Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate H281DRAFT_01311 H281DRAFT_01311 fructose-bisphosphate aldolase
Query= SwissProt::Q56815 (354 letters) >FitnessBrowser__Burk376:H281DRAFT_01311 Length = 345 Score = 474 bits (1220), Expect = e-138 Identities = 239/344 (69%), Positives = 280/344 (81%) Query: 1 MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60 MA +++RQLLDHAA+ YG+PAFNVNNMEQ+ AIM AA T+SPVILQ SAGARKYAGEP Sbjct: 1 MAFIALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEP 60 Query: 61 FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120 +LRHL+ AA+EA+P+IP+V+HQDHGASPAVC AI+SGF+SVMMDGSL D KTPA YDY Sbjct: 61 YLRHLVLAALEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATYDY 120 Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180 NV V+ +VV+ AHAVGVSVEGELGCLGSLETG EDG GA+ L LLTDP EA Sbjct: 121 NVEVSRRVVDAAHAVGVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREAQI 180 Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240 FV++T DALAIAIGTSHGAYKF+R+PTGDILAI RI IH+RIP THLVMHGSSSVPQE Sbjct: 181 FVESTGVDALAIAIGTSHGAYKFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVPQE 240 Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300 L IR +GG+I TYGVPVEEIQ GI +GVRKVNIDTDIRLAM+ A+R+ A ++EFD Sbjct: 241 WLAIIREFGGEIPTTYGVPVEEIQRGIAHGVRKVNIDTDIRLAMSGAMRKSLANARAEFD 300 Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRY 344 PR + AA A+ VC+ RFEAFG AG+A +I+ + LD MA+RY Sbjct: 301 PRAALKAATAAARGVCVERFEAFGCAGQAPRIKPLPLDAMARRY 344 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: 446 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: 354 Length of database: 345 Length adjustment: 29 Effective length of query: 325 Effective length of database: 316 Effective search space: 102700 Effective search space used: 102700 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 H281DRAFT_01311 H281DRAFT_01311 (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.18838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-182 590.3 0.1 6.8e-182 590.1 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01311 H281DRAFT_01311 fructose-bisphos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01311 H281DRAFT_01311 fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 590.1 0.1 6.8e-182 6.8e-182 2 342 .. 4 344 .. 3 345 .] 1.00 Alignments for each domain: == domain 1 score: 590.1 bits; conditional E-value: 6.8e-182 TIGR01521 2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaa 67 i+lrqlldhaae+gygvpafnvnn+eqi aim+aa++t spvilqas+gar+yage++lr+lvlaa lcl|FitnessBrowser__Burk376:H281DRAFT_01311 4 IALRQLLDHAAEHGYGVPAFNVNNMEQIHAIMQAAEETASPVILQASAGARKYAGEPYLRHLVLAA 69 89**************************************************************** PP TIGR01521 68 veeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahav 133 e +pdip+vlhqdhg+spa+c++ai+ gftsvmmdgsl d ktpa ydynv+v+ +vv ahav lcl|FitnessBrowser__Burk376:H281DRAFT_01311 70 LEAHPDIPLVLHQDHGASPAVCQQAIRSGFTSVMMDGSLLPDQKTPATYDYNVEVSRRVVDAAHAV 135 ****************************************************************** PP TIGR01521 134 gasvegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgay 199 g+svegelgclgsletg++++edg+g++g+l r +lltdp ea fv+ t+vdala+aigtshgay lcl|FitnessBrowser__Burk376:H281DRAFT_01311 136 GVSVEGELGCLGSLETGMAGEEDGVGAQGQLTRDDLLTDPREAQIFVESTGVDALAIAIGTSHGAY 201 ****************************************************************** PP TIGR01521 200 kftrkptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgi 265 kf+r+ptg++lai ri eiher+p+thlvmhgsssvpqewl++i e+ggei+ tygvpveei++gi lcl|FitnessBrowser__Burk376:H281DRAFT_01311 202 KFSREPTGDILAIGRIVEIHERIPNTHLVMHGSSSVPQEWLAIIREFGGEIPTTYGVPVEEIQRGI 267 ****************************************************************** PP TIGR01521 266 kfgvrkvnidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskik 331 +gvrkvnidtd rla+++a+r+ +a+ + efdpr lk a a + vc++r+eafg ag+a +ik lcl|FitnessBrowser__Burk376:H281DRAFT_01311 268 AHGVRKVNIDTDIRLAMSGAMRKSLANARAEFDPRAALKAATAAARGVCVERFEAFGCAGQAPRIK 333 ****************************************************************** PP TIGR01521 332 vvsleemarry 342 +++l+ marry lcl|FitnessBrowser__Burk376:H281DRAFT_01311 334 PLPLDAMARRY 344 **********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (345 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: 9.25 // [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