GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aguB in Pseudomonas fluorescens FW300-N1B4

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate Pf1N1B4_1662 N-carbamoylputrescine amidase (3.5.1.53) / Aliphatic amidase AmiE (EC 3.5.1.4)

Query= SwissProt::Q8VYF5
         (299 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662 N-carbamoylputrescine
           amidase (3.5.1.53) / Aliphatic amidase AmiE (EC 3.5.1.4)
          Length = 292

 Score =  375 bits (963), Expect = e-109
 Identities = 183/292 (62%), 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   RIVTVAATQMACSWDLEANIETAEKLVREAAAKGAQIILIQELFEAPYFCQKPNPDYLQL 62

Query: 68  AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127
           A   +++  I   QK+AKEL VV+P+SF+E A  A +NSIAIIDADG++LGIYRKSHIPD
Sbjct: 63  ATTVEDNVAIKHFQKVAKELQVVLPISFYELAGRARFNSIAIIDADGSNLGIYRKSHIPD 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 EPHDKTISSRDHWQRVQQGHAGANLMPLIASNRIGNE----EQDGYDITFYGSSFIANQF 238

Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDGNL 299
           GE V E ++  E +LV  FDLD ++  R +WG FRDRRP+LY  + T+DG+L
Sbjct: 239 GEKVQELNETEEGILVHSFDLDELEHIRSAWGSFRDRRPNLYGAIKTLDGSL 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 Pf1N1B4_1662 (N-carbamoylputrescine amidase (3.5.1.53) / Aliphatic amidase AmiE (EC 3.5.1.4))
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.2528.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.3e-151  488.3   0.0   3.7e-151  488.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662  N-carbamoylputrescine amidase (3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662  N-carbamoylputrescine amidase (3.5.1.53) / Aliphatic amidase AmiE (EC 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.1   0.0  3.7e-151  3.7e-151       1     278 [.       5     282 ..       5     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 488.1 bits;  conditional E-value: 3.7e-151
                                      TIGR03381   1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpvee 64 
                                                    v+vaa+q+a+s+d+e+nie+aeklvreaaakGaqiil++elfeapyfc++ + +y++la++ve+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662   5 VTVAATQMACSWDLEANIETAEKLVREAAAKGAQIILIQELFEAPYFCQKPNPDYLQLATTVED 68 
                                                    79************************************************************** PP

                                      TIGR03381  65 hplikrlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyf 128
                                                    + +ik++qk+akel+vvlp+sf+e ag+a++ns+a+idadG++lg+yrkshiPdgpgy+ek+yf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662  69 NVAIKHFQKVAKELQVVLPISFYELAGRARFNSIAIIDADGSNLGIYRKSHIPDGPGYHEKYYF 132
                                                    **************************************************************** PP

                                      TIGR03381 129 kpGdtGfkvwdtryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWq 192
                                                    +pGdtGfkvw+tryakiGvgicWdqWfpe+ar++al+Gae+l+yPtaiGseP+d++++s++hWq
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662 133 NPGDTGFKVWNTRYAKIGVGICWDQWFPECARSMALQGAEILFYPTAIGSEPHDKTISSRDHWQ 196
                                                    **************************************************************** PP

                                      TIGR03381 193 ramqGhaaanvvpvvaanrigkeveaeleltfyGssfiadetGelvaeadrseeavlvaefdld 256
                                                    r++qGha an++p++a+nrig+e+++++++tfyGssfia++ Ge+v+e++++ee++lv++fdld
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662 197 RVQQGHAGANLMPLIASNRIGNEEQDGYDITFYGSSFIANQFGEKVQELNETEEGILVHSFDLD 260
                                                    **************************************************************** PP

                                      TIGR03381 257 eiakeraawGlfrdrrpelyek 278
                                                    e+++ r+awG frdrrp+ly +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1662 261 ELEHIRSAWGSFRDRRPNLYGA 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.56
//
[ok]

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

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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