Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N1B4

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate Pf1N1B4_71 Glucarate dehydratase (EC 4.2.1.40)

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71
          Length = 447

 Score =  751 bits (1939), Expect = 0.0
 Identities = 355/444 (79%), Positives = 401/444 (90%)

Query: 8   QAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGI 67
           Q A  AP+IT ++VVPVAGHD MLLNLSGAHGP FTRN++IL D++GH GVGEVPGGE I
Sbjct: 4   QEAAKAPIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNVVILKDNAGHTGVGEVPGGERI 63

Query: 68  RKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALL 127
           R+TLEDAR L++   IG YQ +LN+VR  FADRD GGRGLQTFDLRI +HAVT +E+ALL
Sbjct: 64  RQTLEDARALVVGSPIGTYQKILNQVRQTFADRDAGGRGLQTFDLRITIHAVTGLEAALL 123

Query: 128 DLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKE 187
           DLLGQHL VPVAALLGEGQQRD V+MLGYLFYVGDRN+TDL YRSE +ADN+WFR+R+++
Sbjct: 124 DLLGQHLDVPVAALLGEGQQRDEVKMLGYLFYVGDRNETDLAYRSEPDADNDWFRVRHEK 183

Query: 188 ALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWS 247
           A++ ++VV LAEAA+ RYGFKDFKLKGGVL G++EI AVTAL+ERFPDARITLDPNGAWS
Sbjct: 184 AMSADAVVRLAEAAHARYGFKDFKLKGGVLSGDEEIEAVTALAERFPDARITLDPNGAWS 243

Query: 248 LKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHA 307
           LKEA+ LCRDQHHVLAYAEDPCGAEN YSGREVMAEFRR+TGL+TATNMIATDWR+MGHA
Sbjct: 244 LKEAIRLCRDQHHVLAYAEDPCGAENSYSGREVMAEFRRATGLKTATNMIATDWREMGHA 303

Query: 308 IQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGN 367
           IQLQSVDIPLADPHFWT+QGSVRVAQMC+EWGLTWGSHSNNHFDISLAMFTHVAAAAPG 
Sbjct: 304 IQLQSVDIPLADPHFWTLQGSVRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGE 363

Query: 368 ITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGAR 427
           ITAIDTHWIWQDGQRLTK PLQI  G V+VP KPGLGVELD D L KAHE+YK MGLGAR
Sbjct: 364 ITAIDTHWIWQDGQRLTKAPLQIVDGCVQVPTKPGLGVELDMDQLAKAHELYKGMGLGAR 423

Query: 428 DDATAMRYLVSGWEFNNKRPCMVR 451
           DD+ AM++L+ GW+F+NKRPC+VR
Sbjct: 424 DDSVAMQFLIPGWKFDNKRPCLVR 447


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: 696
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: 447
Length adjustment: 33
Effective length of query: 418
Effective length of database: 414
Effective search space:   173052
Effective search space used:   173052
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 Pf1N1B4_71 (Glucarate dehydratase (EC 4.2.1.40))
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.27149.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.7e-271  884.8   0.7   5.4e-271  884.6   0.7    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71  Glucarate dehydratase (EC 4.2.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71  Glucarate dehydratase (EC 4.2.1.40)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  884.6   0.7  5.4e-271  5.4e-271       2     441 .]       8     447 .]       7     447 .] 1.00

  Alignments for each domain:
  == domain 1  score: 884.6 bits;  conditional E-value: 5.4e-271
                                    TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakal 67 
                                                  ++p++t+++vvpvag+d mllnlsgah+pfftrn+vilkd++g+tgvgevpgge+ir+tleda+al
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71   8 KAPIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNVVILKDNAGHTGVGEVPGGERIRQTLEDARAL 73 
                                                  689*************************************************************** PP

                                    TIGR03247  68 vvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallg 133
                                                  vvg ++g+y+++l++vr+tfadrdaggrg+qtfdlr+t+havt+le+alldllgqhl+vpvaallg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71  74 VVGSPIGTYQKILNQVRQTFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQHLDVPVAALLG 139
                                                  ****************************************************************** PP

                                    TIGR03247 134 egqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkd 199
                                                  egqqrdev++lgylf+vgdr++t+l+yrse++a++dw+r+rhe+a++ +avvrlaeaa++rygfkd
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71 140 EGQQRDEVKMLGYLFYVGDRNETDLAYRSEPDADNDWFRVRHEKAMSADAVVRLAEAAHARYGFKD 205
                                                  ****************************************************************** PP

                                    TIGR03247 200 fklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegy 265
                                                  fklkggvl+g+eeieavtala+rfpdaritldpngawsl+eai+lc+d++ vlayaedp+gae++y
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71 206 FKLKGGVLSGDEEIEAVTALAERFPDARITLDPNGAWSLKEAIRLCRDQHHVLAYAEDPCGAENSY 271
                                                  ****************************************************************** PP

                                    TIGR03247 266 sgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeyglt 331
                                                  sgrevmaefrratgl tatnmiatdwre+gha++lq+vdipladphfwtlqgsvrvaq+c+e+glt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71 272 SGREVMAEFRRATGLKTATNMIATDWREMGHAIQLQSVDIPLADPHFWTLQGSVRVAQMCHEWGLT 337
                                                  ****************************************************************** PP

                                    TIGR03247 332 wgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgvel 397
                                                  wgshsnnhfdislamfthvaaaapg++taidthwiwqdgqrltk+pl+i +g+++vp+kpglgvel
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71 338 WGSHSNNHFDISLAMFTHVAAAAPGEITAIDTHWIWQDGQRLTKAPLQIVDGCVQVPTKPGLGVEL 403
                                                  ****************************************************************** PP

                                    TIGR03247 398 dedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                  d+d+++kahelyk +glgardd+vamq+lip+wkfd+krpclvr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_71 404 DMDQLAKAHELYKGMGLGARDDSVAMQFLIPGWKFDNKRPCLVR 447
                                                  *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (447 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: 10.95
//
[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