Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate SM_b21192 SM_b21192 fructose-1,6-bisphosphate aldolase
Query= BRENDA::Q55664 (359 letters) >FitnessBrowser__Smeli:SM_b21192 Length = 347 Score = 469 bits (1207), Expect = e-137 Identities = 229/345 (66%), Positives = 278/345 (80%) Query: 1 MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60 MAL+ +R LLD AAEN Y +PAFNVNN+E I ++M+AAD TDSPVILQASRGAR+YAG+ Sbjct: 1 MALITLRQLLDDAAENDYALPAFNVNNLEYIQAVMRAADATDSPVILQASRGARAYAGDA 60 Query: 61 FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120 FLRHL+LGA E YPHIP+ +H DHG+ P+TC SAI NGFTSVMMDGSLE D KT AS+EY Sbjct: 61 FLRHLILGAAEEYPHIPVCLHLDHGDQPSTCISAITNGFTSVMMDGSLEKDGKTVASYEY 120 Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180 NV VTAEVVK+AH+ G SVEGELGCLG+LETG G+ EDGHGFEGKL +LLTDPE+A++ Sbjct: 121 NVAVTAEVVKIAHAAGVSVEGELGCLGNLETGAGDKEDGHGFEGKLSREELLTDPEQALD 180 Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240 FV+KT VDALAVAIGTSHGAYKFTR+P GE+L+I I +I++ LPNTHLVMHGSSSVP + Sbjct: 181 FVSKTGVDALAVAIGTSHGAYKFTREPDGEILSIETIAKINKRLPNTHLVMHGSSSVPAD 240 Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300 ++ N +GG + +T+GVPV EIQK I GVRKVNIDTD RLA T R+ + P NFD Sbjct: 241 LQELFNAYGGKMKKTWGVPVSEIQKAIPLGVRKVNIDTDLRLAFTGEIRKHHIEHPDNFD 300 Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYA 345 PR++LKP+I +M +VC +R+ F AG ASKI+ L L + A +YA Sbjct: 301 PRNYLKPAIAHMTEVCKERFVAFRAAGQASKIRVLRLPEMAKRYA 345 Lambda K H 0.315 0.131 0.377 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: 448 Number of extensions: 11 Number of successful extensions: 1 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: 359 Length of database: 347 Length adjustment: 29 Effective length of query: 330 Effective length of database: 318 Effective search space: 104940 Effective search space used: 104940 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate SM_b21192 SM_b21192 (fructose-1,6-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (EC 4.1.2.13))
# 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/TIGR01521.hmm # target sequence database: /tmp/gapView.1759.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01521 [M=347] Accession: TIGR01521 Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-178 578.8 0.1 2.1e-178 578.6 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SM_b21192 SM_b21192 fructose-1,6-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b21192 SM_b21192 fructose-1,6-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 578.6 0.1 2.1e-178 2.1e-178 1 344 [. 3 346 .. 3 347 .] 1.00 Alignments for each domain: == domain 1 score: 578.6 bits; conditional E-value: 2.1e-178 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdi 74 li+lrqlld aae+ y +pafnvnnle i a+m+aad+tdspvilqasrgar yag+++lr+l+l+a eeyp+i lcl|FitnessBrowser__Smeli:SM_b21192 3 LITLRQLLDDAAENDYALPAFNVNNLEYIQAVMRAADATDSPVILQASRGARAYAGDAFLRHLILGAAEEYPHI 76 69************************************************************************ PP TIGR01521 75 pvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsle 148 pv+lh dhg++p+tc sai +gftsvmmdgsl++d+kt a+y+ynv vtaevvk+aha g+svegelgclg le lcl|FitnessBrowser__Smeli:SM_b21192 77 PVCLHLDHGDQPSTCISAITNGFTSVMMDGSLEKDGKTVASYEYNVAVTAEVVKIAHAAGVSVEGELGCLGNLE 150 ************************************************************************** PP TIGR01521 149 tgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherl 222 tg g++edghgfeg+l r +lltdpe+a +fv+kt+vdalavaigtshgaykftr+p ge+l+i+ i +i +rl lcl|FitnessBrowser__Smeli:SM_b21192 151 TGAGDKEDGHGFEGKLSREELLTDPEQALDFVSKTGVDALAVAIGTSHGAYKFTREPDGEILSIETIAKINKRL 224 ************************************************************************** PP TIGR01521 223 pdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpse 296 p+thlvmhgsssvp + ++++n+ygg++k+t+gvpv ei+k i gvrkvnidtdlrla t+ +r+ ++p++ lcl|FitnessBrowser__Smeli:SM_b21192 225 PNTHLVMHGSSSVPADLQELFNAYGGKMKKTWGVPVSEIQKAIPLGVRKVNIDTDLRLAFTGEIRKHHIEHPDN 298 ************************************************************************** PP TIGR01521 297 fdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryak 344 fdpr++lk+a+ m +vck+r+ af +ag+aski+v+ l+ema+rya lcl|FitnessBrowser__Smeli:SM_b21192 299 FDPRNYLKPAIAHMTEVCKERFVAFRAAGQASKIRVLRLPEMAKRYAA 346 **********************************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (347 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.09 // [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