Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas fluorescens FW300-N2C3

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate AO356_01240 AO356_01240 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01240
          Length = 447

 Score =  752 bits (1942), Expect = 0.0
 Identities = 358/439 (81%), Positives = 398/439 (90%)

Query: 13  APVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLE 72
           AP+IT ++VVPVAGHD MLLNLSGAHGP FTRNI+IL D++GH GVGEVPGGE IR+TLE
Sbjct: 9   APIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQTLE 68

Query: 73  DARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQ 132
           DAR L++   IG YQ +LN VRNAFADRD GGRGLQTFDLRI +HAVT +E+ALLDLLGQ
Sbjct: 69  DARSLVVGSPIGTYQKILNTVRNAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQ 128

Query: 133 HLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPE 192
           HL VPVAALLGEGQQRD V+MLGYLFYVGDR +TDL YRSE +ADN+WFR+R+++AL  +
Sbjct: 129 HLDVPVAALLGEGQQRDEVKMLGYLFYVGDRQQTDLAYRSEPDADNDWFRVRHEKALDAD 188

Query: 193 SVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAV 252
           +VV LAEAA  RYGF+DFKLKGGVL+G+ EI AVTAL+ERFP ARITLDPNGAWSLKEA+
Sbjct: 189 AVVRLAEAAQARYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLKEAI 248

Query: 253 ALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQS 312
            LCRDQH VLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHAI LQS
Sbjct: 249 RLCRDQHKVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAITLQS 308

Query: 313 VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAID 372
           VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPG+ITAID
Sbjct: 309 VDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAID 368

Query: 373 THWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATA 432
           THWIWQDGQRLTK PLQI+GG V+VPKKPGLG+ELD D L KAHE+YK MGLGARDDA A
Sbjct: 369 THWIWQDGQRLTKAPLQIQGGCVQVPKKPGLGIELDTDQLAKAHELYKGMGLGARDDAVA 428

Query: 433 MRYLVSGWEFNNKRPCMVR 451
           M++L+ GW FNNKRPC+VR
Sbjct: 429 MQFLIPGWTFNNKRPCLVR 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: 19
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 AO356_01240 AO356_01240 (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.15515.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.7e-269  879.7   0.8   1.9e-269  879.5   0.8    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  AO356_01240 glucarate dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  AO356_01240 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  879.5   0.8  1.9e-269  1.9e-269       2     441 .]       8     447 .]       7     447 .] 1.00

  Alignments for each domain:
  == domain 1  score: 879.5 bits;  conditional E-value: 1.9e-269
                                       TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktleda 64 
                                                     ++p++t+++vvpvag+d mllnlsgah+pfftrnivilkd++g+tgvgevpgge+ir+tleda
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240   8 KAPIITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERIRQTLEDA 70 
                                                     689************************************************************ PP

                                       TIGR03247  65 kalvvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevp 127
                                                     ++lvvg ++g+y+++l++vr++fadrdaggrg+qtfdlr+t+havt+le+alldllgqhl+vp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240  71 RSLVVGSPIGTYQKILNTVRNAFADRDAGGRGLQTFDLRITIHAVTGLEAALLDLLGQHLDVP 133
                                                     *************************************************************** PP

                                       TIGR03247 128 vaallgegqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaea 190
                                                     vaallgegqqrdev++lgylf+vgdr++t+l+yrse++a++dw+r+rhe+al  +avvrlaea
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 134 VAALLGEGQQRDEVKMLGYLFYVGDRQQTDLAYRSEPDADNDWFRVRHEKALDADAVVRLAEA 196
                                                     *************************************************************** PP

                                       TIGR03247 191 akdrygfkdfklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvla 253
                                                     a++rygf+dfklkggvl+g+ eieavtala+rfp+aritldpngawsl+eai+lc+d+++vla
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 197 AQARYGFQDFKLKGGVLQGDAEIEAVTALAERFPQARITLDPNGAWSLKEAIRLCRDQHKVLA 259
                                                     *************************************************************** PP

                                       TIGR03247 254 yaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlq 316
                                                     yaedp+gae+gysgrevmaefrratgl tatnmiatdwre+gha+ lq+vdipladphfwt+q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 260 YAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAITLQSVDIPLADPHFWTMQ 322
                                                     *************************************************************** PP

                                       TIGR03247 317 gsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkeple 379
                                                     gsvrvaq+c+e+gltwgshsnnhfdislamfthvaaaapg++taidthwiwqdgqrltk+pl+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 323 GSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQDGQRLTKAPLQ 385
                                                     *************************************************************** PP

                                       TIGR03247 380 ikegkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                     i++g+++vp+kpglg+eld+d+++kahelyk +glgarddavamq+lip+w+f++krpclvr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01240 386 IQGGCVQVPKKPGLGIELDTDQLAKAHELYKGMGLGARDDAVAMQFLIPGWTFNNKRPCLVR 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.97
//
[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