIGDRKKTDLEYASGADGRDDWERVRT 183

Query: 186 KEALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGA 245
           +EA+TPE+VV LAEAA  RYGF DFKLKGGVL G+ EI AVTAL+ERFP AR+TLDPNGA
Sbjct: 184 EEAMTPEAVVRLAEAAQARYGFNDFKLKGGVLPGDAEIEAVTALAERFPKARVTLDPNGA 243

Query: 246 WSLKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMG 305
           WSL EAV LCRDQH VLAYAEDPCGAENGYSGREVMAEFRR+TGL TATNMIATDWRQMG
Sbjct: 244 WSLAEAVRLCRDQHDVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMG 303

Query: 306 HAIQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAP 365
           HAIQLQSVDIPLADPHFWTMQGSVRVAQMCN+WGLTWGSHSNNHFDISLAMFTHVAAAAP
Sbjct: 304 HAIQLQSVDIPLADPHFWTMQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTHVAAAAP 363

Query: 366 GNITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLG 425
           G ITAIDTHWIWQDGQRLT++PL+I GG V+VP+  GLG+ELD D + KAH +Y+  GLG
Sbjct: 364 GKITAIDTHWIWQDGQRLTRDPLRIVGGKVKVPQAAGLGIELDMDEIEKAHALYQQHGLG 423

Query: 426 ARDDATAMRYLVSGWEFNNKRPCMVR 451
           ARDD  AM+YL+  W+F+NKRPC+VR
Sbjct: 424 ARDDGVAMQYLIPNWKFDNKRPCLVR 449


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: 700
Number of extensions: 18
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: 449
Length adjustment: 33
Effective length of query: 418
Effective length of database: 416
Effective search space:   173888
Effective search space used:   173888
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 BPHYT_RS20410 BPHYT_RS20410 (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.31500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.4e-270  882.5   0.9   2.7e-270  882.3   0.9    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS20410  BPHYT_RS20410 glucarate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS20410  BPHYT_RS20410 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  882.3   0.9  2.7e-270  2.7e-270       2     441 .]      10     449 .]       9     449 .] 1.00

  Alignments for each domain:
  == domain 1  score: 882.3 bits;  conditional E-value: 2.7e-270
                                TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgk 71 
                                              atpvvtelrvvpvagrdsmllnlsgah+pfftrnivil+ds+g+tgvgevpgge irkt++da++lvvg+
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410  10 ATPVVTELRVVPVAGRDSMLLNLSGAHGPFFTRNIVILRDSAGHTGVGEVPGGESIRKTIDDARPLVVGQ 79 
                                              69******************************************************************** PP

                                TIGR03247  72 tlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdev 141
                                              ++g+ ++vl+k r++fadrdaggrg+qtfdlr+t+havtale+alldllgqhl+vpvaallgegqqrdev
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410  80 SIGNLQAVLNKARTQFADRDAGGRGLQTFDLRTTIHAVTALEAALLDLLGQHLGVPVAALLGEGQQRDEV 149
                                              ********************************************************************** PP

                                TIGR03247 142 evlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgee 211
                                              e+lgylf++gdrkkt+l+y+s+ + +ddw r+r eea+tpeavvrlaeaa++rygf+dfklkggvl g+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410 150 EMLGYLFYIGDRKKTDLEYASGADGRDDWERVRTEEAMTPEAVVRLAEAAQARYGFNDFKLKGGVLPGDA 219
                                              ********************************************************************** PP

                                TIGR03247 212 eieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrratglp 281
                                              eieavtala+rfp+ar+tldpngawsl ea++lc+d++dvlayaedp+gae+gysgrevmaefrratglp
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410 220 EIEAVTALAERFPKARVTLDPNGAWSLAEAVRLCRDQHDVLAYAEDPCGAENGYSGREVMAEFRRATGLP 289
                                              ********************************************************************** PP

                                TIGR03247 282 tatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamfthva 351
                                              tatnmiatdwr++gha++lq+vdipladphfwt+qgsvrvaq+c+++gltwgshsnnhfdislamfthva
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410 290 TATNMIATDWRQMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTHVA 359
                                              ********************************************************************** PP

                                TIGR03247 352 aaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgveldedavekahelykkkglgarddav 421
                                              aaapgk+taidthwiwqdgqrlt++pl+i +gk+kvp+ +glg+eld+d++ekah ly+++glgardd v
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410 360 AAAPGKITAIDTHWIWQDGQRLTRDPLRIVGGKVKVPQAAGLGIELDMDEIEKAHALYQQHGLGARDDGV 429
                                              ********************************************************************** PP

                                TIGR03247 422 amqllipnwkfdekrpclvr 441
                                              amq+lipnwkfd+krpclvr
  lcl|FitnessBrowser__BFirm:BPHYT_RS20410 430 AMQYLIPNWKFDNKRPCLVR 449
                                              *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (449 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: 00:00:00.01
# Mc/sec: 10.61
//
[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