Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 17999 b3960 argininosuccinate lyase (NCBI)
Query= ecocyc::ARGSUCCINLYA-MONOMER (457 letters) >FitnessBrowser__Keio:17999 Length = 457 Score = 901 bits (2329), Expect = 0.0 Identities = 457/457 (100%), Positives = 457/457 (100%) Query: 1 MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60 MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE Sbjct: 1 MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60 Query: 61 ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120 ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW Sbjct: 61 ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120 Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE Sbjct: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180 Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS Sbjct: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240 Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ Sbjct: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300 Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA Sbjct: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360 Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED Sbjct: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420 Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG 457 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG Sbjct: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG 457 Lambda K H 0.318 0.133 0.386 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: 794 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: 457 Length of database: 457 Length adjustment: 33 Effective length of query: 424 Effective length of database: 424 Effective search space: 179776 Effective search space used: 179776 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate 17999 b3960 (argininosuccinate lyase (NCBI))
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.9085.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-220 717.3 0.0 5e-220 717.1 0.0 1.0 1 lcl|FitnessBrowser__Keio:17999 b3960 argininosuccinate lyase (N Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17999 b3960 argininosuccinate lyase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 717.1 0.0 5e-220 5e-220 1 454 [. 3 456 .. 3 457 .] 1.00 Alignments for each domain: == domain 1 score: 717.1 bits; conditional E-value: 5e-220 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelevda 78 lwggR+++++d+++++fn+sl+fD++lae+Di gs+a++kaL+++g+lt+ee+++l+eaL+ l e+v+++ ++ le+da lcl|FitnessBrowser__Keio:17999 3 LWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEEALNVLLEDVRARpQQILESDA 81 7*******************************************************************9989999**** PP TIGR00838 79 eDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLqr 157 eDiH++vE +lidkvg ++gkklhtgrsRnDqvatdl+l+++d+v+el++a ++l++alve+A+++++++mpgytHLqr lcl|FitnessBrowser__Keio:17999 82 EDIHSWVEGKLIDKVG-QLGKKLHTGRSRNDQVATDLKLWCKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQR 159 ****************.************************************************************** PP TIGR00838 158 AqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEl 236 AqP+t+aH++lay+eml+rD +Rl+dalkR+++sPlG+gAlagt++eidre+la +LgF+++++nsld+vsdRD+++El lcl|FitnessBrowser__Keio:17999 160 AQPVTFAHWCLAYVEMLARDESRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLEL 238 ******************************************************************************* PP TIGR00838 237 lsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaY 315 lsaaa+ mvhlsr+aE+li+f++ E+gfvelsd+v+sgss+mPqKKnpD++EliRgk+grv+G ltg++++lK+lPlaY lcl|FitnessBrowser__Keio:17999 239 LSAAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGALTGMMMTLKGLPLAY 317 ******************************************************************************* PP TIGR00838 316 nkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakai 394 nkD+qEdke+lfdal+t+ ++l++++++l+ ++v++ r++eaa++++a+at+lAdylv+kGvPFReah+ivGe+v++ai lcl|FitnessBrowser__Keio:17999 318 NKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAAQQGYANATELADYLVAKGVPFREAHHIVGEAVVEAI 396 ******************************************************************************* PP TIGR00838 395 ekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeakael 454 ++Gk le+l+l+elqk+s+ ++edv+ +l+l+++++kr+akGG+++++v++ai+ a+a+l lcl|FitnessBrowser__Keio:17999 397 RQGKPLEDLPLSELQKFSQVIDEDVYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARL 456 ********************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (457 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: 00:00:00.01 # Mc/sec: 10.67 // [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