GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguB in Sphingobium czechense LL01

Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate WP_066603038.1 V473_RS09535 N-carbamoylputrescine amidase

Query= SwissProt::Q9XGI9
         (300 letters)



>NCBI__GCF_001046645.1:WP_066603038.1
          Length = 282

 Score =  313 bits (802), Expect = 3e-90
 Identities = 156/280 (55%), Positives = 190/280 (67%), Gaps = 8/280 (2%)

Query: 8   VTVAALQFACTDDVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAK 67
           VTVAALQ + +DD+  N+A     VR A  +GA IIL  ELFEG YFC+ + E  F  A+
Sbjct: 4   VTVAALQLSFSDDMGENIAKVADHVRKAASRGAKIILPPELFEGPYFCRVEDEALFASAQ 63

Query: 68  PYPGHPTIVRMQNLAKELGVVIPVSFFEEANNAHYNSVAIIDADGTDLGLYRKSHIPDGP 127
           P   HP +  M+ LAK+LGV IP SFFE   + HYNS+A+ID  G  +G+YRKSHIPDGP
Sbjct: 64  PIDTHPAVQEMRKLAKQLGVYIPTSFFERDGHHHYNSLAMIDDAGEIMGVYRKSHIPDGP 123

Query: 128 GYQEKYYFNPGDTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGSEP 187
           GY+EKYYF PG+TGFKV+ TKY  IGV ICWDQW+PE AR MAL GAE+LFYPTAIGSEP
Sbjct: 124 GYEEKYYFRPGNTGFKVWSTKYGTIGVGICWDQWYPETARCMALMGAEMLFYPTAIGSEP 183

Query: 188 QDDGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPTGE 247
            D  LD+   WRR M GHA +N +P++A+NRIG E            FYG+SFI    G+
Sbjct: 184 YDSELDTSRMWRRAMIGHAVSNCMPVIAANRIGDE--------DGQLFYGHSFITDEWGD 235

Query: 248 LVAAAGDKEEAVLVAQFDLDKIKSKRHGWGVYRDRRPDLY 287
             A A  K++  LVA  DL K +  R G G +RDRRP+LY
Sbjct: 236 FAAEADAKDQGALVATLDLAKARMHRAGMGFFRDRRPELY 275


Lambda     K      H
   0.319    0.137    0.414 

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: 302
Number of extensions: 10
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: 300
Length of database: 282
Length adjustment: 26
Effective length of query: 274
Effective length of database: 256
Effective search space:    70144
Effective search space used:    70144
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 WP_066603038.1 V473_RS09535 (N-carbamoylputrescine amidase)
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.1902163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-139  448.8   0.0     4e-139  448.6   0.0    1.0  1  NCBI__GCF_001046645.1:WP_066603038.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046645.1:WP_066603038.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.6   0.0    4e-139    4e-139       1     279 []       4     278 ..       4     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 448.6 bits;  conditional E-value: 4e-139
                             TIGR03381   1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplikrlqk 73 
                                           v+vaa+ql++s+d+ eni+k++++vr+aa++Ga+iil+pelfe+pyfc+ ++e+ f+ a+p++ hp++++++k
  NCBI__GCF_001046645.1:WP_066603038.1   4 VTVAALQLSFSDDMGENIAKVADHVRKAASRGAKIILPPELFEGPYFCRVEDEALFASAQPIDTHPAVQEMRK 76 
                                           79*********************************************************************** PP

                             TIGR03381  74 lakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvwdtryakiG 146
                                           lak+l+v +p+sffe++g+++ynsla+id  Ge++gvyrkshiPdgpgyeek+yf+pG+tGfkvw t+y+ iG
  NCBI__GCF_001046645.1:WP_066603038.1  77 LAKQLGVYIPTSFFERDGHHHYNSLAMIDDAGEIMGVYRKSHIPDGPGYEEKYYFRPGNTGFKVWSTKYGTIG 149
                                           ************************************************************************* PP

                             TIGR03381 147 vgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveae 219
                                           vgicWdqW+pe+ar++al+Gae+l+yPtaiGseP+d+eld++++W+ram Gha++n++pv+aanrig+e    
  NCBI__GCF_001046645.1:WP_066603038.1 150 VGICWDQWYPETARCMALMGAEMLFYPTAIGSEPYDSELDTSRMWRRAMIGHAVSNCMPVIAANRIGDE---- 218
                                           *********************************************************************.... PP

                             TIGR03381 220 leltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpelyekl 279
                                             + fyG+sfi+de+G+  aead ++++ lva++dl++++ +ra +G+frdrrpely ++
  NCBI__GCF_001046645.1:WP_066603038.1 219 DGQLFYGHSFITDEWGDFAAEADAKDQGALVATLDLAKARMHRAGMGFFRDRRPELYGRI 278
                                           6899*****************************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (282 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.04
//
[ok]

This GapMind analysis is from Sep 24 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