Alignments for a candidate for prpB in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Paraburkholderia phymatum STM815

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_012403644.1 BPHY_RS21910 methylisocitrate lyase

Query= reanno::Cup4G11:RR42_RS11260
         (302 letters)



>NCBI__GCF_000020045.1:WP_012403644.1
          Length = 303

 Score =  481 bits (1238), Expect = e-141
 Identities = 244/289 (84%), Positives = 264/289 (91%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           SAGA FR A+A E PLQVVG INANHALLA+RAG++AIY+SGGGVAAGSLGLPDLGIS L
Sbjct: 7   SAGAAFRAAVAAEKPLQVVGAINANHALLAQRAGFKAIYVSGGGVAAGSLGLPDLGISTL 66

Query: 71  DDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAKRCG 130
           DDVLTDVRRITDVCD+PLLVDVDTGFG SAFN+ART ++L K GAGAMHIEDQVGAKRCG
Sbjct: 67  DDVLTDVRRITDVCDLPLLVDVDTGFGPSAFNIARTVKALTKAGAGAMHIEDQVGAKRCG 126

Query: 131 HRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGADA 190
           HRPGK IVSQGEM DRIKAAVDARTD +FVIMARTDALAVEGL  AI+RA+ACVEAGAD 
Sbjct: 127 HRPGKAIVSQGEMVDRIKAAVDARTDPDFVIMARTDALAVEGLQSAIDRAMACVEAGADM 186

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IFPEAMT+L MYR+F  AVKVPVLANITEFGATPLFT EEL GA VS+VLYPLSAFRAMN
Sbjct: 187 IFPEAMTELPMYRQFAQAVKVPVLANITEFGATPLFTVEELRGADVSLVLYPLSAFRAMN 246

Query: 251 KAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQG 299
           +AAENVY+AIRRDGTQ+ VVDTMQTR ELY+ IGYHAYEQKLDALF+QG
Sbjct: 247 RAAENVYSAIRRDGTQKAVVDTMQTREELYDRIGYHAYEQKLDALFSQG 295


Lambda     K      H
   0.320    0.134    0.376 

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: 331
Number of extensions: 9
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: 302
Length of database: 303
Length adjustment: 27
Effective length of query: 275
Effective length of database: 276
Effective search space:    75900
Effective search space used:    75900
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 WP_012403644.1 BPHY_RS21910 (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.3794217.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-135  435.4   1.9   4.9e-135  435.2   1.9    1.0  1  NCBI__GCF_000020045.1:WP_012403644.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_012403644.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.2   1.9  4.9e-135  4.9e-135       2     284 ..       9     293 ..       8     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.2 bits;  conditional E-value: 4.9e-135
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 
                                           g+a+r+++++e++lq++Gaina++alla++aGf+a+Y+sG+++aa slglPDlg++tl++v++++rrit+v++
  NCBI__GCF_000020045.1:WP_012403644.1   9 GAAFRAAVAAEKPLQVVGAINANHALLAQRAGFKAIYVSGGGVAAgSLGLPDLGISTLDDVLTDVRRITDVCD 81 
                                           679****************************************999*************************** PP

                             TIGR02317  74 lpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkded 145
                                           lpllvD+DtGfG  a+n+artvk l++ag++a+hieDqv +k+CGh++gk++vs+ emv++ikaav+a++d+d
  NCBI__GCF_000020045.1:WP_012403644.1  82 LPLLVDVDTGFGPsAFNIARTVKALTKAGAGAMHIEDQVGAKRCGHRPGKAIVSQGEMVDRIKAAVDARTDPD 154
                                           ************769********************************************************** PP

                             TIGR02317 146 fvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadel 218
                                           fv++aRtDa aveGl++ai+Ra a veaGad+if+ea++++ ++r+fa+avkvp+lan+tefG tpl+t++el
  NCBI__GCF_000020045.1:WP_012403644.1 155 FVIMARTDALAVEGLQSAIDRAMACVEAGADMIFPEAMTELPMYRQFAQAVKVPVLANITEFGATPLFTVEEL 227
                                           ************************************************************************* PP

                             TIGR02317 219 eelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           + + +++v+yP++a+Ra+++aae+vy+ ++++Gtqk+++d++qtR+elY+ +gy++ye+k++ lf 
  NCBI__GCF_000020045.1:WP_012403644.1 228 RGADVSLVLYPLSAFRAMNRAAENVYSAIRRDGTQKAVVDTMQTREELYDRIGYHAYEQKLDALFS 293
                                           *************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (303 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: 23.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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 2024 update 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