Alignments for a candidate for prpB in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Pseudomonas benzenivorans DSM 8628

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_090438372.1 BLS63_RS00665 methylisocitrate lyase

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



>NCBI__GCF_900100495.1:WP_090438372.1
          Length = 294

 Score =  533 bits (1373), Expect = e-156
 Identities = 272/294 (92%), Positives = 282/294 (95%)

Query: 1   MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60
           MS +TPGQRFRDAVA+EHPLQVVG INANHALLA+RAGFKAIYLSGGGVAAGSLG+PDLG
Sbjct: 1   MSLNTPGQRFRDAVASEHPLQVVGAINANHALLAQRAGFKAIYLSGGGVAAGSLGLPDLG 60

Query: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120
           ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA
Sbjct: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120

Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180
           KRCGHRPNKEIV+QQEMVDRIKAAVDARTD SFVIMARTDALAVEGL SALDRA ACIEA
Sbjct: 121 KRCGHRPNKEIVTQQEMVDRIKAAVDARTDPSFVIMARTDALAVEGLNSALDRAEACIEA 180

Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240
           GADMIFPEAITEL MYK FA R+KAPILANITEFGATPLYTTE+LA  DVSLVLYPLSAF
Sbjct: 181 GADMIFPEAITELAMYKTFAERIKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAF 240

Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           RAMNKAAENVYTA+RRDGTQ+NVIDTMQTRMELYDRI+YH FEQ LDALFAAKK
Sbjct: 241 RAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDRINYHAFEQHLDALFAAKK 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: 345
Number of extensions: 5
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 WP_090438372.1 BLS63_RS00665 (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.25624.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-136  440.1   1.3   1.8e-136  439.9   1.3    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090438372.1  BLS63_RS00665 methylisocitrate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090438372.1  BLS63_RS00665 methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.9   1.3  1.8e-136  1.8e-136       2     284 ..       7     291 ..       6     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.9 bits;  conditional E-value: 1.8e-136
                                 TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearrit 69 
                                               g+++r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+t l++v++++rrit
  lcl|NCBI__GCF_900100495.1:WP_090438372.1   7 GQRFRDAVASEHPLQVVGAINANHALLAQRAGFKAIYLSGGGVAAgSLGLPDLGITGLDDVLTDVRRIT 75 
                                               789****************************************999*********************** PP

                                 TIGR02317  70 rvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaa 137
                                               +v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+v+++emv++ikaa
  lcl|NCBI__GCF_900100495.1:WP_090438372.1  76 DVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIVTQQEMVDRIKAA 144
                                               ****************889************************************************** PP

                                 TIGR02317 138 vkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmte 206
                                               v+a++d++fv++aRtDa aveGl++a++Ra+a +eaGad+if+ea+++++++++fa+++k+p+lan+te
  lcl|NCBI__GCF_900100495.1:WP_090438372.1 145 VDARTDPSFVIMARTDALAVEGLNSALDRAEACIEAGADMIFPEAITELAMYKTFAERIKAPILANITE 213
                                               ********************************************************************* PP

                                 TIGR02317 207 fGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedy 275
                                               fG tpl+t++el+++ +++v+yP++a+Ra++kaae+vy+ l+++Gtqk+++d++qtR elY+ ++y+++
  lcl|NCBI__GCF_900100495.1:WP_090438372.1 214 FGATPLYTTEELASVDVSLVLYPLSAFRAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDRINYHAF 282
                                               ********************************************************************* PP

                                 TIGR02317 276 ekkdkelfk 284
                                               e++++ lf+
  lcl|NCBI__GCF_900100495.1:WP_090438372.1 283 EQHLDALFA 291
                                               ***999985 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.45
//
[ok]

This GapMind analysis is from Sep 24 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