Align Agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate Pf1N1B4_1661 Agmatine deiminase (EC 3.5.3.12)
Query= reanno::pseudo5_N2C3_1:AO356_10030 (368 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 Length = 368 Score = 714 bits (1844), Expect = 0.0 Identities = 335/366 (91%), Positives = 352/366 (96%) Query: 1 MTTLHSTPRADGFHMPAEWATQTQVWMIWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60 MTTL+STPR DGF+MPAEWA QTQ WM+WPERPDNWRLGGKPAQAAHVAVAKAIARFEPV Sbjct: 1 MTTLNSTPRTDGFYMPAEWAPQTQTWMVWPERPDNWRLGGKPAQAAHVAVAKAIARFEPV 60 Query: 61 TVAVSAAQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINDSGEVRGVDWDFNAWGG 120 TVAVSA QYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVIN+ GEVRGVDWDFNAWGG Sbjct: 61 TVAVSAGQYENARARLDVPNIRLVEMSSDDAWVRDTGPTFVINNRGEVRGVDWDFNAWGG 120 Query: 121 FDGGLYAPWNRDSQVASKVLEIERSPRYRTEGFVLEGGSIHVDGEGTVITTEECLLNRNR 180 FDGGLY+PWNRDSQVA K+LEIERSPRYRTEGFVLEGGSIHVDGEGT+ITTEECLLNRNR Sbjct: 121 FDGGLYSPWNRDSQVAGKILEIERSPRYRTEGFVLEGGSIHVDGEGTLITTEECLLNRNR 180 Query: 181 NPHMSREQIEAVLSAQLAVDKVIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQN 240 NPHM R QIEAVLSA LAVDK+IWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQ+ Sbjct: 181 NPHMDRAQIEAVLSANLAVDKIIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQD 240 Query: 241 PNYTRCHAAMDVLQNSTDAKGRPFTVHKMPIPGPMYATEEECAGVDAVEGSQERNPTVRL 300 PNY RC AAM+VLQNSTDAKGRPFTVHKMPIPGP+YATE+ECAGVD V+G+QERNPTVRL Sbjct: 241 PNYPRCQAAMNVLQNSTDAKGRPFTVHKMPIPGPLYATEDECAGVDPVDGTQERNPTVRL 300 Query: 301 AGSYVNFLIVNGGIIAPSFDDPLDAPARDILQNLFPQHEVVMVPGRELLLGGGNIHCLTQ 360 AGSYVNFLIVNGGIIAPSFDDPLD PA++ILQ LFPQHEVVMVPGRELLLGGGNIHCLTQ Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPLDGPAKEILQALFPQHEVVMVPGRELLLGGGNIHCLTQ 360 Query: 361 QQPAPY 366 QQPAP+ Sbjct: 361 QQPAPH 366 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: 700 Number of extensions: 19 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 Pf1N1B4_1661 (Agmatine deiminase (EC 3.5.3.12))
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.25975.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-178 576.9 0.0 8.1e-178 576.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 Agmatine deiminase (EC 3.5.3.12) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 Agmatine deiminase (EC 3.5.3.12) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 576.7 0.0 8.1e-178 8.1e-178 1 357 [] 6 364 .. 6 364 .. 0.99 Alignments for each domain: == domain 1 score: 576.7 bits; conditional E-value: 8.1e-178 TIGR03380 1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqy 64 +tp+ dgf++Pae+++q+++w++WPerpDnWr g+kpaq+a+++vakaia++epvtv+vs+ qy lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 6 STPRTDGFYMPAEWAPQTQTWMVWPERPDNWRLGGKPAQAAHVAVAKAIARFEPVTVAVSAGQY 69 58************************************************************** PP TIGR03380 65 enarkalpe.eirvvemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDd 127 enar++l+ +ir+vemss+Daw+rD+GPtfv+n++ge+rgvdw+fnawgg+++Gly+pW++D+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 70 ENARARLDVpNIRLVEMSSDDAWVRDTGPTFVINNRGEVRGVDWDFNAWGGFDGGLYSPWNRDS 133 *******966****************************************************** PP TIGR03380 128 kvarkvleleridryra.dlvleggsihvDGeGtlltteeclLsegrnpelskeeieeklkeyl 190 +va k+le+er +ryr+ +vleggsihvDGeGtl+tteeclL+++rnp++ +++ie++l + l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 134 QVAGKILEIERSPRYRTeGFVLEGGSIHVDGEGTLITTEECLLNRNRNPHMDRAQIEAVLSANL 197 *****************89********************************************* PP TIGR03380 191 gvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtddesdPqyeiskealevLenetDakG 254 +v+k+iWl++Gl++det+GhvDn++++vrPGev+l+wtdd +dP+y ++++a++vL+n+tDakG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 198 AVDKIIWLPDGLFNDETDGHVDNFCCYVRPGEVLLAWTDDPQDPNYPRCQAAMNVLQNSTDAKG 261 **************************************************************** PP TIGR03380 255 rklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaiilPlfddekDk 318 r ++vhk+++p+pl++te+e++gvd v+gt++r++ rla+syvn+li+n++ii+P+fdd+ D lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 262 RPFTVHKMPIPGPLYATEDECAGVDPVDGTQERNPTVRLAGSYVNFLIVNGGIIAPSFDDPLDG 325 **************************************************************** PP TIGR03380 319 eakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357 ak++lq lfP+++vv+v+ re+llgGGnihc+tqq+pa lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1661 326 PAKEILQALFPQHEVVMVPGRELLLGGGNIHCLTQQQPA 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.18 // [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