Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_041465929.1 CLIM_RS06260 argininosuccinate lyase
Query= BRENDA::Q8DVX5 (460 letters) >NCBI__GCF_000020465.1:WP_041465929.1 Length = 460 Score = 418 bits (1075), Expect = e-121 Identities = 210/460 (45%), Positives = 305/460 (66%) Query: 1 MTTKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDA 60 M+ K LW RF + F +S+ D+ L D++GS AHVTML E+GIIS+E++ Sbjct: 1 MSNKKELLWQSRFSEPFDRDALRFSSSVHVDKALFREDIEGSTAHVTMLAEEGIISEEES 60 Query: 61 ATIKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATD 120 I GL ++ E +AG L +EDIH +E+ L KIG AGK+H+ RSRNDQVATD Sbjct: 61 GQIIRGLREIGAELEAGDLVPHWEDEDIHTVIENRLKEKIGATAGKIHSGRSRNDQVATD 120 Query: 121 MHLYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMF 180 LYL+ ++ + L L+ LV A+ + TI+ GYTHLQ AQPIS GH+ +AY+NMF Sbjct: 121 TRLYLRRQIRTLGTALQGLQKTLVSKAETYRETIIFGYTHLQRAQPISAGHYYLAYFNMF 180 Query: 181 TRDSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFIL 240 RD +R +K ++SPLGAAA AG+T P++ +A+L+ F +SNS+DAVSDRD ++ Sbjct: 181 RRDRDRLTDLLKRVNISPLGAAAFAGSTLPLNPARSAELLDFDGVFSNSIDAVSDRDTVI 240 Query: 241 EFLSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKS 300 EF+S S++MMH+SR E++I W S+E+ ++ +SD F+TGSS+MPQKKN D+AEL+RGK+ Sbjct: 241 EFISVCSMVMMHLSRFAEDLILWSSYEFGYLEISDAFATGSSLMPQKKNADIAELVRGKT 300 Query: 301 GRVYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHM 360 GRVY +L +LT+MK LPL+YN+D+QEDK +FDTAET ++ I +L + ++ + Sbjct: 301 GRVYGSLITMLTIMKGLPLSYNRDMQEDKPPLFDTAETTIESVSIFGKLLEHTTLKEERL 360 Query: 361 AESTQKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDL 420 A+ T D S ATE+A+YL K +PFR AH + G+++ +G L + L+ Y+T S+L Sbjct: 361 AKLTADDLSLATEIAEYLVKKQLPFRDAHRVTGRIVSHSLMSGTTLPGITLDVYRTFSEL 420 Query: 421 IEEDVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460 E D+Y LK +++ + + G F+ V Q+ EAKK L Sbjct: 421 FESDIYAALKPEASIKAKKTHGSCSFDSVAIQLEEAKKLL 460 Lambda K H 0.318 0.132 0.378 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: 565 Number of extensions: 20 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: 460 Length of database: 460 Length adjustment: 33 Effective length of query: 427 Effective length of database: 427 Effective search space: 182329 Effective search space used: 182329 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_041465929.1 CLIM_RS06260 (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.3974.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-181 589.1 0.0 3.8e-181 589.0 0.0 1.0 1 lcl|NCBI__GCF_000020465.1:WP_041465929.1 CLIM_RS06260 argininosuccinate l Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020465.1:WP_041465929.1 CLIM_RS06260 argininosuccinate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 589.0 0.0 3.8e-181 3.8e-181 1 452 [. 8 458 .. 8 460 .] 0.99 Alignments for each domain: == domain 1 score: 589.0 bits; conditional E-value: 3.8e-181 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 lw++R+++ d ++ +f++s++ Dk l+++Diegs+ah+++La++gi++eee ++i++L+e+ e ++ lcl|NCBI__GCF_000020465.1:WP_041465929.1 8 LWQSRFSEPFDRDALRFSSSVHVDKALFREDIEGSTAHVTMLAEEGIISEEESGQIIRGLREIGAELEA 76 7******************************************************************** PP TIGR00838 70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138 g+l +++++eDiH+++E++l +k+g ++k+h+grsRnDqvatd rlylr ++++l +al+ l+k+lv lcl|NCBI__GCF_000020465.1:WP_041465929.1 77 GDLVPHWEDEDIHTVIENRLKEKIG-ATAGKIHSGRSRNDQVATDTRLYLRRQIRTLGTALQGLQKTLV 144 *************************.6666*************************************** PP TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207 kAe+ et++ gytHLqrAqPi+ +H+ lay++m++rD +Rl+d lkRvn sPlG++A+ag+++++++ lcl|NCBI__GCF_000020465.1:WP_041465929.1 145 SKAETYRETIIFGYTHLQRAQPISAGHYYLAYFNMFRRDRDRLTDLLKRVNISPLGAAAFAGSTLPLNP 213 ********************************************************************* PP TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276 ++aelL Fd v +ns+davsdRD +iE++s+++++m+hlsr+aE+lil+ss+Efg++e+sd++++gss lcl|NCBI__GCF_000020465.1:WP_041465929.1 214 ARSAELLDFDGVFSNSIDAVSDRDTVIEFISVCSMVMMHLSRFAEDLILWSSYEFGYLEISDAFATGSS 282 ********************************************************************* PP TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345 +mPqKKn+D+aEl+Rgktgrv+G+l+++lti+K+lPl+Yn+D+qEdk++lfd+ +t+ e+++++ ll+ lcl|NCBI__GCF_000020465.1:WP_041465929.1 283 LMPQKKNADIAELVRGKTGRVYGSLITMLTIMKGLPLSYNRDMQEDKPPLFDTAETTIESVSIFGKLLE 351 ********************************************************************* PP TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414 + ++++erl+++++++ +lat++A+ylv+k +PFR+ah+++G++v +++ +G++l +tl++++ +se lcl|NCBI__GCF_000020465.1:WP_041465929.1 352 HTTLKEERLAKLTADDLSLATEIAEYLVKKQLPFRDAHRVTGRIVSHSLMSGTTLPGITLDVYRTFSEL 420 ********************************************************************* PP TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeaka 452 +e d++ +l++e ++++++++G ++++v+ ++eeak+ lcl|NCBI__GCF_000020465.1:WP_041465929.1 421 FESDIYAALKPEASIKAKKTHGSCSFDSVAIQLEEAKK 458 ***********************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (460 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: 8.55 // [ok]
This GapMind analysis is from Apr 10 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