Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate BPHYT_RS05210 BPHYT_RS05210 argininosuccinate lyase
Query= SwissProt::Q9LAE5 (461 letters) >FitnessBrowser__BFirm:BPHYT_RS05210 Length = 468 Score = 437 bits (1123), Expect = e-127 Identities = 235/461 (50%), Positives = 304/461 (65%), Gaps = 5/461 (1%) Query: 3 KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62 K + WS RF + + R+ +S+ FD L D+ GS AHA MLA II++++ + Sbjct: 8 KGEAWSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLAAQKIIAADDLAAIQ 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 LRGEIDRIGGLLTELRTALLDMAEKNASTIMPGFTHLQVAQPVTFGHHLLAYVEMFSRDA 187 Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242 ER+ D +RVN PLG ALAGT++PIDRH AK L FD I ANSLD VSDRDFAIEF Sbjct: 188 ERMIDCRKRVNRLPLGAAALAGTSYPIDRHAVAKTLGFDGICANSLDAVSDRDFAIEFTA 247 Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302 A++L+M H+SR +EE++LW S F+ L D TGSSIMPQKKNPDVPEL RGKTGRV Sbjct: 248 ASALVMTHVSRFSEELVLWMSPRVGFIDLADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307 Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362 GHL A+L +MKG PLAYNKD QEDKE LFD+V+TV +L ++ G+ + Q + A Sbjct: 308 GHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFAEMV-AGISVKPQAMRDA 366 Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFA- 421 + FS ATD+ADYL RG+PFR+A+ V V+ G L DL LEE ++ P A Sbjct: 367 ALQGFSTATDLADYLVKRGLPFRDAHEAVALAVRVCADRGCDLADLTLEEMRKELPNVAH 426 Query: 422 ---ADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459 D++ ++ VA+RN GGT QV A+ AARA + Sbjct: 427 LIGEDVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARAAL 467 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: 537 Number of extensions: 19 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 BPHYT_RS05210 BPHYT_RS05210 (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.31020.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-186 607.3 0.0 1.2e-186 607.1 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS05210 BPHYT_RS05210 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS05210 BPHYT_RS05210 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 607.1 0.0 1.2e-186 1.2e-186 2 454 .. 12 467 .. 11 468 .] 0.98 Alignments for each domain: == domain 1 score: 607.1 bits; conditional E-value: 1.2e-186 TIGR00838 2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegk 71 w+ R+++ +++ v+++++s+ fDk+la Diegs+ah+ +La + i+ +++ + ++++++++k e+++g+ lcl|FitnessBrowser__BFirm:BPHYT_RS05210 12 WSARFSEPMSELVKRYTSSVFFDKRLALVDIEGSLAHASMLAAQKIIAADDLAAIQRGMAQIKGEIERGE 81 9********************************************************************* PP TIGR00838 72 lelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekA 141 +e++ d eD+Hl++E++l++ +g d+gk+lhtgrsRnDqvatd+rl+lr +++++ l +l++al++ A lcl|FitnessBrowser__BFirm:BPHYT_RS05210 82 FEWQLDLEDVHLNIEARLTALIG-DAGKRLHTGRSRNDQVATDIRLWLRGEIDRIGGLLTELRTALLDMA 150 ***********************.********************************************** PP TIGR00838 142 ekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrella 211 ek+ +t+mpg+tHLq AqP+t++Hhllay+em++rD eR++d kRvn+ PlG++Alagts++idr+++a lcl|FitnessBrowser__BFirm:BPHYT_RS05210 151 EKNASTIMPGFTHLQVAQPVTFGHHLLAYVEMFSRDAERMIDCRKRVNRLPLGAAALAGTSYPIDRHAVA 220 ********************************************************************** PP TIGR00838 212 elLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqK 281 ++LgFd +++nsldavsdRDf+iE+ +a+al+m+h+sr++Eel+l+ s +gf++l+d++++gssimPqK lcl|FitnessBrowser__BFirm:BPHYT_RS05210 221 KTLGFDGICANSLDAVSDRDFAIEFTAASALVMTHVSRFSEELVLWMSPRVGFIDLADRFCTGSSIMPQK 290 ********************************************************************** PP TIGR00838 282 KnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnk 351 KnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++tv ++l++++ +++ + v+ lcl|FitnessBrowser__BFirm:BPHYT_RS05210 291 KNPDVPELARGKTGRVNGHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTVADTLRIFAEMVAGISVKP 360 ********************************************************************** PP TIGR00838 352 erleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqk....lseklee 417 + +++aa ++f++atdlAdylv++G+PFR+ahe v +v+ + ++G +l +ltlee++k + + + e lcl|FitnessBrowser__BFirm:BPHYT_RS05210 361 QAMRDAALQGFSTATDLADYLVKRGLPFRDAHEAVALAVRVCADRGCDLADLTLEEMRKelpnVAHLIGE 430 *******************************************************998733335667899 PP TIGR00838 418 dvlevldleeavekrdakGGtakeevekaieeakael 454 dv++ l+le +v+ r+ GGta+e+v a+++a+a l lcl|FitnessBrowser__BFirm:BPHYT_RS05210 431 DVFSYLTLEGSVASRNHPGGTAPEQVLAAVKAARAAL 467 *********************************9987 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9.34 // [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