Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate BPHYT_RS16260 BPHYT_RS16260 fructose-bisphosphate aldolase
Query= SwissProt::Q56815 (354 letters) >FitnessBrowser__BFirm:BPHYT_RS16260 Length = 354 Score = 513 bits (1321), Expect = e-150 Identities = 253/353 (71%), Positives = 298/353 (84%) Query: 1 MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60 M LVSMRQLLDHAA++ YGLPAFNVNN+EQV+AIM AA ++PVI+Q SAGARKYAGE Sbjct: 1 MPLVSMRQLLDHAAENGYGLPAFNVNNLEQVQAIMAAADKVNAPVIMQASAGARKYAGEA 60 Query: 61 FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120 FLRHLI AAVE+YP IPVVMHQDHG SPAVCM AI+SGF+SVMMDGSL+ DGKT A Y+Y Sbjct: 61 FLRHLIEAAVESYPHIPVVMHQDHGQSPAVCMAAIRSGFTSVMMDGSLEADGKTVASYEY 120 Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180 NV V+ KVVE AH++G++VE ELG LGSLET KG+ EDGHGAE + +LLTDP++AA Sbjct: 121 NVDVSRKVVEAAHSIGITVEAELGVLGSLETMKGDKEDGHGAEGTMTREQLLTDPEQAAD 180 Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240 FVK TQCDALAIAIGTSHGAYKF++KPTGDIL+I RIK IHQRIP THLVMHGSSSVPQE Sbjct: 181 FVKLTQCDALAIAIGTSHGAYKFSKKPTGDILSIQRIKEIHQRIPNTHLVMHGSSSVPQE 240 Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300 LL EIR +GGD+KETYGVPVEEIQEGI+ GVRKVNIDTD+RLA+T AIRR A N S+FD Sbjct: 241 LLAEIREFGGDMKETYGVPVEEIQEGIKNGVRKVNIDTDLRLAITGAIRRYMATNPSKFD 300 Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353 PR ++ A E A K+C+ R+ FG G+A KI+ + LD++A++Y +GEL+QVV Sbjct: 301 PRDYLKPAREAAMKICVERYTQFGCEGQAGKIKPVSLDKIAEKYKAGELSQVV 353 Lambda K H 0.316 0.132 0.369 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: 430 Number of extensions: 10 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: 354 Length of database: 354 Length adjustment: 29 Effective length of query: 325 Effective length of database: 325 Effective search space: 105625 Effective search space used: 105625 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 BPHYT_RS16260 BPHYT_RS16260 (fructose-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.11593.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-185 601.5 1.2 2.8e-185 601.3 1.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS16260 BPHYT_RS16260 fructose-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS16260 BPHYT_RS16260 fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 601.3 1.2 2.8e-185 2.8e-185 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 601.3 bits; conditional E-value: 2.8e-185 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaavee 70 l+s+rqlldhaae+gyg+pafnvnnleq+ aim aadk ++pvi+qas+gar+yage++lr+l++aave lcl|FitnessBrowser__BFirm:BPHYT_RS16260 3 LVSMRQLLDHAAENGYGLPAFNVNNLEQVQAIMAAADKVNAPVIMQASAGARKYAGEAFLRHLIEAAVES 72 69******************************************************************** PP TIGR01521 71 ypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvege 140 yp+ipvv+hqdhg+spa+c++ai+ gftsvmmdgsl++d+kt a+y+ynv+v+ +vv+ ah++g++ve e lcl|FitnessBrowser__BFirm:BPHYT_RS16260 73 YPHIPVVMHQDHGQSPAVCMAAIRSGFTSVMMDGSLEADGKTVASYEYNVDVSRKVVEAAHSIGITVEAE 142 ********************************************************************** PP TIGR01521 141 lgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevl 210 lg lgslet kg++edghg+eg++ r qlltdpe+aa+fvk t+ dala+aigtshgaykf++kptg++l lcl|FitnessBrowser__BFirm:BPHYT_RS16260 143 LGVLGSLETMKGDKEDGHGAEGTMTREQLLTDPEQAADFVKLTQCDALAIAIGTSHGAYKFSKKPTGDIL 212 ********************************************************************** PP TIGR01521 211 aidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrl 280 +i+ri+eih+r+p+thlvmhgsssvpqe l+ i e+gg++ketygvpveei++gik gvrkvnidtdlrl lcl|FitnessBrowser__BFirm:BPHYT_RS16260 213 SIQRIKEIHQRIPNTHLVMHGSSSVPQELLAEIREFGGDMKETYGVPVEEIQEGIKNGVRKVNIDTDLRL 282 ********************************************************************** PP TIGR01521 281 aataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 a+t+a+rr +a++ps+fdpr +lk+a ea ++c++ry +fg g+a kik+vsl+++a++y gel lcl|FitnessBrowser__BFirm:BPHYT_RS16260 283 AITGAIRRYMATNPSKFDPRDYLKPAREAAMKICVERYTQFGCEGQAGKIKPVSLDKIAEKYKAGEL 349 *****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (354 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: 11.34 // [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