Alignments for a candidate for aguA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for aguA in Pseudomonas simiae WCS417

Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate GFF263 PS417_01340 agmatine deiminase

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



>FitnessBrowser__WCS417:GFF263
          Length = 368

 Score =  711 bits (1834), Expect = 0.0
 Identities = 333/366 (90%), Positives = 352/366 (96%)

Query: 1   MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60
           MTTLHSTPRADGF MPAEWA QTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV
Sbjct: 1   MTTLHSTPRADGFRMPAEWAPQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60

Query: 61  TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120
           TVAVSA QYENARARLDVPNIR+VEMSSDDAWVRDTGPTFVINDSGEVRGV+WDFNAWGG
Sbjct: 61  TVAVSAGQYENARARLDVPNIRVVEMSSDDAWVRDTGPTFVINDSGEVRGVNWDFNAWGG 120

Query: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180
           FDGGLY+PWNRDSQV  K+LEIER+PRYRTEGFVLEGGSIHVDGEGT+ITTEECLLNRNR
Sbjct: 121 FDGGLYSPWNRDSQVGGKILEIERTPRYRTEGFVLEGGSIHVDGEGTLITTEECLLNRNR 180

Query: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240
           NPH+ R +IEAVLSA LAVDK+IWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQ+
Sbjct: 181 NPHLDRAEIEAVLSANLAVDKIIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQD 240

Query: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300
           PNY RCHAAMDVLQ+STDA+GR FTVHKMPIPGP+YATEEEC GVD V+G+QERNPTVRL
Sbjct: 241 PNYARCHAAMDVLQSSTDAQGRSFTVHKMPIPGPLYATEEECEGVDPVDGTQERNPTVRL 300

Query: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360
           AGSYVNFLIVNGGIIAPSFDDPLD+ A+ ILQ+LFPQHEVVMVPGRELLLGGGNIHCLTQ
Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPLDSQAKAILQDLFPQHEVVMVPGRELLLGGGNIHCLTQ 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: 683
Number of extensions: 16
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 GFF263 PS417_01340 (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.15334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-178  579.1   0.0   1.7e-178  578.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF263  PS417_01340 agmatine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF263  PS417_01340 agmatine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.9   0.0  1.7e-178  1.7e-178       1     357 []       6     364 ..       6     364 .. 0.99

  Alignments for each domain:
  == domain 1  score: 578.9 bits;  conditional E-value: 1.7e-178
                          TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpe.ei 75 
                                        +tp++dgfr+Pae+++q++vw+iWPerpDnWr g+kpaq+a+++vakaia++epvtv+vs+ qyenar++l+  +i
  lcl|FitnessBrowser__WCS417:GFF263   6 STPRADGFRMPAEWAPQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPVTVAVSAGQYENARARLDVpNI 81 
                                        58*********************************************************************966** PP

                          TIGR03380  76 rvvemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryra.dlvleg 150
                                        rvvemss+Daw+rD+GPtfv+nd+ge+rgv+w+fnawgg+++Gly+pW++D++v  k+le+er++ryr+  +vleg
  lcl|FitnessBrowser__WCS417:GFF263  82 RVVEMSSDDAWVRDTGPTFVINDSGEVRGVNWDFNAWGGFDGGLYSPWNRDSQVGGKILEIERTPRYRTeGFVLEG 157
                                        *********************************************************************89***** PP

                          TIGR03380 151 gsihvDGeGtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGevvls 226
                                        gsihvDGeGtl+tteeclL+++rnp+l ++eie++l + l+v+k+iWl++Gl++det+GhvDn++++vrPGev+l+
  lcl|FitnessBrowser__WCS417:GFF263 158 GSIHVDGEGTLITTEECLLNRNRNPHLDRAEIEAVLSANLAVDKIIWLPDGLFNDETDGHVDNFCCYVRPGEVLLA 233
                                        **************************************************************************** PP

                          TIGR03380 227 wtddesdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyli 302
                                        wtdd +dP+y+++++a++vL+++tDa+Gr ++vhk+++p+pl++teee++gvd v+gt++r++  rla+syvn+li
  lcl|FitnessBrowser__WCS417:GFF263 234 WTDDPQDPNYARCHAAMDVLQSSTDAQGRSFTVHKMPIPGPLYATEEECEGVDPVDGTQERNPTVRLAGSYVNFLI 309
                                        **************************************************************************** PP

                          TIGR03380 303 ankaiilPlfddekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357
                                        +n++ii+P+fdd+ D++ak++lq+lfP+++vv+v+ re+llgGGnihc+tqq+pa
  lcl|FitnessBrowser__WCS417:GFF263 310 VNGGIIAPSFDDPLDSQAKAILQDLFPQHEVVMVPGRELLLGGGNIHCLTQQQPA 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: 7.98
//
[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
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