Alignments for a candidate for gudD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Cupriavidus basilensis 4G11

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate RR42_RS04840 RR42_RS04840 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__Cup4G11:RR42_RS04840
          Length = 452

 Score =  734 bits (1896), Expect = 0.0
 Identities = 350/440 (79%), Positives = 394/440 (89%)

Query: 12  GAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTL 71
           G PVIT+L VVPVAGHDSML+NLSGAHGP FTRNI+IL DS+G+ GVGEVPGGE IR+TL
Sbjct: 13  GTPVITELTVVPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNTGVGEVPGGEAIRQTL 72

Query: 72  EDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLG 131
           EDAR LL  QSIGN+Q+LLN+VR AFA RD GGRGLQTFDLRIA+HAVTA+E+ALLDLLG
Sbjct: 73  EDARELLAGQSIGNHQALLNRVRTAFASRDAGGRGLQTFDLRIAIHAVTALEAALLDLLG 132

Query: 132 QHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTP 191
           +HL VPVAALLGEGQQRDAVEMLGYLFY+GDRN+T LGYRSE EADN+WFR+RN+ A+  
Sbjct: 133 KHLGVPVAALLGEGQQRDAVEMLGYLFYIGDRNRTTLGYRSEPEADNDWFRVRNEAAMNA 192

Query: 192 ESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEA 251
           E VV LA+AAY+RYGF DFKLKGGVLRG++E+ A+ AL+ERFP ARITLDPNGAWSL EA
Sbjct: 193 EGVVRLAQAAYERYGFNDFKLKGGVLRGDEEMEAILALAERFPKARITLDPNGAWSLAEA 252

Query: 252 VALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQ 311
           V LCRD+H VLAYAEDPCGA+ GYSGRE+MAEFR +TGL TATNM+ATDWRQMGHA++LQ
Sbjct: 253 VRLCRDKHGVLAYAEDPCGAQEGYSGREIMAEFRTATGLPTATNMVATDWRQMGHAVRLQ 312

Query: 312 SVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAI 371
           SVDIPLADPHFWTMQGSVRVAQMC EWGLTWGSHSNNHFDISLAMFTHVAAAAPG +TAI
Sbjct: 313 SVDIPLADPHFWTMQGSVRVAQMCAEWGLTWGSHSNNHFDISLAMFTHVAAAAPGRVTAI 372

Query: 372 DTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDAT 431
           DTHWIWQDG+RLTK PL+I+ G V VP +PGLGVELD + L  AHE YK+MGLGARDDA 
Sbjct: 373 DTHWIWQDGERLTKAPLKIENGKVAVPTEPGLGVELDMEQLALAHERYKNMGLGARDDAV 432

Query: 432 AMRYLVSGWEFNNKRPCMVR 451
           AM++L+ GW F+NK PCMVR
Sbjct: 433 AMQFLIPGWTFDNKAPCMVR 452


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: 689
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: 452
Length adjustment: 33
Effective length of query: 418
Effective length of database: 419
Effective search space:   175142
Effective search space used:   175142
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 RR42_RS04840 RR42_RS04840 (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.25989.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-262  856.7   0.6   1.8e-262  856.5   0.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS04840  RR42_RS04840 glucarate dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS04840  RR42_RS04840 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  856.5   0.6  1.8e-262  1.8e-262       2     441 .]      13     452 .]      12     452 .] 1.00

  Alignments for each domain:
  == domain 1  score: 856.5 bits;  conditional E-value: 1.8e-262
                                 TIGR03247   2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvg 70 
                                                tpv+tel vvpvag+dsml+nlsgah+pfftrnivilkds+g+tgvgevpgge+ir+tleda++l+ g
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840  13 GTPVITELTVVPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNTGVGEVPGGEAIRQTLEDARELLAG 81 
                                               69******************************************************************* PP

                                 TIGR03247  71 ktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrd 139
                                               +++g+++++l++vr++fa rdaggrg+qtfdlr+++havtale+alldllg+hl+vpvaallgegqqrd
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840  82 QSIGNHQALLNRVRTAFASRDAGGRGLQTFDLRIAIHAVTALEAALLDLLGKHLGVPVAALLGEGQQRD 150
                                               ********************************************************************* PP

                                 TIGR03247 140 evevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlr 208
                                               +ve+lgylf++gdr++t+l yrse+ea++dw+r+r+e a+  e+vvrla+aa++rygf+dfklkggvlr
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840 151 AVEMLGYLFYIGDRNRTTLGYRSEPEADNDWFRVRNEAAMNAEGVVRLAQAAYERYGFNDFKLKGGVLR 219
                                               ********************************************************************* PP

                                 TIGR03247 209 geeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrra 277
                                               g+ee+ea+ ala+rfp+aritldpngawsl ea++lc+d+++vlayaedp+ga+egysgre+maefr a
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840 220 GDEEMEAILALAERFPKARITLDPNGAWSLAEAVRLCRDKHGVLAYAEDPCGAQEGYSGREIMAEFRTA 288
                                               ********************************************************************* PP

                                 TIGR03247 278 tglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislam 346
                                               tglptatnm+atdwr++gha+rlq+vdipladphfwt+qgsvrvaq+c e+gltwgshsnnhfdislam
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840 289 TGLPTATNMVATDWRQMGHAVRLQSVDIPLADPHFWTMQGSVRVAQMCAEWGLTWGSHSNNHFDISLAM 357
                                               ********************************************************************* PP

                                 TIGR03247 347 fthvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgveldedavekahelykkkglg 415
                                               fthvaaaapg+vtaidthwiwqdg+rltk+pl+i++gk++vp++pglgveld+++++ ahe yk++glg
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840 358 FTHVAAAAPGRVTAIDTHWIWQDGERLTKAPLKIENGKVAVPTEPGLGVELDMEQLALAHERYKNMGLG 426
                                               ********************************************************************* PP

                                 TIGR03247 416 arddavamqllipnwkfdekrpclvr 441
                                               arddavamq+lip+w+fd+k pc+vr
  lcl|FitnessBrowser__Cup4G11:RR42_RS04840 427 ARDDAVAMQFLIPGWTFDNKAPCMVR 452
                                               *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (441 nodes)
Target sequences:                          1  (452 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: 00:00:00.02
# Mc/sec: 8.11
//
[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