Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate Ga0059261_1979 Ga0059261_1979 N-carbamoylputrescine amidase
Query= SwissProt::Q9XGI9 (300 letters) >FitnessBrowser__Korea:Ga0059261_1979 Length = 284 Score = 301 bits (772), Expect = 9e-87 Identities = 152/283 (53%), Positives = 188/283 (66%), Gaps = 10/283 (3%) Query: 8 VTVAALQFACTDDVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAK 67 +TVAALQ A ++DV N+A LVR A KGA ++L ELFEG YFC+ + E F A+ Sbjct: 4 ITVAALQLAFSNDVEQNIANVTDLVREAASKGAQVVLPPELFEGEYFCRVEDEALFATAR 63 Query: 68 PYPGHPTIVRMQNLAKELGVVIPVSFFEEANNAHYNSVAIIDADGTDLGLYRKSHIPDGP 127 P HP + MQ LA EL + IP SFFE YNS+A+I DG G+YRKSHIPDGP Sbjct: 64 PLASHPAVTAMQALAAELQIHIPTSFFEADGPHFYNSLAMIGPDGKVAGVYRKSHIPDGP 123 Query: 128 GYQEKYYFNPGDTGFKVFQ--TKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGS 185 GY+EKYYF PG+TGFKV+ A +GV ICWDQW+PE AR M L GA++LFYPTAIGS Sbjct: 124 GYEEKYYFRPGNTGFKVWDGPADDAALGVGICWDQWYPETARTMMLMGAQLLFYPTAIGS 183 Query: 186 EPQDDGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPT 245 EP D LD+ WRR M GHA +NVVP++ASNRIG E + FYG+SFI Sbjct: 184 EPYDADLDTSRMWRRAMIGHAVSNVVPVIASNRIGTE--------GDQRFYGHSFICDEW 235 Query: 246 GELVAAAGDKEEAVLVAQFDLDKIKSKRHGWGVYRDRRPDLYK 288 G+++A G +E VL A DLD+ + R G G +RDRRP+LY+ Sbjct: 236 GDILAEFGAEETGVLTATLDLDRARKHRAGMGFFRDRRPELYR 278 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: 323 Number of extensions: 12 Number of successful extensions: 3 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: 284 Length adjustment: 26 Effective length of query: 274 Effective length of database: 258 Effective search space: 70692 Effective search space used: 70692 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 Ga0059261_1979 Ga0059261_1979 (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.5155.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-135 435.2 0.0 5.7e-135 435.0 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1979 Ga0059261_1979 N-carbamoylputres Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1979 Ga0059261_1979 N-carbamoylputrescine amidase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.0 0.0 5.7e-135 5.7e-135 1 278 [. 4 279 .. 4 280 .. 0.98 Alignments for each domain: == domain 1 score: 435.0 bits; conditional E-value: 5.7e-135 TIGR03381 1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplik 69 ++vaa+qla+s+dve+ni+++++lvreaa+kGaq++l+pelfe+ yfc+ ++e+ f++a+p+++hp+++ lcl|FitnessBrowser__Korea:Ga0059261_1979 4 ITVAALQLAFSNDVEQNIANVTDLVREAASKGAQVVLPPELFEGEYFCRVEDEALFATARPLASHPAVT 72 79******************************************************************* PP TIGR03381 70 rlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvw 138 ++q+la+el++ +p+sffe +g ++ynsla+i dG+v gvyrkshiPdgpgyeek+yf+pG+tGfkvw lcl|FitnessBrowser__Korea:Ga0059261_1979 73 AMQALAAELQIHIPTSFFEADGPHFYNSLAMIGPDGKVAGVYRKSHIPDGPGYEEKYYFRPGNTGFKVW 141 ********************************************************************* PP TIGR03381 139 d..tryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvp 205 d + a +GvgicWdqW+pe+ar+++l+Ga++l+yPtaiGseP+da+ld++++W+ram Gha++nvvp lcl|FitnessBrowser__Korea:Ga0059261_1979 142 DgpADDAALGVGICWDQWYPETARTMMLMGAQLLFYPTAIGSEPYDADLDTSRMWRRAMIGHAVSNVVP 210 94446899************************************************************* PP TIGR03381 206 vvaanrigkeveaeleltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpe 274 v+a+nrig+e +++fyG+sfi+de+G+++ae++ +e++vl+a++dld+++k+ra +G+frdrrpe lcl|FitnessBrowser__Korea:Ga0059261_1979 211 VIASNRIGTE----GDQRFYGHSFICDEWGDILAEFGAEETGVLTATLDLDRARKHRAGMGFFRDRRPE 275 **********....89***************************************************** PP TIGR03381 275 lyek 278 ly++ lcl|FitnessBrowser__Korea:Ga0059261_1979 276 LYRR 279 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (279 nodes) Target sequences: 1 (284 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: 10.95 // [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