GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguB in Caulobacter crescentus NA1000

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate CCNA_00212 CCNA_00212 N-carbamoylputrescine amidase

Query= SwissProt::Q8VYF5
         (299 letters)



>FitnessBrowser__Caulo:CCNA_00212
          Length = 292

 Score =  322 bits (825), Expect = 6e-93
 Identities = 152/285 (53%), Positives = 200/285 (70%), Gaps = 1/285 (0%)

Query: 8   REVVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKR 67
           R + V+++Q +   D+  N+   E  +REA +KGA +IL  ELF+G YFC AQ E +F +
Sbjct: 3   RTLSVAAIQTSYGMDLQANIKKTEGFIREAASKGAQVILPSELFQGPYFCVAQEERWFAQ 62

Query: 68  AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127
           A P++ HP +  +  LA ELGVVIP+S FE     ++NS+ + DADG+ +G+YRKSHIPD
Sbjct: 63  AHPWREHPVVKAIAPLAGELGVVIPISIFEREGPHYFNSLVMADADGSLMGVYRKSHIPD 122

Query: 128 GPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGS 187
           GPGY EK+YF PGDTGFKV+ T+F +IGV ICWDQW+PE ARAM L GAE LFYPTAIGS
Sbjct: 123 GPGYMEKYYFRPGDTGFKVWDTRFGRIGVGICWDQWYPECARAMALMGAEALFYPTAIGS 182

Query: 188 EPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPT 247
           EP D  LD+   WRR MQGHA +NV+P++ +NRIG E  +      Q TFYG+SF+A   
Sbjct: 183 EPHDASLDTALPWRRAMQGHAVSNVIPVIGANRIGFEPWDGYPNGGQ-TFYGSSFVADHR 241

Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVL 292
           G++V+E     E ++ A FDLD + + R +WG FRDRRP+LY  L
Sbjct: 242 GDLVSELGRADEGLVSATFDLDFLTTHRAAWGFFRDRRPELYTAL 286


Lambda     K      H
   0.321    0.137    0.410 

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: 339
Number of extensions: 9
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: 299
Length of database: 292
Length adjustment: 26
Effective length of query: 273
Effective length of database: 266
Effective search space:    72618
Effective search space used:    72618
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 CCNA_00212 CCNA_00212 (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.10641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-139  447.8   0.0   8.5e-139  447.6   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00212  CCNA_00212 N-carbamoylputrescine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00212  CCNA_00212 N-carbamoylputrescine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.6   0.0  8.5e-139  8.5e-139       2     279 .]       6     286 ..       5     286 .. 0.98

  Alignments for each domain:
  == domain 1  score: 447.6 bits;  conditional E-value: 8.5e-139
                             TIGR03381   2 kvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplikrlqkl 74 
                                           +vaa+q ++  d+++ni+k e ++reaa+kGaq+il+ elf++pyfc +qee++f++a+p++ehp++k+++ l
  lcl|FitnessBrowser__Caulo:CCNA_00212   6 SVAAIQTSYGMDLQANIKKTEGFIREAASKGAQVILPSELFQGPYFCVAQEERWFAQAHPWREHPVVKAIAPL 78 
                                           79*********************************************************************** PP

                             TIGR03381  75 akelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvwdtryakiGv 147
                                           a el+vv+p+s+fe++g +++nsl+++dadG+ +gvyrkshiPdgpgy+ek+yf+pGdtGfkvwdtr+++iGv
  lcl|FitnessBrowser__Caulo:CCNA_00212  79 AGELGVVIPISIFEREGPHYFNSLVMADADGSLMGVYRKSHIPDGPGYMEKYYFRPGDTGFKVWDTRFGRIGV 151
                                           ************************************************************************* PP

                             TIGR03381 148 gicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveae. 219
                                           gicWdqW+pe+ara+al+Gae l+yPtaiGseP+da+ld++  W+ramqGha++nv+pv+ anrig e  ++ 
  lcl|FitnessBrowser__Caulo:CCNA_00212 152 GICWDQWYPECARAMALMGAEALFYPTAIGSEPHDASLDTALPWRRAMQGHAVSNVIPVIGANRIGFEPWDGy 224
                                           ********************************************************************76655 PP

                             TIGR03381 220 ..leltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpelyekl 279
                                               +tfyGssf+ad++G+lv+e++r +e+++ a+fdld ++++raawG+frdrrpely++l
  lcl|FitnessBrowser__Caulo:CCNA_00212 225 pnGGQTFYGSSFVADHRGDLVSELGRADEGLVSATFDLDFLTTHRAAWGFFRDRRPELYTAL 286
                                           5589*******************************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (292 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: 00:00:00.00
# Mc/sec: 10.96
//
[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