Alignments for a candidate for xylE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylE in Cupriavidus basilensis 4G11

Align catechol 2,3-dioxygenase (EC 1.13.11.2) (characterized)
to candidate RR42_RS32655 RR42_RS32655 catechol 2,3-dioxygenase

Query= BRENDA::P06622
         (307 letters)



>FitnessBrowser__Cup4G11:RR42_RS32655
          Length = 310

 Score =  353 bits (906), Expect = e-102
 Identities = 177/307 (57%), Positives = 218/307 (71%), Gaps = 4/307 (1%)

Query: 4   GVMRPGHVQLRVLDMSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEP 63
           GV+RPGHV LRVL++  AL+HY E+LGLIE  RDD+GRVYLKAW E D  S+VLREAD P
Sbjct: 5   GVLRPGHVALRVLELEPALKHYTEVLGLIETARDDKGRVYLKAWDEHDHHSVVLREADSP 64

Query: 64  GMDFMGFKVVDEDALRQLERDLMAYGCA--VEQLPAGELNSCGRRVRFQAPSGHHFELYA 121
           GMD+MGF+V     L  L +++   G A   + +PAGE    G R RF  P+GH  EL+A
Sbjct: 65  GMDYMGFRVDSGRTLEWLAQEVEQSGLASDFQWIPAGEHPRTGVRFRFTIPTGHAIELFA 124

Query: 122 DKEYTGKWGLNDVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDLFTKVLGFYLAEQVL 181
           DK+  G     D NP+ WP DL+GMA  RFDH L+YGD+L  T  LF  VLGF LAE+V+
Sbjct: 125 DKDKLGCL-TGDSNPDPWPDDLRGMAPSRFDHCLLYGDDLDGTVRLFRDVLGFTLAEEVV 183

Query: 182 DENGTR-VAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSID 240
              G   +  FL+ S KAHD+AFI H EK + HH SF+L+ W ++L+AAD+IS  D S+D
Sbjct: 184 AGPGKMMIGAFLTCSNKAHDIAFIRHAEKNKFHHASFNLDNWGEVLKAADIISKKDVSLD 243

Query: 241 IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNE 300
           IGPTRHG+T G TIYFFDPSGNRNEVF GG  +YPD   +TWT ++LGKAIFYHDR LN+
Sbjct: 244 IGPTRHGITRGATIYFFDPSGNRNEVFSGGYIHYPDKPTITWTDNELGKAIFYHDRKLND 303

Query: 301 RFMTVLT 307
            F+ VLT
Sbjct: 304 AFLNVLT 310


Lambda     K      H
   0.322    0.139    0.434 

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: 371
Number of extensions: 17
Number of successful extensions: 4
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: 307
Length of database: 310
Length adjustment: 27
Effective length of query: 280
Effective length of database: 283
Effective search space:    79240
Effective search space used:    79240
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS32655 RR42_RS32655 (catechol 2,3-dioxygenase)
to HMM TIGR03211 (catechol 2,3 dioxygenase (EC 1.13.11.2))

# 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/TIGR03211.hmm
# target sequence database:        /tmp/gapView.3038.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03211  [M=303]
Accession:   TIGR03211
Description: catechol_2_3: catechol 2,3 dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-139  449.2   0.0   3.8e-139  449.1   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS32655  RR42_RS32655 catechol 2,3-dioxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS32655  RR42_RS32655 catechol 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.1   0.0  3.8e-139  3.8e-139       1     303 []       5     310 .]       5     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 449.1 bits;  conditional E-value: 3.8e-139
                                 TIGR03211   1 gvlrlghvelrvldleealkfykdvlGleetgrdeq.svYlkawdewdkysvilteadkagldhvafkv 68 
                                               gvlr+ghv+lrvl+le alk+y++vlGl et+rd++ +vYlkawde+d++sv+l+ead++g+d ++f+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS32655   5 GVLRPGHVALRVLELEPALKHYTEVLGLIETARDDKgRVYLKAWDEHDHHSVVLREADSPGMDYMGFRV 73 
                                               69******************************************************************* PP

                                 TIGR03211  69 eseadLeklekkleaaGv..everieagedlevGeavrfelPsgheleLyaekelvgekkgklnpdpwk 135
                                               +s ++Le l++++e++G+  + ++i+age++++G ++rf++P+gh +eL+a+k+  g  +g+ npdpw+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32655  74 DSGRTLEWLAQEVEQSGLasDFQWIPAGEHPRTGVRFRFTIPTGHAIELFADKDKLGCLTGDSNPDPWP 142
                                               *****************955679********************************************** PP

                                 TIGR03211 136 kelkGvaakrldHvlllaedveenvklltevLgfkltEqvvaedgkeqlaaflsvsnkahdiafvkdpe 204
                                               ++l+G+a++r+dH+ll+++d++ +v+l+++vLgf+l+E+vva++gk++++afl++snkahdiaf++++e
  lcl|FitnessBrowser__Cup4G11:RR42_RS32655 143 DDLRGMAPSRFDHCLLYGDDLDGTVRLFRDVLGFTLAEEVVAGPGKMMIGAFLTCSNKAHDIAFIRHAE 211
                                               ********************************************************************* PP

                                 TIGR03211 205 kgklhHvsflldswedvlkaaDvlskndvkidvgptrHgitrgqtiYvfdPsGnrvElfaggylaypdw 273
                                               k+k+hH+sf+ld+w +vlkaaD++sk+dv++d+gptrHgitrg tiY+fdPsGnr+E+f+ggy++ypd+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32655 212 KNKFHHASFNLDNWGEVLKAADIISKKDVSLDIGPTRHGITRGATIYFFDPSGNRNEVFSGGYIHYPDK 280
                                               ********************************************************************* PP

                                 TIGR03211 274 epitWtedelgrgifyherklnesfltvlt 303
                                               ++itWt++elg++ifyh+rkln++fl+vlt
  lcl|FitnessBrowser__Cup4G11:RR42_RS32655 281 PTITWTDNELGKAIFYHDRKLNDAFLNVLT 310
                                               **************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (303 nodes)
Target sequences:                          1  (310 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: 9.55
//
[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