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.13479.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.80
//
[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