Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N2C3

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate AO356_20865 AO356_20865 2-methylisocitrate lyase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_20865
          Length = 294

 Score =  570 bits (1468), Expect = e-167
 Identities = 293/294 (99%), Positives = 294/294 (100%)

Query: 1   MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60
           MSNSTPGQRFRDAVA+EHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG
Sbjct: 1   MSNSTPGQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60

Query: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120
           ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA
Sbjct: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120

Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180
           KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA
Sbjct: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180

Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240
           GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF
Sbjct: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240

Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK
Sbjct: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294


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: 383
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: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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 AO356_20865 AO356_20865 (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.19723.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   4.1e-135  435.5   1.7   4.8e-135  435.2   1.7    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865  AO356_20865 2-methylisocitrate l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865  AO356_20865 2-methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.2   1.7  4.8e-135  4.8e-135       2     284 ..       7     291 ..       6     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.2 bits;  conditional E-value: 4.8e-135
                                       TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevae 63 
                                                     g+++r+++++e++lq++G+ina++alla++aGf+a+YlsG+++aa slg+PDlg+t l++v++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865   7 GQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAgSLGVPDLGITGLDDVLT 69 
                                                     789****************************************999***************** PP

                                       TIGR02317  64 earritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelv 125
                                                     ++rrit+v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865  70 DVRRITDVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIV 132
                                                     **********************889************************************** PP

                                       TIGR02317 126 skeemvkkikaavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseee 188
                                                     s++emv++ikaav+a++d++fv++aRtDa aveGl++a++Ra a +eaGad+if+ea++++e+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 133 SQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGADMIFPEAITELEM 195
                                                     *************************************************************** PP

                                       TIGR02317 189 frefakavkvpllanmtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkG 251
                                                     ++ fa++vk+p+lan+tefG tpl+t+++l+ + +++v+yP++a+Ra++kaae+vy+ ++++G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 196 YKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAMNKAAENVYTAIRRDG 258
                                                     *************************************************************** PP

                                       TIGR02317 252 tqkelldklqtRkelYellgyedyekkdkelfk 284
                                                     tq++++d++qtR elY+ ++y+++e+k++ lf+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 259 TQQNVIDTMQTRMELYDRIDYHTFEQKLDALFA 291
                                                     ****************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (294 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: 10.83
//
[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