Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate 6935865 Sama_0080 imidazolonepropionase (RefSeq)
Query= reanno::MR1:199292 (408 letters) >FitnessBrowser__SB2B:6935865 Length = 412 Score = 685 bits (1768), Expect = 0.0 Identities = 335/412 (81%), Positives = 374/412 (90%), Gaps = 4/412 (0%) Query: 1 MSWDQVWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRG 60 MSWDQVWID+N+ATMDPS++ YGAIT AA+AVKDGKIAWLG RS+LP FDVL+ PV+RG Sbjct: 1 MSWDQVWIDINIATMDPSMNEAYGAITDAALAVKDGKIAWLGKRSDLPEFDVLATPVHRG 60 Query: 61 KGGWITPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAAL 120 GGW+TPGLIDAHTHLVFAGNRANEFELRL+GA+YEEIARAGGGI+STV ACR+ADEA L Sbjct: 61 HGGWLTPGLIDAHTHLVFAGNRANEFELRLQGASYEEIARAGGGIVSTVKACRDADEAEL 120 Query: 121 FELGRQRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAV 180 F+L R+RLNALAKEGVTTVEIKSGYGLD +TELK+LRVARELG+HHHVDV TTFLGAHAV Sbjct: 121 FDLARRRLNALAKEGVTTVEIKSGYGLDLDTELKLLRVARELGQHHHVDVVTTFLGAHAV 180 Query: 181 PPEYK----GNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAA 236 PPE+K +D YVDL++N+MLPAV+ ENLADA DVFCENIAFNLEQTERVLSAAK Sbjct: 181 PPEFKTLGEAGTDAYVDLVVNEMLPAVVAENLADAADVFCENIAFNLEQTERVLSAAKTL 240 Query: 237 GLQVKLHAEQLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLR 296 GL +KLHAEQLSN+GGSELAARLGAKSVDHIEYLDEAGVKA+++SGTCAVLLPGAFYFLR Sbjct: 241 GLDIKLHAEQLSNLGGSELAARLGAKSVDHIEYLDEAGVKAIAQSGTCAVLLPGAFYFLR 300 Query: 297 ETQKPPIDLLRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAA 356 ET+ PPIDLLRQY VPMVLASDFNPGS PICSTLLMLNMGCTLFRLTPEEALAG+T NAA Sbjct: 301 ETKLPPIDLLRQYQVPMVLASDFNPGSSPICSTLLMLNMGCTLFRLTPEEALAGVTRNAA 360 Query: 357 KALGIEDKVGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVHQ 408 +ALG + +VG L G +ADFCLW I+TPA+LAYSYGVNP DVVK G+L+HQ Sbjct: 361 RALGRDQRVGVLREGMEADFCLWRISTPAELAYSYGVNPLVDVVKGGRLIHQ 412 Lambda K H 0.319 0.136 0.402 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: 633 Number of extensions: 14 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: 408 Length of database: 412 Length adjustment: 31 Effective length of query: 377 Effective length of database: 381 Effective search space: 143637 Effective search space used: 143637 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate 6935865 Sama_0080 (imidazolonepropionase (RefSeq))
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))
# 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/TIGR01224.hmm # target sequence database: /tmp/gapView.8511.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01224 [M=377] Accession: TIGR01224 Description: hutI: imidazolonepropionase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-148 478.7 0.0 6.5e-148 478.5 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6935865 Sama_0080 imidazolonepropionase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6935865 Sama_0080 imidazolonepropionase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.5 0.0 6.5e-148 6.5e-148 2 376 .. 27 408 .. 26 409 .. 0.97 Alignments for each domain: == domain 1 score: 478.5 bits; conditional E-value: 6.5e-148 TIGR01224 2 edaailveegkiaaigqkaalpge..eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeGg 76 daa++v++gkia++g++++lp a+ ++ +G+ +PGl+D+HtHlvfag+R++efel+lqGasY+ei+++Gg lcl|FitnessBrowser__SB2B:6935865 27 TDAALAVKDGKIAWLGKRSDLPEFdvLATPVHRGHGGWLTPGLIDAHTHLVFAGNRANEFELRLQGASYEEIARAGG 103 689*******************9844578889999****************************************** PP TIGR01224 77 GilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttflgaHav 153 Gi+stv+a r+A+e+el++ a+ rl+ l ++G+tt+E+KsGYGLdl++Elk+Lrv+++l ++++vdvvttflgaHav lcl|FitnessBrowser__SB2B:6935865 104 GIVSTVKACRDADEAELFDLARRRLNALAKEGVTTVEIKSGYGLDLDTELKLLRVARELGQHHHVDVVTTFLGAHAV 180 ***************************************************************************** PP TIGR01224 154 Pkevq....ededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelkalgga 226 P+e++ + d+yvd +++e++p+v e+la+a+DvFce+ +F+ eq++r+l+aa+ Gl +klHae+l++lgg+ lcl|FitnessBrowser__SB2B:6935865 181 PPEFKtlgeAGTDAYVDLVVNEMLPAVVAENLADAADVFCENIAFNLEQTERVLSAAKTLGLDIKLHAEQLSNLGGS 257 ***9733324569**************************************************************** PP TIGR01224 227 elaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslq 302 elaa+lga s+dH+e+++++++ka+a++gt avlLPg++++Lr ++ pp++ l++++v++ la+D+nPgssp+ s+ lcl|FitnessBrowser__SB2B:6935865 258 ELAARLGAKSVDHIEYLDEAGVKAIAQSGTCAVLLPGAFYFLReTKLPPIDLLRQYQVPMVLASDFNPGSSPICSTL 334 *******************************************8889****************************** PP TIGR01224 303 lilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknGe 376 l+l++++tl++lt+eeala++t naA alg+ ++ G l+eG +ad+ ++ ++ ++e+aY +gvn + v+k G lcl|FitnessBrowser__SB2B:6935865 335 LMLNMGCTLFRLTPEEALAGVTRNAARALGRDQRVGVLREGMEADFCLWRISTPAELAYSYGVNPLVDVVKGGR 408 ****************************************************************9999998885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 1 (412 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: 9.92 // [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