Alignments for a candidate for prpB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Pseudomonas putida KT2440

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate PP_2334 PP_2334 2-methylisocitrate lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6061
         (294 letters)



>FitnessBrowser__Putida:PP_2334
          Length = 296

 Score =  525 bits (1353), Expect = e-154
 Identities = 267/291 (91%), Positives = 277/291 (95%)

Query: 4   STPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGITG 63
           STPGQRFRDAVA EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLG+PDLGITG
Sbjct: 5   STPGQRFRDAVAAEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGLPDLGITG 64

Query: 64  LDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAKRC 123
           LDDVLTDVRRITDVCDLPLLVDVDTGFG+SAFNVARTV+SM KFGAAAIHIEDQVGAKRC
Sbjct: 65  LDDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVRSMSKFGAAAIHIEDQVGAKRC 124

Query: 124 GHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGAD 183
           GHRPNKEIVSQQEMVDRIKAAVDAR+DDSFVIMARTDALAVEGL +ALDRA AC+EAGAD
Sbjct: 125 GHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLNAALDRAQACVEAGAD 184

Query: 184 MIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAM 243
           MIFPEAITEL+MYK FA RVKAPILANITEFGATPLYTTE+LA  DVSLVLYPLSAFRAM
Sbjct: 185 MIFPEAITELQMYKTFADRVKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAFRAM 244

Query: 244 NKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           NKAAENVYTA+RRDGTQ+NVIDTMQTRMELYD I YH FEQ LDALFA KK
Sbjct: 245 NKAAENVYTALRRDGTQKNVIDTMQTRMELYDAIGYHAFEQSLDALFAQKK 295


Lambda     K      H
   0.320    0.134    0.375 

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: 354
Number of extensions: 6
Number of successful extensions: 1
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: 294
Length of database: 296
Length adjustment: 26
Effective length of query: 268
Effective length of database: 270
Effective search space:    72360
Effective search space used:    72360
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate PP_2334 PP_2334 (2-methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

# 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/TIGR02317.hmm
# target sequence database:        /tmp/gapView.25303.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02317  [M=285]
Accession:   TIGR02317
Description: prpB: methylisocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-136  440.3   1.9   1.6e-136  440.1   1.9    1.0  1  lcl|FitnessBrowser__Putida:PP_2334  PP_2334 2-methylisocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2334  PP_2334 2-methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.1   1.9  1.6e-136  1.6e-136       2     284 ..       8     292 ..       7     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 1.6e-136
                           TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklp 75 
                                         g+++r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+t l++v++++rrit+v++lp
  lcl|FitnessBrowser__Putida:PP_2334   8 GQRFRDAVAAEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAgSLGLPDLGITGLDDVLTDVRRITDVCDLP 82 
                                         789****************************************999***************************** PP

                           TIGR02317  76 llvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvli 149
                                         llvD+DtGfG  a+nvartv+++ + g+aa+hieDqv +k+CGh+++ke+vs++emv++ikaav+a++d++fv++
  lcl|FitnessBrowser__Putida:PP_2334  83 LLVDVDTGFGAsAFNVARTVRSMSKFGAAAIHIEDQVGAKRCGHRPNKEIVSQQEMVDRIKAAVDARSDDSFVIM 157
                                         **********879************************************************************** PP

                           TIGR02317 150 aRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgyk 224
                                         aRtDa aveGl+aa++Ra+a veaGad+if+ea+++++++++fa++vk+p+lan+tefG tpl+t++el+++ ++
  lcl|FitnessBrowser__Putida:PP_2334 158 ARTDALAVEGLNAALDRAQACVEAGADMIFPEAITELQMYKTFADRVKAPILANITEFGATPLYTTEELASVDVS 232
                                         *************************************************************************** PP

                           TIGR02317 225 iviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                         +v+yP++a+Ra++kaae+vy+ l+++Gtqk+++d++qtR elY+ +gy+++e+ ++ lf+
  lcl|FitnessBrowser__Putida:PP_2334 233 LVLYPLSAFRAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDAIGYHAFEQSLDALFA 292
                                         ******************************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (296 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.61
//
[ok]

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

Downloads

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

Related tools

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