Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate PP_2196 PP_2196 agmatinase
Query= SwissProt::Q7X3P1 (306 letters) >FitnessBrowser__Putida:PP_2196 Length = 311 Score = 329 bits (843), Expect = 6e-95 Identities = 161/280 (57%), Positives = 207/280 (73%), Gaps = 6/280 (2%) Query: 31 YSSD---ADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHRWPWHFDMRERLKV 87 YS D D V++GVPFD ATS R G R GP AIR S AW H WPW FD + L V Sbjct: 26 YSRDLRGVDVVVSGVPFDTATSNRPGARFGPRAIRAASVQQAWARH-WPWAFDPFDHLAV 84 Query: 88 VDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPLLRAHAKHFGKMAL 147 +D GD F+ G Q + D ++AH E +L AG LT GGDHF++ PLL+AHA+ G +AL Sbjct: 85 IDYGDCPFDSGTPQSVPDSIEAHAEHILQAGCAMLTLGGDHFISYPLLKAHARRHGPLAL 144 Query: 148 VHFDAHTDTYAN--GSKFDHGTMFYHAPNEGLIDPQHSVQIGIRTEHDTNNGFTVLDAAQ 205 +HFDAH+DT+ + G + DHGTMF+HA EGL+DP HSVQIG+RT +D + GF +LDA Q Sbjct: 145 IHFDAHSDTWPDEAGKRIDHGTMFWHAAREGLVDPAHSVQIGLRTTNDDSQGFAILDARQ 204 Query: 206 VNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGLTTDKALKMLRALQ 265 V+ +G + ++A I++ VG PVYLTFDIDCLDPA+APGTGTPV GGL+T +AL++L L+ Sbjct: 205 VHRQGTEAVIAAIRQRVGERPVYLTFDIDCLDPAYAPGTGTPVCGGLSTVQALEILGGLR 264 Query: 266 PLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYLQAAK 305 +N+VGMDLVEV+PAYD +DITALAGAT+A++ML L AA+ Sbjct: 265 GINLVGMDLVEVAPAYDHADITALAGATLAMEMLCLYAAR 304 Lambda K H 0.321 0.138 0.426 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: 355 Number of extensions: 17 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: 306 Length of database: 311 Length adjustment: 27 Effective length of query: 279 Effective length of database: 284 Effective search space: 79236 Effective search space used: 79236 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate PP_2196 PP_2196 (agmatinase)
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))
# 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/TIGR01230.hmm # target sequence database: /tmp/gapView.7590.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01230 [M=275] Accession: TIGR01230 Description: agmatinase: agmatinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-78 249.1 0.0 4.1e-78 248.8 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2196 PP_2196 agmatinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2196 PP_2196 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.8 0.0 4.1e-78 4.1e-78 13 274 .. 33 299 .. 24 300 .. 0.94 Alignments for each domain: == domain 1 score: 248.8 bits; conditional E-value: 4.1e-78 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvDagdlplaaGdaremvekiee 84 +vv+ g+P+d++ts rpG+r+gp air as++ ++ + ++ ++ l v+D gd p+ G ++ + ++ie+ lcl|FitnessBrowser__Putida:PP_2196 33 VDVVVSGVPFDTATSNRPGARFGPRAIRAASVQQAWAR-HWPWAFDPfdhLAVIDYGDCPFDSGTPQSVPDSIEA 106 699******************************98865.56665554445************************* PP TIGR01230 85 vveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlr.....defegeklshacvmrrvlelgl 154 ++e++l++g ++++GG+H+i++p+++A+++++++la+++fDAH D+ +++++++ ++ ++++++ lcl|FitnessBrowser__Putida:PP_2196 107 HAEHILQAGCAMLTLGGDHFISYPLLKAHARRHGPLALIHFDAHSDTWpdeagKRIDHGTMFWHAAREGLVDPA- 180 ***********************************************9877777799999999999*******9. PP TIGR01230 155 nvlqigiRsgikeeadlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltske 229 +++qig+R+ ++ +++a ++ +v + e +ia ++v ++pvy+t+DiD+lDPa+aPG+gtp+ gGl++ + lcl|FitnessBrowser__Putida:PP_2196 181 HSVQIGLRTTNDDSQGFAILDARQVHRQGTEAVIAAIRQRVGERPVYLTFDIDCLDPAYAPGTGTPVCGGLSTVQ 255 99************************************************************************* PP TIGR01230 230 llklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 +l+ + + ++vG+D+vEvaP+yd++++tal+ a+la+e+l lcl|FitnessBrowser__Putida:PP_2196 256 ALE-ILGGLRGINLVGMDLVEVAPAYDHADITALAGATLAMEMLC 299 ***.67788999*******************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (311 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: 11.56 // [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