GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Herbaspirillum aquaticum IEH 4430

Align 2-methylcitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_088757053.1 CEJ45_RS20845 methylisocitrate lyase

Query= metacyc::MONOMER-13636
         (302 letters)



>NCBI__GCF_002213425.1:WP_088757053.1
          Length = 296

 Score =  496 bits (1278), Expect = e-145
 Identities = 250/292 (85%), Positives = 270/292 (92%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           SAGA FRQA+ +E PLQV+G INANHALLAKRAG+RAIYLSGGGVAAGSLGLPDLGISNL
Sbjct: 5   SAGAAFRQAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAGSLGLPDLGISNL 64

Query: 71  DDVLTDIRRITDVCDTPLLVDVDTGFGASAFNVARTTKSLIKFGAAAMHIEDQVGAKRCG 130
           DDVLTD+RRITDVCD PLLVDVDTGFGASAFNVART KS+IKFGAAAMHIEDQVGAKRCG
Sbjct: 65  DDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVKSMIKFGAAAMHIEDQVGAKRCG 124

Query: 131 HRPNKEIVTQGEMVDRIRAAVDARTDENFVIMARTDALAVEGLDKAIERAVACAEAGADA 190
           HRPNKEIV++ EMVDRI+AAVDARTDENFVIMARTDALAVEGLD AIERAVAC EAGAD 
Sbjct: 125 HRPNKEIVSKQEMVDRIKAAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADM 184

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IFPEA+TDLAMY++F +AVKVP+LANITEFG+TPLFT +EL GA V +VLYPLSAFRAMN
Sbjct: 185 IFPEAITDLAMYKQFANAVKVPILANITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMN 244

Query: 251 KAAENVYAAIRRDGTQKNVVDTMQTRAELYESIGYHDFEQKLDALFAQGKGK 302
           KAAENVY AIRRDGTQKNVVDTMQTR ELY+ I YH +EQ+LDALFAQ K K
Sbjct: 245 KAAENVYQAIRRDGTQKNVVDTMQTRMELYDRIDYHSYEQRLDALFAQQKNK 296


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: 364
Number of extensions: 6
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: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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_088757053.1 CEJ45_RS20845 (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.678551.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-136  438.5   3.5   5.8e-136  438.3   3.5    1.0  1  NCBI__GCF_002213425.1:WP_088757053.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002213425.1:WP_088757053.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.3   3.5  5.8e-136  5.8e-136       2     284 ..       7     291 ..       6     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.3 bits;  conditional E-value: 5.8e-136
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 
                                           g+a+r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+++l++v++++rrit+v++
  NCBI__GCF_002213425.1:WP_088757053.1   7 GAAFRQAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAgSLGLPDLGISNLDDVLTDVRRITDVCD 79 
                                           679****************************************999*************************** PP

                             TIGR02317  74 lpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkded 145
                                           lpllvD+DtGfG  a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+vsk+emv++ikaav+a++de+
  NCBI__GCF_002213425.1:WP_088757053.1  80 LPLLVDVDTGFGAsAFNVARTVKSMIKFGAAAMHIEDQVGAKRCGHRPNKEIVSKQEMVDRIKAAVDARTDEN 152
                                           ************879********************************************************** PP

                             TIGR02317 146 fvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadel 218
                                           fv++aRtDa aveGldaaieRa a veaGad+if+ea+++++++++fa+avkvp+lan+tefG tpl+t+del
  NCBI__GCF_002213425.1:WP_088757053.1 153 FVIMARTDALAVEGLDAAIERAVACVEAGADMIFPEAITDLAMYKQFANAVKVPILANITEFGSTPLFTVDEL 225
                                           ************************************************************************* PP

                             TIGR02317 219 eelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           + + + +v+yP++a+Ra++kaae+vy+ ++++Gtqk+++d++qtR elY+ ++y++ye++++ lf+
  NCBI__GCF_002213425.1:WP_088757053.1 226 KGADVGLVLYPLSAFRAMNKAAENVYQAIRRDGTQKNVVDTMQTRMELYDRIDYHSYEQRLDALFA 291
                                           *************************************************************99986 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.64
//
[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:

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:

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:

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:

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