Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate Pf1N1B4_6037 L-asparaginase (EC 3.5.1.1)
Query= SwissProt::O68897 (362 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 Length = 362 Score = 660 bits (1702), Expect = 0.0 Identities = 341/362 (94%), Positives = 347/362 (95%) Query: 1 MKSALKTFVPGALALLLLFPVAAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQ 60 MKSA TF+PGALALLLL P A QAKEVETK KLANVVILATGGTIAGAGASAANSATYQ Sbjct: 1 MKSAFNTFIPGALALLLLLPTALQAKEVETKQKLANVVILATGGTIAGAGASAANSATYQ 60 Query: 61 AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV 120 AAKVGIEQLIAGVPELSQ+ANVRGEQVMQIASESI N+NLLQLGRRVAELADSKDVDGIV Sbjct: 61 AAKVGIEQLIAGVPELSQLANVRGEQVMQIASESITNDNLLQLGRRVAELADSKDVDGIV 120 Query: 121 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVA SKDARGK Sbjct: 121 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVASSKDARGK 180 Query: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240 GVLVTMNDEIQSGRDVSKMINIKTEAFKS WGPLGMVVEGKSYWFRLPAKRHTMDSEFDI Sbjct: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSAWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240 Query: 241 KTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGV 300 KTIKSL DVEIAY YGNVSDTA KALAQ+GAKAIIHAGTGNGSVSS+VVPALQ LRK GV Sbjct: 241 KTIKSLADVEIAYSYGNVSDTAYKALAQSGAKAIIHAGTGNGSVSSRVVPALQALRKDGV 300 Query: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFW 360 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVA+DLNPQKARILAMVALTKT DSKELQRMFW Sbjct: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVANDLNPQKARILAMVALTKTNDSKELQRMFW 360 Query: 361 EY 362 EY Sbjct: 361 EY 362 Lambda K H 0.315 0.130 0.361 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: 445 Number of extensions: 4 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: 362 Length of database: 362 Length adjustment: 29 Effective length of query: 333 Effective length of database: 333 Effective search space: 110889 Effective search space used: 110889 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 (21.5 bits) S2: 49 (23.5 bits)
Align candidate Pf1N1B4_6037 (L-asparaginase (EC 3.5.1.1))
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))
# 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.carbon/TIGR00520.hmm # target sequence database: /tmp/gapView.31193.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00520 [M=352] Accession: TIGR00520 Description: asnASE_II: L-asparaginase, type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-121 391.7 3.2 1.5e-121 391.5 3.2 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 L-asparaginase (EC 3.5.1.1) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 L-asparaginase (EC 3.5.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 391.5 3.2 1.5e-121 1.5e-121 16 352 .] 26 362 .] 14 362 .] 0.96 Alignments for each domain: == domain 1 score: 391.5 bits; conditional E-value: 1.5e-121 TIGR00520 16 vsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivn 79 +++ +++L n+ ilatGGtiag+g+s a+ a Y++ k+g+e+Li vPel+++an++geq+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 26 KEVETKQKLANVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQLANVRGEQVMQ 89 34556899******************************************************** PP TIGR00520 80 vgsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRp 143 + s+++ ++ ll+l +r+ e +s+dvdGivithGtDtleetayfl+l+ k+dkP+++vG+mRp lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 90 IASESITNDNLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRP 153 **************************************************************** PP TIGR00520 144 atsvsaDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGy 207 t++saDG lnLYnav+va++++++g+Gvlv++nd+i s+r+v k+ ++++fks G lG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 154 GTAMSADGMLNLYNAVAVASSKDARGKGVLVTMNDEIQSGRDVSKMINIKTEAFKSA-WGPLGM 216 ********************************************************9.****** PP TIGR00520 208 iandkieyerepvkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagv 271 ++++k ++ r p+k+ht+++efd++ ++ l +v+i Y+y n++++ ka++++gak i+ ag+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 217 VVEGKSYWFRLPAKRHTMDSEFDIKTIKS-LADVEIAYSYGNVSDTAYKALAQSGAKAIIHAGT 279 *****************************.********************************** PP TIGR00520 272 GnGslsaaalkvleeaakesvvivrssRvadG.vvt.kdaevddkealiasgtLnPqkaRvLLq 333 GnGs+s ++ +l+ + k++v i+rss v+ G v +++++ddk++ + ++ LnPqkaR+L + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 280 GNGSVSSRVVPALQALRKDGVQIIRSSHVNAGgFVLrNAEQPDDKYDWVVANDLNPQKARILAM 343 *****************************9873444155678999******************* PP TIGR00520 334 LaLtktkdlekiqevfeey 352 +aLtkt+d +++q++f ey lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6037 344 VALTKTNDSKELQRMFWEY 362 ****************887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 1 (362 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: 11.15 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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