Alignments for a candidate for aguA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguA in Pseudomonas fluorescens GW456-L13

Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PfGW456L13_397 Agmatine deiminase (EC 3.5.3.12)

Query= reanno::pseudo5_N2C3_1:AO356_10030
         (368 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397
          Length = 368

 Score =  707 bits (1826), Expect = 0.0
 Identities = 331/366 (90%), Positives = 352/366 (96%)

Query: 1   MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60
           MTTL+STPRADGF+MPAEWA QTQ WMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV
Sbjct: 1   MTTLNSTPRADGFYMPAEWAPQTQTWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60

Query: 61  TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120
           TVAVSA QYENARARLDVPNIR+VEMSSDDAWVRD+GPTFVIN+SGEVRGV+WDFNAWGG
Sbjct: 61  TVAVSAGQYENARARLDVPNIRVVEMSSDDAWVRDSGPTFVINNSGEVRGVNWDFNAWGG 120

Query: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180
           FDGGLY+PWNRDSQV  K+LEIERSPRYRTEGFVLEGGSIHVDGEGT+ITTEECLLNRNR
Sbjct: 121 FDGGLYSPWNRDSQVGGKILEIERSPRYRTEGFVLEGGSIHVDGEGTLITTEECLLNRNR 180

Query: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240
           NPHM+R +IEAVLSA LAVDK+IWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQ+
Sbjct: 181 NPHMNRAEIEAVLSANLAVDKIIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQD 240

Query: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300
           PNY RC AAM  LQ+STDAKGRPFTVHKMPIPGP++ATEEECAGVD V+G+QERNPTVRL
Sbjct: 241 PNYPRCQAAMKALQSSTDAKGRPFTVHKMPIPGPLFATEEECAGVDPVDGTQERNPTVRL 300

Query: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360
           AGSYVNFLIVNGGIIAPSFDDP D PA++ILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ
Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPQDGPAKEILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360

Query: 361 QQPAPY 366
           QQPAP+
Sbjct: 361 QQPAPH 366


Lambda     K      H
   0.318    0.136    0.431 

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: 689
Number of extensions: 19
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate PfGW456L13_397 (Agmatine deiminase (EC 3.5.3.12))
to HMM TIGR03380 (aguA: agmatine deiminase (EC 3.5.3.12))

# 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/TIGR03380.hmm
# target sequence database:        /tmp/gapView.25628.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03380  [M=357]
Accession:   TIGR03380
Description: agmatine_aguA: agmatine deiminase
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-177  574.7   0.0   3.8e-177  574.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397  Agmatine deiminase (EC 3.5.3.12)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397  Agmatine deiminase (EC 3.5.3.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.5   0.0  3.8e-177  3.8e-177       1     357 []       6     364 ..       6     364 .. 0.99

  Alignments for each domain:
  == domain 1  score: 574.5 bits;  conditional E-value: 3.8e-177
                                              TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvt 56 
                                                            +tp++dgf++Pae+++q+++w+iWPerpDnWr g+kpaq+a+++vakaia++epvt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397   6 STPRADGFYMPAEWAPQTQTWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPVT 61 
                                                            58****************************************************** PP

                                              TIGR03380  57 vlvskeqyenarkalpe.eirvvemssnDawirDvGPtfvvndkgelrgvdwefna 111
                                                            v+vs+ qyenar++l+  +irvvemss+Daw+rD+GPtfv+n++ge+rgv+w+fna
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397  62 VAVSAGQYENARARLDVpNIRVVEMSSDDAWVRDSGPTFVINNSGEVRGVNWDFNA 117
                                                            ***************966************************************** PP

                                              TIGR03380 112 wgglkdGlyfpWdkDdkvarkvleleridryra.dlvleggsihvDGeGtllttee 166
                                                            wgg+++Gly+pW++D++v  k+le+er +ryr+  +vleggsihvDGeGtl+ttee
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397 118 WGGFDGGLYSPWNRDSQVGGKILEIERSPRYRTeGFVLEGGSIHVDGEGTLITTEE 173
                                                            *********************************89********************* PP

                                              TIGR03380 167 clLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGe 222
                                                            clL+++rnp+++++eie++l + l+v+k+iWl++Gl++det+GhvDn++++vrPGe
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397 174 CLLNRNRNPHMNRAEIEAVLSANLAVDKIIWLPDGLFNDETDGHVDNFCCYVRPGE 229
                                                            ******************************************************** PP

                                              TIGR03380 223 vvlswtddesdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgv 278
                                                            v+l+wtdd +dP+y ++++a++ L+++tDakGr ++vhk+++p+pl++teee++gv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397 230 VLLAWTDDPQDPNYPRCQAAMKALQSSTDAKGRPFTVHKMPIPGPLFATEEECAGV 285
                                                            ******************************************************** PP

                                              TIGR03380 279 davegtlpreagerlaasyvnyliankaiilPlfddekDkeakkllqelfPdrkvv 334
                                                            d v+gt++r++  rla+syvn+li+n++ii+P+fdd++D  ak++lq+lfP+++vv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397 286 DPVDGTQERNPTVRLAGSYVNFLIVNGGIIAPSFDDPQDGPAKEILQNLFPQHEVV 341
                                                            ******************************************************** PP

                                              TIGR03380 335 gvkareillgGGnihcitqqipa 357
                                                            +v+ re+llgGGnihc+tqq+pa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_397 342 MVPGRELLLGGGNIHCLTQQQPA 364
                                                            *********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (368 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: 00:00:00.01
# Mc/sec: 7.07
//
[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