Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 6936063 Sama_0260 argininosuccinate lyase (RefSeq)
Query= ecocyc::ARGSUCCINLYA-MONOMER (457 letters) >FitnessBrowser__SB2B:6936063 Length = 456 Score = 588 bits (1517), Expect = e-173 Identities = 304/453 (67%), Positives = 350/453 (77%) Query: 1 MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60 MALWGGRF A F+ FNDSL DYRL QD+ GS+AW+ A+ +VG+L A+E ++L+ Sbjct: 1 MALWGGRFQGQASALFQLFNDSLPVDYRLFVQDVEGSIAWADAIASVGILNADECSRLKA 60 Query: 61 ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120 AL LLE+V I+ S AEDIHS+VE KLI+KVG LGKKLHTGRSRNDQVATDLKLW Sbjct: 61 ALTELLEEVGEDESAIIGSGAEDIHSFVETKLIEKVGDLGKKLHTGRSRNDQVATDLKLW 120 Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180 CK + L T + AL+ A DAVMPGYTHLQRAQPVTF HWCLAYVEML RD Sbjct: 121 CKASGGLLETKLTAVIQALLALASRELDAVMPGYTHLQRAQPVTFGHWCLAYVEMLERDL 180 Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240 SRL DALKRL+ PLG GALAGTAY IDR +LA LGF T NSLDSVSDRDHV+EL + Sbjct: 181 SRLADALKRLNTCPLGSGALAGTAYAIDRHELAAALGFGGPTLNSLDSVSDRDHVVELCA 240 Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300 AA++ M+HLSR AEDLIFFNTGEA FVEL+D VTSGSSLMPQKKNPDALELIRGK GRV Sbjct: 241 AASVSMMHLSRMAEDLIFFNTGEAAFVELADNVTSGSSLMPQKKNPDALELIRGKTGRVY 300 Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360 G L G++ T+K LPLAYNKDMQEDKEGLFD LD+W CL MAALVL+G++V R ++AA Sbjct: 301 GNLVGILTTMKALPLAYNKDMQEDKEGLFDTLDSWGICLDMAALVLEGVKVNRDNTKQAA 360 Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420 Q GYANATELADYLVAKG+PFREAHH+VGE V+ AI +G+ LE LPL+ LQ F+ VI +D Sbjct: 361 QAGYANATELADYLVAKGMPFREAHHVVGEVVLHAISKGQALEALPLASLQSFAAVIGDD 420 Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQ 453 VYP LSL CL KR GG + +QV A+A Q Sbjct: 421 VYPHLSLDECLAKRDVLGGTAIKQVTAALAAKQ 453 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: 576 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: 457 Length of database: 456 Length adjustment: 33 Effective length of query: 424 Effective length of database: 423 Effective search space: 179352 Effective search space used: 179352 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 6936063 Sama_0260 (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.7767.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-192 624.9 0.0 5.3e-192 624.7 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6936063 Sama_0260 argininosuccinate lyas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936063 Sama_0260 argininosuccinate lyase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 624.7 0.0 5.3e-192 5.3e-192 1 452 [. 3 454 .. 3 456 .] 0.99 Alignments for each domain: == domain 1 score: 624.7 bits; conditional E-value: 5.3e-192 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelev 76 lwggR++++++ ++ fn+sl D++l+ +D+egsia++ a+a +gil+++e ++l++aL+el eev e+ ++ + + lcl|FitnessBrowser__SB2B:6936063 3 LWGGRFQGQASALFQLFNDSLPVDYRLFVQDVEGSIAWADAIASVGILNADECSRLKAALTELLEEVGEDeSAIIGS 79 7*****************************************************************9888588999* PP TIGR00838 77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgyt 153 aeDiH+ vE++li+kvg d+gkklhtgrsRnDqvatdl+l+++++ l ++l ++++al+ +A +e +++mpgyt lcl|FitnessBrowser__SB2B:6936063 80 GAEDIHSFVETKLIEKVG-DLGKKLHTGRSRNDQVATDLKLWCKASGGLLETKLTAVIQALLALASRELDAVMPGYT 155 ******************.********************************************************** PP TIGR00838 154 HLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdR 230 HLqrAqP+t++H++lay+emlerDl+Rl dalkR+n++PlGsgAlagt+++idr+ la+ LgF + nsld+vsdR lcl|FitnessBrowser__SB2B:6936063 156 HLQRAQPVTFGHWCLAYVEMLERDLSRLADALKRLNTCPLGSGALAGTAYAIDRHELAAALGFGGPTLNSLDSVSDR 232 ***************************************************************************** PP TIGR00838 231 DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltgllti 307 D+++El +aa++ m+hlsr+aE+li+f++ E+ fvel+d+v+sgss+mPqKKnpD++EliRgktgrv+Gnl+g+lt+ lcl|FitnessBrowser__SB2B:6936063 233 DHVVELCAAASVSMMHLSRMAEDLIFFNTGEAAFVELADNVTSGSSLMPQKKNPDALELIRGKTGRVYGNLVGILTT 309 ***************************************************************************** PP TIGR00838 308 lKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahe 384 +KalPlaYnkD+qEdke+lfd+l+ + +l++++++l+ +kvn++++++aa++++a+at+lAdylv+kG+PFReah+ lcl|FitnessBrowser__SB2B:6936063 310 MKALPLAYNKDMQEDKEGLFDTLDSWGICLDMAALVLEGVKVNRDNTKQAAQAGYANATELADYLVAKGMPFREAHH 386 ***************************************************************************** PP TIGR00838 385 ivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeaka 452 +vGevv +ai kG+ le l+l+ lq + + +dv+ l+l e+++krd+ GGta ++v+ a+++ ++ lcl|FitnessBrowser__SB2B:6936063 387 VVGEVVLHAISKGQALEALPLASLQSFAAVIGDDVYPHLSLDECLAKRDVLGGTAIKQVTAALAAKQQ 454 **************************************************************998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (456 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: 8.15 // [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