Alignments for a candidate for prpB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Dyella japonica UNC79MFTsu3.2

Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate N515DRAFT_0020 N515DRAFT_0020 methylisocitrate lyase

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



>FitnessBrowser__Dyella79:N515DRAFT_0020
          Length = 295

 Score =  456 bits (1174), Expect = e-133
 Identities = 225/288 (78%), Positives = 253/288 (87%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           S GARFR ALA E PLQV+G INANHALLA+RAGYRAIYLSGGGVAAGSLGLPDLGI+ L
Sbjct: 6   SPGARFRAALAQEQPLQVIGAINANHALLARRAGYRAIYLSGGGVAAGSLGLPDLGINTL 65

Query: 71  DDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAKRCG 130
           DDVLTDVRRITDVCD+PL+VD+DTGFG SAFN+ART +SLIKFGA A HIEDQVGAKRCG
Sbjct: 66  DDVLTDVRRITDVCDLPLMVDIDTGFGPSAFNIARTVKSLIKFGAAACHIEDQVGAKRCG 125

Query: 131 HRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGADA 190
           HRPGKEIVS GEMADR+KAA DA+TD +F ++ARTDA+  EG+D AIERA+ACVEAGAD 
Sbjct: 126 HRPGKEIVSSGEMADRVKAAADAKTDADFFLIARTDAIQTEGVDAAIERAIACVEAGADG 185

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IF EA+ DL  YR+F DAVK PVLANITEFG TPLF+ +EL  AGV +VLYPLSAFRAMN
Sbjct: 186 IFAEAVYDLPTYRRFADAVKAPVLANITEFGKTPLFSVDELRSAGVGIVLYPLSAFRAMN 245

Query: 251 KAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQ 298
           KAAENVY AIRRDG Q+NV+DTMQTR ELY+ IGYH +E++LD LFA+
Sbjct: 246 KAAENVYQAIRRDGHQRNVIDTMQTREELYDRIGYHDFERRLDELFAR 293


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: 323
Number of extensions: 9
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: 295
Length adjustment: 27
Effective length of query: 275
Effective length of database: 268
Effective search space:    73700
Effective search space used:    73700
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 N515DRAFT_0020 N515DRAFT_0020 (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.2807.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.9e-131  421.8   0.4   6.8e-131  421.6   0.4    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020  N515DRAFT_0020 methylisocitrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0020  N515DRAFT_0020 methylisocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.6   0.4  6.8e-131  6.8e-131       2     284 ..       8     292 ..       7     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.6 bits;  conditional E-value: 6.8e-131
                                    TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeear 66 
                                                  g+++r++l++e++lq++Gaina++alla++aG++a+YlsG+++aa slglPDlg+ tl++v++++r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020   8 GARFRAALAQEQPLQVIGAINANHALLARRAGYRAIYLSGGGVAAgSLGLPDLGINTLDDVLTDVR 73 
                                                  689****************************************999******************** PP

                                    TIGR02317  67 ritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemv 131
                                                  rit+v++lpl+vD+DtGfG  a+n+artvk+l++ g+aa+hieDqv +k+CGh++gke+vs  em+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020  74 RITDVCDLPLMVDIDTGFGPsAFNIARTVKSLIKFGAAACHIEDQVGAKRCGHRPGKEIVSSGEMA 139
                                                  *******************769******************************************** PP

                                    TIGR02317 132 kkikaavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavk 197
                                                  +++kaa++ak+d df+liaRtDa  +eG+daaieRa a veaGad if+ea+ ++  +r+fa+avk
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020 140 DRVKAAADAKTDADFFLIARTDAIQTEGVDAAIERAIACVEAGADGIFAEAVYDLPTYRRFADAVK 205
                                                  ****************************************************************** PP

                                    TIGR02317 198 vpllanmtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtR 263
                                                  +p+lan+tefGktpl+++del+++g+ iv+yP++a+Ra++kaae+vy+ ++++G q++++d++qtR
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020 206 APVLANITEFGKTPLFSVDELRSAGVGIVLYPLSAFRAMNKAAENVYQAIRRDGHQRNVIDTMQTR 271
                                                  ****************************************************************** PP

                                    TIGR02317 264 kelYellgyedyekkdkelfk 284
                                                  +elY+ +gy+d+e++++elf+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0020 272 EELYDRIGYHDFERRLDELFA 292
                                                  *****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (295 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: 00:00:00.01
# Mc/sec: 7.11
//
[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
the source code
instructions for running GapMind on your computer

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