Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate 200073 SO_0887 agmatine deiminase (RefSeq)
Query= BRENDA::Q9I6J9 (368 letters) >FitnessBrowser__MR1:200073 Length = 370 Score = 419 bits (1076), Expect = e-122 Identities = 206/361 (57%), Positives = 251/361 (69%), Gaps = 5/361 (1%) Query: 5 TSTPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPVTVCA 64 T+ P DGF MPAEW + WM+WP RPDNWR G AQA FA V AI PV + Sbjct: 12 TTKPSQDGFYMPAEWAAQQAVWMIWPYRPDNWRAAGAYAQATFAKVVDAIGAATPVYMGV 71 Query: 65 SAGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGGFEGG 124 A+ + ++ +VE+ S+D W RDTGPT V++ +G+ RGVDWGFNAWGG GG Sbjct: 72 PKAFLAKAKTVMPS-HVTLVEMDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGG 130 Query: 125 LYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNRNPHL 184 LYFPW +D+QVA+++L ARYR +LEGGSIHVDGEGT +T+ ECLLN NRNP L Sbjct: 131 LYFPWDKDEQVAQQMLAQHGFARYRAP-LILEGGSIHVDGEGTCMTSAECLLNANRNPEL 189 Query: 185 SQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDDPNYL 244 ++ +IE LRDYL V+ IWL +G+Y DETDGH+DN CC+ARPGEV+L WTDD+ DP Y Sbjct: 190 TKEQIEGLLRDYLNVKQFIWLQDGVYMDETDGHIDNMCCFARPGEVILHWTDDESDPQYP 249 Query: 245 RCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGS-QPRDPSIRLAGS 303 R +AAL VL+ + DA+GRKL +H +P PGPLY ++EE GV EG+ PR RLAGS Sbjct: 250 RSKAALEVLQNTVDAQGRKLKIHLLPQPGPLYCSEEESKGV--TEGTGVPRTAGERLAGS 307 Query: 304 YVNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQQQP 363 YVNFLI N I+ P D D A LQ +FPEHE+V VP REILLGGGNIHCITQQ P Sbjct: 308 YVNFLITNHRIVFPLLDPATDDIAAQKLQEIFPEHEIVGVPAREILLGGGNIHCITQQIP 367 Query: 364 A 364 A Sbjct: 368 A 368 Lambda K H 0.319 0.138 0.439 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: 527 Number of extensions: 21 Number of successful extensions: 4 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: 370 Length adjustment: 30 Effective length of query: 338 Effective length of database: 340 Effective search space: 114920 Effective search space used: 114920 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate 200073 SO_0887 (agmatine deiminase (RefSeq))
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.21224.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-180 583.3 0.0 9.3e-180 583.1 0.0 1.0 1 lcl|FitnessBrowser__MR1:200073 SO_0887 agmatine deiminase (RefS Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200073 SO_0887 agmatine deiminase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 583.1 0.0 9.3e-180 9.3e-180 1 357 [] 13 368 .. 13 368 .. 1.00 Alignments for each domain: == domain 1 score: 583.1 bits; conditional E-value: 9.3e-180 TIGR03380 1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpeeirvve 79 t+p++dgf++Pae+++q++vw+iWP+rpDnWr+++ +aq++fa+v++ai ++pv++ v+k+++++a++++p+++++ve lcl|FitnessBrowser__MR1:200073 13 TKPSQDGFYMPAEWAAQQAVWMIWPYRPDNWRAAGAYAQATFAKVVDAIGAATPVYMGVPKAFLAKAKTVMPSHVTLVE 91 589**************************************************************************** PP TIGR03380 80 mssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryradlvleggsihvDGe 158 m+snD+w rD+GPt+vvn +ge+rgvdw fnawgg+++GlyfpWdkD++va+++l+ ++ +ryra+l+leggsihvDGe lcl|FitnessBrowser__MR1:200073 92 MDSNDCWARDTGPTVVVNAEGECRGVDWGFNAWGGHNGGLYFPWDKDEQVAQQMLAQHGFARYRAPLILEGGSIHVDGE 170 ******************************************************************************* PP TIGR03380 159 GtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnfvrPGevvlswtddesdPqye 237 Gt++t++eclL+ +rnpel+ke+ie l++yl+v+++iWl++G+y+det+Gh+Dn+++f+rPGev+l+wtddesdPqy lcl|FitnessBrowser__MR1:200073 171 GTCMTSAECLLNANRNPELTKEQIEGLLRDYLNVKQFIWLQDGVYMDETDGHIDNMCCFARPGEVILHWTDDESDPQYP 249 ******************************************************************************* PP TIGR03380 238 iskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreagerlaasyvnyliankaiilPlfddek 316 +sk+alevL+n++Da+Grklk+h l++p+pl+++eee+kgv++ +g +pr+agerla+syvn+li+n++i++Pl+d ++ lcl|FitnessBrowser__MR1:200073 250 RSKAALEVLQNTVDAQGRKLKIHLLPQPGPLYCSEEESKGVTEGTG-VPRTAGERLAGSYVNFLITNHRIVFPLLDPAT 327 **********************************************.******************************** PP TIGR03380 317 DkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357 D++a+++lqe+fP++++vgv+areillgGGnihcitqqipa lcl|FitnessBrowser__MR1:200073 328 DDIAAQKLQEIFPEHEIVGVPAREILLGGGNIHCITQQIPA 368 ***************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (370 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: 7.83 // [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