Aligments for a candidate for aguB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for aguB in Pseudomonas fluorescens GW456-L13

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate PfGW456L13_2704 N-carbamoylputrescine amidase (3.5.1.53)

Query= SwissProt::Q8VYF5
         (299 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704
          Length = 302

 Score =  317 bits (811), Expect = 3e-91
 Identities = 149/288 (51%), Positives = 206/288 (71%), Gaps = 1/288 (0%)

Query: 10  VVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKRAK 69
           + +++ Q  C+ D+  N+  AE+LVREA AKGA +IL+QELF   YFC  Q       A+
Sbjct: 4   LTIATTQMPCTWDLKHNLDQAEQLVREAAAKGAQVILLQELFATPYFCIEQHHKHLALAE 63

Query: 70  PYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPDGP 129
            Y+    + R   LAKELGVV+P+S++E+A  A++NS+++ DADG  LG+YRK+HIP+  
Sbjct: 64  EYRESHVLQRFAALAKELGVVLPLSWYEKAGNAYFNSLSVADADGRLLGVYRKTHIPNAI 123

Query: 130 GYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGSEP 189
           GYQEK YF+PGD+GF+V+ T F +IG+ ICWDQWFPE AR + L GAE+L +PTAIGSEP
Sbjct: 124 GYQEKEYFSPGDSGFRVWDTAFGRIGLGICWDQWFPETARCLALMGAEVLLFPTAIGSEP 183

Query: 190 QDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPTGE 249
               LDSRDHW+  M+GHA AN++P+VA+NR+G+E   T+    Q++FYG+SFI    G+
Sbjct: 184 GCATLDSRDHWQMTMRGHAAANLLPVVAANRVGREAATTD-PTLQMSFYGSSFICNHKGK 242

Query: 250 IVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDG 297
           ++AEAD  S  VLV   DL  ++  R +WG++RDRRP++Y  LLT DG
Sbjct: 243 LLAEADRDSTGVLVHSLDLAAMREDRLTWGIYRDRRPEMYGALLTQDG 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: 286
Number of extensions: 9
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: 302
Length adjustment: 27
Effective length of query: 272
Effective length of database: 275
Effective search space:    74800
Effective search space used:    74800
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 PfGW456L13_2704 (N-carbamoylputrescine amidase (3.5.1.53))
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.22781.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   6.8e-140  451.2   0.0   7.9e-140  451.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704  N-carbamoylputrescine amidase (3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704  N-carbamoylputrescine amidase (3.5.1.53)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.0   0.0  7.9e-140  7.9e-140       2     278 ..       5     284 ..       4     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 451.0 bits;  conditional E-value: 7.9e-140
                                               TIGR03381   2 kvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyf 56 
                                                             ++a++q+ +++d+++n+++ae+lvreaaakGaq+ill+elf++pyfc eq+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704   5 TIATTQMPCTWDLKHNLDQAEQLVREAAAKGAQVILLQELFATPYFCIEQHHKHL 59 
                                                             89***************************************************** PP

                                               TIGR03381  57 elakpveehplikrlqklakelevvlpvsffekagnalynslavidadGevlgvy 111
                                                             +la++++e+++++r+++lakel+vvlp+s++ekagna++nsl v+dadG+ lgvy
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704  60 ALAEEYRESHVLQRFAALAKELGVVLPLSWYEKAGNAYFNSLSVADADGRLLGVY 114
                                                             ******************************************************* PP

                                               TIGR03381 112 rkshiPdgpgyeekfyfkpGdtGfkvwdtryakiGvgicWdqWfpeaaralalkG 166
                                                             rk+hiP+++gy+ek yf+pGd+Gf+vwdt++++iG+gicWdqWfpe+ar+lal+G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704 115 RKTHIPNAIGYQEKEYFSPGDSGFRVWDTAFGRIGLGICWDQWFPETARCLALMG 169
                                                             ******************************************************* PP

                                               TIGR03381 167 aevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveae.. 219
                                                             aevll+PtaiGseP  a+lds++hWq +m+Ghaaan++pvvaanr+g+e++++  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704 170 AEVLLFPTAIGSEPGCATLDSRDHWQMTMRGHAAANLLPVVAANRVGREAATTdp 224
                                                             *************************************************776566 PP

                                               TIGR03381 220 .leltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrp 273
                                                              l+++fyGssfi++++G+l+aeadr+ ++vlv+++dl++++++r +wG++rdrrp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704 225 tLQMSFYGSSFICNHKGKLLAEADRDSTGVLVHSLDLAAMREDRLTWGIYRDRRP 279
                                                             699**************************************************** PP

                                               TIGR03381 274 elyek 278
                                                             e+y +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704 280 EMYGA 284
                                                             ***86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (302 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: 00:00:00.00
# Mc/sec: 8.61
//
[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, 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

GapMind for catabolism of small carbon sources