Alignments for a candidate for prpD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Burkholderia phytofirmans PsJN

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate dehydratase

Query= BRENDA::P77243
         (483 letters)



>FitnessBrowser__BFirm:BPHYT_RS33975
          Length = 483

 Score =  792 bits (2046), Expect = 0.0
 Identities = 378/483 (78%), Positives = 431/483 (89%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MSA I+N+RP+ D  + DIVDYV +Y I S +A +TA +CL+DTLGCGLEAL YPAC KL
Sbjct: 1   MSAPISNVRPDPDSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           +GPIVPGT+VPNG +VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  MGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LATADWLSR+A+A+GKAPL MK VL AMIKAHEIQGCIALENSFN+VGLDHVLLVK+AST
Sbjct: 121 LATADWLSRSAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVV ++L LTR+E++NAVS A+VDG +LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K
Sbjct: 181 AVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPS LTA  WGFYDV FKG +F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEA 
Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFHAQTAVEAT 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           M L+ Q+ AAG++  DI K+TIRTHEA IRIIDKKGPLNNPADRDHCIQYMVA+PL+ GR
Sbjct: 301 MKLHAQLNAAGRSVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGR 360

Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420
           LTAADYED++AQD RID LR K+ C EDP FT DYHDPEKR+IANA+T+EF DG+ F+EV
Sbjct: 361 LTAADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEV 420

Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480
           +VEYPIGH RRR+DGIP LV+KFK NLAR+FP +QQ  IL+VSLD+ARLE MPVNEY+DL
Sbjct: 421 IVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.406 

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: 787
Number of extensions: 12
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 BPHYT_RS33975 BPHYT_RS33975 (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.14102.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.6e-268  876.2   0.0     3e-268  876.0   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33975  BPHYT_RS33975 2-methylcitrate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33975  BPHYT_RS33975 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.0   0.0    3e-268    3e-268       1     468 []      13     483 .]      13     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 876.0 bits;  conditional E-value: 3e-268
                                TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyq 70 
                                              d+vl di+dyv +y+ids++a++tar++l+dtlgcgl+al yp+ctkl+gp+v+gt+vpnga+vpgts+q
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975  13 DSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKLMGPIVPGTIVPNGAKVPGTSFQ 82 
                                              789******************************************************************* PP

                                TIGR02330  71 ldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikah 140
                                              ldpv+aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr +ia gk+pl +k+vl amikah
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975  83 LDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRSAIAAGKAPLAMKDVLIAMIKAH 152
                                              ********************************************************************** PP

                                TIGR02330 141 eiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrks 210
                                              eiqg++alensfn+vgldhvllvk+astavv +ll +tr+e++na+s+afvdg+alrtyrhapntgsrks
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975 153 EIQGCIALENSFNKVGLDHVLLVKLASTAVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKS 222
                                              ********************************************************************** PP

                                TIGR02330 211 waagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfpaefh 280
                                              waagdatsr+vrlali+++gemgyps+l+a +wgf+dvlfk++ ++++r+ygsyvmenvlfkisfpaefh
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975 223 WAAGDATSRAVRLALISKTGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFH 292
                                              ********************************************************************** PP

                                TIGR02330 281 aqtaveaavklheevker...ldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlv 347
                                              aqtavea++klh +++++   +d+i++i+i+the+airiidkkgpl+npadrdhc+qy+vavpl++g+l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975 293 AQTAVEATMKLHAQLNAAgrsVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGRLT 362
                                              ***************9987789************************************************ PP

                                TIGR02330 348 aedyedavaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrr 417
                                              a+dyed++a+dprid lr k+e+ved++++++y++++krsiana++++f+dgs+++ev veyp+gh+rrr
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975 363 AADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEVIVEYPIGHKRRR 432
                                              ********************************************************************** PP

                                TIGR02330 418 degipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                              ++gip+lv+kfk+nla++f+ k+q  il+++ldqa+lea+pvne++dl+vi
  lcl|FitnessBrowser__BFirm:BPHYT_RS33975 433 EDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDLYVI 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: 11.65
//
[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