Alignments for a candidate for prpD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Pseudomonas fluorescens GW456-L13

Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate PfGW456L13_4114 2-methylcitrate dehydratase (EC 4.2.1.79)

Query= SwissProt::Q937N6
         (484 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114
          Length = 494

 Score =  599 bits (1544), Expect = e-176
 Identities = 304/497 (61%), Positives = 371/497 (74%), Gaps = 16/497 (3%)

Query: 1   MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60
           MS +     RPD D+VL DI DYV  Y+I+S  A DTARNCLIDTLGCGL AL +P CTK
Sbjct: 1   MSANVDLNNRPDYDKVLQDIADYVLNYKIESKEALDTARNCLIDTLGCGLLALRFPECTK 60

Query: 61  LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120
            LGPVV GT+VP GARVPGT ++LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGG
Sbjct: 61  HLGPVVEGTVVPFGARVPGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGG 120

Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180
           ILA AD +S+ H+A G  PLT++ VL AMI AHEIQG IALENSFN+VGLDHV+LVKVAS
Sbjct: 121 ILAVADHLSQKHLANGVAPLTVRTVLEAMIMAHEIQGVIALENSFNRVGLDHVILVKVAS 180

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

Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288
             GEMG P VL+A+ WGFYDVLF              + F F RPYG+YVMEN+L KIS+
Sbjct: 241 MRGEMGIPGVLSARQWGFYDVLFSHTNNDLALKPEDRRAFSFSRPYGSYVMENVLFKISF 300

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

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

Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467
           + V   DG+  + V+VEYP+GH+RRR EGIPLL +KFR NL  RF  ++ + I A   D+
Sbjct: 418 VQVFFKDGSSTENVVVEYPIGHRRRRVEGIPLLEDKFRANLLTRFTSQRSEEIFALCKDR 477

Query: 468 ARLEAMPVNEYLDMYAI 484
            +LEA PVN ++D++ I
Sbjct: 478 QKLEATPVNRFVDLFVI 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: 662
Number of extensions: 24
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 PfGW456L13_4114 (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.18597.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   8.3e-270  881.1   0.0   9.4e-270  880.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114  2-methylcitrate dehydratase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114  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 !  880.9   0.0  9.4e-270  9.4e-270       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 880.9 bits;  conditional E-value: 9.4e-270
                                               TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvveg 55 
                                                             d+vl+diadyvl+y+i+skea+dtar++l+dtlgcgllal++pectk+lgpvveg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114  14 DKVLQDIADYVLNYKIESKEALDTARNCLIDTLGCGLLALRFPECTKHLGPVVEG 68 
                                                             89***************************************************** PP

                                               TIGR02330  56 tlvpngarvpgtsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggila 110
                                                             t+vp garvpgtsy+ldpvkaa++ig++vrwldyndtwlaaewghpsdnlggila
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114  69 TVVPFGARVPGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILA 123
                                                             ******************************************************* PP

                                               TIGR02330 111 vadylsrkriaegkeplkvkevleamikaheiqgvlalensfnrvgldhvllvkv 165
                                                             vad+ls+k++a+g +pl+v+ vleami+aheiqgv+alensfnrvgldhv+lvkv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 124 VADHLSQKHLANGVAPLTVRTVLEAMIMAHEIQGVIALENSFNRVGLDHVILVKV 178
                                                             ******************************************************* PP

                                               TIGR02330 166 astavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrg 220
                                                             astav+akl+ga+re++l+alshaf dgqalrtyrhapn+gsrkswaagda+srg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 179 ASTAVTAKLMGANREQLLSALSHAFADGQALRTYRHAPNAGSRKSWAAGDASSRG 233
                                                             ******************************************************* PP

                                               TIGR02330 221 vrlalialkgemgypsalsapvwgfedvlfkke............klklareygs 263
                                                             vrla++a++gemg+p++lsa +wgf+dvlf+++             ++++r+ygs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 234 VRLADMAMRGEMGIPGVLSARQWGFYDVLFSHTnndlalkpedrrAFSFSRPYGS 288
                                                             ********************************************99********* PP

                                               TIGR02330 264 yvmenvlfkisfpaefhaqtaveaavklheevkerldeierivitthesairiid 318
                                                             yvmenvlfkisfpaefhaqta+eaav+lh++v++rl+ei+rivitthesairii+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 289 YVMENVLFKISFPAEFHAQTACEAAVTLHPQVRNRLHEIDRIVITTHESAIRIIS 343
                                                             ******************************************************* PP

                                               TIGR02330 319 kkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadpridelreklevve 372
                                                             k+gplan adrdhc+qy++avpl+fg+lvae yed  + a+p id lr+k+++ve
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 344 KVGPLANAADRDHCIQYMTAVPLVFGNLVAEYYEDDfHKAHPIIDVLRDKMVIVE 398
                                                             **********************************998999*************** PP

                                               TIGR02330 373 dkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdk 427
                                                             d+r++reyle+dkrsianav+vffkdgs+te+v+veyp+ghrrrr egip+l dk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 399 DPRFTREYLESDKRSIANAVQVFFKDGSSTENVVVEYPIGHRRRRVEGIPLLEDK 453
                                                             ******************************************************* PP

                                               TIGR02330 428 fkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                                             f+anl t+f+s++ e+i+ lc d++kleatpvn+f+dlfvi
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 454 FRANLLTRFTSQRSEEIFALCKDRQKLEATPVNRFVDLFVI 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.84
//
[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