Alignments for a candidate for catA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Herbaspirillum seropedicae SmR1

Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate HSERO_RS18295 HSERO_RS18295 3'-RNA processing protein

Query= BRENDA::Q8GAZ6
         (300 letters)



>FitnessBrowser__HerbieS:HSERO_RS18295
          Length = 303

 Score =  396 bits (1018), Expect = e-115
 Identities = 190/300 (63%), Positives = 236/300 (78%), Gaps = 1/300 (0%)

Query: 1   MDIKTIDALLNKINESATHEGNARTKQVVNRIIRDLFITIDELDVTPNEFWSALNYLGEA 60
           +D K IDA+L KI  +   EGN R K VVNR++RD+F TI+ELDV P EFW+A++YL  A
Sbjct: 1   VDKKAIDAVLQKIESTELAEGNQRVKTVVNRLVRDMFYTIEELDVQPEEFWAAVDYLTSA 60

Query: 61  GQSGELGLLAAGLGFEHFLDVRLDEAEAKAGLQGGTPRTIEGPLYVAGAPESTGHARLDN 120
           G+SGE GL+AAGLGFEHFLD+R+DEAEA+ G+QGGTPRTIEGPLYV+GAPE  G AR+D 
Sbjct: 61  GKSGEFGLIAAGLGFEHFLDLRMDEAEARRGVQGGTPRTIEGPLYVSGAPEQKGFARMDK 120

Query: 121 GNEPGETLVMRGRVLAENGEPVRDALVEVWHANHLGNYSHFDKSQAEFNLRRSIRTDENG 180
             +PG+TL M+G+V  E+G+P+ +ALVEVWHANHLG YS FD  Q+ FNLR SIRTDE G
Sbjct: 121 DPQPGDTLFMQGQVFDEHGKPLANALVEVWHANHLGRYSFFDPDQSPFNLRCSIRTDEQG 180

Query: 181 TYSFRSVVPIGYSVPPQGKTQQLLDLLGRHGHRPAHIHFFVSAPGYRKLTTQINIEGDPY 240
            Y FRS VP+GYSVPP G T +LL  LGRHG RPAHIHFFV+ PGYRKLTTQINI GDPY
Sbjct: 181 RYRFRSRVPVGYSVPPGGATDRLLTKLGRHGSRPAHIHFFVTVPGYRKLTTQINIAGDPY 240

Query: 241 LWDDFAFATREGLVPAVKK-EEGATGKPYGIDGQFALIDFDFSLVKDRDNVPTSEVERVR 299
           LWDDFAFATREGLVP +K   + A  + + +D  F  I+F+F+L+ ++ ++P +++ R R
Sbjct: 241 LWDDFAFATREGLVPELKHVTDPAEIRKHEVDAPFYAIEFNFNLLPEQADLPKADINRPR 300


Lambda     K      H
   0.317    0.137    0.407 

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: 333
Number of extensions: 8
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: 300
Length of database: 303
Length adjustment: 27
Effective length of query: 273
Effective length of database: 276
Effective search space:    75348
Effective search space used:    75348
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: 48 (23.1 bits)

Align candidate HSERO_RS18295 HSERO_RS18295 (3'-RNA processing protein)
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.13209.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.9e-137  441.3   0.0   6.7e-137  441.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS18295  HSERO_RS18295 3'-RNA processing 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS18295  HSERO_RS18295 3'-RNA processing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.1   0.0  6.7e-137  6.7e-137       2     285 .]       3     284 ..       2     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 441.1 bits;  conditional E-value: 6.7e-137
                                  TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelglla 69 
                                                +k ++a+l+k+ ++e ++gn+r+k +v+r+++d+f +ie+ld++++efwaav+yl+++G+++e+gl+a
  lcl|FitnessBrowser__HerbieS:HSERO_RS18295   3 KKAIDAVLQKIESTELAEGNQRVKTVVNRLVRDMFYTIEELDVQPEEFWAAVDYLTSAGKSGEFGLIA 70 
                                                689***************************************************************** PP

                                  TIGR02439  70 aGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvld 137
                                                aGlG+ehfldlr+d+a+a+ g++ggtPrtieGPlyv+Gap+++Gfar+d+++  + ++tl+++Gqv+d
  lcl|FitnessBrowser__HerbieS:HSERO_RS18295  71 AGLGFEHFLDLRMDEAEARRGVQGGTPRTIEGPLYVSGAPEQKGFARMDKDP--QPGDTLFMQGQVFD 136
                                                ***************************************************9..568*********** PP

                                  TIGR02439 138 aeGkpiagakvevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqll 205
                                                ++Gkp+a+a vevwhan+ G ysffd+ qs+fnlr +i+td++G+yr+rs vPvGy+vpp g+t++ll
  lcl|FitnessBrowser__HerbieS:HSERO_RS18295 137 EHGKPLANALVEVWHANHLGRYSFFDPDQSPFNLRCSIRTDEQGRYRFRSRVPVGYSVPPGGATDRLL 204
                                                ******************************************************************** PP

                                  TIGR02439 206 nllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgve 273
                                                 +lGrhG rPah+hffv+ pgyrklttqin++gd+yl+ddfafatreglv+e+k+v+d a++++++v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS18295 205 TKLGRHGSRPAHIHFFVTVPGYRKLTTQINIAGDPYLWDDFAFATREGLVPELKHVTDPAEIRKHEVD 272
                                                ******************************************************************** PP

                                  TIGR02439 274 grfaeiefdlel 285
                                                 +f  ief+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS18295 273 APFYAIEFNFNL 284
                                                *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (303 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: 00:00:00.01
# Mc/sec: 7.06
//
[ok]

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

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

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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