Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate BWI76_RS08720 BWI76_RS08720 imidazolonepropionase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_317 (401 letters) >FitnessBrowser__Koxy:BWI76_RS08720 Length = 405 Score = 426 bits (1095), Expect = e-124 Identities = 222/397 (55%), Positives = 282/397 (71%), Gaps = 7/397 (1%) Query: 2 KTLWQHCHVATM---AQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWV 58 + +W++ +AT+ + Y +++ A++ IE I P GE PAG+ DL G + Sbjct: 8 RVIWRNARLATLDPRSSQPYGLLDHHALLVRNGRIEAIVPEGEAPAGQSI---DLGGRLL 64 Query: 59 TPGLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAA 118 TPGLIDCHTH VFGG+R+ E+EQRL GVSY I+A+GGGI +TVRATR +SE EL A A Sbjct: 65 TPGLIDCHTHLVFGGSRAQEWEQRLNGVSYQTISANGGGINATVRATRDSSEAELLALAR 124 Query: 119 KRLKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYK 178 +RL L+R+GVT++EIKSGYGLDLANERKMLRV ++L A V V T L+AHA PPEYK Sbjct: 125 QRLARLLREGVTTLEIKSGYGLDLANERKMLRVVQQLAATHAVEVSPTLLSAHATPPEYK 184 Query: 179 DRADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAE 238 D YI+ +C +LP L EGL ++VDAFCE + FSP Q ER++ TAQALG+PVK H E Sbjct: 185 GDPDGYINLVCETILPTLWEEGLFESVDAFCENVGFSPTQTERIYSTAQALGIPVKGHVE 244 Query: 239 QLSSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEA 298 QLSSL G+ L +RYH LSADH+E++T + AM++SGTVAVLLPGAFYFL ET+ PP+E Sbjct: 245 QLSSLGGAELVSRYHGLSADHIEYLTPEGVAAMSRSGTVAVLLPGAFYFLNETRRPPVEL 304 Query: 299 LRKHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTH 358 LR++ V +A+A+D NPGTSP SL L +NMAC F +TPEEA AG T HAA ALG +H Sbjct: 305 LREYQVPMAVATDYNPGTSPFASLHLAMNMACVKFGLTPEEAWAGVTRHAAQALGRQASH 364 Query: 359 GSLEVGKVADFVAWQIDRPADLCYWLG-GDLEKRVVR 394 G L G VADF W + P ++ Y G L +RVVR Sbjct: 365 GQLAPGFVADFAIWDAEHPVEMVYEPGRSPLWQRVVR 401 Lambda K H 0.320 0.133 0.399 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: 470 Number of extensions: 18 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: 401 Length of database: 405 Length adjustment: 31 Effective length of query: 370 Effective length of database: 374 Effective search space: 138380 Effective search space used: 138380 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate BWI76_RS08720 BWI76_RS08720 (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.6910.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-144 465.6 0.0 6e-144 465.4 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS08720 BWI76_RS08720 imidazolonepropion Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS08720 BWI76_RS08720 imidazolonepropionase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.4 0.0 6e-144 6e-144 3 377 .] 32 404 .. 30 404 .. 0.99 Alignments for each domain: == domain 1 score: 465.4 bits; conditional E-value: 6e-144 TIGR01224 3 daailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleila 73 ++a+lv++g+i ai ++ ++p+ + idl+G+l +PGl+D+HtHlvf+g+R++e+e++l+G+sY++i a lcl|FitnessBrowser__Koxy:BWI76_RS08720 32 HHALLVRNGRIEAIVPEGEAPA---GQSIDLGGRLLTPGLIDCHTHLVFGGSRAQEWEQRLNGVSYQTISA 99 689*************999998...899******************************************* PP TIGR01224 74 eGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvv 144 +GgGi tvratr+ se+ell+ a++rl++llr+G+ttlE+KsGYGLdl +E kmLrv+++l++++ v+v+ lcl|FitnessBrowser__Koxy:BWI76_RS08720 100 NGGGINATVRATRDSSEAELLALARQRLARLLREGVTTLEIKSGYGLDLANERKMLRVVQQLAATHAVEVS 170 *********************************************************************** PP TIGR01224 145 ttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavkl 215 +t+l aHa P+e+++d+d y++ ++e+++p ee l e+vD+Fce+ +Fs+ q++ri++ aq+ G++vk lcl|FitnessBrowser__Koxy:BWI76_RS08720 171 PTLLSAHATPPEYKGDPDGYINLVCETILPTLWEEGLFESVDAFCENVGFSPTQTERIYSTAQALGIPVKG 241 *********************************************************************** PP TIGR01224 216 HaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekviv 285 H e+l++lggael ++ +++sadH+e++++e+++a+ +gtvavlLPg++++L+ + pp + l++++v++ lcl|FitnessBrowser__Koxy:BWI76_RS08720 242 HVEQLSSLGGAELVSRYHGLSADHIEYLTPEGVAAMSRSGTVAVLLPGAFYFLNeTRRPPVELLREYQVPM 312 ******************************************************8889************* PP TIGR01224 286 alatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesy 356 a+atD nPg+sp++sl+l++++a++++ lt+eea+a++t +aAqalg+++++G+l+ G ad+++++ae++ lcl|FitnessBrowser__Koxy:BWI76_RS08720 313 AVATDYNPGTSPFASLHLAMNMACVKFGLTPEEAWAGVTRHAAQALGRQASHGQLAPGFVADFAIWDAEHP 383 *********************************************************************** PP TIGR01224 357 eeiaYrlgvnvveaviknGev 377 e+ Y+ g + + +++++Ge+ lcl|FitnessBrowser__Koxy:BWI76_RS08720 384 VEMVYEPGRSPLWQRVVRGEI 404 ****************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 1 (405 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: 8.11 // [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