Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate AO353_03470 AO353_03470 arginine deiminase
Query= BRENDA::P13981 (418 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03470 Length = 418 Score = 721 bits (1862), Expect = 0.0 Identities = 343/418 (82%), Positives = 383/418 (91%) Query: 1 MSTEKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVT 60 M+TEK K GVHSEAGKLRKVMVCSPGLAHQRLTP+NCDELLFDDV+WV QAKRDHFDFVT Sbjct: 1 MTTEKVKYGVHSEAGKLRKVMVCSPGLAHQRLTPNNCDELLFDDVLWVAQAKRDHFDFVT 60 Query: 61 KMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLA 120 KMRER IDVLEMHNLLT+ + NPEAL WIL RKITA+SVG+GL E+ +WL SLEPRK+A Sbjct: 61 KMRERDIDVLEMHNLLTDIVANPEALGWILQRKITANSVGVGLVHEVDAWLRSLEPRKIA 120 Query: 121 EYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPM 180 E+LIGGV+ADDLP S G ++M+R++LGHSSF+LPPLPNTQFTRDTTCWIYGGVTLNPM Sbjct: 121 EFLIGGVSADDLPNSFGGKTIEMFRDFLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPM 180 Query: 181 YWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGM 240 +WPARRQETLL +AIYKFHPEF NA+F++WYGDPD++HG++TLEGGDVMPIGNGVVLIGM Sbjct: 181 HWPARRQETLLASAIYKFHPEFTNADFQVWYGDPDQEHGNATLEGGDVMPIGNGVVLIGM 240 Query: 241 GERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKE 300 GER+SRQAIGQ+A +LF A ERVIVAGLPKSRAAMHLDTVFSFCDRDLVT+FPEVV + Sbjct: 241 GERTSRQAIGQLALNLFKHKAVERVIVAGLPKSRAAMHLDTVFSFCDRDLVTIFPEVVSQ 300 Query: 301 IVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNN 360 IV F+LRPD S P G++IRREE +FL+ VA +L LK LRVVETGGNSFAAEREQWDDGNN Sbjct: 301 IVAFTLRPDESKPGGIDIRREETSFLDTVAAALNLKALRVVETGGNSFAAEREQWDDGNN 360 Query: 361 VVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY 418 VV LEPGVV+GYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPI+RDPIDY Sbjct: 361 VVALEPGVVIGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIIRDPIDY 418 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: 673 Number of extensions: 14 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: 418 Length of database: 418 Length adjustment: 32 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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: 50 (23.9 bits)
Align candidate AO353_03470 AO353_03470 (arginine deiminase)
to HMM TIGR01078 (arcA: arginine deiminase (EC 3.5.3.6))
# 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/TIGR01078.hmm # target sequence database: /tmp/gapView.940.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01078 [M=408] Accession: TIGR01078 Description: arcA: arginine 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-167 543.6 0.0 1.5e-167 543.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 AO353_03470 arginine deiminase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 AO353_03470 arginine deiminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 543.4 0.0 1.5e-167 1.5e-167 3 408 .] 10 416 .. 8 416 .. 0.99 Alignments for each domain: == domain 1 score: 543.4 bits; conditional E-value: 1.5e-167 TIGR01078 3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrdngvevllled 67 v+sE+GkL+kv++++Pg ++++ltP+n+delLFdd+l+v +ak++H +Fv+k+r+++++vl++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 10 VHSEAGKLRKVMVCSPGLAHQRLTPNNCDELLFDDVLWVAQAKRDHFDFVTKMRERDIDVLEMHN 74 99*************************************************************** PP TIGR01078 68 LlaEtlaaseakeklldealeeaeilgeelkkelreylksletrelvekllaGvakeelpeeeds 132 Ll++ +a++ea ++l++++++++ +g +l +e+ ++l+sle+r+++e l++Gv +++lp++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 75 LLTDIVANPEALGWILQRKITANS-VGVGLVHEVDAWLRSLEPRKIAEFLIGGVSADDLPNSFGG 138 ************************.9*************************************** PP TIGR01078 133 elslvdlevegdsefvidPlPnllFtRDpsasigngvtlnkmalkaRqrEtlftelifkhHpkfa 197 ++ + + g+s+f+++PlPn++FtRD++++i++gvtln+m ++aR++Etl++++i+k+Hp+f+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 139 KTIEMFRDFLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPMHWPARRQETLLASAIYKFHPEFT 203 ***************************************************************** PP TIGR01078 198 naevevyyd....rsekaslEGGDvlvlskdvlviGiseRtsaqsveklakslfkneaefkkvla 258 na+++v+y+ ++ +a+lEGGDv+ ++++v++iG++eRts+q++++la +lfk+ +++++v++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 204 NADFQVWYGdpdqEHGNATLEGGDVMPIGNGVVLIGMGERTSRQAIGQLALNLFKH-KAVERVIV 267 ********999988999***************************************.99****** PP TIGR01078 259 iklpkkralmHLDtvltmvDkdkftvfpevekelkafsiysltkgneekikveekakleevlaea 323 + lpk+ra+mHLDtv++++D+d +t+fpev+++++af+++ +++++ + +++e++++ + +a+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 268 AGLPKSRAAMHLDTVFSFCDRDLVTIFPEVVSQIVAFTLRPDESKPGGIDIRREETSFLDTVAAA 332 ***************************************************************** PP TIGR01078 324 lgvkklkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnallekaGikvltiagse 388 l++k l++++tg g+s++aeREqw+Dgnnv+a++PGvv++Y+Rn++tn+ll+kaG++v+ti++se lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 333 LNLKALRVVETG-GNSFAAEREQWDDGNNVVALEPGVVIGYDRNTYTNTLLRKAGVEVITISASE 396 ***********9.9*************************************************** PP TIGR01078 389 LsrGrGgprCmsmplvRddi 408 L+rGrGg++Cm++p+ Rd+i lcl|FitnessBrowser__pseudo3_N2E3:AO353_03470 397 LGRGRGGGHCMTCPIIRDPI 416 *****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (408 nodes) Target sequences: 1 (418 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.54 // [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