Alignments for a candidate for prpD in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Pseudomonas fluorescens FW300-N1B4

Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate Pf1N1B4_3823 2-methylcitrate dehydratase (EC 4.2.1.79)

Query= SwissProt::Q937N6
         (484 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823
          Length = 494

 Score =  594 bits (1532), Expect = e-174
 Identities = 303/497 (60%), Positives = 368/497 (74%), Gaps = 16/497 (3%)

Query: 1   MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60
           MS +     RPD D VL DI DYV  ++I+S  A DTARNCL+DTLGCGL AL +P CTK
Sbjct: 1   MSANVDLNIRPDYDTVLQDIADYVLNFKIESPEALDTARNCLMDTLGCGLLALRFPECTK 60

Query: 61  LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120
            LGP+V GT+VP GARVPGT ++LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLG 
Sbjct: 61  HLGPIVEGTVVPFGARVPGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGA 120

Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180
           ILA AD +S+  +A G  PLT++ VL AMI AHEIQG IALENSFN+VG+DHV+LVKVAS
Sbjct: 121 ILAVADHLSQKRLANGDAPLTIRVVLEAMIMAHEIQGVIALENSFNRVGIDHVILVKVAS 180

Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240
           TAV A+++G  R+++L+A+S A+ DGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA
Sbjct: 181 TAVAAKLMGANREQLLSALSHAFADGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240

Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288
             GEMG P VLTAK WGFYDVLF              + F F RP+G+YVMEN+L KIS+
Sbjct: 241 MRGEMGIPGVLTAKQWGFYDVLFSHTNNDLALKPEDKRAFSFSRPFGSYVMENVLFKISF 300

Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348
           PAEFHAQTA EAA+ LH    L      +I  I I THE+ +RII K+GPL+N ADRDHC
Sbjct: 301 PAEFHAQTACEAAVTLH---PLVRNRLHEIDRIVITTHESAIRIISKVGPLANAADRDHC 357

Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407
           IQYM+AVPL+FG L A  YED   A  P ID LR ++  VEDP  TR+Y +P KRSIANA
Sbjct: 358 IQYMIAVPLVFGNLVAEQYEDDFHAVHPIIDVLRDKMVIVEDPRFTREYLEPDKRSIANA 417

Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467
           + V   DG+    V+VEYP+GH+RRRAEGI LL +KF+ NLA RF  ++   I A   DQ
Sbjct: 418 VQVFFKDGSSTKNVVVEYPIGHRRRRAEGIALLEDKFKANLATRFTAQRSAEIFALCKDQ 477

Query: 468 ARLEAMPVNEYLDMYAI 484
           ARLE   VN ++D++ I
Sbjct: 478 ARLEETAVNRFVDLFVI 494


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: 653
Number of extensions: 21
Number of successful extensions: 4
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: 494
Length adjustment: 34
Effective length of query: 450
Effective length of database: 460
Effective search space:   207000
Effective search space used:   207000
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 Pf1N1B4_3823 (2-methylcitrate dehydratase (EC 4.2.1.79))
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.13969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   8.5e-269  877.8   0.1   9.6e-269  877.6   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823  2-methylcitrate dehydratase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823  2-methylcitrate dehydratase (EC 4.2.1.79)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.6   0.1  9.6e-269  9.6e-269       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 877.6 bits;  conditional E-value: 9.6e-269
                                      TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarv 64 
                                                    d+vl+diadyvl+++i+s+ea+dtar++l+dtlgcgllal++pectk+lgp+vegt+vp garv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823  14 DTVLQDIADYVLNFKIESPEALDTARNCLMDTLGCGLLALRFPECTKHLGPIVEGTVVPFGARV 77 
                                                    789************************************************************* PP

                                      TIGR02330  65 pgtsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplk 128
                                                    pgtsy+ldpvkaa++ig++vrwldyndtwlaaewghpsdnlg+ilavad+ls+kr+a+g++pl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823  78 PGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQKRLANGDAPLT 141
                                                    **************************************************************** PP

                                      TIGR02330 129 vkevleamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvd 192
                                                    ++ vleami+aheiqgv+alensfnrvg+dhv+lvkvastav+akl+ga+re++l+alshaf d
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 142 IRVVLEAMIMAHEIQGVIALENSFNRVGIDHVILVKVASTAVAAKLMGANREQLLSALSHAFAD 205
                                                    **************************************************************** PP

                                      TIGR02330 193 gqalrtyrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkke... 253
                                                    gqalrtyrhapn+gsrkswaagda+srgvrla+ia++gemg+p++l+a +wgf+dvlf+++   
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 206 GQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEMGIPGVLTAKQWGFYDVLFSHTnnd 269
                                                    **************************************************************** PP

                                      TIGR02330 254 .........klklareygsyvmenvlfkisfpaefhaqtaveaavklheevkerldeierivit 308
                                                              ++++r++gsyvmenvlfkisfpaefhaqta+eaav+lh+ v++rl+ei+rivit
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 270 lalkpedkrAFSFSRPFGSYVMENVLFKISFPAEFHAQTACEAAVTLHPLVRNRLHEIDRIVIT 333
                                                    ********99****************************************************** PP

                                      TIGR02330 309 thesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadpridelreklevv 371
                                                    thesairii+k+gplan adrdhc+qy++avpl+fg+lvae+yed  +a +p id lr+k+++v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 334 THESAIRIISKVGPLANAADRDHCIQYMIAVPLVFGNLVAEQYEDDfHAVHPIIDVLRDKMVIV 397
                                                    ********************************************9989**************** PP

                                      TIGR02330 372 edkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatk 435
                                                    ed+r++reyle+dkrsianav+vffkdgs+t++v+veyp+ghrrrr+egi +l dkfkanlat+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 398 EDPRFTREYLEPDKRSIANAVQVFFKDGSSTKNVVVEYPIGHRRRRAEGIALLEDKFKANLATR 461
                                                    **************************************************************** PP

                                      TIGR02330 436 fsskkqerilelcldqakleatpvnefldlfvi 468
                                                    f++++ ++i+ lc dqa+le+t+vn+f+dlfvi
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 462 FTAQRSAEIFALCKDQARLEETAVNRFVDLFVI 494
                                                    *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (494 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: 00:00:00.02
# Mc/sec: 11.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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