Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate BPHYT_RS26640 BPHYT_RS26640 agmatinase
Query= SwissProt::Q7X3P1 (306 letters) >FitnessBrowser__BFirm:BPHYT_RS26640 Length = 300 Score = 274 bits (700), Expect = 2e-78 Identities = 145/284 (51%), Positives = 189/284 (66%), Gaps = 7/284 (2%) Query: 29 QPYSSD---ADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHRWPWHFDMRERL 85 +PYS D D ++G+P D+AT+ R GTR GP +R S LA G +PW D + L Sbjct: 11 RPYSRDLTGVDVAVSGIPLDLATTFRPGTRFGPAGVRAASVQLAELG-AFPWGVDPFDHL 69 Query: 86 KVVDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPLLRAHAKHFGK- 144 VVD GD F+ + + D + AH +LA+G R LTFGGDH++T PLL AH + +GK Sbjct: 70 NVVDYGDCWFDAHNPLGIRDAIIAHARGILASGARMLTFGGDHYITYPLLVAHVEKYGKP 129 Query: 145 MALVHFDAHTDTYA--NGSKFDHGTMFYHAPNEGLIDPQHSVQIGIRTEHDTNNGFTVLD 202 ++L+HFDAH DT+ N +HGTMFY A E L+DP SVQIGIRT +D G +LD Sbjct: 130 LSLIHFDAHCDTWPDDNPDSLNHGTMFYKAIRERLVDPARSVQIGIRTWNDDFMGVRILD 189 Query: 203 AAQVNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGLTTDKALKMLR 262 A V+ G + ++ IVG+ P YLTFDIDCLDPAFAPGTGTPV GGL++ +AL+++R Sbjct: 190 APWVHRNGTQAAIDEVLSIVGNAPAYLTFDIDCLDPAFAPGTGTPVAGGLSSAQALEIVR 249 Query: 263 ALQPLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYLQAAKK 306 AL +N+VG D+VEVSP YD SD+TALA A +A DML L +K Sbjct: 250 ALGAVNLVGADVVEVSPPYDHSDVTALAAAHLASDMLCLMRNQK 293 Lambda K H 0.321 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: 323 Number of extensions: 9 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: 306 Length of database: 300 Length adjustment: 27 Effective length of query: 279 Effective length of database: 273 Effective search space: 76167 Effective search space used: 76167 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate BPHYT_RS26640 BPHYT_RS26640 (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.20721.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-72 228.0 0.0 1.1e-71 227.7 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS26640 BPHYT_RS26640 agmatinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS26640 BPHYT_RS26640 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.7 0.0 1.1e-71 1.1e-71 13 274 .. 20 287 .. 8 288 .. 0.93 Alignments for each domain: == domain 1 score: 227.7 bits; conditional E-value: 1.1e-71 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvDagdlplaaGdaremv 79 +v + giP+d +t +rpG+r+gp+ +r as++L++ +++ ++ l+vvD gd + a ++ + lcl|FitnessBrowser__BFirm:BPHYT_RS26640 20 VDVAVSGIPLDLATTFRPGTRFGPAGVRAASVQLAEL-GAFPWGVDPfdhLNVVDYGDCWFDAHNPLGIR 88 58889*****************************976.567765443334******************** PP TIGR01230 80 ekieevveelleegkfvvaiGGeHsitlpvirAvkkkfek.lavvqfDAHtDlr.....defegeklsha 143 + i ++++ +l+ g +++++GG+H it+p++ A+ +k++k l +++fDAH+D+ d +++++++ lcl|FitnessBrowser__BFirm:BPHYT_RS26640 89 DAIIAHARGILASGARMLTFGGDHYITYPLLVAHVEKYGKpLSLIHFDAHCDTWpddnpDSLNHGTMFYK 158 ************************************9965499**********999888999******** PP TIGR01230 144 cvmrrvlelglnvlqigiRsgikeeadlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPaf 213 + +r++++ +++qigiR+ ++ ++ ++ v + + i+evl +v + p y+t+DiD+lDPaf lcl|FitnessBrowser__BFirm:BPHYT_RS26640 159 AIRERLVDPA-RSVQIGIRTWNDDFMGVRILDAPWVHRNGTQAAIDEVLSIVGNAPAYLTFDIDCLDPAF 227 *********9.9********999999999999988888999999************************** PP TIGR01230 214 aPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 aPG+gtp++gGl+s ++l+ v+a ++++vG+DvvEv+P yd+s+vtal+aa la ++l lcl|FitnessBrowser__BFirm:BPHYT_RS26640 228 APGTGTPVAGGLSSAQALE-IVRALGAVNLVGADVVEVSPPYDHSDVTALAAAHLASDMLC 287 *******************.8999**********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (300 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.21 // [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