GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kynB in Acidovorax sp. GW101-3H11

Align Kynurenine formamidase; KFA; KFase; Arylformamidase; N-formylkynurenine formamidase; FKF; EC 3.5.1.9 (characterized)
to candidate Ac3H11_1158 Kynurenine formamidase, bacterial (EC 3.5.1.9)

Query= SwissProt::P0C8P4
         (218 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1158
          Length = 217

 Score =  250 bits (639), Expect = 1e-71
 Identities = 126/214 (58%), Positives = 146/214 (68%), Gaps = 1/214 (0%)

Query: 5   PQLHDGRRIWDISPAVSPATPVWPGDTPFQHDPAWQLDEHCPVNVGRITMSPHTGAHADA 64
           P     RR+WDISP V   +PV+PGDT +       +   CPVNV  ITMSPH GAHADA
Sbjct: 4   PSSPTARRLWDISPPVHAGSPVFPGDTAYSQQWCATIGPGCPVNVSAITMSPHVGAHADA 63

Query: 65  PLHYAADGAPIGAVPLDAYLGPCRVIHCIGAAPRVEPQHIAHALAGT-PPRVLLRTYAQA 123
           PLHY A GA IG V LDA+LGPCRV+H IG  P +  +HIAHA+ GT P RVL+RTY   
Sbjct: 64  PLHYDAQGATIGDVSLDAFLGPCRVVHAIGCGPLITWEHIAHAVDGTLPQRVLVRTYEHM 123

Query: 124 PQGKWDSAFCAVAPETISLLARHGVRLIGIDTPSLDPETSKTMDAHHAVRDHQLAILEGI 183
           P  +WD    A AP TI  LA  GV L+GIDT S+DP  SKT+D+H  +R   L +LE +
Sbjct: 124 PVDRWDGQLAAYAPGTIERLADLGVLLVGIDTASIDPADSKTLDSHQVIRRRGLRVLENL 183

Query: 184 VLDEVPAGDYELIALPLRLATLDASPVRAVLREL 217
           VLD VP GDYELIALPL+L T DASPVRAVLR L
Sbjct: 184 VLDAVPEGDYELIALPLKLTTADASPVRAVLRAL 217


Lambda     K      H
   0.320    0.137    0.444 

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: 271
Number of extensions: 11
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: 218
Length of database: 217
Length adjustment: 22
Effective length of query: 196
Effective length of database: 195
Effective search space:    38220
Effective search space used:    38220
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 (21.8 bits)
S2: 45 (21.9 bits)

Align candidate Ac3H11_1158 (Kynurenine formamidase, bacterial (EC 3.5.1.9))
to HMM TIGR03035 (kynB: arylformamidase (EC 3.5.1.9))

# 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/TIGR03035.hmm
# target sequence database:        /tmp/gapView.5707.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03035  [M=206]
Accession:   TIGR03035
Description: trp_arylform: arylformamidase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    1.2e-92  295.6   0.0    1.3e-92  295.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158  Kynurenine formamidase, bacteria


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158  Kynurenine formamidase, bacterial (EC 3.5.1.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.4   0.0   1.3e-92   1.3e-92       1     206 []      11     217 .]      11     217 .] 0.99

  Alignments for each domain:
  == domain 1  score: 295.4 bits;  conditional E-value: 1.3e-92
                                        TIGR03035   1 rlidisqplnedlatwPGdtpfsqelavsleeegsvnvgritlsvhtGahvdaPlhykndga 62 
                                                      rl+dis+p+++ ++++PGdt++sq++ +++ + ++vnv+ it+s+h+Gah+daPlhy+++ga
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158  11 RLWDISPPVHAGSPVFPGDTAYSQQWCATIGPGCPVNVSAITMSPHVGAHADAPLHYDAQGA 72 
                                                      68************************************************************ PP

                                        TIGR03035  63 kigdveldvylGpcrvidclsalekiekealksalee.apervllrtaekakaeafdediaa 123
                                                       igdv+ld++lGpcrv++++++ ++i+ e++++a+++ +p+rvl+rt+e+++ +++d ++aa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158  73 TIGDVSLDAFLGPCRVVHAIGCGPLITWEHIAHAVDGtLPQRVLVRTYEHMPVDRWDGQLAA 134
                                                      **********************************9973699********************* PP

                                        TIGR03035 124 vapdtiellaekGvrliGvdtpsvdPleskeldahhalakhdlailenlvldevaeGdyeli 185
                                                      +ap tie la  Gv l+G+dt+s+dP++sk+ld+h+ +++++l++lenlvld v eGdyeli
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158 135 YAPGTIERLADLGVLLVGIDTASIDPADSKTLDSHQVIRRRGLRVLENLVLDAVPEGDYELI 196
                                                      ************************************************************** PP

                                        TIGR03035 186 alPlklaeldaspvravlral 206
                                                      alPlkl+++daspvravlral
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1158 197 ALPLKLTTADASPVRAVLRAL 217
                                                      *******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (206 nodes)
Target sequences:                          1  (217 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 6.17
//
[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:

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:

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:

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:

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