Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate 6937151 Sama_1321 succinylarginine dihydrolase (RefSeq)
Query= reanno::SB2B:6937151 (444 letters) >FitnessBrowser__SB2B:6937151 Length = 444 Score = 891 bits (2302), Expect = 0.0 Identities = 444/444 (100%), Positives = 444/444 (100%) Query: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60 MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG Sbjct: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60 Query: 61 MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120 MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS Sbjct: 61 MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120 Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT Sbjct: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180 Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN Sbjct: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240 Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHGNMYFIEVPTAKVSVQ 300 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHGNMYFIEVPTAKVSVQ Sbjct: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHGNMYFIEVPTAKVSVQ 300 Query: 301 DAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSM 360 DAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSM Sbjct: 301 DAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSM 360 Query: 361 QNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLL 420 QNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLL Sbjct: 361 QNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLL 420 Query: 421 MESRTALDELTQIMKLGSVYQFQR 444 MESRTALDELTQIMKLGSVYQFQR Sbjct: 421 MESRTALDELTQIMKLGSVYQFQR 444 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: 803 Number of extensions: 21 Number of successful extensions: 1 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: 444 Length adjustment: 32 Effective length of query: 412 Effective length of database: 412 Effective search space: 169744 Effective search space used: 169744 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 6937151 Sama_1321 (succinylarginine dihydrolase (RefSeq))
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.9783.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-232 755.8 5.1 9.4e-232 755.7 5.1 1.0 1 lcl|FitnessBrowser__SB2B:6937151 Sama_1321 succinylarginine dihyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937151 Sama_1321 succinylarginine dihydrolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 755.7 5.1 9.4e-232 9.4e-232 2 443 .] 4 443 .. 3 443 .. 0.99 Alignments for each domain: == domain 1 score: 755.7 bits; conditional E-value: 9.4e-232 TIGR03241 2 yevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklGfsG 78 +e+nfdGlvG+thnyaGlsfGn+as+sn +vsnpk aakqGl+k kalad+G+ qg+lapqerpdi +lr++Gf+G lcl|FitnessBrowser__SB2B:6937151 4 FEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQGMLAPQERPDIHTLRRVGFTG 80 8**************************************************************************** PP TIGR03241 79 sdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadek 155 sd++vl++aa+ +p+ll a +sassmwtanaatvspsad+ dg++hft+anl k+hrsie tt ++lkaif+de+ lcl|FitnessBrowser__SB2B:6937151 81 SDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADSDDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDER 157 ***************************************************************************** PP TIGR03241 156 kfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlhqleeekv 231 +fa+h+ lp++ ++GdeGaanhtrl+++y+++gve+fvyGr++ + p+p +yparqtleasqavarlhql+++++ lcl|FitnessBrowser__SB2B:6937151 158 YFAHHQHLPEHPHFGDEGAANHTRLCHDYGQAGVEVFVYGRSVAdLSRPAPVKYPARQTLEASQAVARLHQLSDDRT 234 ******************************************997899***************************** PP TIGR03241 232 vyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylf 308 vy+qqnpdvidqGvfhndviav+n++vlf+he+afl++++ l+e+ +k+++ + ievp+a+vsv+dav+sylf lcl|FitnessBrowser__SB2B:6937151 235 VYMQQNPDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHGN---MYFIEVPTAKVSVQDAVKSYLF 308 *************************************************986...999******************* PP TIGR03241 309 nsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnp 385 n+q+++ +dg+m ++ p +c+en+av+ayl+elv+ ++pik v+ fd+++sm+nGGGpaclrlrv++n++elaavnp lcl|FitnessBrowser__SB2B:6937151 309 NTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVKQSMQNGGGPACLRLRVAMNETELAAVNP 385 ***************************************************************************** PP TIGR03241 386 kvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443 +v+++dalfa+ln+wvd+hyrdrls++dladpqll+esrtaldeltqi++lGsvy+fq lcl|FitnessBrowser__SB2B:6937151 386 QVMMNDALFARLNQWVDKHYRDRLSTQDLADPQLLMESRTALDELTQIMKLGSVYQFQ 443 *********************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (444 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.85 // [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