Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate Pf1N1B4_3445 Succinylarginine dihydrolase (EC 3.5.3.23)
Query= reanno::SB2B:6937151 (444 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 Length = 448 Score = 575 bits (1481), Expect = e-168 Identities = 291/446 (65%), Positives = 343/446 (76%), Gaps = 3/446 (0%) Query: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60 MK +E NFDGLVGPTHNY GLS+GNVASQSN+ Q SNPK+AA QGL K KAL +MG QG Sbjct: 1 MKSYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMEMGFQQG 60 Query: 61 MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120 +LAPQERPD+ LRR+GF+G+DA V+ +AAK + LL A SASSMW ANAATVSPSAD+ Sbjct: 61 VLAPQERPDVAALRRLGFSGTDAQVIERAAKEAMPLLVASCSASSMWVANAATVSPSADT 120 Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180 DG++HFT ANL K HRSIE TT +L A+F D+++FAHH LP FGDEGAANHT Sbjct: 121 ADGRVHFTAANLNCKYHRSIEHPTTSRVLGAMFADQKHFAHHAALPAVAQFGDEGAANHT 180 Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240 R C DYG+AGVE FV+GRS D P+P KYPARQTLEASQAVARLH LSDD VY QQN Sbjct: 181 RFCRDYGEAGVEFFVFGRSAFDTRYPSPQKYPARQTLEASQAVARLHGLSDDGVVYAQQN 240 Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKM---HGNMYFIEVPTAKV 297 P VIDQGVFHNDVIAVGN VLFYHE AFL+T+ LAE+ K+ G I VP + V Sbjct: 241 PSVIDQGVFHNDVIAVGNGEVLFYHEDAFLDTEQMLAELQGKLAKAGGKFQSICVPRSAV 300 Query: 298 SVQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVK 357 +V+DAV+SYLFN+Q+++ DG+M +I P +C+ N V YL L + I+ V FD+K Sbjct: 301 TVEDAVRSYLFNSQLLSRPDGSMLLIVPEECRGNERVWQYLQGLTSSGGLIREVKVFDLK 360 Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417 QSMQNGGGPACLRLRVA+NETELAAVN V+M L+ L +WVDKHYRDR++ DLADP Sbjct: 361 QSMQNGGGPACLRLRVALNETELAAVNQGVIMTAPLYGTLTEWVDKHYRDRMTENDLADP 420 Query: 418 QLLMESRTALDELTQIMKLGSVYQFQ 443 QLL+E RTALDELTQI+KLG+VY FQ Sbjct: 421 QLLLECRTALDELTQILKLGAVYPFQ 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: 552 Number of extensions: 15 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 Pf1N1B4_3445 (Succinylarginine dihydrolase (EC 3.5.3.23))
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.22970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-249 813.2 0.1 3.6e-249 813.1 0.1 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 Succinylarginine dihydrolase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 Succinylarginine dihydrolase (EC 3.5.3.23) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 813.1 0.1 3.6e-249 3.6e-249 1 443 [] 3 446 .. 3 446 .. 1.00 Alignments for each domain: == domain 1 score: 813.1 bits; conditional E-value: 3.6e-249 TIGR03241 1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqe 64 +yevnfdGlvG+thny+Gls+Gn+as+sn+++ snpk+aa qGl+kmkal+++Gf+qgvlapqe lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 3 SYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMEMGFQQGVLAPQE 66 69************************************************************** PP TIGR03241 65 rpdiaalrklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaa 128 rpd+aalr+lGfsG d++v+e+aa+ea+ ll+a++sassmw+anaatvspsadtadgrvhftaa lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 67 RPDVAALRRLGFSGTDAQVIERAAKEAMPLLVASCSASSMWVANAATVSPSADTADGRVHFTAA 130 **************************************************************** PP TIGR03241 129 nlnnkfhrsieaettervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelf 192 nln+k+hrsie++tt+rvl a+fad+k+fa+h+alpava++GdeGaanhtr++++y+e+gve+f lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 131 NLNCKYHRSIEHPTTSRVLGAMFADQKHFAHHAALPAVAQFGDEGAANHTRFCRDYGEAGVEFF 194 **************************************************************** PP TIGR03241 193 vyGraal.erepkpkryparqtleasqavarlhqleeekvvyaqqnpdvidqGvfhndviavsn 255 v+Gr+a+ +r+p+p++yparqtleasqavarlh+l+++ vvyaqqnp+vidqGvfhndviav+n lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 195 VFGRSAFdTRYPSPQKYPARQTLEASQAVARLHGLSDDGVVYAQQNPSVIDQGVFHNDVIAVGN 258 *******999****************************************************** PP TIGR03241 256 revlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqllskedgk 319 evlf+he+afl+++q+l+el+ kla g+++++i+vp+++v+vedav+sylfnsqlls+ dg+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 259 GEVLFYHEDAFLDTEQMLAELQGKLAKAGGKFQSICVPRSAVTVEDAVRSYLFNSQLLSRPDGS 322 **************************************************************** PP TIGR03241 320 mllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaav 383 mll+vpeecr ne+vw+yl+ l++++g i+evkvfdl++sm+nGGGpaclrlrv+ln++elaav lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 323 MLLIVPEECRGNERVWQYLQGLTSSGGLIREVKVFDLKQSMQNGGGPACLRLRVALNETELAAV 386 **************************************************************** PP TIGR03241 384 npkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443 n+ v++++ l+ tl++wvd+hyrdr++++dladpqll e+rtaldeltqil+lG+vy+fq lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3445 387 NQGVIMTAPLYGTLTEWVDKHYRDRMTENDLADPQLLLECRTALDELTQILKLGAVYPFQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.62 // [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