Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate AZOBR_RS21725 AZOBR_RS21725 imidazolonepropionase
Query= reanno::Cup4G11:RR42_RS16905 (420 letters) >FitnessBrowser__azobra:AZOBR_RS21725 Length = 404 Score = 514 bits (1323), Expect = e-150 Identities = 262/397 (65%), Positives = 298/397 (75%), Gaps = 2/397 (0%) Query: 12 DGVWHRCHLLPDGDPAKAIRDAALVVQQGRIVWLGMQAELPQAYAALPRHDAGSAWITPG 71 D +W H P +RDA + V+ GRI W+G + P AA HD G W+TPG Sbjct: 4 DSLWFNGHAATMA-PGGVVRDAVIAVKDGRIAWIGAAKDRPAGRAA-EEHDLGGRWVTPG 61 Query: 72 LVDCHTHLVYGGQRADEFAMRLAGAGYEEIARAGGGIVSTVRATRAADEDTLFALAAARL 131 L+DCHTHLV+GG RA EF MRL GA YEEIARAGGGI STV ATRAADED L A AA RL Sbjct: 62 LIDCHTHLVFGGNRAREFEMRLEGATYEEIARAGGGIASTVAATRAADEDGLIASAAVRL 121 Query: 132 APLLAEGVTTLEIKSGYGLDLASERKQLRVARRLGDAFGVTVHTTFLGAHALPPEYAGRA 191 LLAEGVT +E+KSGYGLDLA+ER+ LR AR LG+ F VTV T L AHALPPE+AGRA Sbjct: 122 QRLLAEGVTMVEVKSGYGLDLATERRMLRAARALGERFPVTVRMTGLAAHALPPEFAGRA 181 Query: 192 DDYITLVCETMMPVLADEGLIDAVDAFCESVGFSLAQTERVFQAAERHGLRVKLHAEQLS 251 DDYI LVCE ++P LA EGL+DAVDAFCE + FS QT RVF A+R GL VKLHA+QLS Sbjct: 182 DDYIALVCEDILPALAAEGLLDAVDAFCERIAFSPEQTARVFDTAQRLGLPVKLHADQLS 241 Query: 252 NLGGTALAARYRALSADHLEHLDEAGVVAMAGSGTVAVLLPGAYYFLRDTNLPPIDLLRR 311 + GG ALAARY+ALSADH+EH E G AMA +GTVAVLLPGA+Y LR+T LPPI+L RR Sbjct: 242 DGGGAALAARYKALSADHVEHTGEEGARAMADAGTVAVLLPGAFYTLRETKLPPIELFRR 301 Query: 312 HGVPMAISTDHNPGTSPVTSLLLMMNMACTLFRLTVPEVLAGVTTHAARALGAADRHGLL 371 HGVPMA+STD NPGTSP SLLLM+NMACTLFRLT E LAGVT +AA+ALG A HG L Sbjct: 302 HGVPMAVSTDCNPGTSPAVSLLLMLNMACTLFRLTPQEALAGVTRNAAQALGMAATHGTL 361 Query: 372 AAGRAADFVLWNVDSPAELAYWFGRNPAAAVVRQGKV 408 G+AAD +WNV PAEL YW G NP AAVVR G++ Sbjct: 362 EPGKAADLAVWNVGDPAELCYWLGANPCAAVVRGGRL 398 Lambda K H 0.321 0.134 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: 596 Number of extensions: 22 Number of successful extensions: 3 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: 420 Length of database: 404 Length adjustment: 31 Effective length of query: 389 Effective length of database: 373 Effective search space: 145097 Effective search space used: 145097 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate AZOBR_RS21725 AZOBR_RS21725 (imidazolonepropionase)
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.21347.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-151 488.0 0.0 9.6e-151 487.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS21725 AZOBR_RS21725 imidazolonepropion Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS21725 AZOBR_RS21725 imidazolonepropionase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.8 0.0 9.6e-151 9.6e-151 2 376 .. 22 397 .. 21 398 .. 0.99 Alignments for each domain: == domain 1 score: 487.8 bits; conditional E-value: 9.6e-151 TIGR01224 2 edaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYle 70 da+i+v++g+ia+ig ++ p+ aa+++dl+G+ v+PGl+D+HtHlvf+g+R++efe++l+Ga+Y+e lcl|FitnessBrowser__azobra:AZOBR_RS21725 22 RDAVIAVKDGRIAWIGAAKDRPAGRAAEEHDLGGRWVTPGLIDCHTHLVFGGNRAREFEMRLEGATYEE 90 5899***************************************************************** PP TIGR01224 71 ilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeel 139 i+++GgGi stv atraA+e+ l+++a rl++ll++G+t +EvKsGYGLdl +E +mLr+++al e++ lcl|FitnessBrowser__azobra:AZOBR_RS21725 91 IARAGGGIASTVAATRAADEDGLIASAAVRLQRLLAEGVTMVEVKSGYGLDLATERRMLRAARALGERF 159 ********************************************************************* PP TIGR01224 140 pvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqe 208 pv v t l+aHa+P+e+ ++ d+y++ ++e+++p+ a e l +avD+Fce+ +Fs+eq+ r+++ aq lcl|FitnessBrowser__azobra:AZOBR_RS21725 160 PVTVRMTGLAAHALPPEFAGRADDYIALVCEDILPALAAEGLLDAVDAFCERIAFSPEQTARVFDTAQR 228 ********************************************************************* PP TIGR01224 209 aGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappar 276 Gl+vklHa++l+ gga+laa+ +a+sadH+e++ +e+++a+a+agtvavlLPg++++Lr ++ pp++ lcl|FitnessBrowser__azobra:AZOBR_RS21725 229 LGLPVKLHADQLSDGGGAALAARYKALSADHVEHTGEEGARAMADAGTVAVLLPGAFYTLReTKLPPIE 297 *************************************************************8889**** PP TIGR01224 277 klidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkd 345 ++ ++v++a++tD nPg+sp sl l+l++a+tl++lt++eala++t naAqalg+++++Gtle Gk lcl|FitnessBrowser__azobra:AZOBR_RS21725 298 LFRRHGVPMAVSTDCNPGTSPAVSLLLMLNMACTLFRLTPQEALAGVTRNAAQALGMAATHGTLEPGKA 366 ********************************************************************* PP TIGR01224 346 adlvvlsaesyeeiaYrlgvnvveaviknGe 376 adl+v+++ +++e+ Y+lg+n +av+ G lcl|FitnessBrowser__azobra:AZOBR_RS21725 367 ADLAVWNVGDPAELCYWLGANPCAAVVRGGR 397 ***********************99998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 1 (404 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.64 // [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