GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aguA in Pseudomonas fluorescens FW300-N2C3

Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate AO356_10030 AO356_10030 agmatine deiminase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030 AO356_10030 agmatine
           deiminase
          Length = 368

 Score =  770 bits (1987), Expect = 0.0
 Identities = 368/368 (100%), Positives = 368/368 (100%)

Query: 1   MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60
           MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV
Sbjct: 1   MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60

Query: 61  TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120
           TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG
Sbjct: 61  TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120

Query: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180
           FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR
Sbjct: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180

Query: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240
           NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN
Sbjct: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240

Query: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300
           PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL
Sbjct: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300

Query: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360
           AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ
Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360

Query: 361 QQPAPYVK 368
           QQPAPYVK
Sbjct: 361 QQPAPYVK 368


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: 720
Number of extensions: 13
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 AO356_10030 AO356_10030 (agmatine deiminase)
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.31236.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.4e-179  581.8   0.0   2.7e-179  581.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030  AO356_10030 agmatine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030  AO356_10030 agmatine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.6   0.0  2.7e-179  2.7e-179       1     357 []       6     364 ..       6     364 .. 0.99

  Alignments for each domain:
  == domain 1  score: 581.6 bits;  conditional E-value: 2.7e-179
                                       TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeq 63 
                                                     +tp++dgf++Pae+++q++vw+iWPerpDnWr g+kpaq+a+++vakaia++epvtv+vs++q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030   6 STPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPVTVAVSAAQ 68 
                                                     58************************************************************* PP

                                       TIGR03380  64 yenarkalpe.eirvvemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdk 125
                                                     yenar++l+  +ir+vemss+Daw+rD+GPtfv+nd+ge+rgvdw+fnawgg+++Gly+pW++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030  69 YENARARLDVpNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGGFDGGLYAPWNR 131
                                                     ********966**************************************************** PP

                                       TIGR03380 126 Ddkvarkvleleridryra.dlvleggsihvDGeGtlltteeclLsegrnpelskeeieeklk 187
                                                     D++va+kvle+er +ryr+  +vleggsihvDGeGt++tteeclL+++rnp++s+e+ie++l 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030 132 DSQVASKVLEIERSPRYRTeGFVLEGGSIHVDGEGTVITTEECLLNRNRNPHMSREQIEAVLS 194
                                                     *******************89****************************************** PP

                                       TIGR03380 188 eylgvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtddesdPqyeiskealevLenet 250
                                                     + l+v+kviWl++Gl++det+GhvDn++++vrPGev+l+wtdd ++P+y+++++a++vL+n+t
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030 195 AQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQNPNYTRCHAAMDVLQNST 257
                                                     *************************************************************** PP

                                       TIGR03380 251 DakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaiilPlfd 313
                                                     DakGr ++vhk+++p+p+++teee++gvdaveg+++r++  rla+syvn+li+n++ii+P+fd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030 258 DAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRLAGSYVNFLIVNGGIIAPSFD 320
                                                     *************************************************************** PP

                                       TIGR03380 314 dekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357
                                                     d+ D+ a+++lq+lfP+++vv+v+ re+llgGGnihc+tqq+pa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10030 321 DPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQQQPA 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: 7.32
//
[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:

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. 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:

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