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 GFF4091 HP15_4031 catechol 2,3-dioxygenase

Query= BRENDA::Q8KLV4
         (307 letters)



>FitnessBrowser__Marino:GFF4091
          Length = 307

 Score =  539 bits (1388), Expect = e-158
 Identities = 251/307 (81%), Positives = 275/307 (89%)

Query: 1   MKKGVLRPGHIQLRVLNLESALAHYRDLLGLIEVDRDDFGRVYLKAWTEVDKFSLVLREA 60
           MKKGV+RPGH+Q+RVL+++ AL HY DLLGLIE DRDD GRVYLKAWTEVDKFS+VLR A
Sbjct: 1   MKKGVMRPGHVQIRVLDMDEALKHYTDLLGLIETDRDDHGRVYLKAWTEVDKFSVVLRPA 60

Query: 61  DEPGMDFMGFKVVDEDALRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELY 120
           DEPGMDFM FKVVDE +L+QLE+DL  +G  VEQ+P GEL  CGRRVRF APSGH FELY
Sbjct: 61  DEPGMDFMAFKVVDEASLQQLEKDLADHGVEVEQVPEGELKDCGRRVRFNAPSGHTFELY 120

Query: 121 ADKEYTGKWGVNEVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDLFTKVLGFYLAEQV 180
           ADK+YTGKWG+ EVNPEAWPR L GM AVRFDH L+YG EL ATYDLF  VLGFYLAEQV
Sbjct: 121 ADKKYTGKWGITEVNPEAWPRGLDGMKAVRFDHCLLYGPELAATYDLFVNVLGFYLAEQV 180

Query: 181 LDENGTRVAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDVLRAADLISMTDTSID 240
           LD +GTR+AQFL+LSTKAHD+AFIHH EKG+ HH SF+LETWEDVLRAADLISMTDTSID
Sbjct: 181 LDGDGTRIAQFLTLSTKAHDIAFIHHEEKGKFHHASFYLETWEDVLRAADLISMTDTSID 240

Query: 241 IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNE 300
           IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTW  +QLGKAIFYHDR+LNE
Sbjct: 241 IGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTWQAEQLGKAIFYHDRVLNE 300

Query: 301 RFMTVLT 307
           RF+TVLT
Sbjct: 301 RFLTVLT 307


Lambda     K      H
   0.322    0.140    0.436 

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: 474
Number of extensions: 8
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: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
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 GFF4091 HP15_4031 (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.16723.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.9e-139  448.7   0.1   5.5e-139  448.6   0.1    1.0  1  lcl|FitnessBrowser__Marino:GFF4091  HP15_4031 catechol 2,3-dioxygena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4091  HP15_4031 catechol 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.6   0.1  5.5e-139  5.5e-139       1     303 []       4     307 .]       4     307 .] 0.99

  Alignments for each domain:
  == domain 1  score: 448.6 bits;  conditional E-value: 5.5e-139
                           TIGR03211   1 gvlrlghvelrvldleealkfykdvlGleetgrdeq.svYlkawdewdkysvilteadkagldhvafkveseadL 74 
                                         gv+r+ghv++rvld++ealk+y+d+lGl et+rd++ +vYlkaw+e+dk+sv+l++ad++g+d++afkv +ea+L
  lcl|FitnessBrowser__Marino:GFF4091   4 GVMRPGHVQIRVLDMDEALKHYTDLLGLIETDRDDHgRVYLKAWTEVDKFSVVLRPADEPGMDFMAFKVVDEASL 78 
                                         69************************************************************************* PP

                           TIGR03211  75 eklekkleaaGveverieagedlevGeavrfelPsgheleLyaekelvg.ekkgklnpdpwkkelkGvaakrldH 148
                                         ++lek+l + Gveve++++ge++++G++vrf++Psgh++eLya+k+++g +  +++np++w+++l G++a r+dH
  lcl|FitnessBrowser__Marino:GFF4091  79 QQLEKDLADHGVEVEQVPEGELKDCGRRVRFNAPSGHTFELYADKKYTGkWGITEVNPEAWPRGLDGMKAVRFDH 153
                                         ***********************************************886899********************** PP

                           TIGR03211 149 vlllaedveenvklltevLgfkltEqvvaedgkeqlaaflsvsnkahdiafvkdpekgklhHvsflldswedvlk 223
                                         +ll++++++++ +l+ +vLgf+l+Eqv+++dg++ +a+fl++s+kahdiaf++++ekgk+hH+sf+l++wedvl+
  lcl|FitnessBrowser__Marino:GFF4091 154 CLLYGPELAATYDLFVNVLGFYLAEQVLDGDGTR-IAQFLTLSTKAHDIAFIHHEEKGKFHHASFYLETWEDVLR 227
                                         *********************************6.**************************************** PP

                           TIGR03211 224 aaDvlskndvkidvgptrHgitrgqtiYvfdPsGnrvElfaggylaypdwepitWtedelgrgifyherklnesf 298
                                         aaD++s++d++id+gptrHg+t+g+tiY+fdPsGnr+E+f+gg ++ypd++p+tW++++lg++ifyh+r+lne+f
  lcl|FitnessBrowser__Marino:GFF4091 228 AADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVFCGGDYNYPDHKPVTWQAEQLGKAIFYHDRVLNERF 302
                                         *************************************************************************** PP

                           TIGR03211 299 ltvlt 303
                                         ltvlt
  lcl|FitnessBrowser__Marino:GFF4091 303 LTVLT 307
                                         **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (303 nodes)
Target sequences:                          1  (307 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.63
//
[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