Alignments for a candidate for catA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Pseudomonas stutzeri RCH2

Align subunit of catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate GFF2640 Psest_2692 catechol 1,2-dioxygenase, proteobacterial

Query= metacyc::MONOMER-3422
         (311 letters)



>FitnessBrowser__psRCH2:GFF2640
          Length = 313

 Score =  422 bits (1086), Expect = e-123
 Identities = 216/330 (65%), Positives = 244/330 (73%), Gaps = 40/330 (12%)

Query: 1   MTVKISHTADVQAFFNKVAGLDHAEGNPRFKQIILRVLQDTARLVEDLEITEDEFWHAID 60
           MTVKIS T+DVQ FF + +G  +  G+ R K +I R+L DTA++VEDLEIT+DEFW A+D
Sbjct: 1   MTVKISQTSDVQNFFKEASGFGNDAGSSRMKTVINRILVDTAKIVEDLEITQDEFWKAVD 60

Query: 61  YLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGE 120
           YLNRLGGR+EAGLL AGLG+EHFLDLL+DAKD + GL GGTPRTIEGPLYVAGAP++Q E
Sbjct: 61  YLNRLGGRHEAGLLVAGLGLEHFLDLLEDAKDEQQGLTGGTPRTIEGPLYVAGAPISQAE 120

Query: 121 ARMDDGT--DPGVVMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSEYNLRRR 178
            RMDDG+  D   VMFLQGQV   DGKP+A A VDLWHANT+G YSYFD +QSEYNLRRR
Sbjct: 121 TRMDDGSELDVATVMFLQGQVTGPDGKPVANAVVDLWHANTKGNYSYFDKSQSEYNLRRR 180

Query: 179 IITDAVGRYRARSIVPSGYGCDPQGTTQECLDLLGRHGQRPAHVHFFISAPGFRHLTTQI 238
           I+TD  G YRARSIVPSGYGC   G TQE LD LGRHG+RPAH+HFFISAPG RHLTTQI
Sbjct: 181 IVTDENGNYRARSIVPSGYGCSLDGPTQEVLDHLGRHGRRPAHIHFFISAPGHRHLTTQI 240

Query: 239 NLKMPLPRVIAVFRASALPNCEGDKYLWDDFAYATRDGLIGELRFV-------------- 284
           NL                    GD+YLWDDFAYATRDGL+G++RFV              
Sbjct: 241 NL-------------------AGDEYLWDDFAYATRDGLVGDIRFVEDAEAARARGIEGS 281

Query: 285 -----AFDFHLQAAAAPEAEARSHRPRALQ 309
                 FDF LQAA APEAE RS RPRALQ
Sbjct: 282 RFAELTFDFQLQAAPAPEAEQRSARPRALQ 311


Lambda     K      H
   0.321    0.139    0.424 

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: 372
Number of extensions: 11
Number of successful extensions: 3
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: 311
Length of database: 313
Length adjustment: 27
Effective length of query: 284
Effective length of database: 286
Effective search space:    81224
Effective search space used:    81224
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 GFF2640 Psest_2692 (catechol 1,2-dioxygenase, proteobacterial)
to HMM TIGR02439 (catA: catechol 1,2-dioxygenase (EC 1.13.11.1))

# 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/TIGR02439.hmm
# target sequence database:        /tmp/gapView.10386.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02439  [M=285]
Accession:   TIGR02439
Description: catechol_proteo: catechol 1,2-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     6e-146  470.8   0.2   6.9e-146  470.6   0.2    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2640  Psest_2692 catechol 1,2-dioxygen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2640  Psest_2692 catechol 1,2-dioxygenase, proteobacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.6   0.2  6.9e-146  6.9e-146       2     285 .]       8     292 ..       7     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 470.6 bits;  conditional E-value: 6.9e-146
                           TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGleh 76 
                                         t++vq+++k+++g+ ++ g +r+k +++r+l d++k +edl+it+defw+av+yln+lG ++e+gll+aGlGleh
  lcl|FitnessBrowser__psRCH2:GFF2640   8 TSDVQNFFKEASGFGNDAGSSRMKTVINRILVDTAKIVEDLEITQDEFWKAVDYLNRLGGRHEAGLLVAGLGLEH 82 
                                         789************************************************************************ PP

                           TIGR02439  77 fldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagakvevw 151
                                         fldl+ da+d+++gl+ggtPrtieGPlyvaGap+s+ ++r+ddgse d a++++l+Gqv+  +Gkp+a+a+v++w
  lcl|FitnessBrowser__psRCH2:GFF2640  83 FLDLLEDAKDEQQGLTGGTPRTIEGPLYVAGAPISQAETRMDDGSELDVATVMFLQGQVTGPDGKPVANAVVDLW 157
                                         *************************************************************************** PP

                           TIGR02439 152 hanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhffvsapg 226
                                         han+kGnys+fdksqse+nlrr+i+td++G+yrars+vP+Gyg+  +gptq++l++lGrhG+rPah+hff+sapg
  lcl|FitnessBrowser__psRCH2:GFF2640 158 HANTKGNYSYFDKSQSEYNLRRRIVTDENGNYRARSIVPSGYGCSLDGPTQEVLDHLGRHGRRPAHIHFFISAPG 232
                                         *************************************************************************** PP

                           TIGR02439 227 yrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgveg.rfaeiefdlel 285
                                         +r+lttqinl+gd+yl+ddfa+atr+glv+++++veda+aa++rg+eg rfae++fd++l
  lcl|FitnessBrowser__psRCH2:GFF2640 233 HRHLTTQINLAGDEYLWDDFAYATRDGLVGDIRFVEDAEAARARGIEGsRFAELTFDFQL 292
                                         ***********************************************989********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (313 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: 10.30
//
[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