Alignments for a candidate for prpD in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Pseudomonas fluorescens FW300-N2E3

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate AO353_00880 AO353_00880 2-methylcitrate dehydratase

Query= BRENDA::P74840
         (483 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00880
          Length = 494

 Score =  600 bits (1547), Expect = e-176
 Identities = 306/492 (62%), Positives = 370/492 (75%), Gaps = 16/492 (3%)

Query: 5   ELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPI 64
           +LNIRPD+D+ + DI DYV+N++I SK A DTA  CL+DTLGCGL AL +P C K LGPI
Sbjct: 6   DLNIRPDYDKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPI 65

Query: 65  VPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATA 124
           V GTVVP GARVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGGILA A
Sbjct: 66  VEGTVVPFGARVPGTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVA 125

Query: 125 DWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVASTAVVA 184
           D LS+  VA G APLTM+ VL  MI AHEIQG IALEN+FNRVGLDHVLLVKVASTAV A
Sbjct: 126 DHLSQKRVANGDAPLTMRAVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTA 185

Query: 185 EMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEM 244
           +++G  R+++L A+S A+VDGQ+LRTYRHAPN G+RKSWAAGDA+SR VRLA +A  GEM
Sbjct: 186 KLMGANREQLLAALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEM 245

Query: 245 GYPSALTAKTWGFYDVSFK------------GETFRFQRPYGSYVMENVLFKISFPAEFH 292
           G P  LTA  WGFYDV F               TF   + YG+YVMENVLFKISFPAEFH
Sbjct: 246 GIPGVLTAPQWGFYDVLFSHTNKDLALKPADKRTFSLSQKYGTYVMENVLFKISFPAEFH 305

Query: 293 SQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMV 352
           +QTA EAA+TL+ Q+        +I+K+ I THE+ +RII K G L N ADRDHCIQYM 
Sbjct: 306 AQTACEAAVTLHPQV---SNRLDEIDKIVITTHESAIRIISKVGQLANAADRDHCIQYMT 362

Query: 353 AVPLLFGRLTAADYEDEV-AQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEF 411
           AVPL FG L A  YED+  A    ID LR+K+V  EDP +T +Y + +KR+I NA+ V F
Sbjct: 363 AVPLAFGTLVAEQYEDQFHAAHPIIDELRKKMVIVEDPRYTREYLEADKRSIANALQVFF 422

Query: 412 TDGSRFGEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQ 471
            DGS  G+VVVEYPIGH RRRA+GIP L +KFK NLA +F  ++  +I  +  D+A+LE 
Sbjct: 423 KDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSAQIFALCQDQAKLEA 482

Query: 472 MPVNEYLDLYVI 483
            PVN ++DL+VI
Sbjct: 483 TPVNRFMDLFVI 494


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: 658
Number of extensions: 20
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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 AO353_00880 AO353_00880 (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.28917.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   6.6e-272  888.0   0.1   7.5e-272  887.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  AO353_00880 2-methylcitrate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  AO353_00880 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.8   0.1  7.5e-272  7.5e-272       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 887.8 bits;  conditional E-value: 7.5e-272
                                     TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvp 65 
                                                   d+vl+diadyvl+++i+skea+dtar++l+dtlgcgllal++pectk+lgp+vegt+vp garvp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  14 DKVLQDIADYVLNFKIESKEALDTARNCLMDTLGCGLLALRFPECTKHLGPIVEGTVVPFGARVP 78 
                                                   89*************************************************************** PP

                                     TIGR02330  66 gtsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvk 130
                                                   gt+++ldpvkaa++ig++vrwldyndtwlaaewghpsdnlggilavad+ls+kr+a+g++pl+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880  79 GTHFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRVANGDAPLTMR 143
                                                   ***************************************************************** PP

                                     TIGR02330 131 evleamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqa 195
                                                    vl+ami+aheiqgv+alensfnrvgldhvllvkvastav+akl+ga+re++l+alshafvdgqa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 144 AVLDAMIMAHEIQGVIALENSFNRVGLDHVLLVKVASTAVTAKLMGANREQLLAALSHAFVDGQA 208
                                                   ***************************************************************** PP

                                     TIGR02330 196 lrtyrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkke....... 253
                                                   lrtyrhapn+gsrkswaagda+srgvrla+ia++gemg+p++l+ap+wgf+dvlf+++       
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 209 LRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEMGIPGVLTAPQWGFYDVLFSHTnkdlalk 273
                                                   *********************************************************99****** PP

                                     TIGR02330 254 .....klklareygsyvmenvlfkisfpaefhaqtaveaavklheevkerldeierivitthesa 313
                                                         ++l+++yg+yvmenvlfkisfpaefhaqta+eaav+lh++v +rldei++ivitthesa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 274 padkrTFSLSQKYGTYVMENVLFKISFPAEFHAQTACEAAVTLHPQVSNRLDEIDKIVITTHESA 338
                                                   ****99*********************************************************** PP

                                     TIGR02330 314 iriidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadpridelreklevvedkrys 377
                                                   irii+k+g lan adrdhc+qy++avpl fg lvae+yed+ +aa+p idelr+k+++ved+ry+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 339 IRIISKVGQLANAADRDHCIQYMTAVPLAFGTLVAEQYEDQfHAAHPIIDELRKKMVIVEDPRYT 403
                                                   *****************************************99********************** PP

                                     TIGR02330 378 reyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqe 442
                                                   reyleadkrsiana++vffkdgs+t++v+veyp+ghrrrr+egip+l dkfkanlat+f++++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 404 REYLEADKRSIANALQVFFKDGSSTGQVVVEYPIGHRRRRAEGIPLLEDKFKANLATRFTAQRSA 468
                                                   ***************************************************************** PP

                                     TIGR02330 443 rilelcldqakleatpvnefldlfvi 468
                                                   +i+ lc dqakleatpvn+f+dlfvi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_00880 469 QIFALCQDQAKLEATPVNRFMDLFVI 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: 11.07
//
[ok]

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

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Candidates (tab-delimited)
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