Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate Ac3H11_1866 L-asparaginase (EC 3.5.1.1)
Query= SwissProt::O68897 (362 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1866 Length = 362 Score = 491 bits (1263), Expect = e-143 Identities = 247/327 (75%), Positives = 282/327 (86%), Gaps = 1/327 (0%) Query: 36 NVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIANVRGEQVMQIASESI 95 +VV+LATGGTIAGAGASAANSATY AAKV +++L+AG+PEL+ +A V GEQV QIASES Sbjct: 37 HVVVLATGGTIAGAGASAANSATYAAAKVPVDKLLAGLPELANVAKVSGEQVFQIASESF 96 Query: 96 NNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGT 155 NE+LL+LG+RV+ L+ DVDGIVITHGTDTLEETAYFLNL +T KPI+VVGSMRPGT Sbjct: 97 TNEHLLRLGQRVSALSKQADVDGIVITHGTDTLEETAYFLNLTVRTTKPIVVVGSMRPGT 156 Query: 156 AMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLG 215 A+SADG LNLY+AV VA SKDA GKGVLVTMNDEIQSGRDVSK INIKTEAFKS WGPLG Sbjct: 157 ALSADGALNLYDAVTVAASKDAAGKGVLVTMNDEIQSGRDVSKTINIKTEAFKSQWGPLG 216 Query: 216 MVVEGKSYWFRLPAKRHTMDSEFDIKTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAII 275 MVVEGK+YWFR P KRHT SEF+I IK+LP V+I YGYGN++ T ++A +AG KA+I Sbjct: 217 MVVEGKNYWFRAPVKRHTTQSEFNIDDIKALPAVDIVYGYGNMNTTGIEAYGKAGVKALI 276 Query: 276 HAGTGNGSVSSKVVPALQELRKQGVQIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNP 335 HAGTGNGSV+++ V +L+ LR GVQIIRS+ V GFVLRNAEQPDDKYDWVVAHDL P Sbjct: 277 HAGTGNGSVAAQAVESLKALRASGVQIIRSARV-PDGFVLRNAEQPDDKYDWVVAHDLRP 335 Query: 336 QKARILAMVALTKTQDSKELQRMFWEY 362 QKARILAMVALTKT DSKELQR+FWEY Sbjct: 336 QKARILAMVALTKTNDSKELQRIFWEY 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: 335 Number of extensions: 7 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: 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 Ac3H11_1866 (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.31562.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-120 386.6 1.6 5.6e-120 386.3 1.6 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 L-asparaginase (EC 3.5.1.1) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 L-asparaginase (EC 3.5.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.3 1.6 5.6e-120 5.6e-120 14 352 .] 25 362 .] 16 362 .] 0.97 Alignments for each domain: == domain 1 score: 386.3 bits; conditional E-value: 5.6e-120 TIGR00520 14 lkvsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiege 75 l++ a +++ P++ +latGGtiag+g+s a+ a Y + k+ v++L+ +Pel+++a+++ge lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 25 LSTVALAQAAKPHVVVLATGGTIAGAGASAANSATYAAAKVPVDKLLAGLPELANVAKVSGE 86 55666678899*************************************************** PP TIGR00520 76 qivnvgsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvl 137 q+ ++ s+++ +e+ll+l +r+s+ ++ dvdGivithGtDtleetayfl+ltv+++kP+v+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 87 QVFQIASESFTNEHLLRLGQRVSALSKQADVDGIVITHGTDTLEETAYFLNLTVRTTKPIVV 148 ************************************************************** PP TIGR00520 138 vGamRpatsvsaDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfks 199 vG+mRp t++saDG+lnLY+av+vaa++++ag+Gvlv++nd+i s+r+v kt ++++fks lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 149 VGSMRPGTALSADGALNLYDAVTVAASKDAAGKGVLVTMNDEIQSGRDVSKTINIKTEAFKS 210 ************************************************************** PP TIGR00520 200 eeqGalGyiandkieyerepvkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvda 261 + G lG ++++k ++ r pvk+ht+++ef+++ + lP vdi+Y+y n+ ++ ++a +a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 211 Q-WGPLGMVVEGKNYWFRAPVKRHTTQSEFNIDDIKA-LPAVDIVYGYGNMNTTGIEAYGKA 270 9.*********************************99.************************ PP TIGR00520 262 gakGivlagvGnGslsaaalkvleeaakesvvivrssRvadGvvtkdae.vddkealiasgt 322 g k ++ ag+GnGs+ a+a++ l+ + ++v i+rs Rv+dG v ++ae +ddk++ + + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 271 GVKALIHAGTGNGSVAAQAVESLKALRASGVQIIRSARVPDGFVLRNAEqPDDKYDWVVAHD 332 *******************************************99876527888******** PP TIGR00520 323 LnPqkaRvLLqLaLtktkdlekiqevfeey 352 L PqkaR+L ++aLtkt+d +++q++f ey lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1866 333 LRPQKARILAMVALTKTNDSKELQRIFWEY 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: 10.85 // [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