Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate H281DRAFT_00194 H281DRAFT_00194 argininosuccinate lyase
Query= SwissProt::Q9LAE5 (461 letters) >FitnessBrowser__Burk376:H281DRAFT_00194 Length = 468 Score = 432 bits (1110), Expect = e-125 Identities = 232/462 (50%), Positives = 302/462 (65%), Gaps = 5/462 (1%) Query: 3 KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62 K + WS RF + + R+ +S+ FD L D+ GS AHA ML II++E+ + Sbjct: 8 KGEAWSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLGAQKIIAAEDLAAIQ 67 Query: 63 AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122 G+ QI+ E +G+F +D EDVH +E RLT ++GD GK+LHT RSRNDQV TD RL+ Sbjct: 68 RGMAQIKGEIERGEFEWQLDLEDVHLNIEARLTALIGDAGKRLHTGRSRNDQVATDIRLW 127 Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182 LR +I +I L+E + LLD+AEK+ T++PG+THLQ AQPV+ HHLLAY +M RD Sbjct: 128 LRGEIDRIGGLLKELRTALLDMAEKNASTIMPGFTHLQVAQPVTFGHHLLAYVEMFSRDA 187 Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242 ER+ D +RVN PLG ALAGT++PIDRH AK L FD I ANSLD VSDRDFAIEF Sbjct: 188 ERMLDCRKRVNRLPLGAAALAGTSYPIDRHAVAKTLGFDGICANSLDAVSDRDFAIEFTA 247 Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302 A++L+M H+SR +EE++LW S F+ L D TGSSIMPQKKNPDVPEL RGKTGRV Sbjct: 248 ASALVMTHISRFSEELVLWMSPRVGFIDLADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307 Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362 GHL A+L +MKG PLAYNKD QEDKE LFD+V+TV +L ++ G+ + Q + A Sbjct: 308 GHLMALLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFAEMV-AGISVKPQAMRDA 366 Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFA- 421 + FS ATD+ADYL RG+ FR+A+ V V+ G L DL L+E + P A Sbjct: 367 ALQGFSTATDLADYLVKRGLAFRDAHEAVALAVRICADRGCDLADLTLDEMRAELPNVAH 426 Query: 422 ---ADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460 D++ ++ VA+RN GGT QV A+ AAR ++ Sbjct: 427 LIGDDVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARQALN 468 Lambda K H 0.320 0.135 0.384 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: 544 Number of extensions: 18 Number of successful extensions: 3 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: 461 Length of database: 468 Length adjustment: 33 Effective length of query: 428 Effective length of database: 435 Effective search space: 186180 Effective search space used: 186180 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 H281DRAFT_00194 H281DRAFT_00194 (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.6597.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-185 602.1 0.0 4.3e-185 602.0 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00194 H281DRAFT_00194 argininosuccinat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00194 H281DRAFT_00194 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 602.0 0.0 4.3e-185 4.3e-185 2 454 .. 12 467 .. 11 468 .] 0.98 Alignments for each domain: == domain 1 score: 602.0 bits; conditional E-value: 4.3e-185 TIGR00838 2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeev 67 w+ R+++ +++ v+++++s+ fDk+la Diegs+ah+ +L + i+ +e+ + ++++++++k e+ lcl|FitnessBrowser__Burk376:H281DRAFT_00194 12 WSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLGAQKIIAAEDLAAIQRGMAQIKGEI 77 9***************************************************************** PP TIGR00838 68 kegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdl 133 ++g++e++ d eD+Hl++E++l++ +g d+gk+lhtgrsRnDqvatd+rl+lr +++++ lk+l lcl|FitnessBrowser__Burk376:H281DRAFT_00194 78 ERGEFEWQLDLEDVHLNIEARLTALIG-DAGKRLHTGRSRNDQVATDIRLWLRGEIDRIGGLLKEL 142 ***************************.************************************** PP TIGR00838 134 lkalvekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAla 199 ++al++ Aek+ +t+mpg+tHLq AqP+t++Hhllay+em++rD eR+ld kRvn+ PlG++Ala lcl|FitnessBrowser__Burk376:H281DRAFT_00194 143 RTALLDMAEKNASTIMPGFTHLQVAQPVTFGHHLLAYVEMFSRDAERMLDCRKRVNRLPLGAAALA 208 ****************************************************************** PP TIGR00838 200 gtsfeidrellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfv 265 gts++idr+++a++LgFd +++nsldavsdRDf+iE+ +a+al+m+h+sr++Eel+l+ s +gf+ lcl|FitnessBrowser__Burk376:H281DRAFT_00194 209 GTSYPIDRHAVAKTLGFDGICANSLDAVSDRDFAIEFTAASALVMTHISRFSEELVLWMSPRVGFI 274 ****************************************************************** PP TIGR00838 266 elsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalk 331 +l+d++++gssimPqKKnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++ lcl|FitnessBrowser__Burk376:H281DRAFT_00194 275 DLADRFCTGSSIMPQKKNPDVPELARGKTGRVNGHLMALLTLMKGQPLAYNKDNQEDKEPLFDTVD 340 ****************************************************************** PP TIGR00838 332 tveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekG 397 tv ++l++++ +++ + v+ + +++aa ++f++atdlAdylv++G+ FR+ahe v +v+ + ++G lcl|FitnessBrowser__Burk376:H281DRAFT_00194 341 TVADTLRIFAEMVAGISVKPQAMRDAALQGFSTATDLADYLVKRGLAFRDAHEAVALAVRICADRG 406 ****************************************************************** PP TIGR00838 398 kkleeltleelqk....lsekleedvlevldleeavekrdakGGtakeevekaieeakael 454 +l +ltl+e+++ + + + +dv++ l+le +v+ r+ GGta+e+v a+++a++ l lcl|FitnessBrowser__Burk376:H281DRAFT_00194 407 CDLADLTLDEMRAelpnVAHLIGDDVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARQAL 467 ********9987522226677899********************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (468 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7.19 // [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