Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate GFF4234 PS417_21690 N-succinylarginine dihydrolase
Query= reanno::SB2B:6937151 (444 letters) >FitnessBrowser__WCS417:GFF4234 Length = 448 Score = 582 bits (1501), Expect = e-171 Identities = 298/446 (66%), Positives = 342/446 (76%), Gaps = 3/446 (0%) Query: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60 MK +E NFDGLVGPTHNY GLSFGNVASQSN+ Q SNPK+AA QGL+K KAL DMG VQG Sbjct: 1 MKSYEVNFDGLVGPTHNYGGLSFGNVASQSNSQQHSNPKEAALQGLQKMKALMDMGFVQG 60 Query: 61 MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120 +LAPQERPD+ LR +GF+GSDA V+ QAAK + LL A SASSMW ANAATVSPSAD+ Sbjct: 61 VLAPQERPDVAALRNLGFSGSDAQVIQQAAKDAMPLLVASCSASSMWVANAATVSPSADT 120 Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180 DG++HFT ANL K HRSIE TT +L A+F D+++FAHH LP FGDEGAANHT Sbjct: 121 FDGRVHFTAANLNCKYHRSIEHPTTSRVLGAMFADDKHFAHHAALPAVAQFGDEGAANHT 180 Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240 R C +YG+AGVE FV+GRS D PAP KYPARQTLEASQAVARLH L DD VY QQN Sbjct: 181 RFCREYGEAGVEFFVFGRSAFDPRYPAPQKYPARQTLEASQAVARLHGLKDDGVVYAQQN 240 Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEID---KKMHGNMYFIEVPTAKV 297 P VID GVFHNDVIAVGN VLFYHE AFL T+ LAE+ K+ GN + VP A+V Sbjct: 241 PAVIDAGVFHNDVIAVGNGEVLFYHEDAFLNTEQMLAELQGKLGKLGGNFQSVCVPRAQV 300 Query: 298 SVQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVK 357 SV+DAV+SYLFN+Q+++ +DG+M +I P +C+ N V YL L I+ V FD+K Sbjct: 301 SVEDAVRSYLFNSQLLSRADGSMLLIVPEECRANERVWQYLQSLTATGGLIREVKVFDLK 360 Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417 QSMQNGGGPACLRLRVA+NETELAAVNP V+M L+ L QWVDKHYRD L DLADP Sbjct: 361 QSMQNGGGPACLRLRVALNETELAAVNPGVIMTAPLYDTLTQWVDKHYRDSLRETDLADP 420 Query: 418 QLLMESRTALDELTQIMKLGSVYQFQ 443 QLL+E RTALDELTQI+KLGSVY FQ Sbjct: 421 QLLLECRTALDELTQILKLGSVYPFQ 446 Lambda K H 0.318 0.131 0.380 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: 547 Number of extensions: 14 Number of successful extensions: 2 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: 444 Length of database: 448 Length adjustment: 32 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate GFF4234 PS417_21690 (N-succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))
# 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/TIGR03241.hmm # target sequence database: /tmp/gapView.15278.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03241 [M=443] Accession: TIGR03241 Description: arg_catab_astB: succinylarginine dihydrolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-251 818.6 0.3 8.5e-251 818.4 0.3 1.0 1 lcl|FitnessBrowser__WCS417:GFF4234 PS417_21690 N-succinylarginine d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4234 PS417_21690 N-succinylarginine dihydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 818.4 0.3 8.5e-251 8.5e-251 1 443 [] 3 446 .. 3 446 .. 1.00 Alignments for each domain: == domain 1 score: 818.4 bits; conditional E-value: 8.5e-251 TIGR03241 1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklG 75 +yevnfdGlvG+thny+GlsfGn+as+sn+++ snpk+aa qGl+kmkal+d+Gf qgvlapqerpd+aalr+lG lcl|FitnessBrowser__WCS417:GFF4234 3 SYEVNFDGLVGPTHNYGGLSFGNVASQSNSQQHSNPKEAALQGLQKMKALMDMGFVQGVLAPQERPDVAALRNLG 77 69************************************************************************* PP TIGR03241 76 fsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkai 150 fsGsd++v+++aa++a+ ll+a++sassmw+anaatvspsadt dgrvhftaanln+k+hrsie++tt+rvl a+ lcl|FitnessBrowser__WCS417:GFF4234 78 FSGSDAQVIQQAAKDAMPLLVASCSASSMWVANAATVSPSADTFDGRVHFTAANLNCKYHRSIEHPTTSRVLGAM 152 *************************************************************************** PP TIGR03241 151 fadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlh 224 fad+k+fa+h+alpava++GdeGaanhtr+++ey+e+gve+fv+Gr+a+ r+p+p++yparqtleasqavarlh lcl|FitnessBrowser__WCS417:GFF4234 153 FADDKHFAHHAALPAVAQFGDEGAANHTRFCREYGEAGVEFFVFGRSAFdPRYPAPQKYPARQTLEASQAVARLH 227 *************************************************889*********************** PP TIGR03241 225 qleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsv 299 +l+++ vvyaqqnp+vid+Gvfhndviav+n evlf+he+afln++q+l+el+ kl lg+++++++vp+a+vsv lcl|FitnessBrowser__WCS417:GFF4234 228 GLKDDGVVYAQQNPAVIDAGVFHNDVIAVGNGEVLFYHEDAFLNTEQMLAELQGKLGKLGGNFQSVCVPRAQVSV 302 *************************************************************************** PP TIGR03241 300 edavssylfnsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvv 374 edav+sylfnsqlls++dg+mll+vpeecr ne+vw+yl++l+a++g i+evkvfdl++sm+nGGGpaclrlrv+ lcl|FitnessBrowser__WCS417:GFF4234 303 EDAVRSYLFNSQLLSRADGSMLLIVPEECRANERVWQYLQSLTATGGLIREVKVFDLKQSMQNGGGPACLRLRVA 377 *************************************************************************** PP TIGR03241 375 lndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443 ln++elaavnp v++++ l++tl++wvd+hyrd l ++dladpqll e+rtaldeltqil+lGsvy+fq lcl|FitnessBrowser__WCS417:GFF4234 378 LNETELAAVNPGVIMTAPLYDTLTQWVDKHYRDSLRETDLADPQLLLECRTALDELTQILKLGSVYPFQ 446 ********************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (448 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 6.68 // [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