GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas stutzeri RCH2

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate GFF2276 Psest_2321 methylisocitrate lyase

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



>FitnessBrowser__psRCH2:GFF2276
          Length = 297

 Score =  531 bits (1368), Expect = e-156
 Identities = 272/294 (92%), Positives = 281/294 (95%)

Query: 1   MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60
           M+  + GQRFRDAVA+EHPLQVVG INANHALLAKRAGFKAIYLSGGGVAAGSLG+PDLG
Sbjct: 1   MTLPSAGQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAGSLGLPDLG 60

Query: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120
           ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA
Sbjct: 61  ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120

Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180
           KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGL SALDRAAACIEA
Sbjct: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLNSALDRAAACIEA 180

Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240
           GADMIFPEAITEL MYK FA RVKAPILANITEFGATPLYTTE+LA  DVSLVLYPLSAF
Sbjct: 181 GADMIFPEAITELAMYKTFADRVKAPILANITEFGATPLYTTEELASVDVSLVLYPLSAF 240

Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294
           RAMNKAAENVYTA+RRDGTQ+NVIDTMQTRMELYDRI+YH FEQ LD+LFA KK
Sbjct: 241 RAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDRINYHAFEQHLDSLFAQKK 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: 353
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: 297
Length adjustment: 26
Effective length of query: 268
Effective length of database: 271
Effective search space:    72628
Effective search space used:    72628
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 GFF2276 Psest_2321 (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.31507.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-136  439.8   2.1   2.3e-136  439.6   2.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2276  Psest_2321 methylisocitrate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2276  Psest_2321 methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.6   2.1  2.3e-136  2.3e-136       2     284 ..       7     291 ..       6     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.6 bits;  conditional E-value: 2.3e-136
                           TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtklp 75 
                                         g+++r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+t l++v++++rrit+v++lp
  lcl|FitnessBrowser__psRCH2:GFF2276   7 GQRFRDAVASEHPLQVVGAINANHALLAKRAGFKAIYLSGGGVAAgSLGLPDLGITGLDDVLTDVRRITDVCDLP 81 
                                         789****************************************999***************************** PP

                           TIGR02317  76 llvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfvli 149
                                         llvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+vs++emv++ikaav+a++d++fv++
  lcl|FitnessBrowser__psRCH2:GFF2276  82 LLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIM 156
                                         **********889************************************************************** PP

                           TIGR02317 150 aRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadeleelgyk 224
                                         aRtDa aveGl++a++Ra a +eaGad+if+ea+++++++++fa++vk+p+lan+tefG tpl+t++el+++ ++
  lcl|FitnessBrowser__psRCH2:GFF2276 157 ARTDALAVEGLNSALDRAAACIEAGADMIFPEAITELAMYKTFADRVKAPILANITEFGATPLYTTEELASVDVS 231
                                         *************************************************************************** PP

                           TIGR02317 225 iviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                         +v+yP++a+Ra++kaae+vy+ l+++Gtqk+++d++qtR elY+ ++y+++e+++++lf+
  lcl|FitnessBrowser__psRCH2:GFF2276 232 LVLYPLSAFRAMNKAAENVYTALRRDGTQKNVIDTMQTRMELYDRINYHAFEQHLDSLFA 291
                                         ********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (297 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.85
//
[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