Alignments for a candidate for gudD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas putida KT2440

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate PP_4757 PP_4757 D-glucarate dehydratase / L-idarate epimerase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__Putida:PP_4757
          Length = 448

 Score =  742 bits (1915), Expect = 0.0
 Identities = 352/448 (78%), Positives = 403/448 (89%)

Query: 4   LNQSQAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPG 63
           +N     T  PV+TDL+VVPVAGHDSMLLNLSGAHGP FTRN+++L DS+G+ G+GEVPG
Sbjct: 1   MNMQTLHTSTPVVTDLRVVPVAGHDSMLLNLSGAHGPFFTRNVVVLRDSAGNTGLGEVPG 60

Query: 64  GEGIRKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVE 123
           GE IR+TLEDAR L++ Q IG+YQ +LN +R  FA+RD  GRGLQTFDLRI VHAVTA+E
Sbjct: 61  GEKIRQTLEDARSLVVGQPIGHYQRVLNAMRQTFANRDSAGRGLQTFDLRITVHAVTAIE 120

Query: 124 SALLDLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRL 183
           SALLDLLGQHL VP+AALLGEGQQRDAV+MLGYLFY+GDR +TDL YR+E ++D++WFRL
Sbjct: 121 SALLDLLGQHLNVPMAALLGEGQQRDAVKMLGYLFYIGDRQQTDLAYRNEADSDDDWFRL 180

Query: 184 RNKEALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPN 243
           R+++ALTPE+VV LAEAA  RYGF DFKLKGGVLRGE+E+ AVTAL+ERFP+ARITLDPN
Sbjct: 181 RHEKALTPEAVVRLAEAAKARYGFSDFKLKGGVLRGEEEMEAVTALAERFPEARITLDPN 240

Query: 244 GAWSLKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQ 303
           GAWSLKEA+ALCRD+H+VLAYAEDPCGAENGYSGREVMAEFRR+TGL TATNMIATDWRQ
Sbjct: 241 GAWSLKEAIALCRDKHNVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQ 300

Query: 304 MGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAA 363
           MGHAIQLQSVDIPLADPHFWT+QGSVRVAQMCN+WGLTWGSHSNNHFDISLAMFT VAAA
Sbjct: 301 MGHAIQLQSVDIPLADPHFWTLQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTQVAAA 360

Query: 364 APGNITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMG 423
           APG ITAIDTHWIWQDGQRLT+EPL+I  G V VP +PGLGVELD D L KAHE Y++MG
Sbjct: 361 APGEITAIDTHWIWQDGQRLTREPLRIVDGHVRVPARPGLGVELDEDQLAKAHECYRNMG 420

Query: 424 LGARDDATAMRYLVSGWEFNNKRPCMVR 451
           LGARDD+ AM++L+ GW F+NKRPC+VR
Sbjct: 421 LGARDDSVAMQFLIPGWSFDNKRPCLVR 448


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: 679
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: 448
Length adjustment: 33
Effective length of query: 418
Effective length of database: 415
Effective search space:   173470
Effective search space used:   173470
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 PP_4757 PP_4757 (D-glucarate dehydratase / L-idarate epimerase)
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.18494.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.5e-272  887.9   0.2   6.3e-272  887.7   0.2    1.0  1  lcl|FitnessBrowser__Putida:PP_4757  PP_4757 D-glucarate dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4757  PP_4757 D-glucarate dehydratase / L-idarate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.7   0.2  6.3e-272  6.3e-272       2     441 .]       9     448 .]       8     448 .] 1.00

  Alignments for each domain:
  == domain 1  score: 887.7 bits;  conditional E-value: 6.3e-272
                           TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgktlgey 76 
                                         +tpvvt+lrvvpvag+dsmllnlsgah+pfftrn+v+l+ds+g+tg+gevpggekir+tleda++lvvg+++g+y
  lcl|FitnessBrowser__Putida:PP_4757   9 STPVVTDLRVVPVAGHDSMLLNLSGAHGPFFTRNVVVLRDSAGNTGLGEVPGGEKIRQTLEDARSLVVGQPIGHY 83 
                                         79************************************************************************* PP

                           TIGR03247  77 knvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdevevlgylffvg 151
                                         ++vl+++r+tfa+rd++grg+qtfdlr+tvhavta+esalldllgqhl+vp+aallgegqqrd+v++lgylf++g
  lcl|FitnessBrowser__Putida:PP_4757  84 QRVLNAMRQTFANRDSAGRGLQTFDLRITVHAVTAIESALLDLLGQHLNVPMAALLGEGQQRDAVKMLGYLFYIG 158
                                         *************************************************************************** PP

                           TIGR03247 152 drkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeieavtalakrfpda 226
                                         dr++t+l+yr+e +++ddw+rlrhe+altpeavvrlaeaak+rygf dfklkggvlrgeee+eavtala+rfp+a
  lcl|FitnessBrowser__Putida:PP_4757 159 DRQQTDLAYRNEADSDDDWFRLRHEKALTPEAVVRLAEAAKARYGFSDFKLKGGVLRGEEEMEAVTALAERFPEA 233
                                         *************************************************************************** PP

                           TIGR03247 227 ritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlq 301
                                         ritldpngawsl+eaialc+d+++vlayaedp+gae+gysgrevmaefrratglptatnmiatdwr++gha++lq
  lcl|FitnessBrowser__Putida:PP_4757 234 RITLDPNGAWSLKEAIALCRDKHNVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMGHAIQLQ 308
                                         *************************************************************************** PP

                           TIGR03247 302 avdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltke 376
                                         +vdipladphfwtlqgsvrvaq+c+++gltwgshsnnhfdislamft vaaaapg++taidthwiwqdgqrlt+e
  lcl|FitnessBrowser__Putida:PP_4757 309 SVDIPLADPHFWTLQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTQVAAAAPGEITAIDTHWIWQDGQRLTRE 383
                                         *************************************************************************** PP

                           TIGR03247 377 pleikegkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                         pl+i +g+++vp++pglgvelded+++kahe y+++glgardd+vamq+lip+w+fd+krpclvr
  lcl|FitnessBrowser__Putida:PP_4757 384 PLRIVDGHVRVPARPGLGVELDEDQLAKAHECYRNMGLGARDDSVAMQFLIPGWSFDNKRPCLVR 448
                                         ****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (448 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.18
//
[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