Alignments for a candidate for kynB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynB in Cupriavidus basilensis 4G11

Align Kynurenine formamidase; KFA; KFase; Arylformamidase; N-formylkynurenine formamidase; FKF; EC 3.5.1.9 (characterized)
to candidate RR42_RS15380 RR42_RS15380 kynurenine formamidase

Query= SwissProt::P0C8P4
         (218 letters)



>FitnessBrowser__Cup4G11:RR42_RS15380
          Length = 221

 Score =  341 bits (874), Expect = 7e-99
 Identities = 163/207 (78%), Positives = 176/207 (85%)

Query: 11  RRIWDISPAVSPATPVWPGDTPFQHDPAWQLDEHCPVNVGRITMSPHTGAHADAPLHYAA 70
           R++WDISPA+SP TPVWPGDTPFQ +  WQ+D HCPVNVGRIT+SPHTGAHADAPLHYAA
Sbjct: 14  RQLWDISPALSPDTPVWPGDTPFQLERNWQIDAHCPVNVGRITLSPHTGAHADAPLHYAA 73

Query: 71  DGAPIGAVPLDAYLGPCRVIHCIGAAPRVEPQHIAHALAGTPPRVLLRTYAQAPQGKWDS 130
           DGAPIG V L  YLGPCRVIHCIG AP VEP+HI HALAG PPRVLLRTY QAP  KWD 
Sbjct: 74  DGAPIGEVDLAHYLGPCRVIHCIGVAPLVEPRHIGHALAGAPPRVLLRTYQQAPLAKWDP 133

Query: 131 AFCAVAPETISLLARHGVRLIGIDTPSLDPETSKTMDAHHAVRDHQLAILEGIVLDEVPA 190
            FCAVAPETI+LLA HGV L+GIDTPSLDP+ SKTM AH+ VR H+LAILEG+VLD V  
Sbjct: 134 DFCAVAPETIALLAEHGVMLVGIDTPSLDPQESKTMAAHNMVRRHRLAILEGLVLDAVAE 193

Query: 191 GDYELIALPLRLATLDASPVRAVLREL 217
            DYELIALPLR A LDASPVRAVLR L
Sbjct: 194 ADYELIALPLRFAGLDASPVRAVLRSL 220


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: 336
Number of extensions: 10
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: 218
Length of database: 221
Length adjustment: 22
Effective length of query: 196
Effective length of database: 199
Effective search space:    39004
Effective search space used:    39004
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 RR42_RS15380 RR42_RS15380 (kynurenine formamidase)
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.29835.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-103  330.4   0.0     3e-103  330.2   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS15380  RR42_RS15380 kynurenine formamid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS15380  RR42_RS15380 kynurenine formamidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.2   0.0    3e-103    3e-103       2     206 .]      16     220 ..      15     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 330.2 bits;  conditional E-value: 3e-103
                                 TIGR03035   2 lidisqplnedlatwPGdtpfsqelavsleeegsvnvgritlsvhtGahvdaPlhykndgakigdveld 70 
                                               l+dis++l++d+++wPGdtpf+ e++++++++++vnvgritls+htGah+daPlhy +dga+ig+v+l 
  lcl|FitnessBrowser__Cup4G11:RR42_RS15380  16 LWDISPALSPDTPVWPGDTPFQLERNWQIDAHCPVNVGRITLSPHTGAHADAPLHYAADGAPIGEVDLA 84 
                                               8******************************************************************** PP

                                 TIGR03035  71 vylGpcrvidclsalekiekealksaleeapervllrtaekakaeafdediaavapdtiellaekGvrl 139
                                                ylGpcrvi+c+++++++e++++ +al++ap+rvllrt+++a+  ++d d++avap+ti+llae+Gv l
  lcl|FitnessBrowser__Cup4G11:RR42_RS15380  85 HYLGPCRVIHCIGVAPLVEPRHIGHALAGAPPRVLLRTYQQAPLAKWDPDFCAVAPETIALLAEHGVML 153
                                               ********************************************************************* PP

                                 TIGR03035 140 iGvdtpsvdPleskeldahhalakhdlailenlvldevaeGdyelialPlklaeldaspvravlral 206
                                               +G+dtps+dP+esk+++ah+ +++h+laile+lvld vae dyelialPl++a ldaspvravlr+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS15380 154 VGIDTPSLDPQESKTMAAHNMVRRHRLAILEGLVLDAVAEADYELIALPLRFAGLDASPVRAVLRSL 220
                                               *****************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (206 nodes)
Target sequences:                          1  (221 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: 7.64
//
[ok]

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

Downloads

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

Related tools

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