GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Cupriavidus basilensis 4G11

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate RR42_RS11260 RR42_RS11260 2-methylisocitrate lyase

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



>FitnessBrowser__Cup4G11:RR42_RS11260
          Length = 302

 Score =  587 bits (1513), Expect = e-172
 Identities = 302/302 (100%), Positives = 302/302 (100%)

Query: 1   MTFSTSDLARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSL 60
           MTFSTSDLARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSL
Sbjct: 1   MTFSTSDLARSAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSL 60

Query: 61  GLPDLGISNLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHI 120
           GLPDLGISNLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHI
Sbjct: 61  GLPDLGISNLDDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHI 120

Query: 121 EDQVGAKRCGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERA 180
           EDQVGAKRCGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERA
Sbjct: 121 EDQVGAKRCGHRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERA 180

Query: 181 VACVEAGADAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVL 240
           VACVEAGADAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVL
Sbjct: 181 VACVEAGADAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVL 240

Query: 241 YPLSAFRAMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQGK 300
           YPLSAFRAMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQGK
Sbjct: 241 YPLSAFRAMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQGK 300

Query: 301 AK 302
           AK
Sbjct: 301 AK 302


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: 435
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: 302
Length of database: 302
Length adjustment: 27
Effective length of query: 275
Effective length of database: 275
Effective search space:    75625
Effective search space used:    75625
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 RR42_RS11260 RR42_RS11260 (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.25500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-133  430.8   2.7   1.2e-133  430.6   2.7    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS11260  RR42_RS11260 2-methylisocitrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS11260  RR42_RS11260 2-methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.6   2.7  1.2e-133  1.2e-133       2     284 ..      13     297 ..      12     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.6 bits;  conditional E-value: 1.2e-133
                                 TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearrit 69 
                                               g+++r++l+ e++lq++G+ina++alla++aG++a+YlsG+++aa slglPDlg+++l++v++++rrit
  lcl|FitnessBrowser__Cup4G11:RR42_RS11260  13 GARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAgSLGLPDLGISNLDDVLTDVRRIT 81 
                                               689****************************************999*********************** PP

                                 TIGR02317  70 rvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaa 137
                                               +v+++pllvD+DtGfG  a+nvart ++l++ g++a+hieDqv +k+CGh++gke+vs+ em+++ikaa
  lcl|FitnessBrowser__Cup4G11:RR42_RS11260  82 DVCDVPLLVDVDTGFGAsAFNVARTTRSLIKFGAGAMHIEDQVGAKRCGHRPGKEIVSQGEMADRIKAA 150
                                               ****************879************************************************** PP

                                 TIGR02317 138 vkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmte 206
                                               v+a++de+fv++aRtDa aveGld+aieRa a veaGadaif+ea+++++++r+f +avkvp+lan+te
  lcl|FitnessBrowser__Cup4G11:RR42_RS11260 151 VDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGADAIFPEAMTDLAMYRKFVDAVKVPVLANITE 219
                                               ********************************************************************* PP

                                 TIGR02317 207 fGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedy 275
                                               fG tpl+t++el  +g+++v+yP++a+Ra++kaae+vy+ ++++Gtq++++d++qtR+elYe++gy++y
  lcl|FitnessBrowser__Cup4G11:RR42_RS11260 220 FGATPLFTTEELGGAGVSMVLYPLSAFRAMNKAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAY 288
                                               ********************************************************************* PP

                                 TIGR02317 276 ekkdkelfk 284
                                               e+k++ lf+
  lcl|FitnessBrowser__Cup4G11:RR42_RS11260 289 EQKLDALFA 297
                                               ****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (302 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.49
//
[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:

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