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

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.25615.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.59
//
[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