Alignments for a candidate for gudD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pseudomonas simiae WCS417

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate GFF3692 PS417_18895 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__WCS417:GFF3692
          Length = 441

 Score =  734 bits (1896), Expect = 0.0
 Identities = 350/438 (79%), Positives = 396/438 (90%)

Query: 14  PVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLED 73
           PV+T  +V+PVAGHDSMLLNLSGAHGP FTRNI+IL DSSG+ GVGEVPGGE IR+TLED
Sbjct: 4   PVVTHFQVIPVAGHDSMLLNLSGAHGPYFTRNIVILKDSSGNTGVGEVPGGERIRETLED 63

Query: 74  ARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQH 133
           AR L+I Q IG YQ +LN++R+ FA RD  GRGLQTFDLRI +HAVTA+E+ALLDLLGQ 
Sbjct: 64  ARSLVIGQPIGQYQRILNQMRSTFASRDAAGRGLQTFDLRITIHAVTAMEAALLDLLGQF 123

Query: 134 LQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPES 193
           L VPVAALLGEGQQRDAV+MLGYLFYVGDR+ T L YR+E ++D+EWFRLR++ ALT ++
Sbjct: 124 LDVPVAALLGEGQQRDAVKMLGYLFYVGDRSATPLAYRNEADSDDEWFRLRHETALTADA 183

Query: 194 VVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAVA 253
           VV LAEAA  +YGF DFKLKGGVL G++EI AVTAL+ERFPDARITLDPNGAWSLKEA+ 
Sbjct: 184 VVRLAEAAKAKYGFNDFKLKGGVLSGDEEIQAVTALAERFPDARITLDPNGAWSLKEAIR 243

Query: 254 LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQSV 313
           LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHAIQLQSV
Sbjct: 244 LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAIQLQSV 303

Query: 314 DIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAIDT 373
           DIPLADPHFWT+QGSVRVAQMC+EWGLTWGSHSNNHFDISLAMFT VAAAAPG+ITAIDT
Sbjct: 304 DIPLADPHFWTLQGSVRVAQMCHEWGLTWGSHSNNHFDISLAMFTQVAAAAPGDITAIDT 363

Query: 374 HWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATAM 433
           HWIWQDGQ LTK PL+I+GG V+VP KPGLGVE+D DA+ KAHEVYK MGLGARDD+ AM
Sbjct: 364 HWIWQDGQHLTKAPLKIEGGYVKVPNKPGLGVEIDMDAVAKAHEVYKGMGLGARDDSVAM 423

Query: 434 RYLVSGWEFNNKRPCMVR 451
           ++L+ GW FNNK+PC+VR
Sbjct: 424 QFLIPGWRFNNKQPCLVR 441


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: 683
Number of extensions: 14
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: 441
Length adjustment: 32
Effective length of query: 419
Effective length of database: 409
Effective search space:   171371
Effective search space used:   171371
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 GFF3692 PS417_18895 (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.22785.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-266  869.8   0.5   1.9e-266  869.6   0.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF3692  PS417_18895 glucarate dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3692  PS417_18895 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.6   0.5  1.9e-266  1.9e-266       2     441 .]       2     441 .]       1     441 [] 1.00

  Alignments for each domain:
  == domain 1  score: 869.6 bits;  conditional E-value: 1.9e-266
                           TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgktlgey 76 
                                         +tpvvt+++v+pvag+dsmllnlsgah+p+ftrnivilkdssg+tgvgevpgge+ir+tleda++lv+g+++g+y
  lcl|FitnessBrowser__WCS417:GFF3692   2 TTPVVTHFQVIPVAGHDSMLLNLSGAHGPYFTRNIVILKDSSGNTGVGEVPGGERIRETLEDARSLVIGQPIGQY 76 
                                         79************************************************************************* PP

                           TIGR03247  77 knvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrdevevlgylffvg 151
                                         +++l+++r+tfa rda+grg+qtfdlr+t+havta+e+alldllgq+l+vpvaallgegqqrd+v++lgylf+vg
  lcl|FitnessBrowser__WCS417:GFF3692  77 QRILNQMRSTFASRDAAGRGLQTFDLRITIHAVTAMEAALLDLLGQFLDVPVAALLGEGQQRDAVKMLGYLFYVG 151
                                         *************************************************************************** PP

                           TIGR03247 152 drkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeieavtalakrfpda 226
                                         dr+ t l+yr+e +++d+w+rlrhe alt +avvrlaeaak++ygf+dfklkggvl+g+eei+avtala+rfpda
  lcl|FitnessBrowser__WCS417:GFF3692 152 DRSATPLAYRNEADSDDEWFRLRHETALTADAVVRLAEAAKAKYGFNDFKLKGGVLSGDEEIQAVTALAERFPDA 226
                                         *************************************************************************** PP

                           TIGR03247 227 ritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlq 301
                                         ritldpngawsl+eai+lc+d++ vlayaedp+gae+gysgrevmaefrratgl tatnmiatdwre+gha++lq
  lcl|FitnessBrowser__WCS417:GFF3692 227 RITLDPNGAWSLKEAIRLCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHAIQLQ 301
                                         *************************************************************************** PP

                           TIGR03247 302 avdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltke 376
                                         +vdipladphfwtlqgsvrvaq+c+e+gltwgshsnnhfdislamft vaaaapg++taidthwiwqdgq+ltk+
  lcl|FitnessBrowser__WCS417:GFF3692 302 SVDIPLADPHFWTLQGSVRVAQMCHEWGLTWGSHSNNHFDISLAMFTQVAAAAPGDITAIDTHWIWQDGQHLTKA 376
                                         *************************************************************************** PP

                           TIGR03247 377 pleikegkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                         pl+i++g +kvp+kpglgve+d+dav+kahe+yk +glgardd+vamq+lip+w+f++k+pclvr
  lcl|FitnessBrowser__WCS417:GFF3692 377 PLKIEGGYVKVPNKPGLGVEIDMDAVAKAHEVYKGMGLGARDDSVAMQFLIPGWRFNNKQPCLVR 441
                                         ****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (441 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: 11.95
//
[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