GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Paraburkholderia bryophila 376MFSha3.1

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate H281DRAFT_06607 H281DRAFT_06607 2-methylcitrate dehydratase

Query= BRENDA::P74840
         (483 letters)



>FitnessBrowser__Burk376:H281DRAFT_06607
          Length = 483

 Score =  802 bits (2071), Expect = 0.0
 Identities = 386/483 (79%), Positives = 430/483 (89%)

Query: 1   MSTQELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MS    N+RPD D+ +VDIVDYV++Y+I   +A +TA +CL+DTLGCGLEAL YPAC KL
Sbjct: 1   MSAPISNVRPDPDKVLVDIVDYVLDYQIDGTLALETARHCLIDTLGCGLEALTYPACTKL 60

Query: 61  LGPIVPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           LGPIVPGT+VPNGA+VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  LGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVAST 180
           LATADWLSR A+AAGKAPL MK VL  MIKAHEIQGCIALEN+FN+VGLDHVLLVK+AST
Sbjct: 121 LATADWLSRTAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180

Query: 181 AVVAEMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVV +M+GLTRDE++NAVS A VDGQ+LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K
Sbjct: 181 AVVGQMIGLTRDELINAVSQALVDGQALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240

Query: 241 TGEMGYPSALTAKTWGFYDVSFKGETFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPS LTAKTWGFYDV FKG  F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEAA
Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNEFKFQRPYGSYVMENVLFKISFPAEFHAQTAVEAA 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMVAVPLLFGR 360
           M+L+ Q+Q  G+   DI K+TIRTHEA LRIIDKKGPL+NPADRDHCIQYM+AVPL+FGR
Sbjct: 301 MSLHAQLQLQGRRVEDIRKITIRTHEAALRIIDKKGPLDNPADRDHCIQYMIAVPLIFGR 360

Query: 361 LTAADYEDEVAQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEFTDGSRFGEV 420
           LTAADYED VAQD RID LR K+ C EDP FT DYHDPEKR+I NA+T+EF DGS+F EV
Sbjct: 361 LTAADYEDAVAQDPRIDVLRAKMACVEDPQFTKDYHDPEKRSIANALTIEFNDGSQFDEV 420

Query: 421 VVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQMPVNEYLDL 480
           VVEYPIGH RRR DGIP L+EKFK NLAR+FP +QQ  ILDVSLD+ARLE MPVNEY+DL
Sbjct: 421 VVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.408 

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: 814
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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 H281DRAFT_06607 H281DRAFT_06607 (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.20227.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.9e-270  881.8   0.0   5.6e-270  881.7   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06607  H281DRAFT_06607 2-methylcitrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06607  H281DRAFT_06607 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  881.7   0.0  5.6e-270  5.6e-270       1     468 []      13     483 .]      13     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 881.7 bits;  conditional E-value: 5.6e-270
                                    TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpg 66 
                                                  d+vl+di+dyvl+y+id ++a++tar++l+dtlgcgl+al yp+ctkllgp+v+gt+vpnga+vpg
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607  13 DKVLVDIVDYVLDYQIDGTLALETARHCLIDTLGCGLEALTYPACTKLLGPIVPGTIVPNGAKVPG 78 
                                                  899*************************************************************** PP

                                    TIGR02330  67 tsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkev 132
                                                  ts+qldpv+aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr++ia gk+pl +k+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607  79 TSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRTAIAAGKAPLAMKDV 144
                                                  ****************************************************************** PP

                                    TIGR02330 133 leamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrt 198
                                                  l amikaheiqg++alensfn+vgldhvllvk+astavv +++g+tr+e++na+s+a vdgqalrt
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 145 LIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLASTAVVGQMIGLTRDELINAVSQALVDGQALRT 210
                                                  ****************************************************************** PP

                                    TIGR02330 199 yrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsy 264
                                                  yrhapntgsrkswaagdatsr+vrlali+++gemgyps+l+a +wgf+dvlfk++++k++r+ygsy
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 211 YRHAPNTGSRKSWAAGDATSRAVRLALISKTGEMGYPSVLTAKTWGFYDVLFKGNEFKFQRPYGSY 276
                                                  ****************************************************************** PP

                                    TIGR02330 265 vmenvlfkisfpaefhaqtaveaavklheevk...erldeierivitthesairiidkkgplanpa 327
                                                  vmenvlfkisfpaefhaqtaveaa+ lh +++    r+++i +i+i+the+a riidkkgpl+npa
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 277 VMENVLFKISFPAEFHAQTAVEAAMSLHAQLQlqgRRVEDIRKITIRTHEAALRIIDKKGPLDNPA 342
                                                  *****************************998333459**************************** PP

                                    TIGR02330 328 drdhclqylvavpllfgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianave 393
                                                  drdhc+qy++avpl+fg+l+a+dyedava+dprid lr k+ +ved++++++y++++krsiana++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 343 DRDHCIQYMIAVPLIFGRLTAADYEDAVAQDPRIDVLRAKMACVEDPQFTKDYHDPEKRSIANALT 408
                                                  ****************************************************************** PP

                                    TIGR02330 394 vffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpv 459
                                                  ++f+dgs+++ev+veyp+gh+rrr++gip+lv+kfk+nla++f+ k+q  il+++ldqa+lea+pv
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 409 IEFNDGSQFDEVVVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPV 474
                                                  ****************************************************************** PP

                                    TIGR02330 460 nefldlfvi 468
                                                  ne++dl+vi
  lcl|FitnessBrowser__Burk376:H281DRAFT_06607 475 NEYVDLYVI 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.76
//
[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:

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:

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:

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:

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