Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 7026769 Shewana3_3901 argininosuccinate lyase (RefSeq)
Query= ecocyc::ARGSUCCINLYA-MONOMER (457 letters) >FitnessBrowser__ANA3:7026769 Length = 455 Score = 589 bits (1519), Expect = e-173 Identities = 299/450 (66%), Positives = 351/450 (78%) Query: 1 MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60 MALWGGRF FK FNDSL DYRL EQD+VGS+AW+ A+ +VG++TA E + L++ Sbjct: 1 MALWGGRFQGETSALFKLFNDSLPVDYRLFEQDVVGSIAWADAIASVGIITATECSDLKK 60 Query: 61 ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120 ALN LL +V+ P IL S AEDIHS+VE LI KVG LGKKLHTGRSRNDQVATDLKLW Sbjct: 61 ALNELLVEVKGDPAIILASGAEDIHSFVESALIAKVGDLGKKLHTGRSRNDQVATDLKLW 120 Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180 C+ + L+ + L+S L+ A+ DAVMPGYTHLQRAQPVTF HWCLAYVEM+ RD Sbjct: 121 CQSEGAALVARLQTLRSELIALAEREFDAVMPGYTHLQRAQPVTFGHWCLAYVEMIERDL 180 Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240 SRL DALKR + PLG GALAGTAY++DR LA L FAS T NSLDSVSDRDHV+EL S Sbjct: 181 SRLTDALKRANTCPLGSGALAGTAYQMDRHALAAALNFASPTLNSLDSVSDRDHVVELCS 240 Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300 A+I M+HLSR AEDLIFFN+GEAGF+ LSD VTSGSSLMPQKKNPDALELIRGK GRV Sbjct: 241 TASISMIHLSRMAEDLIFFNSGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVY 300 Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360 G+L G++ T+K LPLAYNKDMQEDKEGLFD +D+W CL MAALVL G+ V RP AA Sbjct: 301 GSLVGILTTMKALPLAYNKDMQEDKEGLFDVVDSWAICLDMAALVLSGLVVNRPNALLAA 360 Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420 QQGYANATELADYLV+KG+PFREAHH+VG AVV AI + PLE L+E + F+ +I++D Sbjct: 361 QQGYANATELADYLVSKGMPFREAHHVVGVAVVAAIAKKIPLEGFTLAEFKTFADIIEDD 420 Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIA 450 VYP L++++CL KR GG + QV QAI+ Sbjct: 421 VYPNLTIEACLAKRDVLGGTALTQVKQAIS 450 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: 548 Number of extensions: 15 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: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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 7026769 Shewana3_3901 (argininosuccinate lyase (RefSeq))
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.19326.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-189 615.7 0.0 3.2e-189 615.6 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026769 Shewana3_3901 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7026769 Shewana3_3901 argininosuccinate lyase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 615.6 0.0 3.2e-189 3.2e-189 1 451 [. 3 453 .. 3 455 .] 0.99 Alignments for each domain: == domain 1 score: 615.6 bits; conditional E-value: 3.2e-189 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelev 76 lwggR+++e++ ++ fn+sl D++l+e+D+ gsia++ a+a +gi+t++e ++l++aL+el evk + ++ l + lcl|FitnessBrowser__ANA3:7026769 3 LWGGRFQGETSALFKLFNDSLPVDYRLFEQDVVGSIAWADAIASVGIITATECSDLKKALNELLVEVKGDpAIILAS 79 7*******************************************************************99789999* PP TIGR00838 77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgyt 153 aeDiH+ vE+ li+kvg d+gkklhtgrsRnDqvatdl+l+++ + l+ +l+ l+++l+ +Ae+e +++mpgyt lcl|FitnessBrowser__ANA3:7026769 80 GAEDIHSFVESALIAKVG-DLGKKLHTGRSRNDQVATDLKLWCQSEGAALVARLQTLRSELIALAEREFDAVMPGYT 155 ******************.********************************************************** PP TIGR00838 154 HLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdR 230 HLqrAqP+t++H++lay+em+erDl+Rl+dalkR+n++PlGsgAlagt++++dr++la+ L F++ + nsld+vsdR lcl|FitnessBrowser__ANA3:7026769 156 HLQRAQPVTFGHWCLAYVEMIERDLSRLTDALKRANTCPLGSGALAGTAYQMDRHALAAALNFASPTLNSLDSVSDR 232 ***************************************************************************** PP TIGR00838 231 DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltgllti 307 D+++El s+a++ m+hlsr+aE+li+f+s E+gf++lsdev+sgss+mPqKKnpD++EliRgktgrv+G+l+g+lt+ lcl|FitnessBrowser__ANA3:7026769 233 DHVVELCSTASISMIHLSRMAEDLIFFNSGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVYGSLVGILTT 309 ***************************************************************************** PP TIGR00838 308 lKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahe 384 +KalPlaYnkD+qEdke+lfd ++ + +l++++++l+ l vn+ ++ aa++++a+at+lAdylv+kG+PFReah+ lcl|FitnessBrowser__ANA3:7026769 310 MKALPLAYNKDMQEDKEGLFDVVDSWAICLDMAALVLSGLVVNRPNALLAAQQGYANATELADYLVSKGMPFREAHH 386 ***************************************************************************** PP TIGR00838 385 ivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeak 451 +vG +v++ai+k + le tl+e++ + +e+dv+ l++e +++krd+ GGta ++v++ai++ k lcl|FitnessBrowser__ANA3:7026769 387 VVGVAVVAAIAKKIPLEGFTLAEFKTFADIIEDDVYPNLTIEACLAKRDVLGGTALTQVKQAISAKK 453 ************99*************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (455 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: 00:00:00.01 # Mc/sec: 11.25 // [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