Alignments for a candidate for gudD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Acidovorax sp. GW101-3H11

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate Ac3H11_338 Glucarate dehydratase (EC 4.2.1.40)

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_338
          Length = 454

 Score =  697 bits (1800), Expect = 0.0
 Identities = 326/443 (73%), Positives = 383/443 (86%)

Query: 9   AATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIR 68
           + +  PVIT+L+VVPVAGHDSML+NLSGAHGP FTRN++IL DS+GH GVGEVPGGE IR
Sbjct: 12  STSSTPVITELRVVPVAGHDSMLMNLSGAHGPFFTRNLIILRDSAGHTGVGEVPGGEKIR 71

Query: 69  KTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLD 128
           +T+EDAR L++   IG++ ++LN +R  FADRD GGRGLQTFDLRI +HAVTAVESA LD
Sbjct: 72  QTIEDARALIVGCPIGHHNAVLNAMRAQFADRDAGGRGLQTFDLRITIHAVTAVESAFLD 131

Query: 129 LLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEA 188
           LLGQHL VPVAALLGEG QR++V+MLGYLFYVGDR KTDL YR+E  ADN+WFRLRN++A
Sbjct: 132 LLGQHLGVPVAALLGEGVQRESVQMLGYLFYVGDRAKTDLAYRTEPGADNDWFRLRNEKA 191

Query: 189 LTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSL 248
           +T E +V LAEAAY+RYGF DFKLKGGVLRGE+E+ A+ AL +RFP+AR+TLDPNG W L
Sbjct: 192 MTAEGIVRLAEAAYERYGFADFKLKGGVLRGEEEVEAIRALHQRFPEARVTLDPNGGWLL 251

Query: 249 KEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAI 308
           K+A+ + RD H V+AYAEDPCGAE  +SGREVMAEFRR+TGL TATNM+ATDWR+M H++
Sbjct: 252 KDAIRITRDLHGVMAYAEDPCGAEGVFSGREVMAEFRRATGLPTATNMVATDWREMAHSL 311

Query: 309 QLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNI 368
            LQSVDIPLADPHFWTM GSVRVAQMC  +GLTWGSHSNNHFD+SLAMFTHV AAAPG +
Sbjct: 312 ALQSVDIPLADPHFWTMAGSVRVAQMCQAFGLTWGSHSNNHFDVSLAMFTHVGAAAPGRV 371

Query: 369 TAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARD 428
           TAIDTHWIWQDG+RLTKEP QIK G +++PKKPGLGVELD D + +AH +Y   GLGARD
Sbjct: 372 TAIDTHWIWQDGERLTKEPFQIKNGFIDLPKKPGLGVELDMDEVERAHRLYLQHGLGARD 431

Query: 429 DATAMRYLVSGWEFNNKRPCMVR 451
           DA AM+YL+ GW+FNNK PCMVR
Sbjct: 432 DAIAMQYLIPGWKFNNKSPCMVR 454


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: 648
Number of extensions: 16
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: 454
Length adjustment: 33
Effective length of query: 418
Effective length of database: 421
Effective search space:   175978
Effective search space used:   175978
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 Ac3H11_338 (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.31047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.2e-260  849.6   0.2   2.5e-260  849.4   0.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338  Glucarate dehydratase (EC 4.2.1.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338  Glucarate dehydratase (EC 4.2.1.40)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  849.4   0.2  2.5e-260  2.5e-260       2     441 .]      15     454 .]      14     454 .] 1.00

  Alignments for each domain:
  == domain 1  score: 849.4 bits;  conditional E-value: 2.5e-260
                                       TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktleda 64 
                                                     +tpv+telrvvpvag+dsml+nlsgah+pfftrn++il+ds+g+tgvgevpggekir+t+eda
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338  15 STPVITELRVVPVAGHDSMLMNLSGAHGPFFTRNLIILRDSAGHTGVGEVPGGEKIRQTIEDA 77 
                                                     79************************************************************* PP

                                       TIGR03247  65 kalvvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevp 127
                                                     +al+vg ++g++++vl+++r++fadrdaggrg+qtfdlr+t+havta+esa+ldllgqhl+vp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338  78 RALIVGCPIGHHNAVLNAMRAQFADRDAGGRGLQTFDLRITIHAVTAVESAFLDLLGQHLGVP 140
                                                     *************************************************************** PP

                                       TIGR03247 128 vaallgegqqrdevevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaea 190
                                                     vaallgeg qr++v++lgylf+vgdr kt+l+yr+e+ a++dw+rlr+e+a+t e++vrlaea
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338 141 VAALLGEGVQRESVQMLGYLFYVGDRAKTDLAYRTEPGADNDWFRLRNEKAMTAEGIVRLAEA 203
                                                     *************************************************************** PP

                                       TIGR03247 191 akdrygfkdfklkggvlrgeeeieavtalakrfpdaritldpngawsleeaialckdlkdvla 253
                                                     a++rygf+dfklkggvlrgeee+ea++al++rfp+ar+tldpng+w l++ai++++dl++v+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338 204 AYERYGFADFKLKGGVLRGEEEVEAIRALHQRFPEARVTLDPNGGWLLKDAIRITRDLHGVMA 266
                                                     *************************************************************** PP

                                       TIGR03247 254 yaedpvgaeegysgrevmaefrratglptatnmiatdwrelghalrlqavdipladphfwtlq 316
                                                     yaedp+gae  +sgrevmaefrratglptatnm+atdwre++h+l lq+vdipladphfwt++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338 267 YAEDPCGAEGVFSGREVMAEFRRATGLPTATNMVATDWREMAHSLALQSVDIPLADPHFWTMA 329
                                                     *************************************************************** PP

                                       TIGR03247 317 gsvrvaqlceeygltwgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkeple 379
                                                     gsvrvaq+c+++gltwgshsnnhfd+slamfthv+aaapg+vtaidthwiwqdg+rltkep++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338 330 GSVRVAQMCQAFGLTWGSHSNNHFDVSLAMFTHVGAAAPGRVTAIDTHWIWQDGERLTKEPFQ 392
                                                     *************************************************************** PP

                                       TIGR03247 380 ikegkikvpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441
                                                     ik+g i++p+kpglgveld+d+ve+ah+ly ++glgardda+amq+lip+wkf++k pc+vr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_338 393 IKNGFIDLPKKPGLGVELDMDEVERAHRLYLQHGLGARDDAIAMQYLIPGWKFNNKSPCMVR 454
                                                     *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (454 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.96
//
[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