Align Agmatinase; EC 3.5.3.11; Agmatine ureohydrolase; AUH (uncharacterized)
to candidate WP_011383513.1 AMB_RS05595 agmatinase
Query= curated2:Q7P0S6 (322 letters) >NCBI__GCF_000009985.1:WP_011383513.1 Length = 297 Score = 207 bits (526), Expect = 3e-58 Identities = 122/274 (44%), Positives = 161/274 (58%), Gaps = 17/274 (6%) Query: 48 VSGIPLDLSVTFRSGARMGPQAIRAASVQLAE-LKPYPWGFDPFEDLAVVDYGDCWFDAH 106 ++GIP DL VT RSGAR GPQA+R AS LA+ P W DP + +++ D GD Sbjct: 26 IAGIPFDLGVTNRSGAREGPQAVRRASRMLADGANPAGWS-DPAQ-MSIADLGDFSL--- 80 Query: 107 NPLTIKPSIIEHARTILASGAKMLTFGGDHYVTYPLLIAHAEKYGKPLALLHFDAHCDTW 166 L P +E A +L GGDH +T LL A ++ G P+ L+HFDAH DTW Sbjct: 81 -ALGDIPRSLEMIEQQAAGIGHLLAVGGDHTITLALLRALVKRTG-PVGLVHFDAHIDTW 138 Query: 167 PDDSPDSLNHGTMFYKAVKEGLIDPKKSVQVGIRT--------WNDDFMGLNVLGAPWVH 218 PD+ L HG+ F+ A++EGL+DP++ +Q+GIR+ W G+ ++ A VH Sbjct: 139 PDNFGQKLAHGSPFFHALREGLVDPRRMIQIGIRSPMPREVYDWTVG-QGVTIVTAEQVH 197 Query: 219 DNGVDATIAEIKKTIGDAPVYVTFDIDCLDPSAAPGTGTPVPGGLTTAQALKIIRNLGDL 278 G I + +G+ Y++FDID +DP APGTGTP GGL T Q + I+R L L Sbjct: 198 AQGPQWVAEAIGRVVGEGLTYLSFDIDAIDPGQAPGTGTPEVGGLFTWQVMAILRRLAGL 257 Query: 279 NIVGMDVVEVAPSYDQSEITAIAAAHIACDMLCL 312 VGMDVVEVAP+YD SEITA+AAA I L L Sbjct: 258 RFVGMDVVEVAPAYDVSEITALAAASILWQYLTL 291 Lambda K H 0.320 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: 268 Number of extensions: 15 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: 322 Length of database: 297 Length adjustment: 27 Effective length of query: 295 Effective length of database: 270 Effective search space: 79650 Effective search space used: 79650 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_011383513.1 AMB_RS05595 (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.15912.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-59 187.9 0.0 1.8e-59 187.6 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383513.1 AMB_RS05595 agmatinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383513.1 AMB_RS05595 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 187.6 0.0 1.8e-59 1.8e-59 13 273 .. 22 289 .. 14 291 .. 0.86 Alignments for each domain: == domain 1 score: 187.6 bits; conditional E-value: 1.8e-59 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremve 80 A i giP+d + r G+r+gp+a+r as L+ + + d a++ ++D+gd++la Gd +++e lcl|NCBI__GCF_000009985.1:WP_011383513.1 22 ATFCIAGIPFDLGVTNRSGAREGPQAVRRASRMLADGANPAGwSDPAQMSIADLGDFSLALGDIPRSLE 90 7889*********************************99999458899********************* PP TIGR01230 81 kieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacv.... 145 +ie++++ + +++a+GG+H+itl+++rA k+ +++ +v+fDAH+D+ + g+kl h ++ lcl|NCBI__GCF_000009985.1:WP_011383513.1 91 MIEQQAAGI----GHLLAVGGDHTITLALLRALVKRTGPVGLVHFDAHIDTWPDNFGQKLAHGSPffha 155 ****99887....579************************************66556666666651111 PP TIGR01230 146 .mrrvlelglnvlqigiRsgikee.adlarennikvlk.relede....iaevlakvldk.pvyvtiDi 206 ++++++ +++qigiRs + +e d+++ +++ +++ +++ + ae++ +v+++ y+++Di lcl|NCBI__GCF_000009985.1:WP_011383513.1 156 lREGLVDPR-RMIQIGIRSPMPREvYDWTVGQGVTIVTaEQVHAQgpqwVAEAIGRVVGEgLTYLSFDI 223 155666666.9*********9877369********9996677777555556666555544145****** PP TIGR01230 207 DvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalell 273 D++DP+ aPG+gtpe+gGl + ++++ ++ + vG+DvvEvaP+yd se+tal+aa + + l lcl|NCBI__GCF_000009985.1:WP_011383513.1 224 DAIDPGQAPGTGTPEVGGLFTWQVMA-ILRRLAGLRFVGMDVVEVAPAYDVSEITALAAASILWQYL 289 **************************.66777899**************************987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (297 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: 00:00:00.00 # Mc/sec: 9.33 // [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