GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Algiphilus aromaticivorans DG1253

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_043764975.1 U743_RS01510 methylisocitrate lyase

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



>NCBI__GCF_000733765.1:WP_043764975.1
          Length = 293

 Score =  473 bits (1217), Expect = e-138
 Identities = 238/290 (82%), Positives = 264/290 (91%)

Query: 8   LARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGI 67
           +  SAGARFR ALA E PLQV+G INANHALLA++AG+RAIYLSGGGVAAGSLGLPDLGI
Sbjct: 1   MIESAGARFRAALAAETPLQVIGAINANHALLAQQAGFRAIYLSGGGVAAGSLGLPDLGI 60

Query: 68  SNLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAK 127
           S LDDVL DVRRITDVCD PLLVDVDTGFG+S FNVARTT+++IK GAGAMHIEDQVGAK
Sbjct: 61  SGLDDVLVDVRRITDVCDTPLLVDVDTGFGSSFFNVARTTKAMIKAGAGAMHIEDQVGAK 120

Query: 128 RCGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAG 187
           RCGHRPGKEIVS+ EM DRIKAAVDARTD +FVIMARTDALAVEGL+ AI+RA ACVEAG
Sbjct: 121 RCGHRPGKEIVSKQEMVDRIKAAVDARTDPDFVIMARTDALAVEGLEAAIDRATACVEAG 180

Query: 188 ADAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFR 247
           AD IFPEAMT+LAMY++F +AV VPVLANITEFG+TPLFT +EL  A VS+VLYPLSAFR
Sbjct: 181 ADMIFPEAMTELAMYKRFAEAVGVPVLANITEFGSTPLFTVDELASADVSLVLYPLSAFR 240

Query: 248 AMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFA 297
           AMNKAA+NVY A+RRDGTQ+NVVDTMQTRAELYE+I YH YE+KLDALF+
Sbjct: 241 AMNKAAQNVYEAVRRDGTQKNVVDTMQTRAELYEAINYHDYERKLDALFS 290


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: 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: 293
Length adjustment: 26
Effective length of query: 276
Effective length of database: 267
Effective search space:    73692
Effective search space used:    73692
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_043764975.1 U743_RS01510 (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.525669.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-133  429.1   2.5     4e-133  428.9   2.5    1.0  1  NCBI__GCF_000733765.1:WP_043764975.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_043764975.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.9   2.5    4e-133    4e-133       2     284 ..       6     290 ..       5     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.9 bits;  conditional E-value: 4e-133
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 
                                           g+++r++l++e +lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg++ l++v+ ++rrit+v++
  NCBI__GCF_000733765.1:WP_043764975.1   6 GARFRAALAAETPLQVIGAINANHALLAQQAGFRAIYLSGGGVAAgSLGLPDLGISGLDDVLVDVRRITDVCD 78 
                                           689****************************************999*************************** PP

                             TIGR02317  74 lpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkded 145
                                            pllvD+DtGfG+  +nvart k +++ag++a+hieDqv +k+CGh++gke+vsk+emv++ikaav+a++d+d
  NCBI__GCF_000733765.1:WP_043764975.1  79 TPLLVDVDTGFGSsFFNVARTTKAMIKAGAGAMHIEDQVGAKRCGHRPGKEIVSKQEMVDRIKAAVDARTDPD 151
                                           ************9568********************************************************* PP

                             TIGR02317 146 fvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadel 218
                                           fv++aRtDa aveGl+aai+Ra+a veaGad+if+ea+++++++++fa+av vp+lan+tefG tpl+t+del
  NCBI__GCF_000733765.1:WP_043764975.1 152 FVIMARTDALAVEGLEAAIDRATACVEAGADMIFPEAMTELAMYKRFAEAVGVPVLANITEFGSTPLFTVDEL 224
                                           ************************************************************************* PP

                             TIGR02317 219 eelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           +++ +++v+yP++a+Ra++kaa++vye ++++Gtqk+++d++qtR+elYe ++y+dye+k++ lf 
  NCBI__GCF_000733765.1:WP_043764975.1 225 ASADVSLVLYPLSAFRAMNKAAQNVYEAVRRDGTQKNVVDTMQTRAELYEAINYHDYERKLDALFS 290
                                           *************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (293 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: 15.58
//
[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