Alignments for a candidate for xylE in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylE in Marinobacter adhaerens HP15

Align catechol 2,3-dioxygenase (EC 1.13.11.2) (characterized)
to candidate GFF1132 HP15_1110 catechol 2,3-dioxygenase

Query= BRENDA::P06622
         (307 letters)



>FitnessBrowser__Marino:GFF1132
          Length = 290

 Score =  492 bits (1266), Expect = e-144
 Identities = 229/290 (78%), Positives = 252/290 (86%)

Query: 18  MSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDFMGFKVVDEDA 77
           M +AL+HY +LLGLIE DRDDQGRVYLKAW+EVDKFS+VLREADEPG DFM FKV+DED 
Sbjct: 1   MDEALQHYTDLLGLIETDRDDQGRVYLKAWSEVDKFSVVLREADEPGCDFMAFKVLDEDT 60

Query: 78  LRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPE 137
           L QLE+DL+ +G  VEQ+PA EL  CGRRVRF  PSGH FEL+ADK+YTGKWGL+ VNPE
Sbjct: 61  LNQLEKDLVTFGVEVEQVPAEELKDCGRRVRFTVPSGHAFELFADKKYTGKWGLSSVNPE 120

Query: 138 AWPRDLKGMAAVRFDHALMYGDELPATYDLFTKVLGFYLAEQVLDENGTRVAQFLSLSTK 197
           AWPR L+GM AVRFDH L YG EL A YD+F  VLGF LAEQVLD  GTRV+QFL++S K
Sbjct: 121 AWPRGLRGMKAVRFDHCLFYGPELAAVYDIFVNVLGFDLAEQVLDPQGTRVSQFLTVSMK 180

Query: 198 AHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSIDIGPTRHGLTHGKTIYFF 257
            HD+AFIHH E G+ HH SFHLETWED+LRAADLI+MTDTSIDIGPTRHGLTHGKTIYFF
Sbjct: 181 EHDIAFIHHEEPGKFHHASFHLETWEDVLRAADLITMTDTSIDIGPTRHGLTHGKTIYFF 240

Query: 258 DPSGNRNEVFCGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNERFMTVLT 307
           DPSGNRNEVFCGGDY YPDHKPVTWTTD+LGKAIFYHDR LNERFM VLT
Sbjct: 241 DPSGNRNEVFCGGDYFYPDHKPVTWTTDELGKAIFYHDRTLNERFMAVLT 290


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: 432
Number of extensions: 13
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: 307
Length of database: 290
Length adjustment: 27
Effective length of query: 280
Effective length of database: 263
Effective search space:    73640
Effective search space used:    73640
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 GFF1132 HP15_1110 (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.23131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.5e-126  405.6   0.1   7.3e-126  405.5   0.1    1.0  1  lcl|FitnessBrowser__Marino:GFF1132  HP15_1110 catechol 2,3-dioxygena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1132  HP15_1110 catechol 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.5   0.1  7.3e-126  7.3e-126      15     303 .]       1     290 []       1     290 [] 0.99

  Alignments for each domain:
  == domain 1  score: 405.5 bits;  conditional E-value: 7.3e-126
                           TIGR03211  15 leealkfykdvlGleetgrdeq.svYlkawdewdkysvilteadkagldhvafkveseadLeklekkleaaGvev 88 
                                         ++eal++y+d+lGl et+rd+q +vYlkaw e+dk+sv+l+ead++g d++afkv +e++L++lek+l  +Gvev
  lcl|FitnessBrowser__Marino:GFF1132   1 MDEALQHYTDLLGLIETDRDDQgRVYLKAWSEVDKFSVVLREADEPGCDFMAFKVLDEDTLNQLEKDLVTFGVEV 75 
                                         79************************************************************************* PP

                           TIGR03211  89 erieagedlevGeavrfelPsgheleLyaekelvg.ekkgklnpdpwkkelkGvaakrldHvlllaedveenvkl 162
                                         e+++a+e++++G++vrf++Psgh +eL+a+k+++g +  +++np++w+++l+G++a r+dH+l++++++++  ++
  lcl|FitnessBrowser__Marino:GFF1132  76 EQVPAEELKDCGRRVRFTVPSGHAFELFADKKYTGkWGLSSVNPEAWPRGLRGMKAVRFDHCLFYGPELAAVYDI 150
                                         *********************************88689************************************* PP

                           TIGR03211 163 ltevLgfkltEqvvaedgkeqlaaflsvsnkahdiafvkdpekgklhHvsflldswedvlkaaDvlskndvkidv 237
                                         + +vLgf l+Eqv++++g++ +++fl+vs k hdiaf++++e+gk+hH+sf l++wedvl+aaD+++++d++id+
  lcl|FitnessBrowser__Marino:GFF1132 151 FVNVLGFDLAEQVLDPQGTR-VSQFLTVSMKEHDIAFIHHEEPGKFHHASFHLETWEDVLRAADLITMTDTSIDI 224
                                         ****************9996.****************************************************** PP

                           TIGR03211 238 gptrHgitrgqtiYvfdPsGnrvElfaggylaypdwepitWtedelgrgifyherklnesfltvlt 303
                                         gptrHg+t+g+tiY+fdPsGnr+E+f+gg + ypd++p+tWt+delg++ifyh+r+lne+f+ vlt
  lcl|FitnessBrowser__Marino:GFF1132 225 GPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYFYPDHKPVTWTTDELGKAIFYHDRTLNERFMAVLT 290
                                         **************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (303 nodes)
Target sequences:                          1  (290 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: 8.50
//
[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