Aligments for a candidate for garD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for garD in Cupriavidus basilensis 4G11

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate RR42_RS29090 RR42_RS29090 galactarate dehydrogenase

Query= reanno::HerbieS:HSERO_RS15800
         (522 letters)



>FitnessBrowser__Cup4G11:RR42_RS29090
          Length = 512

 Score =  820 bits (2118), Expect = 0.0
 Identities = 405/508 (79%), Positives = 453/508 (89%), Gaps = 2/508 (0%)

Query: 15  YIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDVAIG 74
           YI ++  DNVAIV NDGGLP GTVFP GLTL +RVPQGHK+AL DL  G+A+VRY+V IG
Sbjct: 7   YIRIHALDNVAIVANDGGLPEGTVFPCGLTLRERVPQGHKVALVDLAAGDAVVRYNVVIG 66

Query: 75  YAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVGTRN 134
           YA+RD+PKG W+ E +++MP A  LDNLP+ T+   P PPLEGY+FEG+RN DGSVGTRN
Sbjct: 67  YALRDLPKGSWVNERVIEMPVAPGLDNLPVGTRVAEPLPPLEGYSFEGFRNPDGSVGTRN 126

Query: 135 LLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIPIRT 194
           +LAITTTVQCV+GVVEHAV+RIRAELLP+YPNV+DVV LEHTYGCGVAIDAP+A +PIRT
Sbjct: 127 ILAITTTVQCVSGVVEHAVRRIRAELLPQYPNVDDVVGLEHTYGCGVAIDAPDAIVPIRT 186

Query: 195 LRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVVCLQDAEHVGFNSMI 254
           LRNI+LNPNFGG AM+VSLGCEKLQP RLLP   +P     +  VVCLQD EHVGF SMI
Sbjct: 187 LRNIALNPNFGGTAMMVSLGCEKLQPERLLPAGSLPGGL--DVGVVCLQDDEHVGFESMI 244

Query: 255 DSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA 314
           DSIM MA   L  L++RRRETCPAS+LVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA
Sbjct: 245 DSIMAMAHTHLARLDQRRRETCPASELVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA 304

Query: 315 SVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGVDRSANTTPGNKKGG 374
           +VMFSEVTEVRDGIDQLT+RA   EVAQAMIREMDWYD YL++G VDRSANTTPGNKKGG
Sbjct: 305 TVMFSEVTEVRDGIDQLTARAATPEVAQAMIREMDWYDRYLEKGRVDRSANTTPGNKKGG 364

Query: 375 LANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICGTLQLAAGMNLHI 434
           L+NIVEKAMGSIVKSGS+ I+GVLSPG+KL+QKGLIYAATPASDFICGTLQLAAGMNLH+
Sbjct: 365 LSNIVEKAMGSIVKSGSTAITGVLSPGEKLKQKGLIYAATPASDFICGTLQLAAGMNLHV 424

Query: 435 FTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGWELFQLMLD 494
           FTTGRGTPYGLA VPVIKVATR+DLARRWHDLMDVNAGRIA+GEA+IEDVGWELF+LMLD
Sbjct: 425 FTTGRGTPYGLAEVPVIKVATRSDLARRWHDLMDVNAGRIATGEATIEDVGWELFRLMLD 484

Query: 495 VASGKKRTWAEQWKLHNALTLFNPAPVT 522
           VASG+K+TWAE  KLHN+L LFNPAPVT
Sbjct: 485 VASGRKKTWAEHHKLHNSLVLFNPAPVT 512


Lambda     K      H
   0.317    0.134    0.397 

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: 987
Number of extensions: 32
Number of successful extensions: 2
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: 522
Length of database: 512
Length adjustment: 35
Effective length of query: 487
Effective length of database: 477
Effective search space:   232299
Effective search space used:   232299
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate RR42_RS29090 RR42_RS29090 (galactarate dehydrogenase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.18701.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-292  956.4   0.2   1.6e-292  956.3   0.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS29090  RR42_RS29090 galactarate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS29090  RR42_RS29090 galactarate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  956.3   0.2  1.6e-292  1.6e-292       1     507 []       6     512 .]       6     512 .] 1.00

  Alignments for each domain:
  == domain 1  score: 956.3 bits;  conditional E-value: 1.6e-292
                                 TIGR03248   1 lyirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiar 69 
                                               lyir+++ dnvaiv+nd Glp+gt+f++gltl+e++pqghkvalvdl++gda++ry+ viGya++d+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090   6 LYIRIHALDNVAIVANDGGLPEGTVFPCGLTLRERVPQGHKVALVDLAAGDAVVRYNVVIGYALRDLPK 74 
                                               79******************************************************************* PP

                                 TIGR03248  70 GswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdy 138
                                               Gswv+e+++e+p ap l++lp++t+v+e+l+pleGy+feG+rn dGsvGt+nil+itt+vqcv+gvv++
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090  75 GSWVNERVIEMPVAPGLDNLPVGTRVAEPLPPLEGYSFEGFRNPDGSVGTRNILAITTTVQCVSGVVEH 143
                                               ********************************************************************* PP

                                 TIGR03248 139 avkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqp 207
                                               av+ri++ellp+ypnvddvv+l+h+yGcGvaidapdaivpirtlrn+alnpn+GG+a++v+lGceklqp
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 144 AVRRIRAELLPQYPNVDDVVGLEHTYGCGVAIDAPDAIVPIRTLRNIALNPNFGGTAMMVSLGCEKLQP 212
                                               ********************************************************************* PP

                                 TIGR03248 208 erllpeelsavelkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlqcGGs 275
                                               erllp +  + +  d+ v++lqd+++ Gf++m+++i+++a+++l++l++r+ret+paselvvG+qcGGs
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 213 ERLLPAGSLP-GGLDVGVVCLQDDEHvGFESMIDSIMAMAHTHLARLDQRRRETCPASELVVGVQCGGS 280
                                               *******999.8889**********99****************************************** PP

                                 TIGR03248 276 dafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydeylarGe 344
                                               dafsGvtanpavGfa+dllvraGatv+fsevtevrd+i++lt+ra++ eva+a+irem+wyd+yl++G+
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 281 DAFSGVTANPAVGFATDLLVRAGATVMFSEVTEVRDGIDQLTARAATPEVAQAMIREMDWYDRYLEKGR 349
                                               ********************************************************************* PP

                                 TIGR03248 345 adrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcGtlqlas 413
                                               +drsanttpGnkkGGlsniveka+GsivksGs+ai++vlspGek k+kGliyaatpasdf+cGtlqla+
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 350 VDRSANTTPGNKKGGLSNIVEKAMGSIVKSGSTAITGVLSPGEKLKQKGLIYAATPASDFICGTLQLAA 418
                                               ********************************************************************* PP

                                 TIGR03248 414 glnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfrlildvas 482
                                               g+nlhvfttGrGtpyGla+vpvikv+tr++la+rw+dl+d++aGriatGeatiedvGwelfrl+ldvas
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 419 GMNLHVFTTGRGTPYGLAEVPVIKVATRSDLARRWHDLMDVNAGRIATGEATIEDVGWELFRLMLDVAS 487
                                               ********************************************************************* PP

                                 TIGR03248 483 Grkktwaekyklhndlalfnpapvt 507
                                               Grkktwae++klhn+l lfnpapvt
  lcl|FitnessBrowser__Cup4G11:RR42_RS29090 488 GRKKTWAEHHKLHNSLVLFNPAPVT 512
                                               ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (512 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.63
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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