Alignments for a candidate for aguB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguB in Pseudomonas fluorescens FW300-N2E3

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate AO353_11910 AO353_11910 N-carbamoylputrescine amidase

Query= SwissProt::Q8VYF5
         (299 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11910
          Length = 292

 Score =  377 bits (968), Expect = e-109
 Identities = 185/292 (63%), Positives = 222/292 (76%), Gaps = 4/292 (1%)

Query: 8   REVVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKR 67
           R V V++ Q ACS D+  N+  AE+LVREA AKGA IILIQELFE  YFCQ    D+ + 
Sbjct: 3   RIVTVAATQMACSWDLEANIETAEKLVREAAAKGAQIILIQELFETPYFCQKPNPDYLQL 62

Query: 68  AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127
           A   +++  I   QK+AKEL VV+P+SFFE A  A +NSIAIIDADG++LGIYRKSHIPD
Sbjct: 63  ATSVEDNVAIKHFQKVAKELQVVLPISFFELAGRARFNSIAIIDADGSNLGIYRKSHIPD 122

Query: 128 GPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGS 187
           GPGY EK+YFNPGDTGFKV+ T++AKIGV ICWDQWFPE AR+M LQGAEILFYPTAIGS
Sbjct: 123 GPGYHEKYYFNPGDTGFKVWNTRYAKIGVGICWDQWFPECARSMALQGAEILFYPTAIGS 182

Query: 188 EPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPT 247
           EP D+ + SRDHW+RV QGHAGAN++PL+ASNRIG E    E     ITFYG+SFIA   
Sbjct: 183 EPHDKSISSRDHWQRVQQGHAGANLMPLIASNRIGNE----EQDGYDITFYGSSFIANQF 238

Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDGNL 299
           GE V E ++  E VLV  FDLD ++  R +WG FRDRRP+LY  + T+DG+L
Sbjct: 239 GEKVQELNETEEGVLVQSFDLDELEHIRSAWGSFRDRRPNLYGAIKTLDGSL 290


Lambda     K      H
   0.321    0.137    0.410 

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: 302
Number of extensions: 5
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: 299
Length of database: 292
Length adjustment: 26
Effective length of query: 273
Effective length of database: 266
Effective search space:    72618
Effective search space used:    72618
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: 48 (23.1 bits)

Align candidate AO353_11910 AO353_11910 (N-carbamoylputrescine amidase)
to HMM TIGR03381 (aguB: N-carbamoylputrescine amidase (EC 3.5.1.53))

# 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/TIGR03381.hmm
# target sequence database:        /tmp/gapView.26310.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03381  [M=279]
Accession:   TIGR03381
Description: agmatine_aguB: N-carbamoylputrescine amidase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.1e-151  488.0   0.0   4.6e-151  487.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910  AO353_11910 N-carbamoylputrescin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910  AO353_11910 N-carbamoylputrescine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.8   0.0  4.6e-151  4.6e-151       1     278 [.       5     282 ..       5     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.8 bits;  conditional E-value: 4.6e-151
                                     TIGR03381   1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveeh 65 
                                                   v+vaa+q+a+s+d+e+nie+aeklvreaaakGaqiil++elfe+pyfc++ + +y++la++ve++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910   5 VTVAATQMACSWDLEANIETAEKLVREAAAKGAQIILIQELFETPYFCQKPNPDYLQLATSVEDN 69 
                                                   79*************************************************************** PP

                                     TIGR03381  66 plikrlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkp 130
                                                    +ik++qk+akel+vvlp+sffe ag+a++ns+a+idadG++lg+yrkshiPdgpgy+ek+yf+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910  70 VAIKHFQKVAKELQVVLPISFFELAGRARFNSIAIIDADGSNLGIYRKSHIPDGPGYHEKYYFNP 134
                                                   ***************************************************************** PP

                                     TIGR03381 131 GdtGfkvwdtryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqram 195
                                                   GdtGfkvw+tryakiGvgicWdqWfpe+ar++al+Gae+l+yPtaiGseP+d++++s++hWqr++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910 135 GDTGFKVWNTRYAKIGVGICWDQWFPECARSMALQGAEILFYPTAIGSEPHDKSISSRDHWQRVQ 199
                                                   ***************************************************************** PP

                                     TIGR03381 196 qGhaaanvvpvvaanrigkeveaeleltfyGssfiadetGelvaeadrseeavlvaefdldeiak 260
                                                   qGha an++p++a+nrig+e+++++++tfyGssfia++ Ge+v+e++++ee+vlv++fdlde+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910 200 QGHAGANLMPLIASNRIGNEEQDGYDITFYGSSFIANQFGEKVQELNETEEGVLVQSFDLDELEH 264
                                                   ***************************************************************** PP

                                     TIGR03381 261 eraawGlfrdrrpelyek 278
                                                    r+awG frdrrp+ly +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_11910 265 IRSAWGSFRDRRPNLYGA 282
                                                   ****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (292 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.40
//
[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