Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N1B4

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate Pf1N1B4_3819 Methylisocitrate lyase (EC 4.1.3.30)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819
          Length = 296

 Score =  560 bits (1444), Expect = e-164
 Identities = 287/293 (97%), Positives = 291/293 (99%)

Query: 2   SNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 61
           + STPGQRFRDAVA+EHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI
Sbjct: 4   NKSTPGQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 63

Query: 62  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 121
           TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK
Sbjct: 64  TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 123

Query: 122 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 181
           RCGHRPNKEIV+QQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG
Sbjct: 124 RCGHRPNKEIVTQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 183

Query: 182 ADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFR 241
           ADM+FPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLA ADVSLVLYPLSAFR
Sbjct: 184 ADMVFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAAADVSLVLYPLSAFR 243

Query: 242 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK
Sbjct: 244 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 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: 378
Number of extensions: 3
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 Pf1N1B4_3819 (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.25340.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-134  434.1   2.3   1.2e-134  433.9   2.3    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819  Methylisocitrate lyase (EC 4.1.3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819  Methylisocitrate lyase (EC 4.1.3.30)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.9   2.3  1.2e-134  1.2e-134       2     284 ..       9     293 ..       8     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 433.9 bits;  conditional E-value: 1.2e-134
                                      TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaee 64 
                                                    g+++r+++++e++lq++G+ina++alla++aGf+a+YlsG+++aa slg+PDlg+t l++v+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819   9 GQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAgSLGVPDLGITGLDDVLTD 72 
                                                    789****************************************999****************** PP

                                      TIGR02317  65 arritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvsk 127
                                                    +rrit+v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+v++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819  73 VRRITDVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIVTQ 136
                                                    *********************889**************************************** PP

                                      TIGR02317 128 eemvkkikaavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefre 191
                                                    +emv++ikaav+a++d++fv++aRtDa aveGl++a++Ra a +eaGad++f+ea++++e+++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819 137 QEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGADMVFPEAITELEMYKL 200
                                                    **************************************************************** PP

                                      TIGR02317 192 fakavkvpllanmtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqke 255
                                                    fa++vk+p+lan+tefG tpl+t+++l+ + +++v+yP++a+Ra++kaae+vy+ ++++Gtq++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819 201 FASRVKAPILANITEFGATPLYTTEQLAAADVSLVLYPLSAFRAMNKAAENVYTAIRRDGTQQN 264
                                                    **************************************************************** PP

                                      TIGR02317 256 lldklqtRkelYellgyedyekkdkelfk 284
                                                    ++d++qtR elY+ ++y+++e+k++ lf+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3819 265 VIDTMQTRMELYDRIDYHTFEQKLDALFA 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.25
//
[ok]

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

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Protein sequences (fasta format)
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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