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.27740.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.19 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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