Alignments for a candidate for prpD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Cupriavidus basilensis 4G11

Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate RR42_RS14485 RR42_RS14485 2-methylcitrate dehydratase

Query= SwissProt::Q937N6
         (484 letters)



>FitnessBrowser__Cup4G11:RR42_RS14485
          Length = 483

 Score =  847 bits (2187), Expect = 0.0
 Identities = 410/475 (86%), Positives = 442/475 (93%)

Query: 10  RPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTKLLGPVVPGT 69
           RP+PD V+ DIVDYVTRY++KS LAYDTARNCLIDTLGCGLEALSYPACTKLLGP+VPGT
Sbjct: 9   RPEPDPVMADIVDYVTRYQVKSALAYDTARNCLIDTLGCGLEALSYPACTKLLGPIVPGT 68

Query: 70  IVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWIS 129
           +VPNGA+VPGTQFQLDP+QAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADW+S
Sbjct: 69  VVPNGAKVPGTQFQLDPIQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLS 128

Query: 130 RNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVASTAVVAQMLG 189
           RN++AAGRKPLTMK VL  MIKAHEIQGCIALEN+FN+VGLDHVVLVKVASTAVVAQMLG
Sbjct: 129 RNNVAAGRKPLTMKDVLTGMIKAHEIQGCIALENAFNKVGLDHVVLVKVASTAVVAQMLG 188

Query: 190 LTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIARTGEMGYPS 249
           L  DEILNAVSLAWVDGQ+LRTYRHAPN GSRKSWA GDATSRAVRLALIARTGEMGYPS
Sbjct: 189 LAVDEILNAVSLAWVDGQALRTYRHAPNTGSRKSWAAGDATSRAVRLALIARTGEMGYPS 248

Query: 250 VLTAKTWGFYDVLFKGQPFRFQRPYGTYVMENILLKISYPAEFHAQTAVEAAMQLHGALA 309
           VL+AK WGFYDVLFKGQPFRFQRPYGTYVMEN+L KI++PAEFHAQTAVEAAM LHG L 
Sbjct: 249 VLSAKGWGFYDVLFKGQPFRFQRPYGTYVMENVLFKIAFPAEFHAQTAVEAAMTLHGQLC 308

Query: 310 LAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHCIQYMVAVPLLFGRLTAADYED 369
            AG++AA I  +TIRTHEAC+RIIDK GPL+NPADRDHCIQYMVAVPLLFGRL+A DYED
Sbjct: 309 AAGKTAAQIRQVTIRTHEACIRIIDKKGPLANPADRDHCIQYMVAVPLLFGRLSAEDYED 368

Query: 370 RIAADPRIDALRGRITCVEDPALTRDYHDPAKRSIANALTVTLADGTVLDEVLVEYPLGH 429
           +IAADPRIDALR +I CVEDP  T DYHDP KRSIANALTVTL DGTVL EV+V+YPLGH
Sbjct: 369 KIAADPRIDALRDKIVCVEDPRFTADYHDPDKRSIANALTVTLDDGTVLPEVVVDYPLGH 428

Query: 430 KRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQARLEAMPVNEYLDMYAI 484
           KRRR EGIPLLVEKF+TNLARRFP +QQQAILA SLDQARLEAMPVNEY+D+Y I
Sbjct: 429 KRRRDEGIPLLVEKFKTNLARRFPARQQQAILAVSLDQARLEAMPVNEYVDLYVI 483


Lambda     K      H
   0.322    0.136    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: 816
Number of extensions: 17
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: 484
Length of database: 483
Length adjustment: 34
Effective length of query: 450
Effective length of database: 449
Effective search space:   202050
Effective search space used:   202050
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 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate RR42_RS14485 RR42_RS14485 (2-methylcitrate dehydratase)
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

# 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/TIGR02330.hmm
# target sequence database:        /tmp/gapView.2075.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02330  [M=468]
Accession:   TIGR02330
Description: prpD: 2-methylcitrate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-267  871.0   0.0   1.1e-266  870.8   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS14485  RR42_RS14485 2-methylcitrate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14485  RR42_RS14485 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  870.8   0.0  1.1e-266  1.1e-266       1     468 []      13     483 .]      13     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 870.8 bits;  conditional E-value: 1.1e-266
                                 TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsy 69 
                                               d v+ di+dyv  y+++s++aydtar++l+dtlgcgl+al yp+ctkllgp+v+gt+vpnga+vpgt++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485  13 DPVMADIVDYVTRYQVKSALAYDTARNCLIDTLGCGLEALSYPACTKLLGPIVPGTVVPNGAKVPGTQF 81 
                                               66899**************************************************************** PP

                                 TIGR02330  70 qldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamik 138
                                               qldp++aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr+++a g++pl++k+vl+ mik
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485  82 QLDPIQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNNVAAGRKPLTMKDVLTGMIK 150
                                               ********************************************************************* PP

                                 TIGR02330 139 aheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgs 207
                                               aheiqg++alen+fn+vgldhv+lvkvastavva++lg+  +eilna+s+a+vdgqalrtyrhapntgs
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485 151 AHEIQGCIALENAFNKVGLDHVVLVKVASTAVVAQMLGLAVDEILNAVSLAWVDGQALRTYRHAPNTGS 219
                                               ********************************************************************* PP

                                 TIGR02330 208 rkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfp 276
                                               rkswaagdatsr+vrlalia++gemgyps+lsa  wgf+dvlfk++ ++++r+yg+yvmenvlfki+fp
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485 220 RKSWAAGDATSRAVRLALIARTGEMGYPSVLSAKGWGFYDVLFKGQPFRFQRPYGTYVMENVLFKIAFP 288
                                               ********************************************************************* PP

                                 TIGR02330 277 aefhaqtaveaavklheevker...ldeierivitthesairiidkkgplanpadrdhclqylvavpll 342
                                               aefhaqtaveaa++lh ++ ++   +++i +++i+the++iriidkkgplanpadrdhc+qy+vavpll
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485 289 AEFHAQTAVEAAMTLHGQLCAAgktAAQIRQVTIRTHEACIRIIDKKGPLANPADRDHCIQYMVAVPLL 357
                                               ******************988766799****************************************** PP

                                 TIGR02330 343 fgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveypl 411
                                               fg+l aedyed++aadprid+lr+k+++ved+r++++y+++dkrsiana++v+ +dg++  ev+v+ypl
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485 358 FGRLSAEDYEDKIAADPRIDALRDKIVCVEDPRFTADYHDPDKRSIANALTVTLDDGTVLPEVVVDYPL 426
                                               ********************************************************************* PP

                                 TIGR02330 412 ghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                               gh+rrrdegip+lv+kfk+nla++f++++q+ il ++ldqa+lea+pvne++dl+vi
  lcl|FitnessBrowser__Cup4G11:RR42_RS14485 427 GHKRRRDEGIPLLVEKFKTNLARRFPARQQQAILAVSLDQARLEAMPVNEYVDLYVI 483
                                               *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (483 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: 11.47
//
[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