Alignments for a candidate for prpD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Pseudomonas putida KT2440

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate PP_2338 PP_2338 2-methylcitrate dehydratase

Query= SwissProt::P45859
         (472 letters)



>FitnessBrowser__Putida:PP_2338
          Length = 494

 Score =  593 bits (1530), Expect = e-174
 Identities = 292/482 (60%), Positives = 371/482 (76%), Gaps = 13/482 (2%)

Query: 2   PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61
           P  DRV++ + DY L   + S EA  TA + L+DTLGCG+LALR+PECTKLLGP V GT 
Sbjct: 11  PDYDRVLQTLADYALGYRVDSREALDTARNCLMDTLGCGLLALRFPECTKLLGPQVEGTL 70

Query: 62  VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121
           VPNG++VPGTSY LDPV+AA++IGC +RWLDYNDTWLAAEW HPSDNLGGILA AD++S+
Sbjct: 71  VPNGARVPGTSYRLDPVKAAWDIGCTVRWLDYNDTWLAAEWAHPSDNLGGILAVADHLSQ 130

Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181
            R++ G++PL +RDVLE M+ AHEIQGVLALEN+ NRVGLDHV+ VKVA+TAV A+L+G 
Sbjct: 131 KRVAAGEKPLLMRDVLEAMVMAHEIQGVLALENAFNRVGLDHVILVKVASTAVCARLMGA 190

Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241
            RE++ +ALS+A++D  ALRTYRH+PN GSRKSWAAGDA+SRGV LA ++L+GEMG P  
Sbjct: 191 NREQMLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIALRGEMGVPGV 250

Query: 242 LSAPGWGFQDVLFN------------KKEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289
           L+A  WGF DV F+            + E++L + L +YVMENVLFKVS+PAEFHAQTA 
Sbjct: 251 LTASQWGFYDVSFSHTNKDLALKPAGQYELRLPQALGSYVMENVLFKVSFPAEFHAQTAC 310

Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349
           E+AV LHP V+NR+ E+DR+VI T ESAIRII K GPL N ADRDHCLQY+ A+ L+FG 
Sbjct: 311 EAAVTLHPLVRNRLHEVDRIVITTQESAIRIISKSGPLANAADRDHCLQYMVAVPLIFGH 370

Query: 350 ITAQHYE-AETANDPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408
           + A+HYE A  AN P ID+LR+KMEV E+  ++ +YL+P KRSI+NA+QV FKDG+STE 
Sbjct: 371 LVAEHYEDAFHANHPSIDRLREKMEVVEDPRFSREYLEPGKRSIANALQVFFKDGSSTEQ 430

Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468
           V  E+P+GHR RR E +P L  KF  NL T F  ++ + ++E C   + L+   V+ FVD
Sbjct: 431 VVVEYPIGHRRRRGEGIPLLEAKFRANLATRFARQRCQQVFELCKDQQKLEGTAVHRFVD 490

Query: 469 MF 470
           +F
Sbjct: 491 LF 492


Lambda     K      H
   0.319    0.135    0.402 

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: 20
Number of successful extensions: 3
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: 472
Length of database: 494
Length adjustment: 34
Effective length of query: 438
Effective length of database: 460
Effective search space:   201480
Effective search space used:   201480
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate PP_2338 PP_2338 (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.29483.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-265  867.0   0.0   1.7e-265  866.9   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2338  PP_2338 2-methylcitrate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2338  PP_2338 2-methylcitrate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  866.9   0.0  1.7e-265  1.7e-265       1     468 []      14     494 .]      14     494 .] 1.00

  Alignments for each domain:
  == domain 1  score: 866.9 bits;  conditional E-value: 1.7e-265
                           TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldpvk 75 
                                         d+vl+ +ady+l y++ds+ea+dtar++l+dtlgcgllal++pectkllgp vegtlvpngarvpgtsy+ldpvk
  lcl|FitnessBrowser__Putida:PP_2338  14 DRVLQTLADYALGYRVDSREALDTARNCLMDTLGCGLLALRFPECTKLLGPQVEGTLVPNGARVPGTSYRLDPVK 88 
                                         899************************************************************************ PP

                           TIGR02330  76 aafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvlalen 150
                                         aa++ig+ vrwldyndtwlaaew hpsdnlggilavad+ls+kr+a g++pl +++vleam++aheiqgvlalen
  lcl|FitnessBrowser__Putida:PP_2338  89 AAWDIGCTVRWLDYNDTWLAAEWAHPSDNLGGILAVADHLSQKRVAAGEKPLLMRDVLEAMVMAHEIQGVLALEN 163
                                         *************************************************************************** PP

                           TIGR02330 151 sfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsrgvrlal 225
                                         +fnrvgldhv+lvkvastav+a+l+ga+re++l+alshafvdgqalrtyrhapn+gsrkswaagda+srgvrla+
  lcl|FitnessBrowser__Putida:PP_2338 164 AFNRVGLDHVILVKVASTAVCARLMGANREQMLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLAD 238
                                         *************************************************************************** PP

                           TIGR02330 226 ialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefhaqtaveaa 288
                                         ial+gemg+p++l+a++wgf+dv+f+++            +l+l++ +gsyvmenvlfk+sfpaefhaqta+eaa
  lcl|FitnessBrowser__Putida:PP_2338 239 IALRGEMGVPGVLTASQWGFYDVSFSHTnkdlalkpagqyELRLPQALGSYVMENVLFKVSFPAEFHAQTACEAA 313
                                         ***************************9*********************************************** PP

                           TIGR02330 289 vklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadprid 362
                                         v+lh+ v++rl+e++rivitt+esairii+k gplan adrdhclqy+vavpl+fg+lvae+yeda +a++p id
  lcl|FitnessBrowser__Putida:PP_2338 314 VTLHPLVRNRLHEVDRIVITTQESAIRIISKSGPLANAADRDHCLQYMVAVPLIFGHLVAEHYEDAfHANHPSID 388
                                         ******************************************************************99******* PP

                           TIGR02330 363 elreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfs 437
                                         +lrek+evved+r+sreyle+ krsiana++vffkdgs+te+v+veyp+ghrrrr egip+l  kf+anlat+f+
  lcl|FitnessBrowser__Putida:PP_2338 389 RLREKMEVVEDPRFSREYLEPGKRSIANALQVFFKDGSSTEQVVVEYPIGHRRRRGEGIPLLEAKFRANLATRFA 463
                                         *************************************************************************** PP

                           TIGR02330 438 skkqerilelcldqakleatpvnefldlfvi 468
                                          +++++++elc dq+kle t+v +f+dlfvi
  lcl|FitnessBrowser__Putida:PP_2338 464 RQRCQQVFELCKDQQKLEGTAVHRFVDLFVI 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: 00:00:00.01
# Mc/sec: 11.77
//
[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, or view the source code.

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