Aligments for a candidate for prpB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments 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.13156.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.05
//
[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:

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, or view the source code.

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