Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate GFF2966 HP15_2910 fructose-1,6-bisphosphate aldolase
Query= BRENDA::Q602L6 (354 letters) >FitnessBrowser__Marino:GFF2966 Length = 354 Score = 540 bits (1390), Expect = e-158 Identities = 263/354 (74%), Positives = 301/354 (85%) Query: 1 MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60 MALIS+RQ+LDHAAEHGYG+PAFNVNN+EQ++AIMEAA D+PVI+Q SAGAR YAG P Sbjct: 1 MALISMRQMLDHAAEHGYGVPAFNVNNLEQMRAIMEAADRTDSPVIVQASAGARKYAGAP 60 Query: 61 FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120 FLRHL+ AAIE +PHIPV MHQDHG SP+VC RSIQ GFSSVMMDGSL ED KTP Y Y Sbjct: 61 FLRHLILAAIEEFPHIPVVMHQDHGTSPSVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120 Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180 NV+ TR+ VEMAHACGVSVEGELGCLGSLETG+AG+EDG GAEG LDHS +LTDP+EAAD Sbjct: 121 NVDVTRRTVEMAHACGVSVEGELGCLGSLETGQAGEEDGIGAEGTLDHSQMLTDPEEAAD 180 Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240 FV++T VDALAIAIGTSHGAYKFTR PTG +L ID++KAIH RIP HLVMHGSSSVP+E Sbjct: 181 FVKKTHVDALAIAIGTSHGAYKFTRPPTGDILAIDQIKAIHARIPDTHLVMHGSSSVPQE 240 Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300 W ++IN+YGG+I +TYGVPVEEIVEGI+HGVRKVNIDTDLR+AS GA+RRF+ E+ FD Sbjct: 241 WLKIINEYGGEIPETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAVRRFLAENPAEFD 300 Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354 PRK K AMT +C ARYEAFG AG A+KIKP+ LE M YA G+LDP V+ Sbjct: 301 PRKFLKETMKAMTDVCIARYEAFGCAGNASKIKPVNLERMFERYASGELDPKVK 354 Lambda K H 0.320 0.134 0.391 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: 538 Number of extensions: 22 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate GFF2966 HP15_2910 (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.12881.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-210 684.2 0.2 1.9e-210 684.0 0.2 1.0 1 lcl|FitnessBrowser__Marino:GFF2966 HP15_2910 fructose-1,6-bisphosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2966 HP15_2910 fructose-1,6-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.0 0.2 1.9e-210 1.9e-210 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 684.0 bits; conditional E-value: 1.9e-210 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdip 75 lis+rq+ldhaae+gygvpafnvnnleq++aimeaad+tdspvi+qas+gar+yag+++lr+l+laa+ee+p+ip lcl|FitnessBrowser__Marino:GFF2966 3 LISMRQMLDHAAEHGYGVPAFNVNNLEQMRAIMEAADRTDSPVIVQASAGARKYAGAPFLRHLILAAIEEFPHIP 77 69************************************************************************* PP TIGR01521 76 vvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsletg 150 vv+hqdhg+sp++c+++iqlgf+svmmdgsl ed+ktp+dy+ynv+vt ++v++aha+g+svegelgclgsletg lcl|FitnessBrowser__Marino:GFF2966 78 VVMHQDHGTSPSVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEYNVDVTRRTVEMAHACGVSVEGELGCLGSLETG 152 *************************************************************************** PP TIGR01521 151 kgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeiherlpdt 225 ++++edg g+eg+ld+sq+ltdpeeaa+fvkkt+vdala+aigtshgaykftr+ptg++laid+i+ ih+r+pdt lcl|FitnessBrowser__Marino:GFF2966 153 QAGEEDGIGAEGTLDHSQMLTDPEEAADFVKKTHVDALAIAIGTSHGAYKFTRPPTGDILAIDQIKAIHARIPDT 227 *************************************************************************** PP TIGR01521 226 hlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakdpsefdpr 300 hlvmhgsssvpqewl++ineyggei+etygvpveeiv+gik+gvrkvnidtdlrla+t+a+rr++a++p efdpr lcl|FitnessBrowser__Marino:GFF2966 228 HLVMHGSSSVPQEWLKIINEYGGEIPETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAVRRFLAENPAEFDPR 302 *************************************************************************** PP TIGR01521 301 kflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 kflk++++am dvc+aryeafg agnaskik+v+le m++rya+gel lcl|FitnessBrowser__Marino:GFF2966 303 KFLKETMKAMTDVCIARYEAFGCAGNASKIKPVNLERMFERYASGEL 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: 9.07 // [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