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_RS10625 RR42_RS10625 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__Cup4G11:RR42_RS10625
          Length = 452

 Score =  732 bits (1890), Expect = 0.0
 Identities = 349/438 (79%), Positives = 392/438 (89%)

Query: 14  PVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLED 73
           PV+T+L VVPVAGHDSML+NLSGAHGP FTRNI+IL DS+G+ GVGEVPGGE IR+TLED
Sbjct: 15  PVVTELTVVPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNTGVGEVPGGEAIRQTLED 74

Query: 74  ARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQH 133
           AR LL  QSIGN+Q+LLN+VR AFA RD GGRGLQTFDLRIA+HAVTA+E+ALLDLLG+H
Sbjct: 75  ARELLAGQSIGNHQALLNRVRTAFASRDAGGRGLQTFDLRIAIHAVTALEAALLDLLGKH 134

Query: 134 LQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPES 193
           L VPVAALLGEGQQRDAVEMLGYLFY+GDRN+T LGYRSE EADN+WFRLRN+ A+  E 
Sbjct: 135 LGVPVAALLGEGQQRDAVEMLGYLFYIGDRNRTTLGYRSEPEADNDWFRLRNEAAMNAEG 194

Query: 194 VVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAVA 253
           VV LA+AAY+RYGF DFKLKGGVLRG++E+ A+ AL+ERFP ARITLDPNGAWSL EAV 
Sbjct: 195 VVRLAQAAYERYGFNDFKLKGGVLRGDEEMEAILALAERFPKARITLDPNGAWSLAEAVR 254

Query: 254 LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQSV 313
           LCRD+H VLAYAEDPCGA+ GYSGRE+MAEFR +TGL TATNM+ATDWRQMGHA++LQSV
Sbjct: 255 LCRDKHGVLAYAEDPCGAQEGYSGREIMAEFRTATGLPTATNMVATDWRQMGHAVRLQSV 314

Query: 314 DIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAIDT 373
           DIPLADPHFWTMQGSVRVAQMC EWGLTWGSHSNNHFDISLAMFTHVAAAAPG +TAIDT
Sbjct: 315 DIPLADPHFWTMQGSVRVAQMCAEWGLTWGSHSNNHFDISLAMFTHVAAAAPGRVTAIDT 374

Query: 374 HWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATAM 433
           HWIWQDG+RLTK PL+I+ G V VP  PGLGVELD + L  AHE YK+MGLGARDDA AM
Sbjct: 375 HWIWQDGERLTKAPLKIENGKVAVPTAPGLGVELDMEQLALAHERYKNMGLGARDDAVAM 434

Query: 434 RYLVSGWEFNNKRPCMVR 451
           ++L+ GW F+NK PCMVR
Sbjct: 435 QFLIPGWTFDNKAPCMVR 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: 692
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_RS10625 RR42_RS10625 (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.26909.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-262  856.0   0.6   2.9e-262  855.8   0.6    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS10625  RR42_RS10625 glucarate dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS10625  RR42_RS10625 glucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  855.8   0.6  2.9e-262  2.9e-262       3     441 .]      14     452 .]      12     452 .] 1.00

  Alignments for each domain:
  == domain 1  score: 855.8 bits;  conditional E-value: 2.9e-262
                                 TIGR03247   3 tpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggekirktledakalvvgk 71 
                                               tpvvtel vvpvag+dsml+nlsgah+pfftrnivilkds+g+tgvgevpgge+ir+tleda++l+ g+
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625  14 TPVVTELTVVPVAGHDSMLMNLSGAHGPFFTRNIVILKDSAGNTGVGEVPGGEAIRQTLEDARELLAGQ 82 
                                               89******************************************************************* PP

                                 TIGR03247  72 tlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavtalesalldllgqhlevpvaallgegqqrde 140
                                               ++g+++++l++vr++fa rdaggrg+qtfdlr+++havtale+alldllg+hl+vpvaallgegqqrd+
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625  83 SIGNHQALLNRVRTAFASRDAGGRGLQTFDLRIAIHAVTALEAALLDLLGKHLGVPVAALLGEGQQRDA 151
                                               ********************************************************************* PP

                                 TIGR03247 141 vevlgylffvgdrkktsldyrseeeakddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrg 209
                                               ve+lgylf++gdr++t+l yrse+ea++dw+rlr+e a+  e+vvrla+aa++rygf+dfklkggvlrg
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625 152 VEMLGYLFYIGDRNRTTLGYRSEPEADNDWFRLRNEAAMNAEGVVRLAQAAYERYGFNDFKLKGGVLRG 220
                                               ********************************************************************* PP

                                 TIGR03247 210 eeeieavtalakrfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrrat 278
                                               +ee+ea+ ala+rfp+aritldpngawsl ea++lc+d+++vlayaedp+ga+egysgre+maefr at
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625 221 DEEMEAILALAERFPKARITLDPNGAWSLAEAVRLCRDKHGVLAYAEDPCGAQEGYSGREIMAEFRTAT 289
                                               ********************************************************************* PP

                                 TIGR03247 279 glptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeygltwgshsnnhfdislamf 347
                                               glptatnm+atdwr++gha+rlq+vdipladphfwt+qgsvrvaq+c e+gltwgshsnnhfdislamf
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625 290 GLPTATNMVATDWRQMGHAVRLQSVDIPLADPHFWTMQGSVRVAQMCAEWGLTWGSHSNNHFDISLAMF 358
                                               ********************************************************************* PP

                                 TIGR03247 348 thvaaaapgkvtaidthwiwqdgqrltkepleikegkikvpekpglgveldedavekahelykkkglga 416
                                               thvaaaapg+vtaidthwiwqdg+rltk+pl+i++gk++vp+ pglgveld+++++ ahe yk++glga
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625 359 THVAAAAPGRVTAIDTHWIWQDGERLTKAPLKIENGKVAVPTAPGLGVELDMEQLALAHERYKNMGLGA 427
                                               ********************************************************************* PP

                                 TIGR03247 417 rddavamqllipnwkfdekrpclvr 441
                                               rddavamq+lip+w+fd+k pc+vr
  lcl|FitnessBrowser__Cup4G11:RR42_RS10625 428 RDDAVAMQFLIPGWTFDNKAPCMVR 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: 7.71
//
[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