Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate GFF4217 Psest_4290 N-carbamoylputrescine amidase
Query= SwissProt::Q8VYF5 (299 letters) >FitnessBrowser__psRCH2:GFF4217 Length = 293 Score = 376 bits (966), Expect = e-109 Identities = 185/291 (63%), Positives = 221/291 (75%), Gaps = 4/291 (1%) Query: 8 REVVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKR 67 R V V++ Q ACS D N+A A++LVREA AKGA IILIQELFE YFCQ ++ + Sbjct: 3 RVVTVAATQMACSWDRQANIANADKLVREAAAKGAQIILIQELFETPYFCQKPNAEYLQL 62 Query: 68 AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127 A P + +P I QK+A EL VV+P+SFFE A A +NSIAIIDADG LG+YRKSHIPD Sbjct: 63 ATPVEENPAIQHFQKVAAELQVVLPISFFELAGRARFNSIAIIDADGKLLGVYRKSHIPD 122 Query: 128 GPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGS 187 GPGY EK+YFNPGDTGFKV+ T++AKIGVAICWDQWFPE AR+M L GAE+LFYPTAIGS Sbjct: 123 GPGYHEKYYFNPGDTGFKVWNTRYAKIGVAICWDQWFPETARSMALMGAELLFYPTAIGS 182 Query: 188 EPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPT 247 EP D + SRDHW+RV QGHAGAN++PL+ASNRIG+E E ITFYG+SFIA Sbjct: 183 EPHDPNITSRDHWQRVQQGHAGANLMPLIASNRIGRE----EQDGYDITFYGSSFIADQF 238 Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDGN 298 G V E D+ SE VLV QFDLD ++ R +WGVFRDRRP+LY + T+DG+ Sbjct: 239 GAKVEEMDETSEGVLVHQFDLDQLEHIRSAWGVFRDRRPNLYGSIRTLDGS 289 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: 297 Number of extensions: 5 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: 293 Length adjustment: 26 Effective length of query: 273 Effective length of database: 267 Effective search space: 72891 Effective search space used: 72891 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 GFF4217 Psest_4290 (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.18718.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-150 486.7 0.0 1.2e-150 486.5 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF4217 Psest_4290 N-carbamoylputrescine Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF4217 Psest_4290 N-carbamoylputrescine amidase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 486.5 0.0 1.2e-150 1.2e-150 1 278 [. 5 282 .. 5 283 .. 0.99 Alignments for each domain: == domain 1 score: 486.5 bits; conditional E-value: 1.2e-150 TIGR03381 1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplikrlqkla 75 v+vaa+q+a+s+d ++ni++a+klvreaaakGaqiil++elfe+pyfc++ ++ey++la+pvee+p+i+++qk+a lcl|FitnessBrowser__psRCH2:GFF4217 5 VTVAATQMACSWDRQANIANADKLVREAAAKGAQIILIQELFETPYFCQKPNAEYLQLATPVEENPAIQHFQKVA 79 79************************************************************************* PP TIGR03381 76 kelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvwdtryakiGvgic 150 +el+vvlp+sffe ag+a++ns+a+idadG+ lgvyrkshiPdgpgy+ek+yf+pGdtGfkvw+tryakiGv+ic lcl|FitnessBrowser__psRCH2:GFF4217 80 AELQVVLPISFFELAGRARFNSIAIIDADGKLLGVYRKSHIPDGPGYHEKYYFNPGDTGFKVWNTRYAKIGVAIC 154 *************************************************************************** PP TIGR03381 151 WdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveaeleltfy 225 WdqWfpe+ar++al+Gae+l+yPtaiGseP+d+++ s++hWqr++qGha an++p++a+nrig+e+++++++tfy lcl|FitnessBrowser__psRCH2:GFF4217 155 WDQWFPETARSMALMGAELLFYPTAIGSEPHDPNITSRDHWQRVQQGHAGANLMPLIASNRIGREEQDGYDITFY 229 *************************************************************************** PP TIGR03381 226 GssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpelyek 278 Gssfiad+ G++v+e+d++ e+vlv++fdld++++ r+awG+frdrrp+ly + lcl|FitnessBrowser__psRCH2:GFF4217 230 GSSFIADQFGAKVEEMDETSEGVLVHQFDLDQLEHIRSAWGVFRDRRPNLYGS 282 ***************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (279 nodes) Target sequences: 1 (293 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.34 // [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