Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate GFF1960 PGA1_c19930 agmatinase SpeB
Query= SwissProt::Q7X3P1 (306 letters) >FitnessBrowser__Phaeo:GFF1960 Length = 322 Score = 239 bits (610), Expect = 6e-68 Identities = 130/289 (44%), Positives = 177/289 (61%), Gaps = 11/289 (3%) Query: 18 AFGFLRFPLNFQPYSSD---ADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHR 74 A FLR + Y+ D D +TGVPFD A + R GTR GP AIR+ S L Sbjct: 31 ATSFLR-----RKYTKDLTGVDIAVTGVPFDQAVTNRPGTRLGPRAIREASC-LQSPDEP 84 Query: 75 WPWHFDMRERLKVVDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPL 134 + W L + D GDL F+ D L H +LA + GGDH+++ P+ Sbjct: 85 YGWPHKPLSTLAIADYGDLAFDHADVPAFPAALTDHIRGILATETASVVLGGDHYISFPI 144 Query: 135 LRAHAKHFGKMALVHFDAHTDTYA--NGSKFDHGTMFYHAPNEGLIDPQHSVQIGIRTEH 192 L+A+A+ G ++L+ FDAHTDT+ N + DHGTMFY A GL+DP+ SVQ+GIRT + Sbjct: 145 LKAYAEKHGPISLLQFDAHTDTWPDDNMDRIDHGTMFYKAVKMGLVDPKTSVQVGIRTTN 204 Query: 193 DTNNGFTVLDAAQVNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGL 252 D G ++DA V+D G + +IK I+G P YLTFDIDCLDPA+APGTGTPV GGL Sbjct: 205 DDTLGVNIIDAPTVHDIGPVETAKRIKAILGDRPTYLTFDIDCLDPAYAPGTGTPVWGGL 264 Query: 253 TTDKALKMLRALQPLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYL 301 T+ +A ++LR + +NI G D+VEVSP +D + TA+AGA +A +++ L Sbjct: 265 TSAQASRILREIAGINIKGGDVVEVSPPFDTTGATAIAGAHVATEIICL 313 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: 321 Number of extensions: 10 Number of successful extensions: 3 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: 322 Length adjustment: 27 Effective length of query: 279 Effective length of database: 295 Effective search space: 82305 Effective search space used: 82305 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 GFF1960 PGA1_c19930 (agmatinase SpeB)
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.32322.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-63 199.0 0.0 7.5e-63 198.7 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1960 PGA1_c19930 agmatinase SpeB Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1960 PGA1_c19930 agmatinase SpeB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 198.7 0.0 7.5e-63 7.5e-63 13 273 .. 46 311 .. 36 313 .. 0.95 Alignments for each domain: == domain 1 score: 198.7 bits; conditional E-value: 7.5e-63 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeld...rdlallkvvDagdlplaaGdaremvekieev 85 ++ ++g+P+d+++ rpG+r gp aireas L++ +e ++ + l++l ++D gdl + d + ++++ lcl|FitnessBrowser__Phaeo:GFF1960 46 VDIAVTGVPFDQAVTNRPGTRLGPRAIREASC-LQSPDEPYGwphKPLSTLAIADYGDLAFDHADVPAFPAALTDH 120 57889**************************7.88888888855567999************************** PP TIGR01230 86 veelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlr.....defegeklshacvmrrvlelglnv 156 ++ +l+ v++GG+H i++p+++A ++k++++ ++qfDAHtD+ d +++++++ +v+ ++++++ + lcl|FitnessBrowser__Phaeo:GFF1960 121 IRGILATETASVVLGGDHYISFPILKAYAEKHGPISLLQFDAHTDTWpddnmDRIDHGTMFYKAVKMGLVDPK-TS 195 **********************************************998888899*****************9.99 PP TIGR01230 157 lqigiRsgikeeadlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltskellk 232 +q+giR+ ++ + ++ v ++ ++ ++ +a++ d+p y+t+DiD+lDPa+aPG+gtp+ gGlts ++ + lcl|FitnessBrowser__Phaeo:GFF1960 196 VQVGIRTTNDDTLGVNIIDAPTVHDIGPVETAKRIKAILGDRPTYLTFDIDCLDPAYAPGTGTPVWGGLTSAQASR 271 *************************9999999******************************************** PP TIGR01230 233 lfvlaekekkvvGlDvvEvaPvydssevtaltaaklalell 273 +++ +++G DvvEv+P +d++ ta++ a +a e++ lcl|FitnessBrowser__Phaeo:GFF1960 272 -ILREIAGINIKGGDVVEVSPPFDTTGATAIAGAHVATEII 311 .7899999******************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (322 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: 7.53 // [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