Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_106719047.1 CU100_RS23360 argininosuccinate lyase
Query= BRENDA::Q8DVX5 (460 letters) >NCBI__GCF_003010935.1:WP_106719047.1 Length = 466 Score = 432 bits (1111), Expect = e-125 Identities = 228/457 (49%), Positives = 302/457 (66%), Gaps = 1/457 (0%) Query: 5 NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64 ++++WGGRF +G A +EE ASI FDQKL D++GS+AH ML + GIIS +D I Sbjct: 7 SNEMWGGRFASGPAAIMEEINASIGFDQKLYAQDIQGSLAHAAMLAKTGIISGDDHDKIA 66 Query: 65 AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124 GL +L E + G+ F EDIHMN+ES L IG AG+LHTARSRNDQVA D L+ Sbjct: 67 KGLNTILSEIETGKFIFSRKLEDIHMNIESRLAELIGAPAGRLHTARSRNDQVAVDFRLW 126 Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184 +KA+ ++ L L + A +H T+MPG+THLQ AQP++FGHH MAY MF RD Sbjct: 127 VKAEFEKTAIALKMLIEAFLKRAAEHATTLMPGFTHLQTAQPVTFGHHCMAYVEMFGRDL 186 Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244 R ++ D SPLGAAALAGT FPIDR MTA+ +GF EP NSLD+VSDRD+ LEFLS Sbjct: 187 SRVRDAIERMDESPLGAAALAGTGFPIDRHMTAKALGFREPTRNSLDSVSDRDYALEFLS 246 Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304 A+I H+SR+ EE++ W + ++ FV LSD+FSTGSSIMPQKKNPD AEL+R K+GR+ Sbjct: 247 TAAITATHLSRLAEEIVIWSTPQFGFVRLSDSFSTGSSIMPQKKNPDAAELVRAKTGRIT 306 Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364 +L GLLTVMK LPL Y+KD+QEDKE +FD AET+ +A+ + GM+ M +N M ++ Sbjct: 307 GSLVGLLTVMKGLPLTYSKDMQEDKEAVFDAAETLELAIAAMTGMVGDMTINTAAMKKAA 366 Query: 365 QKDFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEE 423 +S AT+LAD+L + G+PFR+AH + G+ + + L + LE Q I I + Sbjct: 367 GSGYSTATDLADWLVRELGLPFREAHHVTGRAVALAERQKVDLGKLALEDMQAIHPGITD 426 Query: 424 DVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460 V+ L +V R S GGT +V+ QI +K L Sbjct: 427 AVFGYLTIDKSVRSRKSYGGTAPGEVRRQIRFWQKRL 463 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: 578 Number of extensions: 27 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: 466 Length adjustment: 33 Effective length of query: 427 Effective length of database: 433 Effective search space: 184891 Effective search space used: 184891 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_106719047.1 CU100_RS23360 (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.980818.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-187 608.2 0.0 6e-187 608.1 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106719047.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106719047.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 608.1 0.0 6e-187 6e-187 1 454 [. 10 463 .. 10 464 .. 0.99 Alignments for each domain: == domain 1 score: 608.1 bits; conditional E-value: 6e-187 TIGR00838 1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 +wggR+++++ ++e nas+ fD++l+++Di+gs+ah+++Lak+gi++ ++++k+ ++L+++ +e++ gk+ NCBI__GCF_003010935.1:WP_106719047.1 10 MWGGRFASGPAAIMEEINASIGFDQKLYAQDIQGSLAHAAMLAKTGIISGDDHDKIAKGLNTILSEIETGKFI 82 6************************************************************************ PP TIGR00838 74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146 ++ + eDiH+++E++l + +g +g +lht+rsRnDqva+d+rl+++++ ++ a alk l++a++++A+++ NCBI__GCF_003010935.1:WP_106719047.1 83 FSRKLEDIHMNIESRLAELIGAPAG-RLHTARSRNDQVAVDFRLWVKAEFEKTAIALKMLIEAFLKRAAEHAT 154 *********************7777.*********************************************** PP TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219 tlmpg+tHLq AqP+t++Hh++ay+em+ rDl+R+ da++R+++sPlG++Alagt+f+idr+++a+ LgF + NCBI__GCF_003010935.1:WP_106719047.1 155 TLMPGFTHLQTAQPVTFGHHCMAYVEMFGRDLSRVRDAIERMDESPLGAAALAGTGFPIDRHMTAKALGFREP 227 ************************************************************************* PP TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292 ++nsld+vsdRD+++E+ls+aa++++hlsrlaEe++++s+ fgfv lsd++s+gssimPqKKnpD+aEl+R+ NCBI__GCF_003010935.1:WP_106719047.1 228 TRNSLDSVSDRDYALEFLSTAAITATHLSRLAEEIVIWSTPQFGFVRLSDSFSTGSSIMPQKKNPDAAELVRA 300 ************************************************************************* PP TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365 ktgr++G+l+gllt++K+lPl+Y kD+qEdkea+fda +t+e ++ ++tg++ ++++n+ +++aa +++++a NCBI__GCF_003010935.1:WP_106719047.1 301 KTGRITGSLVGLLTVMKGLPLTYSKDMQEDKEAVFDAAETLELAIAAMTGMVGDMTINTAAMKKAAGSGYSTA 373 ************************************************************************* PP TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437 tdlAd+lvr+ G+PFReah+++G++va a+++ ++l +l+le +q++++ +++ v+ l++ ++v+ r+++GG NCBI__GCF_003010935.1:WP_106719047.1 374 TDLADWLVRElGLPFREAHHVTGRAVALAERQKVDLGKLALEDMQAIHPGITDAVFGYLTIDKSVRSRKSYGG 446 ********************************99*************************************** PP TIGR00838 438 takeevekaieeakael 454 ta+ ev+++i +++l NCBI__GCF_003010935.1:WP_106719047.1 447 TAPGEVRRQIRFWQKRL 463 **********9988776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (466 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17.27 // [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