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

GapMind for catabolism of small carbon sources

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

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate PfGW456L13_4118 Methylisocitrate lyase (EC 4.1.3.30)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118
          Length = 296

 Score =  559 bits (1440), Expect = e-164
 Identities = 285/294 (96%), Positives = 292/294 (99%)

Query: 1   MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60
           ++ STPGQRFRDAVA+EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG
Sbjct: 3   LNKSTPGQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 62

Query: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120
           ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA
Sbjct: 63  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 122

Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180
           KRCGHRPNKEIV+QQEMVDRIKAAVDAR+DDSFVIMARTDALAVEGLESALDRAAACIEA
Sbjct: 123 KRCGHRPNKEIVTQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLESALDRAAACIEA 182

Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240
           GADM+FPEAITELEMYKLFA+RVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF
Sbjct: 183 GADMVFPEAITELEMYKLFANRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 242

Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK
Sbjct: 243 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 296


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: 375
Number of extensions: 4
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 PfGW456L13_4118 (Methylisocitrate lyase (EC 4.1.3.30))
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.14072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     7e-135  434.7   2.0   8.1e-135  434.5   2.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118  Methylisocitrate lyase (EC 4.1.3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118  Methylisocitrate lyase (EC 4.1.3.30)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.5   2.0  8.1e-135  8.1e-135       2     284 ..       9     293 ..       8     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 434.5 bits;  conditional E-value: 8.1e-135
                                               TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlgl 55 
                                                             g+++r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slg+PDlg+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118   9 GQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAgSLGVPDLGI 63 
                                                             789****************************************999********* PP

                                               TIGR02317  56 ttleevaeearritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieD 109
                                                             t l++v++++rrit+v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieD
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118  64 TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIED 118
                                                             ******************************889********************** PP

                                               TIGR02317 110 qvapkkCGhldgkelvskeemvkkikaavkakkdedfvliaRtDaraveGldaai 164
                                                             qv +k+CGh+++ke+v+++emv++ikaav+a++d++fv++aRtDa aveGl++a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118 119 QVGAKRCGHRPNKEIVTQQEMVDRIKAAVDARSDDSFVIMARTDALAVEGLESAL 173
                                                             ******************************************************* PP

                                               TIGR02317 165 eRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadele 219
                                                             +Ra a +eaGad++f+ea++++e+++ fa++vk+p+lan+tefG tpl+t+++l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118 174 DRAAACIEAGADMVFPEAITELEMYKLFANRVKAPILANITEFGATPLYTTEQLA 228
                                                             ******************************************************* PP

                                               TIGR02317 220 elgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyed 274
                                                              + +++v+yP++a+Ra++kaae+vy+ ++++Gtq++++d++qtR elY+ ++y++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118 229 GADVSLVLYPLSAFRAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHT 283
                                                             ******************************************************* PP

                                               TIGR02317 275 yekkdkelfk 284
                                                             +e+k++ lf+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4118 284 FEQKLDALFA 293
                                                             *****99985 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: 9.96
//
[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