GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguA in Shewanella oneidensis MR-1

Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 200073 SO_0887 agmatine deiminase (RefSeq)

Query= BRENDA::Q9I6J9
         (368 letters)



>FitnessBrowser__MR1:200073
          Length = 370

 Score =  419 bits (1076), Expect = e-122
 Identities = 206/361 (57%), Positives = 251/361 (69%), Gaps = 5/361 (1%)

Query: 5   TSTPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCA 64
           T+ P  DGF MPAEW   +  WM+WP RPDNWR  G  AQA FA V  AI    PV +  
Sbjct: 12  TTKPSQDGFYMPAEWAAQQAVWMIWPYRPDNWRAAGAYAQATFAKVVDAIGAATPVYMGV 71

Query: 65  SAGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGG 124
                  A+  +   ++ +VE+ S+D W RDTGPT V++ +G+ RGVDWGFNAWGG  GG
Sbjct: 72  PKAFLAKAKTVMPS-HVTLVEMDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGG 130

Query: 125 LYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHL 184
           LYFPW +D+QVA+++L     ARYR    +LEGGSIHVDGEGT +T+ ECLLN NRNP L
Sbjct: 131 LYFPWDKDEQVAQQMLAQHGFARYRAP-LILEGGSIHVDGEGTCMTSAECLLNANRNPEL 189

Query: 185 SQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYL 244
           ++ +IE  LRDYL V+  IWL +G+Y DETDGH+DN CC+ARPGEV+L WTDD+ DP Y 
Sbjct: 190 TKEQIEGLLRDYLNVKQFIWLQDGVYMDETDGHIDNMCCFARPGEVILHWTDDESDPQYP 249

Query: 245 RCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGS-QPRDPSIRLAGS 303
           R +AAL VL+ + DA+GRKL +H +P PGPLY ++EE  GV   EG+  PR    RLAGS
Sbjct: 250 RSKAALEVLQNTVDAQGRKLKIHLLPQPGPLYCSEEESKGV--TEGTGVPRTAGERLAGS 307

Query: 304 YVNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQP 363
           YVNFLI N  I+ P  D   D  A   LQ +FPEHE+V VP REILLGGGNIHCITQQ P
Sbjct: 308 YVNFLITNHRIVFPLLDPATDDIAAQKLQEIFPEHEIVGVPAREILLGGGNIHCITQQIP 367

Query: 364 A 364
           A
Sbjct: 368 A 368


Lambda     K      H
   0.319    0.138    0.439 

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: 527
Number of extensions: 21
Number of successful extensions: 4
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: 370
Length adjustment: 30
Effective length of query: 338
Effective length of database: 340
Effective search space:   114920
Effective search space used:   114920
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 200073 SO_0887 (agmatine deiminase (RefSeq))
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.21224.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     8e-180  583.3   0.0   9.3e-180  583.1   0.0    1.0  1  lcl|FitnessBrowser__MR1:200073  SO_0887 agmatine deiminase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200073  SO_0887 agmatine deiminase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.1   0.0  9.3e-180  9.3e-180       1     357 []      13     368 ..      13     368 .. 1.00

  Alignments for each domain:
  == domain 1  score: 583.1 bits;  conditional E-value: 9.3e-180
                       TIGR03380   1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpeeirvve 79 
                                     t+p++dgf++Pae+++q++vw+iWP+rpDnWr+++ +aq++fa+v++ai  ++pv++ v+k+++++a++++p+++++ve
  lcl|FitnessBrowser__MR1:200073  13 TKPSQDGFYMPAEWAAQQAVWMIWPYRPDNWRAAGAYAQATFAKVVDAIGAATPVYMGVPKAFLAKAKTVMPSHVTLVE 91 
                                     589**************************************************************************** PP

                       TIGR03380  80 mssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryradlvleggsihvDGe 158
                                     m+snD+w rD+GPt+vvn +ge+rgvdw fnawgg+++GlyfpWdkD++va+++l+ ++ +ryra+l+leggsihvDGe
  lcl|FitnessBrowser__MR1:200073  92 MDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGGLYFPWDKDEQVAQQMLAQHGFARYRAPLILEGGSIHVDGE 170
                                     ******************************************************************************* PP

                       TIGR03380 159 GtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtddesdPqye 237
                                     Gt++t++eclL+ +rnpel+ke+ie  l++yl+v+++iWl++G+y+det+Gh+Dn+++f+rPGev+l+wtddesdPqy 
  lcl|FitnessBrowser__MR1:200073 171 GTCMTSAECLLNANRNPELTKEQIEGLLRDYLNVKQFIWLQDGVYMDETDGHIDNMCCFARPGEVILHWTDDESDPQYP 249
                                     ******************************************************************************* PP

                       TIGR03380 238 iskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaiilPlfddek 316
                                     +sk+alevL+n++Da+Grklk+h l++p+pl+++eee+kgv++ +g +pr+agerla+syvn+li+n++i++Pl+d ++
  lcl|FitnessBrowser__MR1:200073 250 RSKAALEVLQNTVDAQGRKLKIHLLPQPGPLYCSEEESKGVTEGTG-VPRTAGERLAGSYVNFLITNHRIVFPLLDPAT 327
                                     **********************************************.******************************** PP

                       TIGR03380 317 DkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357
                                     D++a+++lqe+fP++++vgv+areillgGGnihcitqqipa
  lcl|FitnessBrowser__MR1:200073 328 DDIAAQKLQEIFPEHEIVGVPAREILLGGGNIHCITQQIPA 368
                                     ***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (370 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: 7.83
//
[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:

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