Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate PP_0266 PP_0266 Agmatine deiminase
Query= reanno::pseudo5_N2C3_1:AO356_10030 (368 letters) >FitnessBrowser__Putida:PP_0266 Length = 368 Score = 665 bits (1717), Expect = 0.0 Identities = 311/365 (85%), Positives = 335/365 (91%) Query: 1 MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60 M TL+STPRADGFHMPAEWA QTQVWM+WPERPDNWRLGGKPAQAAHV +AKAIARFEPV Sbjct: 1 MKTLNSTPRADGFHMPAEWAPQTQVWMVWPERPDNWRLGGKPAQAAHVTLAKAIARFEPV 60 Query: 61 TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120 TVAVSA QYENAR +LD PNIR+VE+S+DDAWVRDTGPTFVIND GEVRGVDW FNAWGG Sbjct: 61 TVAVSAGQYENARRQLDQPNIRVVEISNDDAWVRDTGPTFVINDHGEVRGVDWGFNAWGG 120 Query: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180 FDGGLYAPWNRD ++A+KVLE+ER RY+TEGFVLEGGSIHVDGEGTVITTEECLLNRNR Sbjct: 121 FDGGLYAPWNRDEELAAKVLEMERCQRYQTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180 Query: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240 NPH+SREQIEAVL LAVD V+WLPDGL+NDETDGHVDNFCCYVRPGEVLLAWTDD + Sbjct: 181 NPHLSREQIEAVLRDHLAVDTVVWLPDGLYNDETDGHVDNFCCYVRPGEVLLAWTDDSND 240 Query: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300 PNY RCHAAMDVL+N+ DAKGR F VHKMPIPGP++AT EECAGVD V GSQER+P+VRL Sbjct: 241 PNYARCHAAMDVLKNTRDAKGREFIVHKMPIPGPLFATAEECAGVDQVAGSQERDPSVRL 300 Query: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360 AGSYVNFLIVNGGIIAPSFDDP DA AR IL +FP HEVVM+PGRELLLGGGNIHCLTQ Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPADAEARAILARIFPDHEVVMIPGRELLLGGGNIHCLTQ 360 Query: 361 QQPAP 365 QQPAP Sbjct: 361 QQPAP 365 Lambda K H 0.318 0.136 0.431 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: 643 Number of extensions: 18 Number of successful extensions: 1 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate PP_0266 PP_0266 (Agmatine deiminase)
to HMM TIGR03380 (aguA: agmatine deiminase (EC 3.5.3.12))
# 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/TIGR03380.hmm # target sequence database: /tmp/gapView.8401.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03380 [M=357] Accession: TIGR03380 Description: agmatine_aguA: agmatine deiminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-178 579.1 0.0 1.8e-178 578.9 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_0266 PP_0266 Agmatine deiminase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0266 PP_0266 Agmatine deiminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 578.9 0.0 1.8e-178 1.8e-178 1 357 [] 6 364 .. 6 364 .. 0.99 Alignments for each domain: == domain 1 score: 578.9 bits; conditional E-value: 1.8e-178 TIGR03380 1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpe.e 74 +tp++dgf++Pae+++q++vw++WPerpDnWr g+kpaq+a++++akaia++epvtv+vs+ qyenar++l++ + lcl|FitnessBrowser__Putida:PP_0266 6 STPRADGFHMPAEWAPQTQVWMVWPERPDNWRLGGKPAQAAHVTLAKAIARFEPVTVAVSAGQYENARRQLDQpN 80 58*********************************************************************988* PP TIGR03380 75 irvvemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryra.dlvl 148 irvve+s++Daw+rD+GPtfv+nd+ge+rgvdw fnawgg+++Gly+pW++D+++a kvle+er +ry++ +vl lcl|FitnessBrowser__Putida:PP_0266 81 IRVVEISNDDAWVRDTGPTFVINDHGEVRGVDWGFNAWGGFDGGLYAPWNRDEELAAKVLEMERCQRYQTeGFVL 155 **********************************************************************89*** PP TIGR03380 149 eggsihvDGeGtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGev 223 eggsihvDGeGt++tteeclL+++rnp+ls+e+ie++l+++l+v+ v+Wl++Gly+det+GhvDn++++vrPGev lcl|FitnessBrowser__Putida:PP_0266 156 EGGSIHVDGEGTVITTEECLLNRNRNPHLSREQIEAVLRDHLAVDTVVWLPDGLYNDETDGHVDNFCCYVRPGEV 230 *************************************************************************** PP TIGR03380 224 vlswtddesdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyv 298 +l+wtdd++dP+y+++++a++vL+n++DakGr++ vhk+++p+pl++t+ee++gvd+v g+++r+++ rla+syv lcl|FitnessBrowser__Putida:PP_0266 231 LLAWTDDSNDPNYARCHAAMDVLKNTRDAKGREFIVHKMPIPGPLFATAEECAGVDQVAGSQERDPSVRLAGSYV 305 *************************************************************************** PP TIGR03380 299 nyliankaiilPlfddekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357 n+li+n++ii+P+fdd+ D+ea+++l+++fPd++vv+++ re+llgGGnihc+tqq+pa lcl|FitnessBrowser__Putida:PP_0266 306 NFLIVNGGIIAPSFDDPADAEARAILARIFPDHEVVMIPGRELLLGGGNIHCLTQQQPA 364 *********************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (368 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: 00:00:00.01 # Mc/sec: 9.41 // [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