Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate PP_4960 PP_4960 Fructose-bisphosphate aldolase
Query= BRENDA::A0Q7I9 (354 letters) >FitnessBrowser__Putida:PP_4960 Length = 354 Score = 571 bits (1471), Expect = e-167 Identities = 276/349 (79%), Positives = 311/349 (89%) Query: 1 MALVSLRQLLDHAAEHGYGLPAFNVNNLEQVRAVMEAADKVNSPVILQGSAGARKYAGAS 60 MAL+S+RQ+LDHAAE GYG+PAFNVNNLEQ+RA+MEAADK +SPVI+Q SAGARKYAGA Sbjct: 1 MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60 Query: 61 FIRHLVLAAIEEYPHIPVCMHQDHGTSPSVCQRSIQLGFSSVMMDGSLKSDGKTPADYEY 120 F+RHL+LAAIEE+PHIPVCMHQDHGTSP VCQRSIQLGFSSVMMDGSL DGKTP DYEY Sbjct: 61 FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120 Query: 121 NVNVTKTVSDMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLSMDQLLTDPEEAAD 180 NV VT+ MAHACGVSVEGELGCLGSLETG AGEEDGIGAEG L Q+LTDPEEAAD Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180 Query: 181 FVRRTKVDALAIAIGTSHGAYKFTKPPTGDVLSIKRVKEIHARIPDTHLVMHGSSSVPQD 240 FV++T+VDALAIAIGTSHGAYKFTKPPTGDVL+I R+KEIH RIP+THLVMHGSSSVPQ+ Sbjct: 181 FVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240 Query: 241 WLEVINTYGGAMGETYGVPVEEIVEAIKYGVRKINIDTDLRMAATGAIRRFLAENPAEFD 300 WL +IN YGG + ETYGVPVEEIVE IK+GVRK+NIDTDLR+A+TGA+RR +A+NP+EFD Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNPSEFD 300 Query: 301 PRKYNAVAKAAMSEICAARYEAFGSAGMASKIKPISLETMFQRYESGEL 349 PRK+ AM ++C ARYEAFG+AG ASKIKPISLE M+QRY GEL Sbjct: 301 PRKFFGETIKAMRDVCIARYEAFGTAGNASKIKPISLEGMYQRYLKGEL 349 Lambda K H 0.316 0.132 0.380 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: 526 Number of extensions: 13 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 PP_4960 PP_4960 (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.aa/TIGR01521.hmm # target sequence database: /tmp/gapView.21722.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-215 699.3 0.2 4.9e-215 699.1 0.2 1.0 1 lcl|FitnessBrowser__Putida:PP_4960 PP_4960 Fructose-bisphosphate al Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4960 PP_4960 Fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 699.1 0.2 4.9e-215 4.9e-215 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 699.1 bits; conditional E-value: 4.9e-215 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdip 75 lis+rq+ldhaae+gygvpafnvnnleq++aimeaadktdspvi+qas+gar+yag+++lr+l+laa+ee+p+ip lcl|FitnessBrowser__Putida:PP_4960 3 LISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIP 77 69************************************************************************* PP TIGR01521 76 vvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletg 150 v++hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt+++v++aha+g+svegelgclgsletg lcl|FitnessBrowser__Putida:PP_4960 78 VCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVRVTQQTVAMAHACGVSVEGELGCLGSLETG 152 *************************************************************************** PP TIGR01521 151 kgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdt 225 ++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykft++ptg+vlaidri+eih+r+p+t lcl|FitnessBrowser__Putida:PP_4960 153 MAGEEDGIGAEGVLDHSQMLTDPEEAADFVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNT 227 *************************************************************************** PP TIGR01521 226 hlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdpr 300 hlvmhgsssvpqewl++in+ygg+iketygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++psefdpr lcl|FitnessBrowser__Putida:PP_4960 228 HLVMHGSSSVPQEWLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNPSEFDPR 302 *************************************************************************** PP TIGR01521 301 kflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 kf+ ++++am+dvc+aryeafgtagnaskik++sle+m++ry kgel lcl|FitnessBrowser__Putida:PP_4960 303 KFFGETIKAMRDVCIARYEAFGTAGNASKIKPISLEGMYQRYLKGEL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.23 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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