Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_085218001.1 B9N75_RS06120 argininosuccinate lyase
Query= BRENDA::Q8DVX5 (460 letters) >NCBI__GCF_900177405.1:WP_085218001.1 Length = 458 Score = 407 bits (1047), Expect = e-118 Identities = 212/454 (46%), Positives = 294/454 (64%), Gaps = 1/454 (0%) Query: 8 LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67 +WGGRF G + + E ASI FD++L D+ GS AHV ML +GI++ DA I GL Sbjct: 1 MWGGRFADGPSAVMREINASIPFDKRLWRQDIAGSKAHVAMLAAQGIVAAADAGAIAKGL 60 Query: 68 EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127 + + EY+A + D++ EDIHM++E L IGP AG+LHTARSRNDQVATD L+++ Sbjct: 61 DAIAAEYEADGVAEDLALEDIHMHVEHRLAELIGPAAGRLHTARSRNDQVATDFRLWVRD 120 Query: 128 KLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSERF 187 +D V LA + L+D A +H T+MPG+THLQ AQP++ GHHLMAY+ M RD RF Sbjct: 121 AIDAVDAGLAAFQRALLDRAAEHADTVMPGFTHLQVAQPVTLGHHLMAYHAMADRDRSRF 180 Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247 + PLGAAALAGT+FPIDR TA +GF P +NSLD+VSDRDF L++L+ A+ Sbjct: 181 ADARARLNRCPLGAAALAGTSFPIDRAATAAALGFDGPTANSLDSVSDRDFALDYLTAAA 240 Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307 +H+SR+ EE I W S + FV L D +STGSSIMPQK+NPD AEL+RG +GR+ + Sbjct: 241 QCALHLSRLAEEFILWASQPFGFVALPDAYSTGSSIMPQKRNPDAAELVRGHAGRIVGAM 300 Query: 308 FGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQKD 367 L+ MK LPLAY+KD+Q+DK +F+ + + +++ + GM+ S M + Sbjct: 301 TSLMITMKGLPLAYSKDMQDDKPPLFEAHDLLALSIAAMTGMVESAAFVPDRMRAALTAG 360 Query: 368 FSNATELADYLAS-KGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426 + AT+LAD+L G+PFR+AH I G ++ + G L D+PL+ +Q I I+ V+ Sbjct: 361 HATATDLADWLVRVAGIPFREAHHITGGVVKAADEAGLPLWDMPLDAFQAIDPRIDASVF 420 Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460 + L +V+ R S GGT +QV+ +IAEAK AL Sbjct: 421 DVLSIEASVKSRTSFGGTAPDQVRARIAEAKAAL 454 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: 585 Number of extensions: 20 Number of successful extensions: 2 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: 458 Length adjustment: 33 Effective length of query: 427 Effective length of database: 425 Effective search space: 181475 Effective search space used: 181475 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_085218001.1 B9N75_RS06120 (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.739008.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-179 581.1 0.0 1e-178 580.9 0.0 1.0 1 NCBI__GCF_900177405.1:WP_085218001.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085218001.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 580.9 0.0 1e-178 1e-178 1 454 [. 1 454 [. 1 455 [. 0.99 Alignments for each domain: == domain 1 score: 580.9 bits; conditional E-value: 1e-178 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 +wggR++++++ ++e nas+ fDk+l ++Di gs+ah+++La +gi+ + +a + ++L+ ++ e++++ + NCBI__GCF_900177405.1:WP_085218001.1 1 MWGGRFADGPSAVMREINASIPFDKRLWRQDIAGSKAHVAMLAAQGIVAAADAGAIAKGLDAIAAEYEADGVA 73 6************************************************************************ PP TIGR00838 74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146 ++ eDiH+ vE++l + +g ++++lht+rsRnDqvatd+rl++rd+++ + l ++++al+++A+++ + NCBI__GCF_900177405.1:WP_085218001.1 74 EDLALEDIHMHVEHRLAELIG-PAAGRLHTARSRNDQVATDFRLWVRDAIDAVDAGLAAFQRALLDRAAEHAD 145 *********************.7778*********************************************** PP TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219 t+mpg+tHLq AqP+tl+Hhl+ay+ m +rD +R+ da R+n++PlG++Alagtsf+idr ++a+ LgFd NCBI__GCF_900177405.1:WP_085218001.1 146 TVMPGFTHLQVAQPVTLGHHLMAYHAMADRDRSRFADARARLNRCPLGAAALAGTSFPIDRAATAAALGFDGP 218 ************************************************************************* PP TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292 ++nsld+vsdRDf+++ l+aaa +++hlsrlaEe+il++s+ fgfv l+d++s+gssimPqK+npD+aEl+Rg NCBI__GCF_900177405.1:WP_085218001.1 219 TANSLDSVSDRDFALDYLTAAAQCALHLSRLAEEFILWASQPFGFVALPDAYSTGSSIMPQKRNPDAAELVRG 291 ************************************************************************* PP TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365 ++gr++G +t+l++++K+lPlaY kD+q+dk++lf+a + + ++ ++tg++++ + +r++ a ++++a+a NCBI__GCF_900177405.1:WP_085218001.1 292 HAGRIVGAMTSLMITMKGLPLAYSKDMQDDKPPLFEAHDLLALSIAAMTGMVESAAFVPDRMRAALTAGHATA 364 ************************************************************************* PP TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437 tdlAd+lvr G+PFReah+i+G vv++a e+G+ l +++l+ +q+++++++ v++vl++e +v+ r++ GG NCBI__GCF_900177405.1:WP_085218001.1 365 TDLADWLVRVaGIPFREAHHITGGVVKAADEAGLPLWDMPLDAFQAIDPRIDASVFDVLSIEASVKSRTSFGG 437 *********99************************************************************** PP TIGR00838 438 takeevekaieeakael 454 ta+++v+ +i+eaka l NCBI__GCF_900177405.1:WP_085218001.1 438 TAPDQVRARIAEAKAAL 454 **************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (458 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: 17.55 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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