Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate Echvi_3852 Echvi_3852 argininosuccinate lyase
Query= reanno::Cola:Echvi_3852 (444 letters) >FitnessBrowser__Cola:Echvi_3852 Length = 444 Score = 887 bits (2293), Expect = 0.0 Identities = 444/444 (100%), Positives = 444/444 (100%) Query: 1 MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK 60 MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK Sbjct: 1 MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK 60 Query: 61 GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY 120 GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY Sbjct: 61 GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY 120 Query: 121 RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME 180 RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME Sbjct: 121 RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME 180 Query: 181 LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF 240 LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF Sbjct: 181 LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF 240 Query: 241 AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ 300 AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ Sbjct: 241 AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ 300 Query: 301 SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF 360 SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF Sbjct: 301 SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF 360 Query: 361 YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT 420 YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT Sbjct: 361 YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT 420 Query: 421 KMETALAKFDFSAIETSYQKLLEA 444 KMETALAKFDFSAIETSYQKLLEA Sbjct: 421 KMETALAKFDFSAIETSYQKLLEA 444 Lambda K H 0.319 0.135 0.389 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: 826 Number of extensions: 14 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
Align candidate Echvi_3852 Echvi_3852 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))
# 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.aa/TIGR00838.hmm # target sequence database: /tmp/gapView.23474.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00838 [M=455] Accession: TIGR00838 Description: argH: argininosuccinate lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-104 336.2 0.1 2.3e-104 335.8 0.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3852 Echvi_3852 argininosuccinate lya Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3852 Echvi_3852 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.8 0.1 2.3e-104 2.3e-104 11 387 .. 11 388 .. 3 396 .. 0.94 Alignments for each domain: == domain 1 score: 335.8 bits; conditional E-value: 2.3e-104 TIGR00838 11 dkavaefn..aslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiH 82 k+v++f+ + +fD la D+ gs+ah+++L+ +lt+ee + l+++L+++++e++eg++++++ +eD+H lcl|FitnessBrowser__Cola:Echvi_3852 11 TKEVEQFTigRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKKGLKDIYQEIQEGTFTIDPGVEDVH 84 45666665225679************************************************************ PP TIGR00838 83 lavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLq 156 ++vE l+++ g dvgkklh+grsRnDqva+dl+ly r+ ++e+++ k+l + l+ +Aek+++ lmpgytH q lcl|FitnessBrowser__Cola:Echvi_3852 85 SQVEFLLTERYG-DVGKKLHSGRSRNDQVAVDLKLYYRAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQ 157 ************.************************************************************* PP TIGR00838 157 rAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdR 230 A P +++ ++ a ae+l++D+e l a++ ++++PlGs+A g+sf+++r+++++lLgF+++ n ++a +R lcl|FitnessBrowser__Cola:Echvi_3852 158 LAMPSSFGLWFGAMAESLAEDMELWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNR 231 ************************************************************************** PP TIGR00838 231 DfiiEll.saaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltg 303 ++ +a+a ++ l rl+ ++i+f + fgfv+++d++++gssimP KKnpDv EliR+k+ +++ + lcl|FitnessBrowser__Cola:Echvi_3852 232 GKTEKAIaFAMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQSGPQN 305 98766542556667789********************************************************* PP TIGR00838 304 lltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGv 377 l++ + + + Y +Dlq ke+ f ++++++l++ +++l++++++ + le++ k+ ++ + lv +G+ lcl|FitnessBrowser__Cola:Echvi_3852 306 LMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKFYKH-LFSVEVVNDLVLQGM 378 **************************************************88777665.567899999****** PP TIGR00838 378 PFReaheivG 387 PFR+a++ vG lcl|FitnessBrowser__Cola:Echvi_3852 379 PFRDAYKKVG 388 *******999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 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: 9.69 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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