Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate RR42_RS26140 RR42_RS26140 glutaminase
Query= SwissProt::O68897 (362 letters) >FitnessBrowser__Cup4G11:RR42_RS26140 Length = 373 Score = 418 bits (1074), Expect = e-121 Identities = 206/341 (60%), Positives = 264/341 (77%), Gaps = 1/341 (0%) Query: 22 AAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIAN 81 AA A ++ + AN+VI+ TGGTIAGAGA+A N+A YQ+A V ++++IA VPE+S+IAN Sbjct: 34 AAGAPTQASEARKANIVIIGTGGTIAGAGAAATNTAAYQSAVVPVDKIIASVPEISKIAN 93 Query: 82 VRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKT 141 V+GEQV QI SES NNE LL+LG+RV+EL DVDGIVITHGTDT+EET YFLNL K+ Sbjct: 94 VKGEQVFQIGSESFNNERLLKLGKRVSELLKQPDVDGIVITHGTDTIEETTYFLNLTLKS 153 Query: 142 DKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMIN 201 DKP++VVGSMRPGTA+ ADG LNLY+AV VA S ++RGKG L +NDEI +GRDV+K Sbjct: 154 DKPVVVVGSMRPGTALGADGALNLYDAVLVASSPESRGKGTLAVLNDEIHTGRDVTKSNT 213 Query: 202 IKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDIKTIKSLPDVEIAYGYGNVSDT 261 K E F+SP+GPLG VVEG++ ++RLPA+ HTM +E+DI I LP+V + Y YGNV+ Sbjct: 214 FKIETFRSPFGPLGYVVEGRTLYYRLPARPHTMQTEWDIDKIDKLPEVAVVYAYGNVNPA 273 Query: 262 AVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGVQIIRSSHVNAGGFVLRNAEQP 321 ++ A + GAKAI++A TGNGSV +V L+ R +GVQI+R+S GG V+RNAEQP Sbjct: 274 SIDAAVKNGAKAIVYAATGNGSVGDYMVEPLKAARAKGVQIVRASR-TGGGVVVRNAEQP 332 Query: 322 DDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFWEY 362 DDKYDW+V D PQKARIL +ALTKT D+KELQ++FW+Y Sbjct: 333 DDKYDWLVTDDQLPQKARILMALALTKTNDTKELQKIFWKY 373 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: 325 Number of extensions: 8 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: 373 Length adjustment: 30 Effective length of query: 332 Effective length of database: 343 Effective search space: 113876 Effective search space used: 113876 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 RR42_RS26140 RR42_RS26140 (glutaminase)
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.7803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-125 402.6 0.6 7.6e-125 402.3 0.6 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS26140 RR42_RS26140 glutaminase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS26140 RR42_RS26140 glutaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.3 0.6 7.6e-125 7.6e-125 21 352 .] 43 373 .] 27 373 .] 0.95 Alignments for each domain: == domain 1 score: 402.3 bits; conditional E-value: 7.6e-125 TIGR00520 21 aksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneev 89 ++ ni i++tGGtiag+g+ ++ta+Y++ ++ v+++i +vPe+++ian++geq+ ++gs+++n+e lcl|FitnessBrowser__Cup4G11:RR42_RS26140 43 EARKANIVIIGTGGTIAGAGAAATNTAAYQSAVVPVDKIIASVPEISKIANVKGEQVFQIGSESFNNER 111 445579*************************************************************** PP TIGR00520 90 llklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYna 158 llkl kr+se l++ dvdGivithGtDt+eet yfl+lt+ksdkPvv+vG+mRp t++ aDG+lnLY+a lcl|FitnessBrowser__Cup4G11:RR42_RS26140 112 LLKLGKRVSELLKQPDVDGIVITHGTDTIEETTYFLNLTLKSDKPVVVVGSMRPGTALGADGALNLYDA 180 ********************************************************************* PP TIGR00520 159 vsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtlet 227 v va++++s+g+G+l vlnd+i +r+vtk nt +++tf+s G lGy++++ + y+r p+++ht++t lcl|FitnessBrowser__Cup4G11:RR42_RS26140 181 VLVASSPESRGKGTLAVLNDEIHTGRDVTKSNTFKIETFRSP-FGPLGYVVEGRTLYYRLPARPHTMQT 248 *****************************************9.************************** PP TIGR00520 228 efdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivr 296 e+d++k d+ lP+v ++Yay n+ ++ ++a+v++gak iv a++GnGs+ + +++ l+ a ++v ivr lcl|FitnessBrowser__Cup4G11:RR42_RS26140 249 EWDIDKIDK-LPEVAVVYAYGNVNPASIDAAVKNGAKAIVYAATGNGSVGDYMVEPLKAARAKGVQIVR 316 *********.*********************************************************** PP TIGR00520 297 ssRvadGvvtkdae.vddkealiasgtLnPqkaRvLLqLaLtktkdlekiqevfeey 352 +sR+ Gvv ++ae +ddk++ + + PqkaR+L+ LaLtkt+d++++q++f +y lcl|FitnessBrowser__Cup4G11:RR42_RS26140 317 ASRTGGGVVVRNAEqPDDKYDWLVTDDQLPQKARILMALALTKTNDTKELQKIFWKY 373 *******9998765277887766666667*************************765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 1 (373 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: 10.71 // [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