Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2E2

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate Pf6N2E2_2116 Glucarate dehydratase (EC 4.2.1.40)

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116
          Length = 447

 Score =  751 bits (1940), Expect = 0.0
 Identities = 357/442 (80%), Positives = 399/442 (90%)

Query: 10  ATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRK 69
           A+ AP+IT +++VPVAGHD MLLNLSGAHGP FTRNI+IL D++GH GVGEVPGGE IR+
Sbjct: 6   ASKAPIITSMQIVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQ 65

Query: 70  TLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDL 129
           TLEDAR L++   IG YQ +LN VR AFADRD GGRGLQTFDLRI +HAVT +E+ALLDL
Sbjct: 66  TLEDARSLVVGSPIGTYQKILNTVRQAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDL 125

Query: 130 LGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEAL 189
           LGQHL VPVAALLGEGQQRD V+MLGYLFYVGDR +TDL YRSE +ADN+WFR+R+++AL
Sbjct: 126 LGQHLDVPVAALLGEGQQRDEVKMLGYLFYVGDRQQTDLPYRSEPDADNDWFRVRHEKAL 185

Query: 190 TPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLK 249
             ++VV LAEAA+ RYGF+DFKLKGGVL+G+ EI AVTAL+ERFP ARITLDPNGAWSLK
Sbjct: 186 DADAVVRLAEAAHSRYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLK 245

Query: 250 EAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQ 309
           EA+ LCRDQH VLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHAI 
Sbjct: 246 EAIRLCRDQHKVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAIT 305

Query: 310 LQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNIT 369
           LQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPG IT
Sbjct: 306 LQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGEIT 365

Query: 370 AIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDD 429
           AIDTHWIWQDGQRLTK PLQI+GG V+VPKKPGLG+ELD D L KAHE+YK MGLGARDD
Sbjct: 366 AIDTHWIWQDGQRLTKAPLQIQGGCVQVPKKPGLGIELDTDQLAKAHELYKGMGLGARDD 425

Query: 430 ATAMRYLVSGWEFNNKRPCMVR 451
           A AM++L+ GW FNNKRPC+VR
Sbjct: 426 AVAMQFLIPGWTFNNKRPCLVR 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: 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: 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 Pf6N2E2_2116 (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.24944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   9.9e-270  880.5   0.4   1.1e-269  880.3   0.4    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116  Glucarate dehydratase (EC 4.2.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116  Glucarate dehydratase (EC 4.2.1.40)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.3   0.4  1.1e-269  1.1e-269       2     441 .]       8     447 .]       7     447 .] 1.00

  Alignments for each domain:
  == domain 1  score: 880.3 bits;  conditional E-value: 1.1e-269
                                      TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledak 65 
                                                    ++p++t++++vpvag+d mllnlsgah+pfftrnivilkd++g+tgvgevpgge+ir+tleda+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116   8 KAPIITSMQIVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQTLEDAR 71 
                                                    689************************************************************* PP

                                      TIGR03247  66 alvvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpva 129
                                                    +lvvg ++g+y+++l++vr++fadrdaggrg+qtfdlr+t+havt+le+alldllgqhl+vpva
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116  72 SLVVGSPIGTYQKILNTVRQAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQHLDVPVA 135
                                                    **************************************************************** PP

                                      TIGR03247 130 allgegqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakd 193
                                                    allgegqqrdev++lgylf+vgdr++t+l+yrse++a++dw+r+rhe+al  +avvrlaeaa+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116 136 ALLGEGQQRDEVKMLGYLFYVGDRQQTDLPYRSEPDADNDWFRVRHEKALDADAVVRLAEAAHS 199
                                                    **************************************************************** PP

                                      TIGR03247 194 rygfkdfklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaed 257
                                                    rygf+dfklkggvl+g+ eieavtala+rfp+aritldpngawsl+eai+lc+d+++vlayaed
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116 200 RYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLKEAIRLCRDQHKVLAYAED 263
                                                    **************************************************************** PP

                                      TIGR03247 258 pvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrv 321
                                                    p+gae+gysgrevmaefrratgl tatnmiatdwre+gha+ lq+vdipladphfwt+qgsvrv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116 264 PCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAITLQSVDIPLADPHFWTMQGSVRV 327
                                                    **************************************************************** PP

                                      TIGR03247 322 aqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleikegki 385
                                                    aq+c+e+gltwgshsnnhfdislamfthvaaaapg++taidthwiwqdgqrltk+pl+i++g++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116 328 AQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGEITAIDTHWIWQDGQRLTKAPLQIQGGCV 391
                                                    **************************************************************** PP

                                      TIGR03247 386 kvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                    +vp+kpglg+eld+d+++kahelyk +glgarddavamq+lip+w+f++krpclvr
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2116 392 QVPKKPGLGIELDTDQLAKAHELYKGMGLGARDDAVAMQFLIPGWTFNNKRPCLVR 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: 12.51
//
[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